Since 1997, the UCSD Genetics Training Program has served graduate trainees interested in genetics and genomics, including trainees supported by our institutional training grant and trainees who participated in the program while supported from other sources. Trainees over this period had a 93% degree completion rate. Average time to degree for students who completed the PhD during the five years ending May 2021 was 5.4 years. Our alumni have succeeded in a variety of professional careers based on their training. Program alumni, irrespective of support, along with publications they contributed with their graduate mentors are listed by year of trainee entry into the Genetics Training Program.

 

Summary data

Histogram shows high completion rate for each entry year

Bar plot shows frequencies for first position after completion by category

 Bar plot shows current position of alumni in 2021 by employment sector

 

Alumni self-reported satisfaction at 10 years post-degree:

Histogram shows strong alumni satisfaction 10 years after degree

2017 Trainees

Josh Chiou

Entry program: Biomedical Sciences
Advisor: Kyle Gaulton
Next position: Senior Computational Geneticist, Pfizer
Current position: Senior Computational Geneticist, Pfizer
email: Joshua.chiou@pfizer.com
 

Publications

Aylward A, Okino ML, Benaglio P, Chiou J, Beebe E, Padilla JA, Diep S, Gaulton KJ (2021) Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes. PLoS Genet 17:e1009531. PMC8183998

Chiou J, Geusz RJ, Okino ML, Han JY, Miller M, Melton R, Beebe E, Benaglio P, Huang S, Korgaonkar K, Heller S, Kleger A, et al (2021) Interpreting type 1 diabetes risk with genetics and single-cell epigenomics. Nature 594:398-402.

Chiou J, Zeng C, Cheng Z, Han JY, Schlichting M, Miller M, Mendez R, Huang S, Wang J, Sui Y, Deogaygay A, Okino ML, et al (2021) Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk. Nat Genet 53:455-466.

Geusz RJ, Wang A, Chiou J, Lancman JJ, Wetton N, Kefalopoulou S, Wang J, Qiu Y, Yan J, Aylward A, Ren B, Dong PDS, Gaulton KJ, Sander M (2021) Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development. Elife 10. PMC7864636

Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, et al (2021) Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature 589:E4. PMC8064906

Hocker JD, Poirion OB, Zhu F, Buchanan J, Zhang K, Chiou J, Wang TM, Zhang Q, Hou X, Li YE, Zhang Y, Farah EN, et al (2021) Cardiac cell type-specific gene regulatory programs and disease risk association. Sci Adv 7. PMC8121433

Yan J, Qiu Y, Ribeiro Dos Santos AM, Yin Y, Li YE, Vinckier N, Nariai N, Benaglio P, Raman A, Li X, Fan S, Chiou J, et al (2021) Systematic analysis of binding of transcription factors to noncoding variants. Nature 591:147-151.

Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, et al (2020) An atlas of dynamic chromatin landscapes in mouse fetal development. Nature 583:744-751. PMC7398618

Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, et al (2020) Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature 586:E31. PMC7962567

Wang A, Chiou J, Poirion OB, Buchanan J, Valdez MJ, Verheyden JM, Hou X, Kudtarkar P, Narendra S, Newsome JM, Guo M, Faddah DA, et al (2020) Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes. Elife 9. PMC7688309

Gorkin DU, Qiu Y, Hu M, Fletez-Brant K, Liu T, Schmitt AD, Noor A, Chiou J, Gaulton KJ, Sebat J, Li Y, Hansen KD, Ren B (2019) Common DNA sequence variation influences 3-dimensional conformation of the human genome. Genome Biol 20:255. PMC6883528

Greenwald WW, Chiou J, Yan J, Qiu Y, Dai N, Wang A, Nariai N, Aylward A, Han JY, Kadakia N, Regue L, Okino ML, et al (2019) Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk. Nat Commun 10:2078. PMC6505525

Zhang Q, Chao TC, Patil VS, Qin Y, Tiwari SK, Chiou J, Dobin A, Tsai CM, Li Z, Dang J, Gupta S, Urdahl K, et al (2019) The long noncoding RNA ROCKI regulates inflammatory gene expression. EMBO J 38. PMC6463213

Aylward A, Chiou J, Okino ML, Kadakia N, Gaulton KJ (2018) Shared genetic risk contributes to type 1 and type 2 diabetes etiology. Hum Mol Genet.

Udler MS, Kim J, von Grotthuss M, Bonas-Guarch S, Cole JB, Chiou J, Christopher DAoboM, the I, Boehnke M, Laakso M, Atzmon G, Glaser B, et al (2018) Type 2 diabetes genetic loci informed by multi-trait associations point to disease mechanisms and subtypes: A soft clustering analysis. PLoS Med 15:e1002654. PMC6150463

 

Ryan Geusz

Entry program: Biomedical Sciences
Advisor: Maike Sander
Next position: 
Current position: in training
email: 

Publications

Chiou J, Geusz RJ, Okino ML, Han JY, Miller M, Melton R, Beebe E, Benaglio P, Huang S, Korgaonkar K, Heller S, Kleger A, et al (2021) Interpreting type 1 diabetes risk with genetics and single-cell epigenomics. Nature 594:398-402.

Geusz RJ, Wang A, Chiou J, Lancman JJ, Wetton N, Kefalopoulou S, Wang J, Qiu Y, Yan J, Aylward A, Ren B, Dong PDS, Gaulton KJ, Sander M (2021) Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development. Elife 10. PMC7864636

Vinckier NK, Patel NA, Geusz RJ, Wang A, Wang J, Matta I, Harrington AR, Wortham M, Wetton N, Wang J, Jhala US, Rosenfeld MG, et al (2020) LSD1-mediated enhancer silencing attenuates retinoic acid signalling during pancreatic endocrine cell development. Nat Commun 11:2082. PMC7190832

  

Emily Griffin

Entry program: Biomedical Sciences
Advisor: Susan Ackerman
Next position: 
Current position: in training
email: 
LinkedIn profile:  
 

Publications

Griffin EN, and Ackerman SL (2020). Lipid Metabolism and Axon Degeneration: An ACOX1 Balancing Act. Neuron 106:551-553.

 

Krystyna Kolodziej

Entry program: Biomedical Sciences
Advisor: Bing Ren and Eran Mukamel
Next position: Pre-doctoral student, Exercise physiology, Colorado State University
Current position: in training
LinkedIn profile:  
 

Madeline Luth

Entry program: Biomedical Sciences
Advisor: Elizabeth Winzeler
Next position: 
Current position: in training
 

Publications

Ellis KM, Lucantoni L, Chavchich M, Abraham M, De Paoli A, Luth MR, Zeeman AM, Delves MJ, Teran FS, Straschil U, Baum J, Kocken CH, et al (2021) The novel bis-1,2,4-triazine MIPS-0004373 demonstrates rapid and potent activity against all blood stages of the malaria parasite. Antimicrob Agents Chemother:AAC0031121.

Rocamora F, Gupta P, Istvan ES, Luth MR, Carpenter EF, Kumpornsin K, Sasaki E, Calla J, Mittal N, Carolino K, Owen E, Llinas M, et al (2021) PfMFR3: A Multidrug-Resistant Modulator in Plasmodium falciparum. ACS Infect Dis 7:811-825. PMC8042660

Summers RL, Pasaje CFA, Pisco JP, Striepen J, Luth MR, Kumpornsin K, Carpenter EF, Munro JT, Lin, Plater A, Punekar AS, Shepherd AM, et al (2021) Chemogenomics identifies acetyl-coenzyme A synthetase as a target for malaria treatment and prevention. Cell Chem Biol.

Abraham M, Gagaring K, Martino ML, Vanaerschot M, Plouffe DM, Calla J, Godinez-Macias KP, Du AY, Wree M, Antonova-Koch Y, Eribez K, Luth MR, et al (2020) Probing the Open Global Health Chemical Diversity Library for Multistage- Active Starting Points for Next-Generation Antimalarials. ACS Infect Dis 6:613-628. PMC7155171

LaMonte GM, Rocamora F, Marapana DS, Gnadig NF, Ottilie S, Luth MR, Worgall TS, Goldgof GM, Mohunlal R, Santha Kumar TR, Thompson JK, Vigil E, et al (2020) Pan-active imidazolopiperazine antimalarials target the Plasmodium falciparum intracellular secretory pathway. Nat Commun 11:1780. PMC7156427

Luth MR, Winzeler EA (2020) SnapShot: Antimalarial Drugs. Cell 183:554-554 e551.

Mandt REK, Lafuente-Monasterio MJ, Sakata-Kato T, Luth MR, Segura D, Pablos-Tanarro A, Viera S, Magan N, Ottilie S, Winzeler EA, Lukens AK, Gamo FJ, Wirth DF (2019) In vitro selection predicts malaria parasite resistance to dihydroorotate dehydrogenase inhibitors in a mouse infection model. Sci Transl Med 11. PMC7444640

Rosenberg A, Luth MR, Winzeler EA, Behnke M, Sibley LD (2019) Evolution of resistance in vitro reveals mechanisms of artemisinin activity in Toxoplasma gondii. Proc Natl Acad Sci U S A. PMC6936365

Stokes BH, Yoo E, Murithi JM, Luth MR, Afanasyev P, da Fonseca PCA, Winzeler EA, Ng CL, Bogyo M, Fidock DA (2019) Covalent Plasmodium falciparum-selective proteasome inhibitors exhibit a low propensity for generating resistance in vitro and synergize with multiple antimalarial agents. PLoS Pathog 15:e1007722. PMC6553790

Antonova-Koch Y, Meister S, Abraham M, Luth MR, Ottilie S, Lukens AK, Sakata-Kato T, Vanaerschot M, Owen E, Jado JC, Maher SP, Calla J, et al (2018) Open-source discovery of chemical leads for next-generation chemoprotective antimalarials. Science 362. PMC6516198

Luth MR, Gupta P, Ottilie S, Winzeler EA (2018) Using in Vitro Evolution and Whole Genome Analysis To Discover Next Generation Targets for Antimalarial Drug Discovery. ACS Infect Dis 4:301-314. PMC5848146

Xie SC, Gillett DL, Spillman NJ, Tsu C, Luth MR, Ottilie S, Duffy S, Gould AE, Hales P, Seager BA, Charron CL, Bruzzese F, et al (2018) Target Validation and Identification of Novel Boronate Inhibitors of the Plasmodium falciparum Proteasome. J Med Chem 61:10053-10066. PMC6257627

 

Tunmise Olayinka

Entry program: Neurosciences/MSTP
Advisor: Alysson Muotri and Bradley Voytek
Next position: 
Current position:  

  

Saugat Poudel

Entry program: Biomedical Sciences
Advisor: Victor Nizet
Next position: 
Current position: in training
email: 
 

Publications

Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Seif Y, Lamsa A, Dillon N, Vrbanac A, Sugie J, Dahesh S, et al (2021) Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media. Gigascience 10. PMC7794652

Sastry AV, Dillon N, Anand A, Poudel S, Hefner Y, Xu S, Szubin R, Feist AM, Nizet V, Palsson B (2021) Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility. mSphere 6:e0044321. PMC8386450

Poudel S, Tsunemoto H, Seif Y, Sastry AV, Szubin R, Xu S, Machado H, Olson CA, Anand A, Pogliano J, Nizet V, Palsson BO (2020) Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response. Proc Natl Acad Sci U S A 117:17228-17239. PMC7382225

Gao NJ, Al-Bassam MM, Poudel S, Wozniak JM, Gonzalez DJ, Olson J, Zengler K, Nizet V, Valderrama JA (2019) Functional and Proteomic Analysis of Streptococcus pyogenes Virulence Upon Loss of Its Native Cas9 Nuclease. Front Microbiol 10:1967. PMC6714885

Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, et al (2019) Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Sci Data 6:43. PMC6486602

Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, et al (2019) Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media. Sci Data 6:322. PMC6917727

 

Mike Valdez

Entry program: Biomedical Sciences

Advisor: Xin Sun
Next position: 
Current position: in training
email: 
 

Publications

Garcia AN, Casanova NG, Valera DG, Sun X, Song JH, Kempf CL, Moreno-Vinasco L, Burns K, Bermudez T, Valdez M, Cuellar G, Gregory T, et al (2021) Involvement of eNAMPT/TLR4 signaling in murine radiation pneumonitis: protection by eNAMPT neutralization. Transl Res.

Wang A, Chiou J, Poirion OB, Buchanan J, Valdez MJ, Verheyden JM, Hou X, Kudtarkar P, Narendra S, Newsome JM, Guo M, Faddah DA, et al (2020) Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes. Elife 9. PMC7688309

 

2016 Trainees

Andrew Cooper

Entry program: Biological Sciences
Advisor: Julian Schroeder
Next position: Lecturer, UC San Diego Division of Biological Sciences
Current position:Lecturer, UC San Diego Division of Biological Sciences
 

Publications

Cooper AM, Felix D, Alcantara F, Zaslavsky I, Work A, Watson PL, Pezzoli K, Yu Q, Zhu D, Scavo AJ, Zarabi Y, Schroeder JI (2020) Monitoring and mitigation of toxic heavy metals and arsenic accumulation in food crops: A case study of an urban community garden. Plant Direct 4:e00198. PMC6957986

 

Elie Farah

Entry program: Biomedical Sciences
Advisor: Neil Chi
Next position: 
Current position: in training 
 

Publications

Hocker JD, Poirion OB, Zhu F, Buchanan J, Zhang K, Chiou J, Wang TM, Zhang Q, Hou X, Li YE, Zhang Y, Farah EN, et al (2021) Cardiac cell type-specific gene regulatory programs and disease risk association. Sci Adv 7. PMC8121433

Deacon DC, Happe CL, Chen C, Tedeschi N, Manso AM, Li T, Dalton ND, Peng Q, Farah EN, Gu Y, Tenerelli KP, Tran VD, et al (2019) Combinatorial interactions of genetic variants in human cardiomyopathy. Nat Biomed Eng 3:147-157. PMC6433174

Ren J, Han P, Ma X, Farah EN, Bloomekatz J, Zeng XI, Zhang R, Swim MM, Witty AD, Knight HG, Deshpande R, Xu W, et al (2019) Canonical Wnt5b Signaling Directs Outlying Nkx2.5+ Mesoderm into Pacemaker Cardiomyocytes. Dev Cell 50:729-743 e725. PMC6759400

Zhang Y, Li T, Preissl S, Amaral ML, Grinstein JD, Farah EN, Destici E, Qiu Y, Hu R, Lee AY, Chee S, Ma K, et al (2019) Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. Nat Genet 51:1380-1388. PMC6722002

Veevers J, Farah EN, Corselli M, Witty AD, Palomares K, Vidal JG, Emre N, Carson CT, Ouyang K, Liu C, van Vliet P, Zhu M, et al (2018) Cell-Surface Marker Signature for Enrichment of Ventricular Cardiomyocytes Derived from Human Embryonic Stem Cells. Stem Cell Reports 11:828-841. PMC6135222

Nina Gao

Entry program: Biomedical Sciences
Advisor: Victor Nizet
Next position: Clinical microbiology postdoctoral fellow (University of Maryland, Baltimore)
Current position: Clinical microbiology postdoctoral fellow (University of Maryland, Baltimore)
email: aninoag@gmail.com
"Come for the bagels, stay for the critical discussions."
 

Publications

Gao NJ, Al-Bassam MM, Poudel S, Wozniak JM, Gonzalez DJ, Olson J, Zengler K, Nizet V, Valderrama JA (2019) Functional and Proteomic Analysis of Streptococcus pyogenes Virulence Upon Loss of Its Native Cas9 Nuclease. Front Microbiol 10:1967. PMC6714885

Valderrama JA, Riestra AM, Gao NJ, LaRock CN, Gupta N, Ali SR, Hoffman HM, Ghosh P, Nizet V (2017) Group A streptococcal M protein activates the NLRP3 inflammasome. Nat Microbiol 2:1425-1434. PMC5750061

 

Shereen Georges Ghosh

Entry program: Biomedical Sciences
Advisor: Joseph Gleeson
Next position: Business Support Scientist, Bionano Genomics
Current position: Business Support Scientist, Bionano Genomics
email: shereenghosh@gmail.com

Publications

Ghosh SG, Breuss MW, Schlachetzki Z, Chai G, Ross D, Stanley V, Sonmez FM, Topaloglu H, Zaki MS, Hosny H, Gad S, Gleeson JG (2021) Biallelic hypomorphic mutations in HEATR5B, encoding HEAT repeat-containing protein 5B, in a neurological syndrome with pontocerebellar hypoplasia. Eur J Hum Genet 29:957-964. PMC8187379

Ghosh SG, Lee S, Fabunan R, Chai G, Zaki MS, Abdel-Salam G, Sultan T, Ben-Omran T, Alvi JR, McEvoy-Venneri J, Stanley V, Patel A, et al (2021) Biallelic variants in HPDL, encoding 4-hydroxyphenylpyruvate dioxygenase-like protein, lead to an infantile neurodegenerative condition. Genet Med 23:524-533.

Ghosh SG, Scala M, Beetz C, Helman G, Stanley V, Yang X, Breuss MW, Mazaheri N, Selim L, Hadipour F, Pais L, Stutterd CA, et al (2021) A relatively common homozygous TRAPPC4 splicing variant is associated with an early-infantile neurodegenerative syndrome. Eur J Hum Genet 29:271-279. PMC7868361

Wang L, Li Z, Sievert D, Smith DEC, Mendes MI, Chen DY, Stanley V, Ghosh S, Wang Y, Kara M, Aslanger AD, Rosti RO, et al (2021) Author Correction: Loss of NARS1 impairs progenitor proliferation in cortical brain organoids and leads to microcephaly. Nat Commun 12:1192. PMC7884391

Ghosh SG, Wang L, Breuss MW, Green JD, Stanley V, Yang X, Ross D, Traynor BJ, Alhashem AM, Azam M, Selim L, Bastaki L, et al (2020) Recurrent homozygous damaging mutation in TMX2, encoding a protein disulfide isomerase, in four families with microlissencephaly. J Med Genet 57:274-282. PMC7405652

Hanzlikova H, Prokhorova E, Krejcikova K, Cihlarova Z, Kalasova I, Kubovciak J, Sachova J, Hailstone R, Brazina J, Ghosh S, Cirak S, Gleeson JG, Ahel I, Caldecott KW (2020) Pathogenic ARH3 mutations result in ADP-ribose chromatin scars during DNA strand break repair. Nat Commun 11:3391. PMC7341855

Wang L, Li Z, Sievert D, Smith DEC, Mendes MI, Chen DY, Stanley V, Ghosh S, Wang Y, Kara M, Aslanger AD, Rosti RO, et al (2020) Loss of NARS1 impairs progenitor proliferation in cortical brain organoids and leads to microcephaly. Nat Commun 11:4038. PMC7424529

Wenderski W, Wang L, Krokhotin A, Walsh JJ, Li H, Shoji H, Ghosh S, George RD, Miller EL, Elias L, Gillespie MA, Son EY, et al (2020) Loss of the neural-specific BAF subunit ACTL6B relieves repression of early response genes and causes recessive autism. Proc Natl Acad Sci U S A 117:10055-10066. PMC7211998

Ghosh SG, Becker K, Huang H, Dixon-Salazar T, Chai G, Salpietro V, Al-Gazali L, Waisfisz Q, Wang H, Vaux KK, Stanley V, Manole A, et al (2018) Biallelic Mutations in ADPRHL2, Encoding ADP-Ribosylhydrolase 3, Lead to a Degenerative Pediatric Stress-Induced Epileptic Ataxia Syndrome. Am J Hum Genet 103:431-439. PMC6128219

  

Natalie Hollingsworth

Entry program: Biomedical Sciences
Advisor: Karen Oegema and Arshad Desai
Next position: 
Current position: on leave
LinkedIn profile:  

  

Ryan Marina

Entry program: Biomedical Sciences
Advisor: Gene Yeo
Next position: 
Current position: in training
email: rmarina4251@gmail.com
LinkedIn profile: https://www.linkedin.com/in/ryan-marina-bb25a3221/ 
 
"Graduate school is hard...you often feel lost and clueless. Despite the doubt that may shroud your journey, remember to never let that drown out your curiosity. Talk with your peers, request feedback, and share your work. And most importantly, learn to reflect often and appreciate your personal and professional growth, however incremental it might seem."
"GTP was a great experience. From informal discussions to in depth research dissections, I learned a tremendous amount from both students and faculty members alike."

Publications

Brannan KW, Chaim IA, Marina RJ, Yee BA, Kofman ER, Lorenz DA, Jagannatha P, Dong KD, Madrigal AA, Underwood JG, Yeo GW (2021) Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. Nat Methods 18:507-519. PMC8148648

Marina RJ, Brannan KW, Dong KD, Yee BA, Yeo GW (2020) Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing. Cell Rep 33:108350.

Batra R, Nelles DA, Pirie E, Blue SM, Marina RJ, Wang H, Chaim IA, Thomas JD, Zhang N, Nguyen V, Aigner S, Markmiller S, et al (2017) Elimination of Toxic Microsatellite Repeat Expansion RNA by RNA-Targeting Cas9. Cell 170:899-912 e810. PMC5873302

 

Caroline Sferrazza

Entry program: Neurosciences
Advisor: Larry Goldstein
Next position: Science Writer/Analyst at Rose Li & Associates, Inc.
Current position: Science Writer/Analyst at Rose Li & Associates, Inc.

  

2015 Trainees

Michael Baughn

Entry program: Biomedical Sciences
Advisor: Don Cleveland
Next position: Postdoc, UC San Diego
Current position: Postdoc, UC San Diego
email: mbaughn@ucsd.edu
"All of old. Nothing else ever. Ever tried. Ever failed. No matter. Try again. Fail again. Fail better." -- Samuel Beckett
 

Publications

Melamed Z, Lopez-Erauskin J, Baughn MW, Zhang O, Drenner K, Sun Y, Freyermuth F, McMahon MA, Beccari MS, Artates JW, Ohkubo T, Rodriguez M, et al (2019) Premature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration. Nat Neurosci 22:180-190. PMC6348009

Krach F, Batra R, Wheeler EC, Vu AQ, Wang R, Hutt K, Rabin SJ, Baughn MW, Libby RT, Diaz-Garcia S, Stauffer J, Pirie E, et al (2018) Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS. Acta Neuropathol 136:405-423. PMC6215775

Lopez-Erauskin J, Tadokoro T, Baughn MW, Myers B, McAlonis-Downes M, Chillon-Marinas C, Asiaban JN, Artates J, Bui AT, Vetto AP, Lee SK, Le AV, et al (2018) ALS/FTD-Linked Mutation in FUS Suppresses Intra-axonal Protein Synthesis and Drives Disease Without Nuclear Loss-of-Function of FUS. Neuron 100:816-830 e817. PMC6277851

Saberi S, Stauffer JE, Jiang J, Garcia SD, Taylor AE, Schulte D, Ohkubo T, Schloffman CL, Maldonado M, Baughn M, Rodriguez MJ, Pizzo D, Cleveland D, Ravits J (2018) Sense-encoded poly-GR dipeptide repeat proteins correlate to neurodegeneration and uniquely co-localize with TDP-43 in dendrites of repeat-expanded C9orf72 amyotrophic lateral sclerosis. Acta Neuropathol 135:459-474. PMC5935138

Batra R, Hutt K, Vu A, Rabin SJ, Baughn MW, Libby RT, Hoon S, Ravits J, Yeo GW (2016) Gene Expression Signatures of Sporadic ALS Motor Neuron Populations. bioRxiv:038448.

Brandler WM, Antaki D, Gujral M, Noor A, Rosanio G, Chapman TR, Barrera DJ, Lin GN, Malhotra D, Watts AC, Wong LC, Estabillo JA, et al (2016) Frequency and Complexity of De Novo Structural Mutation in Autism. Am J Hum Genet 98:667-679. PMC4833290

Jiang J, Zhu Q, Gendron TF, Saberi S, McAlonis-Downes M, Seelman A, Stauffer JE, Jafar-Nejad P, Drenner K, Schulte D, Chun S, Sun S, et al (2016) Gain of Toxicity from ALS/FTD-Linked Repeat Expansions in C9ORF72 Is Alleviated by Antisense Oligonucleotides Targeting GGGGCC-Containing RNAs. Neuron 90:535-550. PMC4860075

Lagier-Tourenne C, Baughn M, Rigo F, Sun S, Liu P, Li HR, Jiang J, Watt AT, Chun S, Katz M, Qiu J, Sun Y, et al (2013) Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for ALS and frontotemporal degeneration. Proc Natl Acad Sci U S A 110:E4530-4539. PMC3839752

Lagier-Tourenne C, Polymenidou M, Hutt KR, Vu AQ, Baughn M, Huelga SC, Clutario KM, Ling SC, Liang TY, Mazur C, Wancewicz E, Kim AS, et al (2012) Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs. Nat Neurosci 15:1488-1497. PMC3586380

  

Spencer Goodman

Entry program: Biomedical Sciences
Advisor: Stephanie Cherqui
Next position: Postdoc, Genomics Institute of the Novartis Foundation
Current position: Postdoc, Genomics Institute of the Novartis Foundation
email: goodman.spencer27@gmail.com

Publications 

Bengali M, Goodman S, Sun X, Dohil MA, Dohil R, Newbury R, Lobry T, Hernandez L, Antignac C, Jain S, Cherqui S (2021) Non-invasive intradermal imaging of cystine crystals in cystinosis. PLoS One 16:e0247846. PMC7932553 following competing interests: Stephanie Cherqui is inventor on a patent entitled "Methods of treating mitochondrial disorders" (#20378-201301) and co-inventor on a patent entitled "Methods of treating lysosomal disorders" (#20378-202488). She is a cofounder, shareholder and a member of both the Scientific Board and Board of Directors of Stelios Therapeutics Inc. Stephanie Cherqui also serves as a member of the Scientific Review Board and Board of Trustees of the Cystinosis Research Foundation. The terms of this arrangement have been reviewed and approved by the University of California San Diego in accordance with its conflict of interest policies. This does not alter our adherence to PLOS ONE policies on sharing data and materials. There are no other patents, products in development or marketed products associated with this research to declare.

Goodman S, Naphade S, Khan M, Sharma J, Cherqui S (2019) Macrophage polarization impacts tunneling nanotube formation and intercellular organelle trafficking. Sci Rep 9:14529. PMC6787037

Ariazi J, Benowitz A, De Biasi V, Den Boer ML, Cherqui S, Cui H, Douillet N, Eugenin EA, Favre D, Goodman S, Gousset K, Hanein D, et al (2017) Tunneling Nanotubes and Gap Junctions-Their Role in Long-Range Intercellular Communication during Development, Health, and Disease Conditions. Front Mol Neurosci 10:333. PMC5651011

Rocca CJ, Goodman SM, Dulin JN, Haquang JH, Gertsman I, Blondelle J, Smith JLM, Heyser CJ, Cherqui S (2017) Transplantation of wild-type mouse hematopoietic stem and progenitor cells ameliorates deficits in a mouse model of Friedreich's ataxia. Sci Transl Med 9. PMC5735830

 

Samuel Lin

Entry program: Biological Sciences
Advisor: Steven Wasserman
Next position: Postdoc, Sumit Chanda lab, Sanford-Burnham-Prebys Discovery Institute
Current position: Postdoc, Sumimt Chanda lab, Sanford-Burnham-Prebys Discovery Institute
"I learned a lot in journal club. I think Bruce does an amazing job pointing out things in the papers that can be changed, which we can then use to improve our own work. Bruce did not pay me to make this statement."
 

Publications 

Cohen LB, Lindsay SA, Xu Y, Lin SJH, Wasserman SA (2020) The Daisho Peptides Mediate Drosophila Defense Against a Subset of Filamentous Fungi. Front Immunol 11:9. PMC6989431

Lin SJH, Cohen LB, Wasserman SA (2020) Effector specificity and function in Drosophila innate immunity: Getting AMPed and dropping Boms. PLoS Pathog 16:e1008480. PMC7255597

Lin SJH, Fulzele A, Cohen LB, Bennett EJ, Wasserman SA (2019) Bombardier Enables Delivery of Short-Form Bomanins in the Drosophila Toll Response. Front Immunol 10:3040. PMC6965162

Lindsay SA, Lin SJH, Wasserman SA (2018) Short-Form Bomanins Mediate Humoral Immunity in Drosophila. J Innate Immun 10:306-314. PMC6158068

 

Alannah Miranda

Entry program: Biomedical Sciences
Advisor: John Kelsoe
Next position: Postdoc, UC San Diego
Current position: Postdoc, UC San Diego

Publications 

Nakajima K, Miranda A, Craig DW, Shekhtman T, Kmoch S, Bleyer A, Szelinger S, Kato T, Kelsoe JR (2020) Ntrk1 mutation co-segregating with bipolar disorder and inherited kidney disease in a multiplex family causes defects in neuronal growth and depression-like behavior in mice. Transl Psychiatry 10:407. PMC7687911

Miranda A, Shekhtman T, McCarthy M, DeModena A, Leckband SG, Kelsoe JR (2019) Study of 45 candidate genes suggests CACNG2 may be associated with lithium response in bipolar disorder. J Affect Disord 248:175-179. PMC7292366

Cross-Disorder Group of the Psychiatric Genomics C, Lee SH, Ripke S, Neale BM, Faraone SV, Purcell SM, Perlis RH, Mowry BJ, Thapar A, Goddard ME, Witte JS, Absher D, et al (2013) Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nat Genet 45:984-994. PMC3800159

 

Shanna Newton Lavalle

Entry program: Biomedical Sciences
Advisor: Pamela Mellon
Next position: Postdoc, Graham McVicker lab, Salk Institute
Current position: Postdoc, Graham McVicker lab, Salk Institute
"The path to your PhD requires hard work, planning, commitment, networking and more. Doing these things will set you up for success, but the real challenges come from the things you cannot plan for. Building resiliency in the face of adversity and unforeseen obstacles is what makes our degrees truly valuable. So if I have one piece of advice to offer, it is to always put yourself and your personal needs first, so that you can retain the mental stamina to push through the most challenging of times and excel in ways you never anticipated."
 

Publications 

Lavalle SN, Chou T, Hernandez J, Naing NCP, Tonsfeldt KJ, Hoffmann HM, Mellon PL (2021) Kiss1 is differentially regulated in male and female mice by the homeodomain transcription factor VAX1. Mol Cell Endocrinol 534:111358. PMC8319105

 

Alison Parisian

Entry program: Biomedical Sciences
Advisor: Frank Furnari
Next position: Scientist I at Olema Oncology
Current position: Scientist I at Olema Oncology
 

Publications 

Benitez JA, Finlay D, Castanza A, Parisian AD, Ma J, Longobardi C, Campos A, Vadla R, Izurieta A, Scerra G, Koga T, Long T, et al (2021) PTEN deficiency leads to proteasome addiction: a novel vulnerability in glioblastoma. Neuro Oncol 23:1072-1086.

Banisadr A, Eick M, Beri P, Parisian AD, Yeoman B, Placone JK, Engler AJ, Furnari F (2020) EGFRvIII uses intrinsic and extrinsic mechanisms to reduce glioma adhesion and increase migration. J Cell Sci 133. PMC7774888

Koga T, Chaim IA, Benitez JA, Markmiller S, Parisian AD, Hevner RF, Turner KM, Hessenauer FM, D'Antonio M, Nguyen ND, Saberi S, Ma J, et al (2020) Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells. Nat Commun 11:550. PMC6987220

Parisian AD, Koga T, Miki S, Johann PD, Kool M, Crawford JR, Furnari FB (2020) SMARCB1 loss interacts with neuronal differentiation state to block maturation and impact cell stability. Genes Dev 34:1316-1329. PMC7528703

Jameson NM, Ma J, Benitez J, Izurieta A, Han JY, Mendez R, Parisian A, Furnari F (2019) Intron 1-Mediated Regulation of EGFR Expression in EGFR-Dependent Malignancies Is Mediated by AP-1 and BET Proteins. Mol Cancer Res 17:2208-2220. PMC6825583

Orellana L, Thorne AH, Lema R, Gustavsson J, Parisian AD, Hospital A, Cordeiro TN, Bernado P, Scott AM, Brun-Heath I, Lindahl E, Cavenee WK, Furnari FB, Orozco M (2019) Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope. Proc Natl Acad Sci U S A 116:10009-10018. PMC6525488

Zanca C, Villa GR, Benitez JA, Thorne AH, Koga T, D'Antonio M, Ikegami S, Ma J, Boyer AD, Banisadr A, Jameson NM, Parisian AD, et al (2017) Glioblastoma cellular cross-talk converges on NF-kappaB to attenuate EGFR inhibitor sensitivity. Genes Dev 31:1212-1227. PMC5558924

  

Brian Reilly

Entry program: Biomedical Sciences/DPharm
Advisor: Rafael Bejar
Next position: Intern Pharmacist
Current position: Research Scientist, Metrum Research Group
 

Publications

Reilly BM, Luger T, Park S, Lio CJ, Gonzalez-Avalos E, Wheeler EC, Lee M, Williamson L, Tanaka T, Diep D, Zhang K, Huang Y, Rao A, Bejar R (2021) 5-Azacytidine Transiently Restores Dysregulated Erythroid Differentiation Gene Expression in TET2-Deficient Erythroleukemia Cells. Mol Cancer Res 19:451-464. PMC7925369

Reilly B, Tanaka TN, Diep D, Yeerna H, Tamayo P, Zhang K, Bejar R (2019) DNA methylation identifies genetically and prognostically distinct subtypes of myelodysplastic syndromes. Blood Adv 3:2845-2858. PMC6784525

 

Emily Wheeler

Entry program: Biomedical Sciences
Advisor: Gene Yeo
Next position: Postdoc, Zuzana Tothova lab, Dana Farber Cancer Center
Current position: Postdoc, Zuzana Tothova lab, Dana Farber Cancer Center
email: ecwheeler91@gmail.com
 
"Take advantage of your fellow trainees and academic advisors in GTP to talk about your science, career goals, etc. I got tons of informal advice about interviewing, job searching, and my research from participating in the program events and interacting with our members."
 

Publications 

Tan FE, Sathe S, Wheeler EC, Yeo GW (2021) Non-microRNA binding competitively inhibits LIN28 regulation. Cell Rep 36:109517.

Trujillo CA, Rice ES, Schaefer NK, Chaim IA, Wheeler EC, Madrigal AA, Buchanan J, Preissl S, Wang A, Negraes PD, Szeto RA, Herai RH, et al (2021) Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment. Science 371. PMC8006534

Marcheva B, Perelis M, Weidemann BJ, Taguchi A, Lin H, Omura C, Kobayashi Y, Newman MV, Wyatt EJ, McNally EM, Fox JEM, Hong H, et al (2020) A role for alternative splicing in circadian control of exocytosis and glucose homeostasis. Genes Dev 34:1089-1105. PMC7397853

Van Nostrand EL, Pratt GA, Yee BA, Wheeler EC, Blue SM, Mueller J, Park SS, Garcia KE, Gelboin-Burkhart C, Nguyen TB, Rabano I, Stanton R, et al (2020) Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins. Genome Biol 21:90. PMC7137325

Wheeler EC, Vu AQ, Einstein JM, DiSalvo M, Ahmed N, Van Nostrand EL, Shishkin AA, Jin W, Allbritton NL, Yeo GW (2020) Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors. Nat Methods 17:636-642. PMC7357298

Ganem NS, Ben-Asher N, Manning AC, Deffit SN, Washburn MC, Wheeler EC, Yeo GW, Zgayer OB, Mantsur E, Hundley HA, Lamm AT (2019) Disruption in A-to-I Editing Levels Affects C. elegans Development More Than a Complete Lack of Editing. Cell Rep 27:1244-1253 e1244. PMC8139731

Tan FE, Sathe S, Wheeler EC, Nussbacher JK, Peter S, Yeo GW (2019) A Transcriptome-wide Translational Program Defined by LIN28B Expression Level. Mol Cell 73:304-313.e303. PMC6338497

Krach F, Batra R, Wheeler EC, Vu AQ, Wang R, Hutt K, Rabin SJ, Baughn MW, Libby RT, Diaz-Garcia S, Stauffer J, Pirie E, et al (2018) Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS. Acta Neuropathol 136:405-423. PMC6215775

Wheeler EC, Van Nostrand EL, Yeo GW (2018) Advances and challenges in the detection of transcriptome-wide protein- RNA interactions. Wiley Interdiscip Rev RNA 9. PMC5739989

Carter H, Marty R, Hofree M, Gross AM, Jensen J, Fisch KM, Wu X, DeBoever C, Van Nostrand EL, Song Y, Wheeler E, Kreisberg JF, et al (2017) Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. Cancer Discov 7:410-423. PMC5460679

Deffit SN, Yee BA, Manning AC, Rajendren S, Vadlamani P, Wheeler EC, Domissy A, Washburn MC, Yeo GW, Hundley HA (2017) The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis. Elife 6. PMC5644944

Batra R, Stark TJ, Clark E, Belzile JP, Wheeler EC, Yee BA, Huang H, Gelboin-Burkhart C, Huelga SC, Aigner S, Roberts BT, Bos TJ, et al (2016) RNA-binding protein CPEB1 remodels host and viral RNA landscapes. Nat Struct Mol Biol 23:1101-1110. PMC5140759

  

2014 Trainees

Danny Antaki

Entry program: Biomedical Sciences
Advisor: Jonathan Sebat
Next position: Postdoc, Joe Gleeson lab, UC San Diego
Current position: Bioinformatics Scientist, Twist Bioscience
 

Publications 

Urresti J, Zhang P, Moran-Losada P, Yu NK, Negraes PD, Trujillo CA, Antaki D, Amar M, Chau K, Pramod AB, Diedrich J, Tejwani L, et al (2021) Cortical organoids model early brain development disrupted by 16p11.2 copy number variants in autism. Mol Psychiatry.

Yang X, Breuss MW, Xu X, Antaki D, James KN, Stanley V, Ball LL, George RD, Wirth SA, Cao B, Nguyen A, McEvoy-Venneri J, et al (2021) Developmental and temporal characteristics of clonal sperm mosaicism. Cell 184:4772-4783 e4715.

Breuss MW, Antaki D, George RD, Kleiber M, James KN, Ball LL, Hong O, Mitra I, Yang X, Wirth SA, Gu J, Garcia CAB, et al (2020) Autism risk in offspring can be assessed through quantification of male sperm mosaicism. Nat Med 26:143-150. PMC7032648

Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, et al (2019) Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat Commun 10:1784. PMC6467913

Pagel KA, Antaki D, Lian A, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P (2019) Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. PLoS Comput Biol 15:e1007112. PMC6594643

Antaki D, Brandler WM, Sebat J (2018) SV2: accurate structural variation genotyping and de novo mutation detection from whole genomes. Bioinformatics 34:1774-1777. PMC5946924

Brandler WM, Antaki D, Gujral M, Kleiber ML, Whitney J, Maile MS, Hong O, Chapman TR, Tan S, Tandon P, Pang T, Tang SC, et al (2018) Paternally inherited cis-regulatory structural variants are associated with autism. Science 360:327-331. PMC6449150

Marshall CR, Howrigan DP, Merico D, Thiruvahindrapuram B, Wu W, Greer DS, Antaki D, Shetty A, Holmans PA, Pinto D, Gujral M, Brandler WM, et al (2017) Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects. Nat Genet 49:27-35. PMC5737772

Brandler WM, Antaki D, Gujral M, Noor A, Rosanio G, Chapman TR, Barrera DJ, Lin GN, Malhotra D, Watts AC, Wong LC, Estabillo JA, et al (2016) Frequency and Complexity of De Novo Structural Mutation in Autism. Am J Hum Genet 98:667-679. PMC4833290

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, et al (2015) An integrated map of structural variation in 2,504 human genomes. Nature 526:75-81. PMC4617611

 

Daniel Chen

Entry program: Biomedical Sciences
Advisor: Kang Zhang
Next position: Postdoc, Stanford University
Current position: Scientist, Spring Discovery
"Choose an advisor that cares about training their students, not just getting papers published. Then work hard, but don't forget to enjoy beautiful San Diego!" 
 

Publications 

Chen D, Chao DL, Rocha L, Kolar M, Nguyen Huu VA, Krawczyk M, Dasyani M, Wang T, Jafari M, Jabari M, Ross KD, Saghatelian A, et al (2020) The lipid elongation enzyme ELOVL2 is a molecular regulator of aging in the retina. Aging Cell 19:e13100. PMC6996962

Fritsche LG, Igl W, Bailey JN, Grassmann F, Sengupta S, Bragg-Gresham JL, Burdon KP, Hebbring SJ, Wen C, Gorski M, Kim IK, Cho D, et al (2016) A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants. Nat Genet 48:134-143. PMC4745342

Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, Morsey BM, Swindells S, Shen H, Ng CT, Flagg K, Chen D, et al (2016) Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. Mol Cell 62:157-168. PMC4995115

Lin H, Ouyang H, Zhu J, Huang S, Liu Z, Chen S, Cao G, Li G, Signer RA, Xu Y, Chung C, Zhang Y, et al (2016) Lens regeneration using endogenous stem cells with gain of visual function. Nature 531:323-328. PMC6061995

Li G, Xu F, Zhu J, Krawczyk M, Zhang Y, Yuan J, Patel S, Wang Y, Lin Y, Zhang M, Cai H, Chen D, et al (2015) Transcription Factor PAX6 (Paired Box 6) Controls Limbal Stem Cell Lineage in Development and Disease. J Biol Chem 290:20448-20454. PMC4536450

Skowronska-Krawczyk D, Zhao L, Zhu J, Weinreb RN, Cao G, Luo J, Flagg K, Patel S, Wen C, Krupa M, Luo H, Ouyang H, et al (2015) P16INK4a Upregulation Mediated by SIX6 Defines Retinal Ganglion Cell Pathogenesis in Glaucoma. Mol Cell 59:931-940. PMC4648709

Zhao L, Chen XJ, Zhu J, Xi YB, Yang X, Hu LD, Ouyang H, Patel SH, Jin X, Lin D, Wu F, Flagg K, et al (2015) Lanosterol reverses protein aggregation in cataracts. Nature 523:607-611.

 

Wilmer Del Cid

Entry program: Neurosciences
Advisor: Chih-Ying Su
Next position: 
Current position: 

  

Elaine Guo

Entry program: Biomedical Sciences
Advisor: Richard Kolodner
Next position: Scientist, Bristol Myers Squibb
Current position: Research Scientist, Blacksmith Medicines
 

Publications 

Guo E, Ishii Y, Mueller J, Srivatsan A, Gahman T, Putnam CD, Wang JYJ, Kolodner RD (2020) FEN1 endonuclease as a therapeutic target for human cancers with defects in homologous recombination. Proc Natl Acad Sci U S A 117:19415-19424. PMC7431096

 

Jennifer Kuo

Entry program: Biomedical Sciences
Advisor: Albert La Spada
Next position: R&D Intern in Epigenetics, Celgene
Current position: Data Scientist, Mint Mobile
 

Publications

Gilmore-Hall S, Kuo J, Ward JM, Zahra R, Morrison RS, Perkins G, La Spada AR (2019) CCP1 promotes mitochondrial fusion and motility to prevent Purkinje cell neuron loss in pcd mice. J Cell Biol 218:206-219. PMC6314562

 

Nathan Jameson

Entry program: Biomedical Sciences
Advisor: Frank Furnari
Next position: Scientist I, Omniome Inc
Current position: Scientist, Zentalis Pharmaceuticals
email: nathan.m.jameson@gmail.com
"Don't be afraid to reach out to former students for career advice, PhD advisor advice, or just to talk about their or your experience. Chances are someone else had a similar experience or career aspirations as you do and they can help you work through it." 
 

Publications 

Jameson NM, Ma J, Benitez J, Izurieta A, Han JY, Mendez R, Parisian A, Furnari F (2019) Intron 1-Mediated Regulation of EGFR Expression in EGFR-Dependent Malignancies Is Mediated by AP-1 and BET Proteins. Mol Cancer Res 17:2208-2220. PMC6825583

Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, et al (2019) Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature 575:699-703. PMC7094777

Benitez JA, Ma J, D'Antonio M, Boyer A, Camargo MF, Zanca C, Kelly S, Khodadadi-Jamayran A, Jameson NM, Andersen M, Miletic H, Saberi S, et al (2017) PTEN regulates glioblastoma oncogenesis through chromatin-associated complexes of DAXX and histone H3.3. Nat Commun 8:15223. PMC5437297

Zanca C, Villa GR, Benitez JA, Thorne AH, Koga T, D'Antonio M, Ikegami S, Ma J, Boyer AD, Banisadr A, Jameson NM, Parisian AD, et al (2017) Glioblastoma cellular cross-talk converges on NF-kappaB to attenuate EGFR inhibitor sensitivity. Genes Dev 31:1212-1227. PMC5558924

  

Terry Solomon

Entry program: Biomedical Sciences
Advisor: Kelly Frazer
Next position: Regulatory Affairs Specialist
Current position: Regulatory Affairs Specialist, Pulmonx
email: ter.solomon@gmail.com

Publications 

Horvei LD, Braekkan SK, Smith EN, Solomon T, Hindberg K, Frazer KA, Rosendaal FR, Hansen JB (2018) Joint effects of prothrombotic genotypes and body height on the risk of venous thromboembolism: the Tromso study. J Thromb Haemost 16:83-89.

Jensen SB, Hindberg K, Solomon T, Smith EN, Lapek JD, Jr., Gonzalez DJ, Latysheva N, Frazer KA, Braekkan SK, Hansen JB (2018) Discovery of novel plasma biomarkers for future incident venous thromboembolism by untargeted synchronous precursor selection mass spectrometry proteomics. J Thromb Haemost 16:1763-1774. PMC6123273

Solomon T, Lapek JD, Jr., Jensen SB, Greenwald WW, Hindberg K, Matsui H, Latysheva N, Braekken SK, Gonzalez DJ, Frazer KA, Smith EN, Hansen JB (2018) Identification of Common and Rare Genetic Variation Associated With Plasma Protein Levels Using Whole-Exome Sequencing and Mass Spectrometry. Circ Genom Precis Med 11:e002170. PMC6301071

Brandler WM, Antaki D, Gujral M, Noor A, Rosanio G, Chapman TR, Barrera DJ, Lin GN, Malhotra D, Watts AC, Wong LC, Estabillo JA, et al (2016) Frequency and Complexity of De Novo Structural Mutation in Autism. Am J Hum Genet 98:667-679. PMC4833290

Gran OV, Smith EN, Braekkan SK, Jensvoll H, Solomon T, Hindberg K, Wilsgaard T, Rosendaal FR, Frazer KA, Hansen JB (2016) Joint effects of cancer and variants in the factor 5 gene on the risk of venous thromboembolism. Haematologica 101:1046-1053. PMC5060021

Solomon T, Smith EN, Matsui H, Braekkan SK, Consortium I, Wilsgaard T, Njolstad I, Mathiesen EB, Hansen JB, Frazer KA (2016) Associations Between Common and Rare Exonic Genetic Variants and Serum Levels of 20 Cardiovascular-Related Proteins: The Tromso Study. Circ Cardiovasc Genet 9:375-383. PMC4982757

  

Jenhan Tao

Entry program: Bioinformatics & Systems Biology
Advisor: Chris Glass
Next position: Bioinformatics Scientist, Illumina
Current position: Scientist II, Computational Biology, Generate Biomedicines
email: jenhantao@gmail.com
"It matters because it matters to you."
 

Publications 

Shamie I, Duttke SH, Karottki KJC, Han CZ, Hansen AH, Hefzi H, Xiong K, Li S, Roth SJ, Tao J, Lee GM, Glass CK, et al (2021) A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells. NAR Genom Bioinform 3:lqab061. PMC8276764

Schlachetzki JCM, Prots I, Tao J, Chun HB, Saijo K, Gosselin D, Winner B, Glass CK, Winkler J (2020) Author Correction: A monocyte gene expression signature in the early clinical course of Parkinson's disease. Sci Rep 10:6261. PMC7136204

Fonseca GJ, Tao J, Westin EM, Duttke SH, Spann NJ, Strid T, Shen Z, Stender JD, Sakai M, Link VM, Benner C, Glass CK (2019) Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages. Nat Commun 10:414. PMC6345992

Link VM, Duttke SH, Chun HB, Holtman IR, Westin E, Hoeksema MA, Abe Y, Skola D, Romanoski CE, Tao J, Fonseca GJ, Troutman TD, et al (2018) Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell 173:1796-1809 e1717. PMC6003872

Muse ED, Yu S, Edillor CR, Tao J, Spann NJ, Troutman TD, Seidman JS, Henke A, Roland JT, Ozeki KA, Thompson BM, McDonald JG, et al (2018) Cell-specific discrimination of desmosterol and desmosterol mimetics confers selective regulation of LXR and SREBP in macrophages. Proc Natl Acad Sci U S A 115:E4680-E4689. PMC5960280

Schlachetzki JCM, Prots I, Tao J, Chun HB, Saijo K, Gosselin D, Winner B, Glass CK, Winkler J (2018) A monocyte gene expression signature in the early clinical course of Parkinson's disease. Sci Rep 8:10757. PMC6050266

Shemer A, Grozovski J, Tay TL, Tao J, Volaski A, Suss P, Ardura-Fabregat A, Gross-Vered M, Kim JS, David E, Chappell-Maor L, Thielecke L, et al (2018) Engrafted parenchymal brain macrophages differ from microglia in transcriptome, chromatin landscape and response to challenge. Nat Commun 9:5206. PMC6284018

Oishi Y, Spann NJ, Link VM, Muse ED, Strid T, Edillor C, Kolar MJ, Matsuzaka T, Hayakawa S, Tao J, Kaikkonen MU, Carlin AF, et al (2017) SREBP1 Contributes to Resolution of Pro-inflammatory TLR4 Signaling by Reprogramming Fatty Acid Metabolism. Cell Metab 25:412-427. PMC5568699

Eichenfield DZ, Troutman TD, Link VM, Lam MT, Cho H, Gosselin D, Spann NJ, Lesch HP, Tao J, Muto J, Gallo RL, Evans RM, Glass CK (2016) Tissue damage drives co-localization of NF-kappaB, Smad3, and Nrf2 to direct Rev-erb sensitive wound repair in mouse macrophages. Elife 5. PMC4963201

 

Tina Wang

Entry program: Biomedical Sciences
Advisor: Trey Ideker
Next position: Freelance Computational Biology Consultant
Current position: Scientist, Bioinformatics and Data Analysis, Janssen Pharmaceuticals
 

Publications 

Lew BJ, Schantell MD, O'Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW (2021) Reductions in Gray Matter Linked to Epigenetic HIV-Associated Accelerated Aging. Cereb Cortex 31:3752-3763. PMC8258439

Spooner RK, Taylor BK, L'Heureux E, Schantell M, Arif Y, May PE, Morsey B, Wang T, Ideker T, Fox HS, Wilson TW (2021) Stress-induced aberrations in sensory processing predict worse cognitive outcomes in healthy aging adults. Aging (Albany NY) 13:19996-20015. PMC8436901

Proskovec AL, Rezich MT, O'Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW (2020) Association of Epigenetic Metrics of Biological Age With Cortical Thickness. JAMA Netw Open 3:e2015428. PMC7490648

Wang T, Ma J, Hogan AN, Fong S, Licon K, Tsui B, Kreisberg JF, Adams PD, Carvunis AR, Bannasch DL, Ostrander EA, Ideker T (2020) Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome. Cell Syst 11:176-185.e176. PMC7484147

Wiesman AI, Rezich MT, O'Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW (2020) Epigenetic Markers of Aging Predict the Neural Oscillations Serving Selective Attention. Cereb Cortex 30:1234-1243. PMC7132912

Bui N, Huang JK, Bojorquez-Gomez A, Licon K, Sanchez KS, Tang SN, Beckett AN, Wang T, Zhang W, Shen JP, Kreisberg JF, Ideker T (2018) Disruption of NSD1 in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to Hypomethylation. Mol Cancer Ther 17:1585-1594. PMC6030464

Field AE, Robertson NA, Wang T, Havas A, Ideker T, Adams PD (2018) DNA Methylation Clocks in Aging: Categories, Causes, and Consequences. Mol Cell 71:882-895. PMC6520108

Cole JJ, Robertson NA, Rather MI, Thomson JP, McBryan T, Sproul D, Wang T, Brock C, Clark W, Ideker T, Meehan RR, Miller RA, Brown-Borg HM, Adams PD (2017) Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions. Genome Biol 18:58. PMC5370462

Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T (2017) Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biol 18:57. PMC5371228

Carvunis AR, Wang T, Skola D, Yu A, Chen J, Kreisberg JF, Ideker T (2015) Evidence for a common evolutionary rate in metazoan transcriptional networks. Elife 4. PMC4764585

  

2013 Trainees

Alexandra Buckley

Entry program: Biomedical Sciences
Advisor: Nik Schork
Next position: Bioinformatics Scientist, Helix
Current position: Data Scientist, Invitae
 

Publications

Buckley AR, Ideker T, Carter H, Schork NJ (2019) Rare variant phasing using paired tumor:normal sequence data. BMC Bioinformatics 20:265. PMC6537421

Buckley AR, Ideker T, Carter H, Harismendy O, Schork NJ (2018) Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas. Genome Med 10:69. PMC6138910

Buckley AR, Standish KA, Bhutani K, Ideker T, Lasken RS, Carter H, Harismendy O, Schork NJ (2017) Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls. BMC Genomics 18:458. PMC5467262

 

Victoria (Doroski) Corey

Entry program: Biomedical Sciences
Advisor: Elizabeth Winzeler
Next position: Associate Bioinformatics Scientist, Illumina
Current position: Bioinformatics Scientist II, Illumina
 

Publications

Cowell AN, Istvan ES, Lukens AK, Gomez-Lorenzo MG, Vanaerschot M, Sakata-Kato T, Flannery EL, Magistrado P, Owen E, Abraham M, LaMonte G, Painter HJ, et al (2018) Mapping the malaria parasite druggable genome by using in vitro evolution and chemogenomics. Science 359:191-199. PMC5925756

Istvan ES, Mallari JP, Corey VC, Dharia NV, Marshall GR, Winzeler EA, Goldberg DE (2017) Esterase mutation is a mechanism of resistance to antimalarial compounds. Nat Commun 8:14240. PMC5263872

Vanaerschot M, Lucantoni L, Li T, Combrinck JM, Ruecker A, Kumar TRS, Rubiano K, Ferreira PE, Siciliano G, Gulati S, Henrich PP, Ng CL, et al (2017) Hexahydroquinolines are antimalarial candidates with potent blood-stage and transmission-blocking activity. Nat Microbiol 2:1403-1414. PMC5708124

Corey VC, Lukens AK, Istvan ES, Lee MCS, Franco V, Magistrado P, Coburn-Flynn O, Sakata-Kato T, Fuchs O, Gnadig NF, Goldgof G, Linares M, et al (2016) A broad analysis of resistance development in the malaria parasite. Nat Commun 7:11901. PMC4912613

Kato N, Comer E, Sakata-Kato T, Sharma A, Sharma M, Maetani M, Bastien J, Brancucci NM, Bittker JA, Corey V, Clarke D, Derbyshire ER, et al (2016) Diversity-oriented synthesis yields novel multistage antimalarial inhibitors. Nature 538:344-349. PMC5515376

LaMonte G, Lim MY, Wree M, Reimer C, Nachon M, Corey V, Gedeck P, Plouffe D, Du A, Figueroa N, Yeung B, Bifani P, Winzeler EA (2016) Mutations in the Plasmodium falciparum Cyclic Amine Resistance Locus (PfCARL) Confer Multidrug Resistance. mBio 7. PMC4958248

Lehmann JS, Corey VC, Ricaldi JN, Vinetz JM, Winzeler EA, Matthias MA (2016) Whole Genome Shotgun Sequencing Shows Selection on Leptospira Regulatory Proteins During in vitro Culture Attenuation. Am J Trop Med Hyg 94:302-313. PMC4751964

Lim MY, LaMonte G, Lee MCS, Reimer C, Tan BH, Corey V, Tjahjadi BF, Chua A, Nachon M, Wintjens R, Gedeck P, Malleret B, et al (2016) UDP-galactose and acetyl-CoA transporters as Plasmodium multidrug resistance genes. Nat Microbiol 1:16166. PMC5575994

Magistrado PA, Corey VC, Lukens AK, LaMonte G, Sasaki E, Meister S, Wree M, Winzeler E, Wirth DF (2016) Plasmodium falciparum Cyclic Amine Resistance Locus (PfCARL), a Resistance Mechanism for Two Distinct Compound Classes. ACS Infect Dis 2:816-826. PMC5109296

Ng CL, Siciliano G, Lee MC, de Almeida MJ, Corey VC, Bopp SE, Bertuccini L, Wittlin S, Kasdin RG, Le Bihan A, Clozel M, Winzeler EA, Alano P, Fidock DA (2016) CRISPR-Cas9-modified pfmdr1 protects Plasmodium falciparum asexual blood stages and gametocytes against a class of piperazine-containing compounds but potentiates artemisinin-based combination therapy partner drugs. Mol Microbiol 101:381-393. PMC4958522

Swann J, Corey V, Scherer CA, Kato N, Comer E, Maetani M, Antonova-Koch Y, Reimer C, Gagaring K, Ibanez M, Plouffe D, Zeeman AM, et al (2016) High-Throughput Luciferase-Based Assay for the Discovery of Therapeutics That Prevent Malaria. ACS Infect Dis 2:281-293. PMC4890880

Flannery EL, Wang T, Akbari A, Corey VC, Gunawan F, Bright AT, Abraham M, Sanchez JF, Santolalla ML, Baldeviano GC, Edgel KA, Rosales LA, et al (2015) Next-Generation Sequencing of Plasmodium vivax Patient Samples Shows Evidence of Direct Evolution in Drug-Resistance Genes. ACS Infect Dis 1:367-379. PMC4692371

Manary MJ, Singhakul SS, Flannery EL, Bopp SE, Corey VC, Bright AT, McNamara CW, Walker JR, Winzeler EA (2014) Identification of pathogen genomic variants through an integrated pipeline. BMC Bioinformatics 15:63. PMC3945619

  

Sophia Espanola

Entry program: Biomedical Sciences
Advisor: David Traver
Next position: Research Scientist, Vertex Pharmaceuticals
Current position: Research Scientist, Vertex Pharmaceuticals
email: sdespanola@gmail.com

Publications

Espanola SG, Song H, Ryu E, Saxena A, Kim ES, Manegold JE, Nasamran CA, Sahoo D, Oh CK, Bickers C, Shin U, Grainger S, et al (2020) Haematopoietic stem cell-dependent Notch transcription is mediated by p53 through the Histone chaperone Supt16h. Nat Cell Biol 22:1411-1422. PMC8092813

Bickers C, Espanola SD, Grainger S, Pouget C, Traver D (2018) Zebrafish snai2 mutants fail to phenocopy morphant phenotypes. PLoS One 13:e0202747. PMC6135377

 

Greg Goldgof

Entry program: Biomedical Sciences/MSTP
Advisor: Elizabeth Winzeler
Next position: Resident, UC San Francisco
Current position: Clinical Instructor, UC San Francisco
 

Publications

LaMonte GM, Rocamora F, Marapana DS, Gnadig NF, Ottilie S, Luth MR, Worgall TS, Goldgof GM, Mohunlal R, Santha Kumar TR, Thompson JK, Vigil E, et al (2020) Pan-active imidazolopiperazine antimalarials target the Plasmodium falciparum intracellular secretory pathway. Nat Commun 11:1780. PMC7156427

LaMonte GM, Almaliti J, Bibo-Verdugo B, Keller L, Zou BY, Yang J, Antonova-Koch Y, Orjuela-Sanchez P, Boyle CA, Vigil E, Wang L, Goldgof GM, et al (2017) Development of a Potent Inhibitor of the Plasmodium Proteasome with Reduced Mammalian Toxicity. J Med Chem 60:6721-6732. PMC5554889

Ottilie S, Goldgof GM, Calvet CM, Jennings GK, LaMonte G, Schenken J, Vigil E, Kumar P, McCall LI, Lopes ES, Gunawan F, Yang J, et al (2017) Rapid Chagas Disease Drug Target Discovery Using Directed Evolution in Drug-Sensitive Yeast. ACS Chem Biol 12:422-434. PMC5649375

Bertin MJ, Demirkiran O, Navarro G, Moss NA, Lee J, Goldgof GM, Vigil E, Winzeler EA, Valeriote FA, Gerwick WH (2016) Kalkipyrone B, a marine cyanobacterial gamma-pyrone possessing cytotoxic and anti-fungal activities. Phytochemistry 122:113-118. PMC4724546

Corey VC, Lukens AK, Istvan ES, Lee MCS, Franco V, Magistrado P, Coburn-Flynn O, Sakata-Kato T, Fuchs O, Gnadig NF, Goldgof G, Linares M, et al (2016) A broad analysis of resistance development in the malaria parasite. Nat Commun 7:11901. PMC4912613

Goldgof GM, Durrant JD, Ottilie S, Vigil E, Allen KE, Gunawan F, Kostylev M, Henderson KA, Yang J, Schenken J, LaMonte GM, Manary MJ, et al (2016) Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor. Sci Rep 6:27806. PMC4904242

Van Voorhis WC, Adams JH, Adelfio R, Ahyong V, Akabas MH, Alano P, Alday A, Aleman Resto Y, Alsibaee A, Alzualde A, Andrews KT, Avery SV, et al (2016) Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond. PLoS Pathog 12:e1005763. PMC4965013

Suzuki Y, Assad-Garcia N, Kostylev M, Noskov VN, Wise KS, Karas BJ, Stam J, Montague MG, Hanly TJ, Enriquez NJ, Ramon A, Goldgof GM, et al (2015) Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling. Genome Res 25:435-444. PMC4352883

Karas BJ, Jablanovic J, Sun L, Ma L, Goldgof GM, Stam J, Ramon A, Manary MJ, Winzeler EA, Venter JC, Weyman PD, Gibson DG, et al (2013) Direct transfer of whole genomes from bacteria to yeast. Nat Methods 10:410-412. PMC4034675

 

Bernardo Lara

Entry program: Biomedical Sciences
Advisor: Antonio De Maio
Next position: Senior Research Assistant, MD Anderson Cancer Center
Current position: QC Analytical Specialist II at Catalent Pharma Solutions
 

Publications

Liu Z, Cauvi DM, Bernardino EMA, Lara B, Lizardo RE, Hawisher D, Bickler S, De Maio A (2018) Isolation and characterization of human urine extracellular vesicles. Cell Stress Chaperones 23:943-953. PMC6111092

 

Kevin Ross

Entry program: Biomedical Sciences
Advisor: Bruce Hamilton
Next position: Postdoc, Bruce Hamilton lab, UC San Diego
Current position: 
 

Publications

Ross KD, Ren J, Zhang R, Chi NC, Hamilton BA (2021) Ankfn1 vestibular defects in zebrafish require mutations in both ancestral and derived paralogs. bioRxiv:2021.2009.2011.459924.

Hernandez J, Ross KD, Hamilton BA (2021) Inducible Yeast Two-Hybrid with Quantitative Measures. bioRxiv:2021.2007.2001.450807.

Chen D, Chao DL, Rocha L, Kolar M, Nguyen Huu VA, Krawczyk M, Dasyani M, Wang T, Jafari M, Jabari M, Ross KD, Saghatelian A, et al (2020) The lipid elongation enzyme ELOVL2 is a molecular regulator of aging in the retina. Aging Cell 19:e13100. PMC6996962

Thomas GD, Hanna RN, Vasudevan NT, Hamers AA, Romanoski CE, McArdle S, Ross KD, Blatchley A, Yoakum D, Hamilton BA, Mikulski Z, Jain MK, Glass CK, Hedrick CC (2016) Deleting an Nr4a1 Super-Enhancer Subdomain Ablates Ly6C(low) Monocytes while Preserving Macrophage Gene Function. Immunity 45:975-987. PMC5694686

Concepcion D, Ross KD, Hutt KR, Yeo GW, Hamilton BA (2015) Nxf1 natural variant E610G is a semi-dominant suppressor of IAP-induced RNA processing defects. PLoS Genet 11:e1005123. PMC4383553

Zhang S, Ross KD, Seidner GA, Gorman MR, Poon TH, Wang X, Keithley EM, Lee PN, Martindale MQ, Joiner WJ, Hamilton BA (2015) Nmf9 Encodes a Highly Conserved Protein Important to Neurological Function in Mice and Flies. PLoS Genet 11:e1005344. PMC4488434

  

Genevieve Ryan

Entry program: Biomedical Sciences
Advisor: Pamela Mellon
Next position: Postdoc, Emma Farley lab, UC San Diego
Current position: Postdoc, Emma Farley lab, UC San Diego
 

Publications 

Ho EV, Shi C, Cassin J, He MY, Nguyen RD, Ryan GE, Tonsfeldt KJ, Mellon PL (2021) Reproductive Deficits Induced by Prenatal Anti-Mullerian Hormone Exposure Require Androgen Receptor in Kisspeptin Cells. Endocrinology. In Press. PMID:34529765

Ryan GE, Bohaczuk SC, Cassin J, Witham EA, Shojaei S, Ho EV, Thackray VG, Mellon PL (2021) Androgen receptor positively regulates gonadotropin-releasing hormone receptor in pituitary gonadotropes. Mol Cell Endocrinol 530:111286. PMC8177864

Ryan GE, Malik S, Mellon PL (2018) Antiandrogen Treatment Ameliorates Reproductive and Metabolic Phenotypes in the Letrozole-Induced Mouse Model of PCOS. Endocrinology 159:1734-1747. PMC6097580

Kauffman AS, Thackray VG, Ryan GE, Tolson KP, Glidewell-Kenney CA, Semaan SJ, Poling MC, Iwata N, Breen KM, Duleba AJ, Stener-Victorin E, Shimasaki S, Webster NJ, Mellon PL (2015) A Novel Letrozole Model Recapitulates Both the Reproductive and Metabolic Phenotypes of Polycystic Ovary Syndrome in Female Mice. Biol Reprod 93:69. PMC4710190

 

Anthony Schmitt

Entry program: Biomedical Sciences
Advisor: Bing Ren
Next position: Director of Genomics at Arima Genomics, Inc.
Current position: Senior Vice President, Science, Arima Genomics, Inc.
 

Publications 

Dall'Agnese A, Caputo L, Nicoletti C, di Iulio J, Schmitt A, Gatto S, Diao Y, Ye Z, Forcato M, Perera R, Bicciato S, Telenti A, Ren B, Puri PL (2019) Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation. Mol Cell 76:453-472 e458. PMC6842445

Gorkin DU, Qiu Y, Hu M, Fletez-Brant K, Liu T, Schmitt AD, Noor A, Chiou J, Gaulton KJ, Sebat J, Li Y, Hansen KD, Ren B (2019) Common DNA sequence variation influences 3-dimensional conformation of the human genome. Genome Biol 20:255. PMC6883528

Jung I, Schmitt A, Diao Y, Lee AJ, Liu T, Yang D, Tan C, Eom J, Chan M, Chee S, Chiang Z, Kim C, et al (2019) A compendium of promoter-centered long-range chromatin interactions in the human genome. Nat Genet 51:1442-1449. PMC6778519

Rosa-Garrido M, Chapski DJ, Schmitt AD, Kimball TH, Karbassi E, Monte E, Balderas E, Pellegrini M, Shih TT, Soehalim E, Liem D, Ping P, et al (2017) High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure. Circulation 136:1613-1625. PMC5648689

Fang R, Yu M, Li G, Chee S, Liu T, Schmitt AD, Ren B (2016) Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res 26:1345-1348. PMC5143423

Schmitt AD, Hu M, Jung I, Xu Z, Qiu Y, Tan CL, Li Y, Lin S, Lin Y, Barr CL, Ren B (2016) A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. Cell Rep 17:2042-2059. PMC5478386

Schmitt AD, Hu M, Ren B (2016) Genome-wide mapping and analysis of chromosome architecture. Nat Rev Mol Cell Biol 17:743-755. PMC5763923

Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, et al (2016) Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation. Nature 530:242.

Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, et al (2015) Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature 518:350-354. PMC4449149

Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, et al (2015) Human body epigenome maps reveal noncanonical DNA methylation variation. Nature 523:212-216. PMC4499021

Selvaraj S, Schmitt AD, Dixon JR, Ren B (2015) Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq. BMC Genomics 16:900. PMC4636068

Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B (2013) A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503:290-294. PMC3838900

  

Sam Stoner

Entry program: Biomedical Sciences
Advisor: Dong-Er Zhang
Next position: Senior Scientist, Pfizer
Current position: Senior Scientist, Pfizer
 

Publications 

Davis AG, Johnson DT, Zheng D, Wang R, Jayne ND, Liu M, Shin J, Wang L, Stoner SA, Zhou JH, Ball ED, Tian B, Zhang DE (2021) Alternative polyadenylation dysregulation contributes to the differentiation block of acute myeloid leukemia. Blood.

Stoner SA, Liu KTH, Andrews ET, Liu M, Arimoto KI, Yan M, Davis AG, Weng S, Dow M, Xian S, DeKelver RC, Carter H, Zhang DE (2020) The RUNX1-ETO target gene RASSF2 suppresses t(8;21) AML development and regulates Rac GTPase signaling. Blood Cancer J 10:16. PMC7005177

Stoner SA, Yan M, Liu KTH, Arimoto KI, Shima T, Wang HY, Johnson DT, Bejar R, Jamieson C, Guan KL, Zhang DE (2019) Hippo kinase loss contributes to del(20q) hematologic malignancies through chronic innate immune activation. Blood 134:1730-1744. PMC6856986

Arimoto KI, Miyauchi S, Stoner SA, Fan JB, Zhang DE (2018) Negative regulation of type I IFN signaling. J Leukoc Biol.

Arimoto KI, Lochte S, Stoner SA, Burkart C, Zhang Y, Miyauchi S, Wilmes S, Fan JB, Heinisch JJ, Li Z, Yan M, Pellegrini S, et al (2017) STAT2 is an essential adaptor in USP18-mediated suppression of type I interferon signaling. Nat Struct Mol Biol 24:279-289. PMC5365074

Weng S, Matsuura S, Mowery CT, Stoner SA, Lam K, Ran D, Davis AG, Lo MC, Zhang DE (2017) Restoration of MYC-repressed targets mediates the negative effects of GM-CSF on RUNX1-ETO leukemogenicity. Leukemia 31:159-169. PMC5214981

Weng S, Stoner SA, Zhang DE (2016) Sex chromosome loss and the pseudoautosomal region genes in hematological malignancies. Oncotarget 7:72356-72372. PMC5342167

  

2012 Trainees

Karmel Allison

Entry program: Bioinformatics & Systems Biology
Advisor: Chris Glass
Next position: Data Scientist at Genia Technologies
Current position: Technical Advisor in the Office of the CTO, Microsoft
email: karmel@arcaio.com
"Happy to talk to anyone about: AI, AI/ML as applied to bio, working in Big Tech, balancing work & family, being a woman in engineering, and whatever’s on your mind."
 

Publications

Delpoux A, Marcel N, Hess Michelini R, Katayama CD, Allison KA, Glass CK, Quinones-Parra SM, Murre C, Loh L, Kedzierska K, Lappas M, Hedrick SM, Doedens AL (2021) FOXO1 constrains activation and regulates senescence in CD8 T cells. Cell Rep 34:108674.

Allison KA, Sajti E, Collier JG, Gosselin D, Troutman TD, Stone EL, Hedrick SM, Glass CK (2016) Affinity and dose of TCR engagement yield proportional enhancer and gene activity in CD4+ T cells. Elife 5. PMC4931909

Davis-Turak JC, Allison K, Shokhirev MN, Ponomarenko P, Tsimring LS, Glass CK, Johnson TL, Hoffmann A (2015) Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing. Nucleic Acids Res 43:699-707. PMC4333389

Allison KA, Kaikkonen MU, Gaasterland T, Glass CK (2014) Vespucci: a system for building annotated databases of nascent transcripts. Nucleic Acids Res 42:2433-2447. PMC3936758

Heinz S, Romanoski CE, Benner C, Allison KA, Kaikkonen MU, Orozco LD, Glass CK (2013) Effect of natural genetic variation on enhancer selection and function. Nature 503:487-492. PMC3994126

Kaikkonen MU, Spann NJ, Heinz S, Romanoski CE, Allison KA, Stender JD, Chun HB, Tough DF, Prinjha RK, Benner C, Glass CK (2013) Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol Cell 51:310-325. PMC3779836

 

Babette Hammerling

Entry program: Biomedical Sciences
Advisor: Åsa Gustafsson
Next position: Technical Applications Scientist I, Illumina
Current position: Senior Technical Applications Scientist, Illumina

Publications

Hammerling BC, Shires SE, Leon LJ, Cortez MQ, Gustafsson AB (2020) Isolation of Rab5-positive endosomes reveals a new mitochondrial degradation pathway utilized by BNIP3 and Parkin. Small GTPases 11:69-76. PMC6959301

Lampert MA, Orogo AM, Najor RH, Hammerling BC, Leon LJ, Wang BJ, Kim T, Sussman MA, Gustafsson AB (2019) BNIP3L/NIX and FUNDC1-mediated mitophagy is required for mitochondrial network remodeling during cardiac progenitor cell differentiation. Autophagy 15:1182-1198. PMC6613840

Hammerling BC, Najor RH, Cortez MQ, Shires SE, Leon LJ, Gonzalez ER, Boassa D, Phan S, Thor A, Jimenez RE, Li H, Kitsis RN, et al (2017) A Rab5 endosomal pathway mediates Parkin-dependent mitochondrial clearance. Nat Commun 8:14050. PMC5290275

Hammerling BC, Gustafsson AB (2014) Mitochondrial quality control in the myocardium: cooperation between protein degradation and mitophagy. J Mol Cell Cardiol 75:122-130. PMC4159946

  

Cynthia Hsu

Entry program: Biomedical Sciences/MSTP
Advisor: Albert La Spada
Next position: Gastroenterology Fellow, UC San Diego
Current position: Gastroenterology Fellow, UC San Diego
 
Publications

Hsu CL, Lee EX, Gordon KL, Paz EA, Shen WC, Ohnishi K, Meisenhelder J, Hunter T, La Spada AR (2018) MAP4K3 mediates amino acid-dependent regulation of autophagy via phosphorylation of TFEB. Nat Commun 9:942. PMC5838220

Dickey AS, Sanchez DN, Arreola M, Sampat KR, Fan W, Arbez N, Akimov S, Van Kanegan MJ, Ohnishi K, Gilmore-Hall SK, Flores AL, Nguyen JM, et al (2017) PPARdelta activation by bexarotene promotes neuroprotection by restoring bioenergetic and quality control homeostasis. Sci Transl Med 9. PMC5748332

Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, Adachi H, Adams CM, Adams PD, Adeli K, Adhihetty PJ, Adler SG, et al (2016) Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy 12:1-222. PMC4835977

Dubinsky AN, Dastidar SG, Hsu CL, Zahra R, Djakovic SN, Duarte S, Esau CC, Spencer B, Ashe TD, Fischer KM, MacKenna DA, Sopher BL, et al (2014) Let-7 coordinately suppresses components of the amino acid sensing pathway to repress mTORC1 and induce autophagy. Cell Metab 20:626-638. PMC4245205

 

Fernando Martinez

Entry program: Biomedical Sciences
Advisor: Gene Yeo
Next position: Scientist, Verge Genomics
Current position: Senior Scientist, Fountain Therapeutics
 

Publications

Pirie E, Oh CK, Zhang X, Han X, Cieplak P, Scott HR, Deal AK, Ghatak S, Martinez FJ, Yeo GW, Yates JR, 3rd, Nakamura T, Lipton SA (2021) S-nitrosylated TDP-43 triggers aggregation, cell-to-cell spread, and neurotoxicity in hiPSCs and in vivo models of ALS/FTD. Proc Natl Acad Sci U S A 118. PMC7980404

Kapeli K, Martinez FJ, Yeo GW (2017) Genetic mutations in RNA-binding proteins and their roles in ALS. Hum Genet 136:1193-1214. PMC5602095

Kapeli K, Pratt GA, Vu AQ, Hutt KR, Martinez FJ, Sundararaman B, Batra R, Freese P, Lambert NJ, Huelga SC, Chun SJ, Liang TY, et al (2016) Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. Nat Commun 7:12143. PMC4935974

Martinez FJ, Pratt GA, Van Nostrand EL, Batra R, Huelga SC, Kapeli K, Freese P, Chun SJ, Ling K, Gelboin-Burkhart C, Fijany L, Wang HC, et al (2016) Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System. Neuron 92:780-795. PMC5123850

Lee SR, Pratt GA, Martinez FJ, Yeo GW, Lykke-Andersen J (2015) Target Discrimination in Nonsense-Mediated mRNA Decay Requires Upf1 ATPase Activity. Mol Cell 59:413-425. PMC4673969

 

Gabriel Pratt

Entry program: Bioinformatics & Systems Biology
Advisor: Gene Yeo
Next position: Bioinformatics Scientist, TwinStrand Biosciences
Current position: Applied Scientist, Amazon
email: 
 

Publications

Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R, Blue SM, Chen JY, Cody NAL, Dominguez D, Olson S, Sundararaman B, et al (2021) Author Correction: A large-scale binding and functional map of human RNA-binding proteins. Nature 589:E5. PMC7962576

Luo EC, Nathanson JL, Tan FE, Schwartz JL, Schmok JC, Shankar A, Markmiller S, Yee BA, Sathe S, Pratt GA, Scaletta DB, Ha Y, et al (2020) Large-scale tethered function assays identify factors that regulate mRNA stability and translation. Nat Struct Mol Biol 27:989-1000. PMC8221285

Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R, Blue SM, Chen JY, Cody NAL, Dominguez D, Olson S, Sundararaman B, et al (2020) A large-scale binding and functional map of human RNA-binding proteins. Nature 583:711-719. PMC7410833

Van Nostrand EL, Pratt GA, Yee BA, Wheeler EC, Blue SM, Mueller J, Park SS, Garcia KE, Gelboin-Burkhart C, Nguyen TB, Rabano I, Stanton R, et al (2020) Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins. Genome Biol 21:90. PMC7137325

Quinones-Valdez G, Tran SS, Jun HI, Bahn JH, Yang EW, Zhan L, Brummer A, Wei X, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Xiao X (2019) Regulation of RNA editing by RNA-binding proteins in human cells. Commun Biol 2:19. PMC6331435 scientific advisory boards of Locana, Eclipse Bioinnovations and Aquinnah Pharmaceuticals. E.V.N is a co-founder and member of the scientific advisory board of Eclipse BioInnovations. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. The remaining authors declare no competing interests.

Tran SS, Jun HI, Bahn JH, Azghadi A, Ramaswami G, Van Nostrand EL, Nguyen TB, Hsiao YE, Lee C, Pratt GA, Martinez-Cerdeno V, Hagerman RJ, et al (2019) Widespread RNA editing dysregulation in brains from autistic individuals. Nat Neurosci 22:25-36. PMC6375307

Yang EW, Bahn JH, Hsiao EY, Tan BX, Sun Y, Fu T, Zhou B, Van Nostrand EL, Pratt GA, Freese P, Wei X, Quinones-Valdez G, et al (2019) Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA. Nat Commun 10:1338. PMC6430814

Yee BA, Pratt GA, Graveley BR, Van Nostrand EL, Yeo GW (2019) RBP-Maps enables robust generation of splicing regulatory maps. RNA 25:193-204. PMC6348990

Dominguez D, Freese P, Alexis MS, Su A, Hochman M, Palden T, Bazile C, Lambert NJ, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Burge CB (2018) Sequence, Structure, and Context Preferences of Human RNA Binding Proteins. Mol Cell 70:854-867 e859. PMC6062212

Van Nostrand EL, Gelboin-Burkhart C, Wang R, Pratt GA, Blue SM, Yeo GW (2017) CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins. Methods 118-119:50-59. PMC5411315

Van Nostrand EL, Nguyen TB, Gelboin-Burkhart C, Wang R, Blue SM, Pratt GA, Louie AL, Yeo GW (2017) Erratum to: Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP). Methods Mol Biol 1648:E1.

Van Nostrand EL, Nguyen TB, Gelboin-Burkhart C, Wang R, Blue SM, Pratt GA, Louie AL, Yeo GW (2017) Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP). Methods Mol Biol 1648:177-200. PMC5991800

Van Nostrand EL, Shishkin AA, Pratt GA, Nguyen TB, Yeo GW (2017) Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions. Methods 126:29-37. PMC5582984

Brannan KW, Jin W, Huelga SC, Banks CA, Gilmore JM, Florens L, Washburn MP, Van Nostrand EL, Pratt GA, Schwinn MK, Daniels DL, Yeo GW (2016) SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes. Mol Cell 64:282-293. PMC5074894

Conway AE, Van Nostrand EL, Pratt GA, Aigner S, Wilbert ML, Sundararaman B, Freese P, Lambert NJ, Sathe S, Liang TY, Essex A, Landais S, et al (2016) Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. Cell Rep 15:666-679. PMC4839292

Kapeli K, Pratt GA, Vu AQ, Hutt KR, Martinez FJ, Sundararaman B, Batra R, Freese P, Lambert NJ, Huelga SC, Chun SJ, Liang TY, et al (2016) Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. Nat Commun 7:12143. PMC4935974

Martinez FJ, Pratt GA, Van Nostrand EL, Batra R, Huelga SC, Kapeli K, Freese P, Chun SJ, Ling K, Gelboin-Burkhart C, Fijany L, Wang HC, et al (2016) Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System. Neuron 92:780-795. PMC5123850

Rentas S, Holzapfel N, Belew MS, Pratt G, Voisin V, Wilhelm BT, Bader GD, Yeo GW, Hope KJ (2016) Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells. Nature 532:508-511. PMC4880456

Sundararaman B, Zhan L, Blue SM, Stanton R, Elkins K, Olson S, Wei X, Van Nostrand EL, Pratt GA, Huelga SC, Smalec BM, Wang X, et al (2016) Resources for the Comprehensive Discovery of Functional RNA Elements. Mol Cell 61:903-913. PMC4839293

Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang MY, Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, Stanton R, Rigo F, Guttman M, Yeo GW (2016) Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13:508-514. PMC4887338

Hung T, Pratt GA, Sundararaman B, Townsend MJ, Chaivorapol C, Bhangale T, Graham RR, Ortmann W, Criswell LA, Yeo GW, Behrens TW (2015) The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. Science 350:455-459. PMC4691329

Lee SR, Pratt GA, Martinez FJ, Yeo GW, Lykke-Andersen J (2015) Target Discrimination in Nonsense-Mediated mRNA Decay Requires Upf1 ATPase Activity. Mol Cell 59:413-425. PMC4673969

Singh G, Pratt G, Yeo GW, Moore MJ (2015) The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion. Annu Rev Biochem 84:325-354. PMC4804868

Lovci MT, Ghanem D, Marr H, Arnold J, Gee S, Parra M, Liang TY, Stark TJ, Gehman LT, Hoon S, Massirer KB, Pratt GA, et al (2013) Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol 20:1434-1442. PMC3918504

  

Eric Scott

Entry program: Bioinformatics & Systems Biology
Advisor: Joseph Gleeson
Next position: Bioinformatics Scientist II
Current position: Associate Director of Bioinformatics, Grail Inc.
email: escott55@gmail.com

Publications 

Maffucci P, Bigio B, Rapaport F, Cobat A, Borghesi A, Lopez M, Patin E, Bolze A, Shang L, Bendavid M, Scott EM, Stenson PD, et al (2019) Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis. Proc Natl Acad Sci U S A 116:950-959. PMC6338851

Marin-Valencia I, Novarino G, Johansen A, Rosti B, Issa MY, Musaev D, Bhat G, Scott E, Silhavy JL, Stanley V, Rosti RO, Gleeson JW, et al (2018) A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features. J Med Genet 55:48-54. PMC6056005

Schaffer AE, Breuss MW, Caglayan AO, Al-Sanaa N, Al-Abdulwahed HY, Kaymakcalan H, Yilmaz C, Zaki MS, Rosti RO, Copeland B, Baek ST, Musaev D, et al (2018) Biallelic loss of human CTNNA2, encoding alphaN-catenin, leads to ARP2/3 complex overactivity and disordered cortical neuronal migration. Nat Genet 50:1093-1101. PMC6072555

Breuss MW, Nguyen T, Srivatsan A, Leca I, Tian G, Fritz T, Hansen AH, Musaev D, McEvoy-Venneri J, James KN, Rosti RO, Scott E, et al (2017) Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability. Hum Mol Genet 26:258-269. PMC6075555

Lardelli RM, Schaffer AE, Eggens VR, Zaki MS, Grainger S, Sathe S, Van Nostrand EL, Schlachetzki Z, Rosti B, Akizu N, Scott E, Silhavy JL, et al (2017) Biallelic mutations in the 3' exonuclease TOE1 cause pontocerebellar hypoplasia and uncover a role in snRNA processing. Nat Genet 49:457-464. PMC5325768

Breuss MW, Sultan T, James KN, Rosti RO, Scott E, Musaev D, Furia B, Reis A, Sticht H, Al-Owain M, Alkuraya FS, Reuter MS, et al (2016) Autosomal-Recessive Mutations in the tRNA Splicing Endonuclease Subunit TSEN15 Cause Pontocerebellar Hypoplasia and Progressive Microcephaly. Am J Hum Genet 99:785. PMC5011070

Breuss MW, Sultan T, James KN, Rosti RO, Scott E, Musaev D, Furia B, Reis A, Sticht H, Al-Owain M, Alkuraya FS, Reuter MS, et al (2016) Autosomal-Recessive Mutations in the tRNA Splicing Endonuclease Subunit TSEN15 Cause Pontocerebellar Hypoplasia and Progressive Microcephaly. Am J Hum Genet 99:228-235. PMC5005448

Itan Y, Shang L, Boisson B, Ciancanelli MJ, Markle JG, Martinez-Barricarte R, Scott E, Shah I, Stenson PD, Gleeson J, Cooper DN, Quintana-Murci L, et al (2016) The mutation significance cutoff: gene-level thresholds for variant predictions. Nat Methods 13:109-110. PMC4980758

Kim JH, Ki SM, Joung JG, Scott E, Heynen-Genel S, Aza-Blanc P, Kwon CH, Kim J, Gleeson JG, Lee JE (2016) Genome-wide screen identifies novel machineries required for both ciliogenesis and cell cycle arrest upon serum starvation. Biochim Biophys Acta 1863:1307-1318. PMC4886714

Scott EM, Halees A, Itan Y, Spencer EG, He Y, Azab MA, Gabriel SB, Belkadi A, Boisson B, Abel L, Clark AG, Greater Middle East Variome C, et al (2016) Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery. Nat Genet 48:1071-1076. PMC5019950

Akizu N, Cantagrel V, Zaki MS, Al-Gazali L, Wang X, Rosti RO, Dikoglu E, Gelot AB, Rosti B, Vaux KK, Scott EM, Silhavy JL, et al (2015) Biallelic mutations in SNX14 cause a syndromic form of cerebellar atrophy and lysosome-autophagosome dysfunction. Nat Genet 47:528-534. PMC4414867

Guemez-Gamboa A, Nguyen LN, Yang H, Zaki MS, Kara M, Ben-Omran T, Akizu N, Rosti RO, Rosti B, Scott E, Schroth J, Copeland B, et al (2015) Inactivating mutations in MFSD2A, required for omega-3 fatty acid transport in brain, cause a lethal microcephaly syndrome. Nat Genet 47:809-813. PMC4547531

Itan Y, Shang L, Boisson B, Patin E, Bolze A, Moncada-Velez M, Scott E, Ciancanelli MJ, Lafaille FG, Markle JG, Martinez-Barricarte R, de Jong SJ, et al (2015) The human gene damage index as a gene-level approach to prioritizing exome variants. Proc Natl Acad Sci U S A 112:13615-13620. PMC4640721

Roosing S, Hofree M, Kim S, Scott E, Copeland B, Romani M, Silhavy JL, Rosti RO, Schroth J, Mazza T, Miccinilli E, Zaki MS, et al (2015) Functional genome-wide siRNA screen identifies KIAA0586 as mutated in Joubert syndrome. Elife 4:e06602. PMC4477441

Akizu N, Silhavy JL, Rosti RO, Scott E, Fenstermaker AG, Schroth J, Zaki MS, Sanchez H, Gupta N, Kabra M, Kara M, Ben-Omran T, et al (2014) Mutations in CSPP1 lead to classical Joubert syndrome. Am J Hum Genet 94:80-86. PMC3882909

Law R, Dixon-Salazar T, Jerber J, Cai N, Abbasi AA, Zaki MS, Mittal K, Gabriel SB, Rafiq MA, Khan V, Nguyen M, Ali G, et al (2014) Biallelic truncating mutations in FMN2, encoding the actin-regulatory protein Formin 2, cause nonsyndromic autosomal-recessive intellectual disability. Am J Hum Genet 95:721-728. PMC4259997

Novarino G, Fenstermaker AG, Zaki MS, Hofree M, Silhavy JL, Heiberg AD, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, et al (2014) Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science 343:506-511. PMC4157572

Schaffer AE, Eggens VR, Caglayan AO, Reuter MS, Scott E, Coufal NG, Silhavy JL, Xue Y, Kayserili H, Yasuno K, Rosti RO, Abdellateef M, et al (2014) CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration. Cell 157:651-663. PMC4128918

Akizu N, Cantagrel V, Schroth J, Cai N, Vaux K, McCloskey D, Naviaux RK, Van Vleet J, Fenstermaker AG, Silhavy JL, Scheliga JS, Toyama K, et al (2013) AMPD2 regulates GTP synthesis and is mutated in a potentially treatable neurodegenerative brainstem disorder. Cell 154:505-517. PMC3815927

Akizu N, Shembesh NM, Ben-Omran T, Bastaki L, Al-Tawari A, Zaki MS, Koul R, Spencer E, Rosti RO, Scott E, Nickerson E, Gabriel S, et al (2013) Whole-exome sequencing identifies mutated c12orf57 in recessive corpus callosum hypoplasia. Am J Hum Genet 92:392-400. PMC3591854

Kim S, Jeong K, Bhutani K, Lee J, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V (2013) Virmid: accurate detection of somatic mutations with sample impurity inference. Genome Biol 14:R90. PMC4054681

Travaglini L, Brancati F, Silhavy J, Iannicelli M, Nickerson E, Elkhartoufi N, Scott E, Spencer E, Gabriel S, Thomas S, Ben-Zeev B, Bertini E, et al (2013) Phenotypic spectrum and prevalence of INPP5E mutations in Joubert syndrome and related disorders. Eur J Hum Genet 21:1074-1078. PMC3778343

Lee JH, Huynh M, Silhavy JL, Kim S, Dixon-Salazar T, Heiberg A, Scott E, Bafna V, Hill KJ, Collazo A, Funari V, Russ C, et al (2012) De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly. Nat Genet 44:941-945. PMC4417942

Novarino G, El-Fishawy P, Kayserili H, Meguid NA, Scott EM, Schroth J, Silhavy JL, Kara M, Khalil RO, Ben-Omran T, Ercan-Sencicek AG, Hashish AF, et al (2012) Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy. Science 338:394-397. PMC3704165

  

Naomi (Frank) Searle

Entry program: Biomedical Sciences
Advisor: Lorraine Pillus
Next position: Annotation Scientist, Invivoscribe
Current position: Annotation Scientist, Invivoscribe

Publications

Searle NE, Pillus L (2018) Critical genomic regulation mediated by Enhancer of Polycomb. Curr Genet 64:147-154. PMC6287951

Searle NE, Torres-Machorro AL, Pillus L (2017) Chromatin Regulation by the NuA4 Acetyltransferase Complex Is Mediated by Essential Interactions Between Enhancer of Polycomb (Epl1) and Esa1. Genetics 205:1125-1137. PMC5340328

  

Michael Yu

Entry program: Bioinformatics & Systems Biology
Advisor: Trey Ideker
Next position: Postdoctoral Fellow, UC San Diego
Current position: Research Assistant Professor at Toyota Technological Institute at Chicago
email: 
 

Publications

van de Haar J, Canisius S, Yu MK, Voest EE, Wessels LFA, Ideker T (2019) Identifying Epistasis in Cancer Genomes: A Delicate Affair. Cell 177:1375-1383. PMC6816465

Yu MK, Ma J, Ono K, Zheng F, Fong SH, Gary A, Chen J, Demchak B, Pratt D, Ideker T (2019) DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies. Cell Syst 8:267-273 e263. PMC7042149

Huang JK, Carlin DE, Yu MK, Zhang W, Kreisberg JF, Tamayo P, Ideker T (2018) Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. Cell Syst 6:484-495 e485. PMC5920724

Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T (2018) Using deep learning to model the hierarchical structure and function of a cell. Nat Methods 15:290-298. PMC5882547

Wang S, Ma J, Yu MK, Zheng F, Huang EW, Han J, Peng J, Ideker T (2018) Annotating gene sets by mining large literature collections with protein networks. Pac Symp Biocomput 23:602-613. PMC5806628

Yu MK, Ma J, Fisher J, Kreisberg JF, Raphael BJ, Ideker T (2018) Visible Machine Learning for Biomedicine. Cell 173:1562-1565. PMC6483071

Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, et al (2018) A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genet 50:613-620. PMC5893414

Kramer MH, Farre JC, Mitra K, Yu MK, Ono K, Demchak B, Licon K, Flagg M, Balakrishnan R, Cherry JM, Subramani S, Ideker T (2017) Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. Mol Cell 65:761-774 e765. PMC5439305

Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T (2017) Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biol 18:57. PMC5371228

Yu MK, Kramer M, Dutkowski J, Srivas R, Licon K, Kreisberg J, Ng CT, Krogan N, Sharan R, Ideker T (2016) Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems. Cell Syst 2:77-88. PMC4772745

Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T (2014) NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res 42:D1269-1274. PMC3965056

Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T (2014) Inferring gene ontologies from pairwise similarity data. Bioinformatics 30:i34-42. PMC4058954

  

2011 Trainees

Jacqueline Benthuysen (PhD, 2016)

Entry program: Biomedical Sciences
Advisor: Maike Sander
Next position: Postdoctoral Fellow, Celgene
Current position: Technical Application Specialist II, Luminex/Diasorin

Publications 

Wortham M, Benthuysen JR, Wallace M, Savas JN, Mulas F, Divakaruni AS, Liu F, Albert V, Taylor BL, Sui Y, Saez E, Murphy AN, et al (2018) Integrated In Vivo Quantitative Proteomics and Nutrient Tracing Reveals Age-Related Metabolic Rewiring of Pancreatic beta Cell Function. Cell Rep 25:2904-2918 e2908. PMC6317899

Benthuysen JR, Carrano AC, Sander M (2016) Advances in beta cell replacement and regeneration strategies for treating diabetes. J Clin Invest 126:3651-3660. PMC5096826

Taylor BL, Benthuysen J, Sander M (2015) Postnatal beta-cell proliferation and mass expansion is dependent on the transcription factor Nkx6.1. Diabetes 64:897-903. PMC4338594

Schaffer AE, Taylor BL, Benthuysen JR, Liu J, Thorel F, Yuan W, Jiao Y, Kaestner KH, Herrera PL, Magnuson MA, May CL, Sander M (2013) Nkx6.1 controls a gene regulatory network required for establishing and maintaining pancreatic Beta cell identity. PLoS Genet 9:e1003274. PMC3561089

 

Christopher DeBoever

Entry program: Bioinformatics & Systems Biology
Advisor: Kelly Frazer
Next position: Postdoctoral Researcher, Stanford University
Current position: Senior Scientist Statistical Genetics, Takeda Development Center Americas
  

Publications 

Benaglio P, D'Antonio-Chronowska A, Ma W, Yang F, Young Greenwald WW, Donovan MKR, DeBoever C, Li H, Drees F, Singhal S, Matsui H, van Setten J, et al (2019) Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits. Nat Genet 51:1506-1517. PMC6858543

DeBoever C, Li H, Jakubosky D, Benaglio P, Reyna J, Olson KM, Huang H, Biggs W, Sandoval E, D'Antonio M, Jepsen K, Matsui H, et al (2017) Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells. Cell Stem Cell 20:533-546 e537. PMC5444918

M DA, Weghorn D, A DA-C, Coulet F, Olson KM, DeBoever C, Drees F, Arias A, Alakus H, Richardson AL, Schwab RB, Farley EK, Sunyaev SR, Frazer KA (2017) Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer. Nat Commun 8:436. PMC5585396

Nariai N, Greenwald WW, DeBoever C, Li H, Frazer KA (2017) Efficient Prioritization of Multiple Causal eQTL Variants via Sparse Polygenic Modeling. Genetics 207:1301-1312. PMC5714449

Panopoulos AD, D'Antonio M, Benaglio P, Williams R, Hashem SI, Schuldt BM, DeBoever C, Arias AD, Garcia M, Nelson BC, Harismendy O, Jakubosky DA, et al (2017) iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types. Stem Cell Reports 8:1086-1100. PMC5390244

Cui B, Ghia EM, Chen L, Rassenti LZ, DeBoever C, Widhopf GF, 2nd, Yu J, Neuberg DS, Wierda WG, Rai KR, Kay NE, Brown JR, et al (2016) High-level ROR1 associates with accelerated disease progression in chronic lymphocytic leukemia. Blood 128:2931-2940. PMC5179332

Barrett CL, DeBoever C, Jepsen K, Saenz CC, Carson DA, Frazer KA (2015) Systematic transcriptome analysis reveals tumor-specific isoforms for ovarian cancer diagnosis and therapy. Proc Natl Acad Sci U S A 112:E3050-3057. PMC4466751

DeBoever C, Ghia EM, Shepard PJ, Rassenti L, Barrett CL, Jepsen K, Jamieson CH, Carson D, Kipps TJ, Frazer KA (2015) Transcriptome sequencing reveals potential mechanism of cryptic 3' splice site selection in SF3B1-mutated cancers. PLoS Comput Biol 11:e1004105. PMC4358997

Smith EN, Ghia EM, DeBoever CM, Rassenti LZ, Jepsen K, Yoon KA, Matsui H, Rozenzhak S, Alakus H, Shepard PJ, Dai Y, Khosroheidari M, et al (2015) Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development. Blood Cancer J 5:e303. PMC4450323

Cheng CP, DeBoever C, Frazer KA, Liu YC, Tseng VS (2014) MiningABs: mining associated biomarkers across multi-connected gene expression datasets. BMC Bioinformatics 15:173. PMC4068973

DeBoever C, Reid EG, Smith EN, Wang X, Dumaop W, Harismendy O, Carson D, Richman D, Masliah E, Frazer KA (2013) Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas. PLoS One 8:e73956. PMC3762708

  

Lawrence Du

Entry program: Biological Sciences
Advisor: Scott Rifkin
Next position: Machine Learning Consultant for Juno Diagnostics (4 person startup at the time)
Current position: 23andme - Software Engineer Machine Learning
email: larrydu88@gmail.com
 

Publications 

Du L, Tracy S, Rifkin SA (2016) Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements. Dev Biol 412:160-170. PMC4814310

 

Lauren Fong

Entry program: Biomedical Sciences
Advisor: Larry Goldstein
Next position: Biotech
Current position: Senior Scientist, Fate Therapeutics
 

Publications 

Almenar-Queralt A, Merkurjev D, Kim HS, Navarro M, Ma Q, Chaves RS, Allegue C, Driscoll SP, Chen AG, Kohlnhofer B, Fong LK, Woodruff G, et al (2019) Chromatin establishes an immature version of neuronal protocadherin selection during the naive-to-primed conversion of pluripotent stem cells. Nat Genet 51:1691-1701. PMC7061033

van der Kant R, Langness VF, Herrera CM, Williams DA, Fong LK, Leestemaker Y, Steenvoorden E, Rynearson KD, Brouwers JF, Helms JB, Ovaa H, Giera M, et al (2019) Cholesterol Metabolism Is a Druggable Axis that Independently Regulates Tau and Amyloid-beta in iPSC-Derived Alzheimer's Disease Neurons. Cell Stem Cell 24:363-375 e369. PMC6414424

Fong LK, Yang MM, Dos Santos Chaves R, Reyna SM, Langness VF, Woodruff G, Roberts EA, Young JE, Goldstein LSB (2018) Full-length amyloid precursor protein regulates lipoprotein metabolism and amyloid-beta clearance in human astrocytes. J Biol Chem 293:11341-11357. PMC6065173

Young JE, Fong LK, Frankowski H, Petsko GA, Small SA, Goldstein LSB (2018) Stabilizing the Retromer Complex in a Human Stem Cell Model of Alzheimer's Disease Reduces TAU Phosphorylation Independently of Amyloid Precursor Protein. Stem Cell Reports 10:1046-1058. PMC5919412

   

Jonathan Grinstein

Entry program: Biomedical Sciences
Advisor: Neil Chi
Next position: Science Writer, 101 Network
Current position: Science Writer and Editor 
  

Publications 

Zhang Y, Li T, Preissl S, Amaral ML, Grinstein JD, Farah EN, Destici E, Qiu Y, Hu R, Lee AY, Chee S, Ma K, et al (2019) Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. Nat Genet 51:1380-1388. PMC6722002

Veevers J, Farah EN, Corselli M, Witty AD, Palomares K, Vidal JG, Emre N, Carson CT, Ouyang K, Liu C, van Vliet P, Zhu M, et al (2018) Cell-Surface Marker Signature for Enrichment of Ventricular Cardiomyocytes Derived from Human Embryonic Stem Cells. Stem Cell Reports 11:828-841. PMC6135222

Panopoulos AD, D'Antonio M, Benaglio P, Williams R, Hashem SI, Schuldt BM, DeBoever C, Arias AD, Garcia M, Nelson BC, Harismendy O, Jakubosky DA, et al (2017) iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types. Stem Cell Reports 8:1086-1100. PMC5390244

Han P, Bloomekatz J, Ren J, Zhang R, Grinstein JD, Zhao L, Burns CG, Burns CE, Anderson RM, Chi NC (2016) Coordinating cardiomyocyte interactions to direct ventricular chamber morphogenesis. Nature 534:700-704. PMC5330678

 

Amanda Mason

Entry program: 
Advisor: Albert La Spada
Next position: Postdoc, Leiden University Medical Center
Current position: Technical Support Specialist, MRC Holland
 

Publications 

Mason AG, Garza RM, McCormick MA, Patel B, Kennedy BK, Pillus L, La Spada AR (2017) The replicative lifespan-extending deletion of SGF73 results in altered ribosomal gene expression in yeast. Aging Cell 16:785-796. PMC5506417

Mason AG, Tome S, Simard JP, Libby RT, Bammler TK, Beyer RP, Morton AJ, Pearson CE, La Spada AR (2014) Expression levels of DNA replication and repair genes predict regional somatic repeat instability in the brain but are not altered by polyglutamine disease protein expression or age. Hum Mol Genet 23:1606-1618. PMC3929096

McCormick MA, Mason AG, Guyenet SJ, Dang W, Garza RM, Ting MK, Moller RM, Berger SL, Kaeberlein M, Pillus L, La Spada AR, Kennedy BK (2014) The SAGA histone deubiquitinase module controls yeast replicative lifespan via Sir2 interaction. Cell Rep 8:477-486. PMC4284099

Bennett CL, Chen Y, Vignali M, Lo RS, Mason AG, Unal A, Huq Saifee NP, Fields S, La Spada AR (2013) Protein interaction analysis of senataxin and the ALS4 L389S mutant yields insights into senataxin post-translational modification and uncovers mutant-specific binding with a brain cytoplasmic RNA-encoded peptide. PLoS One 8:e78837. PMC3823977

Chakrabarti L, Zahra R, Jackson SM, Kazemi-Esfarjani P, Sopher BL, Mason AG, Toneff T, Ryu S, Shaffer S, Kansy JW, Eng J, Merrihew G, et al (2010) Mitochondrial dysfunction in NnaD mutant flies and Purkinje cell degeneration mice reveals a role for Nna proteins in neuronal bioenergetics. Neuron 66:835-847. PMC3101252

  

Panid Sharifnia

Entry program: Neurosciences/MSTP
Advisor: Yishi Jin
Next position: Resident Physician, UC San Francisco
Current position: Psychiatrist, San Francisco
 

Publications 

Andrusiak MG, Sharifnia P, Lyu X, Wang Z, Dickey AM, Wu Z, Chisholm AD, Jin Y (2019) Inhibition of Axon Regeneration by Liquid-like TIAR-2 Granules. Neuron 104:290-304 e298. PMC6813885

Sharifnia P, Kim KW, Wu Z, Jin Y (2017) Distinct cis elements in the 3' UTR of the C. elegans cebp-1 mRNA mediate its regulation in neuronal development. Dev Biol 429:240-248. PMC5828015

Sharifnia P, Jin Y (2014) Regulatory roles of RNA binding proteins in the nervous system of C. elegans. Front Mol Neurosci 7:100. PMC4290612

Kurup N, Sharifnia P, Jin Y (2013) Spatial and temporal dynamics of neurite regrowth. Curr Opin Neurobiol 23:1011-1017. PMC3833091

  

2010 Trainees

Allen Acab

Entry program: Biomedical Sciences
Advisor: Alysson Muotri
Next position: Scientist I, Prognosys Biosciences
Current position: Scientist at Quest Diagnostics
 
Publications

Trujillo CA, Adams JW, Negraes PD, Carromeu C, Tejwani L, Acab A, Tsuda B, Thomas CA, Sodhi N, Fichter KM, Romero S, Zanella F, et al (2021) Pharmacological reversal of synaptic and network pathology in human MECP2-KO neurons and cortical organoids. EMBO Mol Med 13:e12523. PMC7799367

Zhang ZN, Freitas BC, Qian H, Lux J, Acab A, Trujillo CA, Herai RH, Nguyen Huu VA, Wen JH, Joshi-Barr S, Karpiak JV, Engler AJ, et al (2016) Layered hydrogels accelerate iPSC-derived neuronal maturation and reveal migration defects caused by MeCP2 dysfunction. Proc Natl Acad Sci U S A 113:3185-3190. PMC4812712

Acab A, Muotri AR (2015) The Use of Induced Pluripotent Stem Cell Technology to Advance Autism Research and Treatment. Neurotherapeutics 12:534-545. PMC4489954

Griesi-Oliveira K, Acab A, Gupta AR, Sunaga DY, Chailangkarn T, Nicol X, Nunez Y, Walker MF, Murdoch JD, Sanders SJ, Fernandez TV, Ji W, et al (2015) Modeling non-syndromic autism and the impact of TRPC6 disruption in human neurons. Mol Psychiatry 20:1350-1365. PMC4427554

Chailangkarn T, Acab A, Muotri AR (2012) Modeling neurodevelopmental disorders using human neurons. Curr Opin Neurobiol 22:785-790. PMC3587787

Marchetto MC, Carromeu C, Acab A, Yu D, Yeo GW, Mu Y, Chen G, Gage FH, Muotri AR (2010) A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells. Cell 143:527-539. PMC3003590

  

Alexa Clemmons

Entry program: Biological Sciences
Advisor: Steven Wasserman
Next position: Postdoctoral Research Associate
Current position: Director of Product at Codon Learning 
 

Publications 

Clemmons AW, Lindsay SA, Wasserman SA (2015) An effector Peptide family required for Drosophila toll-mediated immunity. PLoS Pathog 11:e1004876. PMC4411088

Clemmons AW, Wasserman SA (2013) Combinatorial effects of transposable elements on gene expression and phenotypic robustness in Drosophila melanogaster development. G3 (Bethesda) 3:1531-1538. PMC3755913

 

Jennifer Higginbotham

Entry program: Biomedical Sciences
Advisor: Clodagh O'Shea
Next position: Technical Writing Consultant, Allele Biotechnology
Current position: CMC Senior Writer, Global Regulatory Writing & Consulting
 

Publictions 

Higginbotham JM, O'Shea CC (2015) Adenovirus E4-ORF3 Targets PIAS3 and Together with E1B-55K Remodels SUMO Interactions in the Nucleus and at Virus Genome Replication Domains. J Virol 89:10260-10272. PMC4580165

 

Jason Lehmann

Entry program: Biomedical Sciences
Advisor: Victor Nizet
Next position: Postdoc, University of Florida
Current position: Product Marketing Manager at Codex DNA
 

Publications 

Lehmann JS, Corey VC, Ricaldi JN, Vinetz JM, Winzeler EA, Matthias MA (2016) Whole Genome Shotgun Sequencing Shows Selection on Leptospira Regulatory Proteins During in vitro Culture Attenuation. Am J Trop Med Hyg 94:302-313. PMC4751964

Lehmann JS, Matthias MA, Vinetz JM, Fouts DE (2014) Leptospiral pathogenomics. Pathogens 3:280-308. PMC4243447

Lehmann JS, Fouts DE, Haft DH, Cannella AP, Ricaldi JN, Brinkac L, Harkins D, Durkin S, Sanka R, Sutton G, Moreno A, Vinetz JM, Matthias MA (2013) Pathogenomic inference of virulence-associated genes in Leptospira interrogans. PLoS Negl Trop Dis 7:e2468. PMC3789758

Ricaldi JN, Fouts DE, Selengut JD, Harkins DM, Patra KP, Moreno A, Lehmann JS, Purushe J, Sanka R, Torres M, Webster NJ, Vinetz JM, Matthias MA (2012) Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. PLoS Negl Trop Dis 6:e1853. PMC3493377

 

Sol Reyna

Entry program: Biomedical Sciences
Advisor: Larry Goldstein
Next position: Life Sciences Specialist, L.E.K. Consulting
Current position: Director, Head of Strategic Operations at Laronde
 

Publications 

Fong LK, Yang MM, Dos Santos Chaves R, Reyna SM, Langness VF, Woodruff G, Roberts EA, Young JE, Goldstein LSB (2018) Full-length amyloid precursor protein regulates lipoprotein metabolism and amyloid-beta clearance in human astrocytes. J Biol Chem 293:11341-11357. PMC6065173

D'Antonio M, Woodruff G, Nathanson JL, D'Antonio-Chronowska A, Arias A, Matsui H, Williams R, Herrera C, Reyna SM, Yeo GW, Goldstein LSB, Panopoulos AD, Frazer KA (2017) High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells. Stem Cell Reports 8:1101-1111. PMC5390243

Woodruff G, Reyna SM, Dunlap M, Van Der Kant R, Callender JA, Young JE, Roberts EA, Goldstein LS (2016) Defective Transcytosis of APP and Lipoproteins in Human iPSC-Derived Neurons with Familial Alzheimer's Disease Mutations. Cell Rep 17:759-773. PMC5796664

Goldstein LS, Reyna S, Woodruff G (2015) Probing the secrets of Alzheimer's disease using human-induced pluripotent stem cell technology. Neurotherapeutics 12:121-125. PMC4322074

Niederst ED, Reyna SM, Goldstein LS (2015) Axonal amyloid precursor protein and its fragments undergo somatodendritic endocytosis and processing. Mol Biol Cell 26:205-217. PMC4294669

Weissmiller AM, Natera-Naranjo O, Reyna SM, Pearn ML, Zhao X, Nguyen P, Cheng S, Goldstein LS, Tanzi RE, Wagner SL, Mobley WC, Wu C (2015) A gamma-secretase inhibitor, but not a gamma-secretase modulator, induced defects in BDNF axonal trafficking and signaling: evidence for a role for APP. PLoS One 10:e0118379. PMC4339551

Heinzen EL, Swoboda KJ, Hitomi Y, Gurrieri F, Nicole S, de Vries B, Tiziano FD, Fontaine B, Walley NM, Heavin S, Panagiotakaki E, European Alternating Hemiplegia of Childhood Genetics C, et al (2012) De novo mutations in ATP1A3 cause alternating hemiplegia of childhood. Nat Genet 44:1030-1034. PMC3442240

Israel MA, Yuan SH, Bardy C, Reyna SM, Mu Y, Herrera C, Hefferan MP, Van Gorp S, Nazor KL, Boscolo FS, Carson CT, Laurent LC, et al (2012) Probing sporadic and familial Alzheimer's disease using induced pluripotent stem cells. Nature 482:216-220. PMC3338985

   

Suzannah Szumowski

Entry program: Biological Sciences
Advisor: Emily Troemel
Next position: Scientist, ThermoFisher
Current position: Technical Applications Scientist, Illumina
 

Publications 

Szumowski SC, Estes KA, Popovich JJ, Botts MR, Sek G, Troemel ER (2016) Small GTPases promote actin coat formation on microsporidian pathogens traversing the apical membrane of Caenorhabditis elegans intestinal cells. Cell Microbiol 18:30-45. PMC5522806

Szumowski SC, Troemel ER (2015) Microsporidia-host interactions. Curr Opin Microbiol 26:10-16. PMC4577307

Szumowski SC, Botts MR, Popovich JJ, Smelkinson MG, Troemel ER (2014) The small GTPase RAB-11 directs polarized exocytosis of the intracellular pathogen N. parisii for fecal-oral transmission from C. elegans. Proc Natl Acad Sci U S A 111:8215-8220. PMC4050618

Szumowski SC, Estes KA, Troemel ER (2012) Preparing a discreet escape: Microsporidia reorganize host cytoskeleton prior to non-lytic exit from C. elegans intestinal cells. Worm 1:207-211. PMC3670220

Estes KA, Szumowski SC, Troemel ER (2011) Non-lytic, actin-based exit of intracellular parasites from C. elegans intestinal cells. PLoS Pathog 7:e1002227. PMC3174248

 

Tiffany Taylor

Entry program: Biomedical Sciences
Advisor: Frank Furnari
Next position: Christine Mirzayan Science and Technology Policy Fellow, The National Academies of Sciences, Engineering, and Medicine
Current position: Program Officer, The National Academies of Sciences, Engineering, and Medicine
 

Publications 

Wykosky J, Hu J, Gomez GG, Taylor T, Villa GR, Pizzo D, VandenBerg SR, Thorne AH, Chen CC, Mischel PS, Gonias SL, Cavenee WK, Furnari FB (2015) A urokinase receptor-Bim signaling axis emerges during EGFR inhibitor resistance in mutant EGFR glioblastoma. Cancer Res 75:394-404. PMC4297573

Taylor TE, Furnari FB, Cavenee WK (2012) Targeting EGFR for treatment of glioblastoma: molecular basis to overcome resistance. Curr Cancer Drug Targets 12:197-209. PMC3464093

  

Grace Woodruff

Entry program: Biomedical Sciences
Advisor: Larry Goldstein
Next position: Postdoc, The Janssen Pharmaceutical Companies of Johnson & Johnson
Current position: Senior Scientist, The Janssen Pharmaceutical Companies of Johnson & Johnson
 

Publications 

Almenar-Queralt A, Merkurjev D, Kim HS, Navarro M, Ma Q, Chaves RS, Allegue C, Driscoll SP, Chen AG, Kohlnhofer B, Fong LK, Woodruff G, et al (2019) Chromatin establishes an immature version of neuronal protocadherin selection during the naive-to-primed conversion of pluripotent stem cells. Nat Genet 51:1691-1701. PMC7061033

Fong LK, Yang MM, Dos Santos Chaves R, Reyna SM, Langness VF, Woodruff G, Roberts EA, Young JE, Goldstein LSB (2018) Full-length amyloid precursor protein regulates lipoprotein metabolism and amyloid-beta clearance in human astrocytes. J Biol Chem 293:11341-11357. PMC6065173

D'Antonio M, Woodruff G, Nathanson JL, D'Antonio-Chronowska A, Arias A, Matsui H, Williams R, Herrera C, Reyna SM, Yeo GW, Goldstein LSB, Panopoulos AD, Frazer KA (2017) High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells. Stem Cell Reports 8:1101-1111. PMC5390243

Woodruff G, Reyna SM, Dunlap M, Van Der Kant R, Callender JA, Young JE, Roberts EA, Goldstein LS (2016) Defective Transcytosis of APP and Lipoproteins in Human iPSC-Derived Neurons with Familial Alzheimer's Disease Mutations. Cell Rep 17:759-773. PMC5796664

Goldstein LS, Reyna S, Woodruff G (2015) Probing the secrets of Alzheimer's disease using human-induced pluripotent stem cell technology. Neurotherapeutics 12:121-125. PMC4322074

Young JE, Boulanger-Weill J, Williams DA, Woodruff G, Buen F, Revilla AC, Herrera C, Israel MA, Yuan SH, Edland SD, Goldstein LS (2015) Elucidating molecular phenotypes caused by the SORL1 Alzheimer's disease genetic risk factor using human induced pluripotent stem cells. Cell Stem Cell 16:373-385. PMC4388804

Liu Q, Waltz S, Woodruff G, Ouyang J, Israel MA, Herrera C, Sarsoza F, Tanzi RE, Koo EH, Ringman JM, Goldstein LS, Wagner SL, Yuan SH (2014) Effect of potent gamma-secretase modulator in human neurons derived from multiple presenilin 1-induced pluripotent stem cell mutant carriers. JAMA Neurol 71:1481-1489. PMC4374637

Lu P, Woodruff G, Wang Y, Graham L, Hunt M, Wu D, Boehle E, Ahmad R, Poplawski G, Brock J, Goldstein LS, Tuszynski MH (2014) Long-distance axonal growth from human induced pluripotent stem cells after spinal cord injury. Neuron 83:789-796. PMC4144679

Woodruff G, Young JE, Martinez FJ, Buen F, Gore A, Kinaga J, Li Z, Yuan SH, Zhang K, Goldstein LS (2013) The presenilin-1 DeltaE9 mutation results in reduced gamma-secretase activity, but not total loss of PS1 function, in isogenic human stem cells. Cell Rep 5:974-985. PMC3867011

 

2009 Trainees

Gordon Bean

Entry program: Bioinformatics & Systems Biology
Advisor: Trey Ideker
Next position: Bioinformatics Scientist, Illumina
Current position: Senior Bioinformatics Scientist, Illumina
 

Publications 

Ming Sun S, Batte A, Elmer M, van der Horst SC, van Welsem T, Bean G, Ideker T, van Leeuwen F, van Attikum H (2020) A genetic interaction map centered on cohesin reveals auxiliary factors involved in sister chromatid cohesion in S. cerevisiae. J Cell Sci 133. PMC7325435

Silva E, Michaca M, Munson B, Bean GJ, Jaeger PA, Licon K, Winzeler EA, Ideker T (2020) Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response. G3 (Bethesda) 10:2981-2988. PMC7466999

Bean GJ, Jaeger PA, Bahr S, Ideker T (2014) Development of ultra-high-density screening tools for microbial "omics". PLoS One 9:e85177. PMC3897414

Bean GJ, Ideker T (2012) Differential analysis of high-throughput quantitative genetic interaction data. Genome Biol 13:R123. PMC4056373

  

Anne (Conway) Gable

Entry program: Biomedical Sciences
Advisor: Leanne Jones and Gene Yeo
Next position: Postdoc, UC San Diego
Current position: Senior Marketing Product Manager, Miltenyi Biotec
  

Publications 

Conway AE, Van Nostrand EL, Pratt GA, Aigner S, Wilbert ML, Sundararaman B, Freese P, Lambert NJ, Sathe S, Liang TY, Essex A, Landais S, et al (2016) Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. Cell Rep 15:666-679. PMC4839292

  

Michael Lam

Entry program: Biomedical Sciences/MSTP
Advisor: Chris Glass
Next position: 
Current position: Associate Physician, UC San Diego
  

Publications  

Hogan NT, Whalen MB, Stolze LK, Hadeli NK, Lam MT, Springstead JR, Glass CK, Romanoski CE (2017) Transcriptional networks specifying homeostatic and inflammatory programs of gene expression in human aortic endothelial cells. Elife 6. PMC5461113

Oishi Y, Spann NJ, Link VM, Muse ED, Strid T, Edillor C, Kolar MJ, Matsuzaka T, Hayakawa S, Tao J, Kaikkonen MU, Carlin AF, et al (2017) SREBP1 Contributes to Resolution of Pro-inflammatory TLR4 Signaling by Reprogramming Fatty Acid Metabolism. Cell Metab 25:412-427. PMC5568699

Eichenfield DZ, Troutman TD, Link VM, Lam MT, Cho H, Gosselin D, Spann NJ, Lesch HP, Tao J, Muto J, Gallo RL, Evans RM, Glass CK (2016) Tissue damage drives co-localization of NF-kappaB, Smad3, and Nrf2 to direct Rev-erb sensitive wound repair in mouse macrophages. Elife 5. PMC4963201

Lam MT, Li W, Rosenfeld MG, Glass CK (2014) Enhancer RNAs and regulated transcriptional programs. Trends Biochem Sci 39:170-182. PMC4266492

Lam MT, Cho H, Lesch HP, Gosselin D, Heinz S, Tanaka-Oishi Y, Benner C, Kaikkonen MU, Kim AS, Kosaka M, Lee CY, Watt A, et al (2013) Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature 498:511-515. PMC3839578

Shibata N, Carlin AF, Spann NJ, Saijo K, Morello CS, McDonald JG, Romanoski CE, Maurya MR, Kaikkonen MU, Lam MT, Crotti A, Reichart D, et al (2013) 25-Hydroxycholesterol activates the integrated stress response to reprogram transcription and translation in macrophages. J Biol Chem 288:35812-35823. PMC3861632

Cho H, Zhao X, Hatori M, Yu RT, Barish GD, Lam MT, Chong LW, DiTacchio L, Atkins AR, Glass CK, Liddle C, Auwerx J, et al (2012) Regulation of circadian behaviour and metabolism by REV-ERB-alpha and REV-ERB-beta. Nature 485:123-127. PMC3367514

Harmon GS, Lam MT, Glass CK (2011) PPARs and lipid ligands in inflammation and metabolism. Chem Rev 111:6321-6340. PMC3437919

Kaikkonen MU, Lam MT, Glass CK (2011) Non-coding RNAs as regulators of gene expression and epigenetics. Cardiovasc Res 90:430-440. PMC3096308

 

Mark Moyle

Entry program: Biomedical Sciences
Advisor: Arshad Desai
Next position: Postdoc, Daniel Colón-Ramos lab, Yale
Current position: Postdoc, Daniel Colón-Ramos lab, Yale
  

Publications 

Lara-Gonzalez P, Moyle MW, Budrewicz J, Mendoza-Lopez J, Oegema K, Desai A (2019) The G2-to-M Transition Is Ensured by a Dual Mechanism that Protects Cyclin B from Degradation by Cdc20-Activated APC/C. Dev Cell 51:313-325 e310. PMC7778526

Hattersley N, Cheerambathur D, Moyle M, Stefanutti M, Richardson A, Lee KY, Dumont J, Oegema K, Desai A (2016) A Nucleoporin Docks Protein Phosphatase 1 to Direct Meiotic Chromosome Segregation and Nuclear Assembly. Dev Cell 38:463-477. PMC5094371

Kim T, Moyle MW, Lara-Gonzalez P, De Groot C, Oegema K, Desai A (2016) Correction: Kinetochore-localized BUB-1/BUB-3 complex promotes anaphase onset in C. elegans. J Cell Biol 212:737. PMC4792070

Kim T, Moyle MW, Lara-Gonzalez P, De Groot C, Oegema K, Desai A (2015) Kinetochore-localized BUB-1/BUB-3 complex promotes anaphase onset in C. elegans. J Cell Biol 209:507-517. PMC4442812

Moyle MW, Kim T, Hattersley N, Espeut J, Cheerambathur DK, Oegema K, Desai A (2014) A Bub1-Mad1 interaction targets the Mad1-Mad2 complex to unattached kinetochores to initiate the spindle checkpoint. J Cell Biol 204:647-657. PMC3941058

  

Chloe Rivera

Entry program: Biomedical Sciences
Advisor: Bing Ren
Next position: Engagement Manager, McKinsey & Company
Current position: Senior Director, Transformation in R & D, AbbVie
  

Publications 

Larsson AJM, Johnsson P, Hagemann-Jensen M, Hartmanis L, Faridani OR, Reinius B, Segerstolpe A, Rivera CM, Ren B, Sandberg R (2019) Genomic encoding of transcriptional burst kinetics. Nature 565:251-254. PMC7610481

Yan J, Chen SA, Local A, Liu T, Qiu Y, Dorighi KM, Preissl S, Rivera CM, Wang C, Ye Z, Ge K, Hu M, Wysocka J, Ren B (2018) Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers. Cell Res 28:387. PMC5835777

Yan J, Chen SA, Local A, Liu T, Qiu Y, Dorighi KM, Preissl S, Rivera CM, Wang C, Ye Z, Ge K, Hu M, Wysocka J, Ren B (2018) Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers. Cell Res 28:204-220. PMC5799818

Li Y, Rivera CM, Ishii H, Jin F, Selvaraj S, Lee AY, Dixon JR, Ren B (2014) CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells. PLoS One 9:e114485. PMC4259346

Rivera CM, Ren B (2013) Mapping human epigenomes. Cell 155:39-55. PMC3838898

  

Thomas Stark

Entry program: Biological Sciences
Advisor: Gene Yeo
Next position: Postdoc, CDC
Current position: Health Scientist Informatics, CDC
  

Publications 

Gould TW, Dominguez B, de Winter F, Yeo GW, Liu P, Sundararaman B, Stark T, Vu A, Degen JL, Lin W, Lee KF (2019) Glial cells maintain synapses by inhibiting an activity-dependent retrograde protease signal. PLoS Genet 15:e1007948. PMC6417855

Batra R, Stark TJ, Clark E, Belzile JP, Wheeler EC, Yee BA, Huang H, Gelboin-Burkhart C, Huelga SC, Aigner S, Roberts BT, Bos TJ, et al (2016) RNA-binding protein CPEB1 remodels host and viral RNA landscapes. Nat Struct Mol Biol 23:1101-1110. PMC5140759

Belzile JP, Stark TJ, Yeo GW, Spector DH (2014) Human cytomegalovirus infection of human embryonic stem cell-derived primitive neural stem cells is restricted at several steps but leads to the persistence of viral DNA. J Virol 88:4021-4039. PMC3993748

Van Wynsberghe PM, Finnegan EF, Stark T, Angelus EP, Homan KE, Yeo GW, Pasquinelli AE (2014) The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans. Dev Biol 390:126-135. PMC4077587

Lovci MT, Ghanem D, Marr H, Arnold J, Gee S, Parra M, Liang TY, Stark TJ, Gehman LT, Hoon S, Massirer KB, Pratt GA, et al (2013) Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol 20:1434-1442. PMC3918504

Stark TJ, Arnold JD, Spector DH, Yeo GW (2012) High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection. J Virol 86:226-235. PMC3255895

Wilbert ML, Huelga SC, Kapeli K, Stark TJ, Liang TY, Chen SX, Yan BY, Nathanson JL, Hutt KR, Lovci MT, Kazan H, Vu AQ, et al (2012) LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance. Mol Cell 48:195-206. PMC3483422

  

Melissa Wilbert

Entry program: Biomedical Sciences
Advisor: Gene Yeo
Next position: Computational Biologist, Novartis Institutes for BioMedical Research
Current position: Senior Clinical Informatics Specialist, Roswell Park Comprehensive Cancer Center
  

Publications 

Conway AE, Van Nostrand EL, Pratt GA, Aigner S, Wilbert ML, Sundararaman B, Freese P, Lambert NJ, Sathe S, Liang TY, Essex A, Landais S, et al (2016) Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. Cell Rep 15:666-679. PMC4839292

Wilbert ML, Huelga SC, Kapeli K, Stark TJ, Liang TY, Chen SX, Yan BY, Nathanson JL, Hutt KR, Lovci MT, Kazan H, Vu AQ, et al (2012) LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance. Mol Cell 48:195-206. PMC3483422

Wilbert ML, Yeo GW (2011) Genome-wide approaches in the study of microRNA biology. Wiley Interdiscip Rev Syst Biol Med 3:491-512. PMC3482411

Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo GW (2010) Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat Struct Mol Biol 17:173-179. PMC2834287

 

Susan Zhang

Entry program: Biomedical Sciences
Advisor: Bruce Hamilton
Next position: Postdoc, Vijay Kalra lab, USC
Current position: Postdoc, Vijay Kalra lab, USC
  

Publications 

Zhang S, Ross KD, Seidner GA, Gorman MR, Poon TH, Wang X, Keithley EM, Lee PN, Martindale MQ, Joiner WJ, Hamilton BA (2015) Nmf9 Encodes a Highly Conserved Protein Important to Neurological Function in Mice and Flies. PLoS Genet 11:e1005344. PMC4488434

  

2008 Trainees

A. Taylor Bright

Entry program: Biomedical Sciences
Advisor: Elizabeth Winzeler
Next position: Co-founder and Chief Operating Officer, Novoron Biosciences
Current position: Co-founder and Chief Operating Officer, Novoron Biosciences
 

Publications 

Flannery EL, Wang T, Akbari A, Corey VC, Gunawan F, Bright AT, Abraham M, Sanchez JF, Santolalla ML, Baldeviano GC, Edgel KA, Rosales LA, et al (2015) Next-Generation Sequencing of Plasmodium vivax Patient Samples Shows Evidence of Direct Evolution in Drug-Resistance Genes. ACS Infect Dis 1:367-379. PMC4692371

Bright AT, Manary MJ, Tewhey R, Arango EM, Wang T, Schork NJ, Yanow SK, Winzeler EA (2014) A high resolution case study of a patient with recurrent Plasmodium vivax infections shows that relapses were caused by meiotic siblings. PLoS Negl Trop Dis 8:e2882. PMC4046966

Manary MJ, Singhakul SS, Flannery EL, Bopp SE, Corey VC, Bright AT, McNamara CW, Walker JR, Winzeler EA (2014) Identification of pathogen genomic variants through an integrated pipeline. BMC Bioinformatics 15:63. PMC3945619

Bopp SE, Manary MJ, Bright AT, Johnston GL, Dharia NV, Luna FL, McCormack S, Plouffe D, McNamara CW, Walker JR, Fidock DA, Denchi EL, Winzeler EA (2013) Mitotic evolution of Plasmodium falciparum shows a stable core genome but recombination in antigen families. PLoS Genet 9:e1003293. PMC3567157

Bright AT, Alenazi T, Shokoples S, Tarning J, Paganotti GM, White NJ, Houston S, Winzeler EA, Yanow SK (2013) Genetic analysis of primaquine tolerance in a patient with relapsing vivax malaria. Emerg Infect Dis 19:802-805. PMC3647516

Bright AT, Winzeler EA (2013) Epidemiology: resistance mapping in malaria. Nature 498:446-447.

McCarthy JS, Griffin PM, Sekuloski S, Bright AT, Rockett R, Looke D, Elliott S, Whiley D, Sloots T, Winzeler EA, Trenholme KR (2013) Experimentally induced blood-stage Plasmodium vivax infection in healthy volunteers. J Infect Dis 208:1688-1694. PMC3888148

Bright AT, Tewhey R, Abeles S, Chuquiyauri R, Llanos-Cuentas A, Ferreira MU, Schork NJ, Vinetz JM, Winzeler EA (2012) Whole genome sequencing analysis of Plasmodium vivax using whole genome capture. BMC Genomics 13:262. PMC3410760

Harbut MB, Patel BA, Yeung BK, McNamara CW, Bright AT, Ballard J, Supek F, Golde TE, Winzeler EA, Diagana TT, Greenbaum DC (2012) Targeting the ERAD pathway via inhibition of signal peptide peptidase for antiparasitic therapeutic design. Proc Natl Acad Sci U S A 109:21486-21491. PMC3535666

Bright AT, Winzeler EA (2011) Noncoding RNA, antigenic variation, and the virulence genes of Plasmodium falciparum. BMC Biol 9:50. PMC3141604

Meister S, Plouffe DM, Kuhen KL, Bonamy GM, Wu T, Barnes SW, Bopp SE, Borboa R, Bright AT, Che J, Cohen S, Dharia NV, et al (2011) Imaging of Plasmodium liver stages to drive next-generation antimalarial drug discovery. Science 334:1372-1377. PMC3473092

Dharia NV, Bright AT, Westenberger SJ, Barnes SW, Batalov S, Kuhen K, Borboa R, Federe GC, McClean CM, Vinetz JM, Neyra V, Llanos-Cuentas A, et al (2010) Whole-genome sequencing and microarray analysis of ex vivo Plasmodium vivax reveal selective pressure on putative drug resistance genes. Proc Natl Acad Sci U S A 107:20045-20050. PMC2993397

Dvorin JD, Martyn DC, Patel SD, Grimley JS, Collins CR, Hopp CS, Bright AT, Westenberger S, Winzeler E, Blackman MJ, Baker DA, Wandless TJ, Duraisingh MT (2010) A plant-like kinase in Plasmodium falciparum regulates parasite egress from erythrocytes. Science 328:910-912. PMC3109083

   

Britt Flaherty

Entry program: Biological Sciences
Advisor: Tracy Johnson and James Golden
Next position: Technical Applications Scientist, Illumina
Current position: Executive Sequencing Specialist, Illumina
email: brittflaherty@gmail.com
"Informational interviews are critical in planning your first steps after grad school. What you do in the 5 years after you graduate sets up your career for life, so learn about and explore your options now."
 

Publications  

Flaherty BL, Johnson DB, Golden JW (2014) Deep sequencing of HetR-bound DNA reveals novel HetR targets in Anabaena sp. strain PCC7120. BMC Microbiol 14:255. PMC4192349

Flaherty BL, Van Nieuwerburgh F, Head SR, Golden JW (2011) Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation. BMC Genomics 12:332. PMC3141674

   

David Kochman

Entry program: Biomedical Sciences
Advisor: Joseph Gleeson
Next position: Contractor, OrchidGene
Current position: Principle Scientist, Novoron Bioscience
 

 

Julianne McCall

Entry program: Biomedical Sciences
Advisor: Mark Tuszynski and Armin Blesch
Next position: Transfer to University of Heidelberg
Current position: Co-Director of Precision Medicine, California Governor's Office of Planning & Research
 

Publications 

McCall J, Nicholson L, Weidner N, Blesch A (2012) Optimization of adult sensory neuron electroporation to study mechanisms of neurite growth. Front Mol Neurosci 5:11. PMC3274834

McCall J, Weidner N, Blesch A (2012) Neurotrophic factors in combinatorial approaches for spinal cord regeneration. Cell Tissue Res 349:27-37. PMC3376183

  

Jeff Nelson

Entry program: Biological Sciences
Advisor: Steve Kay
Next position: Postdoc, James Thomson lab, Morgridge Institute for Research
Current position: Product Manager at Promega Corporation 
   

Pagkapol Pongsawakul

Entry program: Biological Sciences
Advisor: Steve Kay
Next position: 
Current position: Lecturer, Mahidol University, Thailind
  

Publications 

Hirota T, Lee JW, St John PC, Sawa M, Iwaisako K, Noguchi T, Pongsawakul PY, Sonntag T, Welsh DK, Brenner DA, Doyle FJ, 3rd, Schultz PG, Kay SA (2012) Identification of small molecule activators of cryptochrome. Science 337:1094-1097. PMC3589997

Zhang EE, Liu Y, Dentin R, Pongsawakul PY, Liu AC, Hirota T, Nusinow DA, Sun X, Landais S, Kodama Y, Brenner DA, Montminy M, Kay SA (2010) Cryptochrome mediates circadian regulation of cAMP signaling and hepatic gluconeogenesis. Nat Med 16:1152-1156. PMC2952072

Zhang EE, Liu AC, Hirota T, Miraglia LJ, Welch G, Pongsawakul PY, Liu X, Atwood A, Huss JW, 3rd, Janes J, Su AI, Hogenesch JB, Kay SA (2009) A genome-wide RNAi screen for modifiers of the circadian clock in human cells. Cell 139:199-210. PMC2777987

   

Erilynn (Russo) Heinrichsen

Entry program: Biomedical Sciences
Advisor: Gabriel Haddad
Next position: IRACDA Postdoc, UC San Diego
Current position: Education Specialist, Engaged Teaching, Teaching + Learning Commons, UC San Diego
 

Publications 

Stobdan T, Sahoo D, Azad P, Hartley I, Heinrichsen E, Zhou D, Haddad GG (2019) High fat diet induces sex-specific differential gene expression in Drosophila melanogaster. PLoS One 14:e0213474. PMC6413938

Heinrichsen ET, Zhang H, Robinson JE, Ngo J, Diop S, Bodmer R, Joiner WJ, Metallo CM, Haddad GG (2014) Metabolic and transcriptional response to a high-fat diet in Drosophila melanogaster. Mol Metab 3:42-54. PMC3929909

Heinrichsen ET, Haddad GG (2012) Role of high-fat diet in stress response of Drosophila. PLoS One 7:e42587. PMC3411628

Azad P, Zhou D, Russo E, Haddad GG (2009) Distinct mechanisms underlying tolerance to intermittent and constant hypoxia in Drosophila melanogaster. PLoS One 4:e5371. PMC2670512

  

Deanna Stevens

Entry program: Biomedical Sciences
Advisor: Arshad Desai
 

Publications 

Monen J, Hattersley N, Muroyama A, Stevens D, Oegema K, Desai A (2015) Separase Cleaves the N-Tail of the CENP-A Related Protein CPAR-1 at the Meiosis I Metaphase-Anaphase Transition in C. elegans. PLoS One 10:e0125382. PMC4412405

Shen Y, Li J, Nitta M, Futalan D, Steed T, Treiber JM, Taich Z, Stevens D, Wykosky J, Chen HZ, Carter BS, Becher OJ, et al (2015) Orthogonal targeting of EGFRvIII expressing glioblastomas through simultaneous EGFR and PLK1 inhibition. Oncotarget 6:11751-11767. PMC4494902

Stevens D, Oegema K, Desai A (2013) Meiotic double-strand breaks uncover and protect against mitotic errors in the C. elegans germline. Curr Biol 23:2400-2406. PMC3885542

Stevens D, Gassmann R, Oegema K, Desai A (2011) Uncoordinated loss of chromatid cohesion is a common outcome of extended metaphase arrest. PLoS One 6:e22969. PMC3149067 

  

Emily (Witham) Meadows

Entry program: Biomedical Sciences
Advisor: Pamela Mellon
Next position: Postdoc, Supriya Srinivasan lab, The Scripps Research Institute
Current position: Scientist II at Novartis Gene Therapies
 

Publications 

Ryan GE, Bohaczuk SC, Cassin J, Witham EA, Shojaei S, Ho EV, Thackray VG, Mellon PL (2021) Androgen receptor positively regulates gonadotropin-releasing hormone receptor in pituitary gonadotropes. Mol Cell Endocrinol 530:111286. PMC8177864

Witham EA, Meadows JD, Hoffmann HM, Shojaei S, Coss D, Kauffman AS, Mellon PL (2013) Kisspeptin regulates gonadotropin genes via immediate early gene induction in pituitary gonadotropes. Mol Endocrinol 27:1283-1294. PMC3725344

Xie H, Cherrington BD, Meadows JD, Witham EA, Mellon PL (2013) Msx1 homeodomain protein represses the alphaGSU and GnRH receptor genes during gonadotrope development. Mol Endocrinol 27:422-436. PMC3589667

Witham EA, Meadows JD, Shojaei S, Kauffman AS, Mellon PL (2012) Prenatal exposure to low levels of androgen accelerates female puberty onset and reproductive senescence in mice. Endocrinology 153:4522-4532. PMC3423623

 

2007 Trainees

Thomas Cohen

Entry program: Biomedical Sciences
Advisor: Fred Levine
Next position: Postdoc, Rob Mitra lab, Washington University School of Medicine
Current position: Senior Analyst, BioGenerator Ventures
 

Publications 

Cohen T, Sundaresh S, Levine F (2013) Antipsychotics activate the TGFbeta pathway effector SMAD3. Mol Psychiatry 18:347-357. PMC3991551

Lee SH, Athavankar S, Cohen T, Piran R, Kiselyuk A, Levine F (2013) Identification of alverine and benfluorex as HNF4alpha activators. ACS Chem Biol 8:1730-1736. PMC3922238

Kiselyuk A, Lee SH, Farber-Katz S, Zhang M, Athavankar S, Cohen T, Pinkerton AB, Ye M, Bushway P, Richardson AD, Hostetler HA, Rodriguez-Lee M, et al (2012) HNF4alpha antagonists discovered by a high-throughput screen for modulators of the human insulin promoter. Chem Biol 19:806-818. PMC3447631

Kiselyuk A, Farber-Katz S, Cohen T, Lee SH, Geron I, Azimi B, Heynen-Genel S, Singer O, Price J, Mercola M, Itkin-Ansari P, Levine F (2010) Phenothiazine neuroleptics signal to the human insulin promoter as revealed by a novel high-throughput screen. J Biomol Screen 15:663-670. PMC3374493

 

Rafael Gomez-Amaro

Entry program: Biomedical Sciences
Advisor: Sylvia Evans
Next position: Postdoc, Michael Petrascheck lab, The Scripps Research Institute
Current position: Scientific Advisor, BD Biosciences
email: rgomezamaro1@gmail.com

Publications 

Moore-Morris T, Guimaraes-Camboa N, Banerjee I, Zambon AC, Kisseleva T, Velayoudon A, Stallcup WB, Gu Y, Dalton ND, Cedenilla M, Gomez-Amaro R, Zhou B, et al (2014) Resident fibroblast lineages mediate pressure overload-induced cardiac fibrosis. J Clin Invest 124:2921-2934. PMC4071409

Ouyang K, Leandro Gomez-Amaro R, Stachura DL, Tang H, Peng X, Fang X, Traver D, Evans SM, Chen J (2014) Loss of IP3R-dependent Ca2+ signalling in thymocytes leads to aberrant development and acute lymphoblastic leukemia. Nat Commun 5:4814. PMC5537137

  

Stephanie Nissen Bussen

Entry program: Biomedical Sciences
Advisor: John Kelsoe
Next position: Clinical Data Coordinator, Synteract
Current position: Associate Director, Data Management, BioAtla
 

Publications

Nissen S, Liang S, Shehktman T, Kelsoe JR, Bipolar Genome S, Greenwood TA, Nievergelt CM, McKinney R, Shilling PD, Smith EN, Schork NJ, Bloss CS, et al (2012) Evidence for association of bipolar disorder to haplotypes in the 22q12.3 region near the genes stargazin, IFT27 and parvalbumin. Am J Med Genet B Neuropsychiatr Genet 159B:941-950. PMC3665332

McCarthy MJ, Barrett TB, Nissen S, Kelsoe JR, Turner EE (2010) Allele specific analysis of the ADRBK2 gene in lymphoblastoid cells from bipolar disorder patients. J Psychiatr Res 44:201-208. PMC2830298

  

Morgan Pence

Entry program: Biomedical Sciences
Advisor: Victor Nizet
Next position: 
Current position: Director, Clinical and Molecular Microbiology at Cook Children's Health Care System
  

Publications 

Pence MA, Haste NM, Meharena HS, Olson J, Gallo RL, Nizet V, Kristian SA (2015) Beta-Lactamase Repressor BlaI Modulates Staphylococcus aureus Cathelicidin Antimicrobial Peptide Resistance and Virulence. PLoS One 10:e0136605. PMC4549145

Gonzalez DJ, Okumura CY, Hollands A, Kersten R, Akong-Moore K, Pence MA, Malone CL, Derieux J, Moore BS, Horswill AR, Dixon JE, Dorrestein PC, Nizet V (2012) Novel phenol-soluble modulin derivatives in community-associated methicillin-resistant Staphylococcus aureus identified through imaging mass spectrometry. J Biol Chem 287:13889-13898. PMC3340166

Cole JN, Pence MA, von Kockritz-Blickwede M, Hollands A, Gallo RL, Walker MJ, Nizet V (2010) M protein and hyaluronic acid capsule are essential for in vivo selection of covRS mutations characteristic of invasive serotype M1T1 group A Streptococcus. mBio 1. PMC2934611

Hollands A, Pence MA, Timmer AM, Osvath SR, Turnbull L, Whitchurch CB, Walker MJ, Nizet V (2010) Genetic switch to hypervirulence reduces colonization phenotypes of the globally disseminated group A streptococcus M1T1 clone. J Infect Dis 202:11-19. PMC2880657

Pence MA, Rooijakkers SH, Cogen AL, Cole JN, Hollands A, Gallo RL, Nizet V (2010) Streptococcal inhibitor of complement promotes innate immune resistance phenotypes of invasive M1T1 group A Streptococcus. J Innate Immun 2:587-595. PMC3219503

Courtney HS, Ofek I, Penfound T, Nizet V, Pence MA, Kreikemeyer B, Podbielski A, Hasty DL, Dale JB (2009) Relationship between expression of the family of M proteins and lipoteichoic acid to hydrophobicity and biofilm formation in Streptococcus pyogenes. PLoS One 4:e4166. PMC2613554

Cox KH, Ruiz-Bustos E, Courtney HS, Dale JB, Pence MA, Nizet V, Aziz RK, Gerling I, Price SM, Hasty DL (2009) Inactivation of DltA modulates virulence factor expression in Streptococcus pyogenes. PLoS One 4:e5366. PMC2671602

Mitchell DA, Lee SW, Pence MA, Markley AL, Limm JD, Nizet V, Dixon JE (2009) Structural and functional dissection of the heterocyclic peptide cytotoxin streptolysin S. J Biol Chem 284:13004-13012. PMC2676033

Timmer AM, Timmer JC, Pence MA, Hsu LC, Ghochani M, Frey TG, Karin M, Salvesen GS, Nizet V (2009) Streptolysin O promotes group A Streptococcus immune evasion by accelerated macrophage apoptosis. J Biol Chem 284:862-871. PMC2613605

Zinkernagel AS, Timmer AM, Pence MA, Locke JB, Buchanan JT, Turner CE, Mishalian I, Sriskandan S, Hanski E, Nizet V (2008) The IL-8 protease SpyCEP/ScpC of group A Streptococcus promotes resistance to neutrophil killing. Cell Host Microbe 4:170-178. PMC2631432

  

Eveline (Sun) Arnold

Entry program: Biomedical Sciences
Advisor: Don Cleveland
Next position: Postdoc, Kenneth Fischbeck lab, National Institutes of Health
Current position: Senior Scientific Reviewer, U.S. Food and Drug Administration 
  

Publications 

Ditsworth D, Maldonado M, McAlonis-Downes M, Sun S, Seelman A, Drenner K, Arnold E, Ling SC, Pizzo D, Ravits J, Cleveland DW, Da Cruz S (2017) Mutant TDP-43 within motor neurons drives disease onset but not progression in amyotrophic lateral sclerosis. Acta Neuropathol 133:907-922. PMC5427168

Mitchell JC, Constable R, So E, Vance C, Scotter E, Glover L, Hortobagyi T, Arnold ES, Ling SC, McAlonis M, Da Cruz S, Polymenidou M, et al (2015) Wild type human TDP-43 potentiates ALS-linked mutant TDP-43 driven progressive motor and cortical neuron degeneration with pathological features of ALS. Acta Neuropathol Commun 3:36. PMC4479086

Arnold ES, Ling SC, Huelga SC, Lagier-Tourenne C, Polymenidou M, Ditsworth D, Kordasiewicz HB, McAlonis-Downes M, Platoshyn O, Parone PA, Da Cruz S, Clutario KM, et al (2013) ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43. Proc Natl Acad Sci U S A 110:E736-745. PMC3581922

Polymenidou M, Lagier-Tourenne C, Hutt KR, Huelga SC, Moran J, Liang TY, Ling SC, Sun E, Wancewicz E, Mazur C, Kordasiewicz H, Sedaghat Y, et al (2011) Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. Nat Neurosci 14:459-468. PMC3094729

  

Shannon Weiman

Entry program: Biomedical Sciences
Advisor: Victor Nizet
Next position: Correspondent, MySDScience.com
Current position: Feelance Science and Biomedical Writer, Editor
 

Publications 

Weiman S, Uchiyama S, Lin FY, Chaffin D, Varki A, Nizet V, Lewis AL (2010) O-Acetylation of sialic acid on Group B Streptococcus inhibits neutrophil suppression and virulence. Biochem J 428:163-168. PMC3640289

Uchiyama S, Carlin AF, Khosravi A, Weiman S, Banerjee A, Quach D, Hightower G, Mitchell TJ, Doran KS, Nizet V (2009) The surface-anchored NanA protein promotes pneumococcal brain endothelial cell invasion. J Exp Med 206:1845-1852. PMC2737157

Weiman S, Dahesh S, Carlin AF, Varki A, Nizet V, Lewis AL (2009) Genetic and biochemical modulation of sialic acid O-acetylation on group B Streptococcus: phenotypic and functional impact. Glycobiology 19:1204-1213. PMC2757575

 

Leah Boyer

Entry program: Biomedical Sciences
Advisor: Fred (Rusty) Gage
Next position: Director, Stem Cell Core Laboratory
Current position: Freelance Stem Cell Biologist
 

Publications 

Havlicek S, Kohl Z, Mishra HK, Prots I, Eberhardt E, Denguir N, Wend H, Plotz S, Boyer L, Marchetto MC, Aigner S, Sticht H, et al (2014) Gene dosage-dependent rescue of HSP neurite defects in SPG4 patients' neurons. Hum Mol Genet 23:2527-2541. PMC3990156

Vilchez D, Boyer L, Lutz M, Merkwirth C, Morantte I, Tse C, Spencer B, Page L, Masliah E, Berggren WT, Gage FH, Dillin A (2013) FOXO4 is necessary for neural differentiation of human embryonic stem cells. Aging Cell 12:518-522. PMC4864013

Boyer LF, Campbell B, Larkin S, Mu Y, Gage FH (2012) Dopaminergic differentiation of human pluripotent cells. Curr Protoc Stem Cell Biol Chapter 1:Unit1H 6.

Vilchez D, Boyer L, Morantte I, Lutz M, Merkwirth C, Joyce D, Spencer B, Page L, Masliah E, Berggren WT, Gage FH, Dillin A (2012) Increased proteasome activity in human embryonic stem cells is regulated by PSMD11. Nature 489:304-308. PMC5215918

Winner B, Regensburger M, Schreglmann S, Boyer L, Prots I, Rockenstein E, Mante M, Zhao C, Winkler J, Masliah E, Gage FH (2012) Role of alpha-synuclein in adult neurogenesis and neuronal maturation in the dentate gyrus. J Neurosci 32:16906-16916. PMC4962062

Marchetto MC, Brennand KJ, Boyer LF, Gage FH (2011) Induced pluripotent stem cells (iPSCs) and neurological disease modeling: progress and promises. Hum Mol Genet 20:R109-115. PMC4447776

Winner B, Jappelli R, Maji SK, Desplats PA, Boyer L, Aigner S, Hetzer C, Loher T, Vilar M, Campioni S, Tzitzilonis C, Soragni A, et al (2011) In vivo demonstration that alpha-synuclein oligomers are toxic. Proc Natl Acad Sci U S A 108:4194-4199. PMC3053976

Saijo K, Winner B, Carson CT, Collier JG, Boyer L, Rosenfeld MG, Gage FH, Glass CK (2009) A Nurr1/CoREST pathway in microglia and astrocytes protects dopaminergic neurons from inflammation-induced death. Cell 137:47-59. PMC2754279

  

2006 Trainees

Molly Bush Lettman

Entry program: Biomedical Sciences
Advisor: Karen Oegema
Next position: Senior Scientist, PPD
Current position: Research Scientist, University of Wisconsin-Madison
 

Publications 

Shimanovskaya E, Viscardi V, Lesigang J, Lettman MM, Qiao R, Svergun DI, Round A, Oegema K, Dong G (2014) Structure of the C. elegans ZYG-1 cryptic polo box suggests a conserved mechanism for centriolar docking of Plk4 kinases. Structure 22:1090-1104. PMC4126857

Lettman MM, Wong YL, Viscardi V, Niessen S, Chen SH, Shiau AK, Zhou H, Desai A, Oegema K (2013) Direct binding of SAS-6 to ZYG-1 recruits SAS-6 to the mother centriole for cartwheel assembly. Dev Cell 25:284-298. PMC3655416

  

Ohn Chow

Entry program: Biomedical Sciences
Advisor: Victor Nizet and Chris Glass
Next position: Medical Student, Duke University School of Medicine
Current position: Clinical Research Director, Sanofi
  

Publications 

Akong-Moore K, Chow OA, von Kockritz-Blickwede M, Nizet V (2012) Influences of chloride and hypochlorite on neutrophil extracellular trap formation. PLoS One 7:e42984. PMC3418225

Lin FY, Zhang Y, Hensler M, Liu YL, Chow OA, Zhu W, Wang K, Pang R, Thienphrapa W, Nizet V, Oldfield E (2012) Dual dehydrosqualene/squalene synthase inhibitors: leads for innate immune system-based therapeutics. ChemMedChem 7:561-564. PMC3471559

Chow OA, von Kockritz-Blickwede M, Bright AT, Hensler ME, Zinkernagel AS, Cogen AL, Gallo RL, Monestier M, Wang Y, Glass CK, Nizet V (2010) Statins enhance formation of phagocyte extracellular traps. Cell Host Microbe 8:445-454. PMC3008410

von Kockritz-Blickwede M, Chow OA, Nizet V (2009) Fetal calf serum contains heat-stable nucleases that degrade neutrophil extracellular traps. Blood 114:5245-5246. PMC2792215

 

Dan Clark

Entry program: Biological Sciences
Advisor: Pamela Mellon
Next position: Adjunct Instructor, UC San Diego
Current position: Professor, Ventura College

Publications 

Hoffmann HM, Larder R, Lee JS, Hu RJ, Trang C, Devries BM, Clark DD, Mellon PL (2019) Differential CRE Expression in Lhrh-cre and GnRH-cre Alleles and the Impact on Fertility in Otx2-Flox Mice. Neuroendocrinology 108:328-342. PMC6753941

Schoeller EL, Clark DD, Dey S, Cao NV, Semaan SJ, Chao LW, Kauffman AS, Stowers L, Mellon PL (2016) Bmal1 Is Required for Normal Reproductive Behaviors in Male Mice. Endocrinology 157:4914-4929. PMC5133342

Clark DD, Gorman MR, Hatori M, Meadows JD, Panda S, Mellon PL (2013) Aberrant development of the suprachiasmatic nucleus and circadian rhythms in mice lacking the homeodomain protein Six6. J Biol Rhythms 28:15-25. PMC3586279

Larder R, Kimura I, Meadows J, Clark DD, Mayo S, Mellon PL (2013) Gene dosage of Otx2 is important for fertility in male mice. Mol Cell Endocrinol 377:16-22. PMC3771655

Larder R, Clark DD, Miller NL, Mellon PL (2011) Hypothalamic dysregulation and infertility in mice lacking the homeodomain protein Six6. J Neurosci 31:426-438. PMC3103738

  

Ali Torkamani

Entry program: Biomedical Sciences
Advisor: Nik Schork
Next position:Research Scientist, The Scripps Research Institute
Current position: Association Professor, The Scripps Research Institute
email: atorkama@scripps.edu
"Arnold said it best: trust yourself, break some rules, don't be afraid to fail, ignore the naysayers, work like hell, and give something back."
  

Publications 

Lahiry P, Torkamani A, Schork NJ, Hegele RA (2010) Kinase mutations in human disease: interpreting genotype-phenotype relationships. Nat Rev Genet 11:60-74.

Torkamani A, Dean B, Schork NJ, Thomas EA (2010) Coexpression network analysis of neural tissue reveals perturbations in developmental processes in schizophrenia. Genome Res 20:403-412. PMC2847743

Dixit A, Yi L, Gowthaman R, Torkamani A, Schork NJ, Verkhivker GM (2009) Sequence and structure signatures of cancer mutation hotspots in protein kinases. PLoS One 4:e7485. PMC2759519

Torkamani A, Schork NJ (2009) Identification of rare cancer driver mutations by network reconstruction. Genome Res 19:1570-1578. PMC2752121

Torkamani A, Schork NJ (2009) Pathway and network analysis with high-density allelic association data. Methods Mol Biol 563:289-301.

 

2005 Trainees

Emily (Davis) Niederst

Entry program: Biomedical Sciences
Advisor: Larry Goldstein
Next position: Postdoc, Mustafa Sahin lab, Boston Children's Hsopital
Current position: Director of Scientific Initiatives, Picower Institute for Learning and Memory, MIT
  

Publications 

Niederst ED, Reyna SM, Goldstein LS (2015) Axonal amyloid precursor protein and its fragments undergo somatodendritic endocytosis and processing. Mol Biol Cell 26:205-217. PMC4294669

Almenar-Queralt A, Falzone TL, Shen Z, Lillo C, Killian RL, Arreola AS, Niederst ED, Ng KS, Kim SN, Briggs SP, Williams DS, Goldstein LS (2014) UV irradiation accelerates amyloid precursor protein (APP) processing and disrupts APP axonal transport. J Neurosci 34:3320-3339. PMC3935090

Shah SB, Nolan R, Davis E, Stokin GB, Niesman I, Canto I, Glabe C, Goldstein LS (2009) Examination of potential mechanisms of amyloid-induced defects in neuronal transport. Neurobiol Dis 36:11-25.

 

Jarrod Heck

Entry program: Biological Sciences
Advisor: Randy Hampton
Next position: Postdoc, Fred Hutchinson Cancer Research Center
Current position: Clinical Laboratory Director, Adaptive Biotechnologies Corp.
  

Publications 

Singh A, Vashistha N, Heck J, Tang X, Wipf P, Brodsky JL, Hampton RY (2020) Direct involvement of Hsp70 ATP hydrolysis in Ubr1-dependent quality control. Mol Biol Cell 31:2669-2686. PMC7927186

Heck JW, Cheung SK, Hampton RY (2010) Cytoplasmic protein quality control degradation mediated by parallel actions of the E3 ubiquitin ligases Ubr1 and San1. Proc Natl Acad Sci U S A 107:1106-1111. PMC2824284

 

Natalie Kardos

Entry program: Biomedical Sciences
Advisor: Anthony Wynshaw-Boris
Next position: Research Associate, La Jolla Bioengineering Institute
Current position: Staff Field Applications Scientist, Illumina
   

Publications  

Etheridge SL, Ray S, Li S, Hamblet NS, Lijam N, Tsang M, Greer J, Kardos N, Wang J, Sussman DJ, Chen P, Wynshaw-Boris A (2008) Murine dishevelled 3 functions in redundant pathways with dishevelled 1 and 2 in normal cardiac outflow tract, cochlea, and neural tube development. PLoS Genet 4:e1000259. PMC2576453

 

Alice Kiselyuk

Entry program: Bioengineering and Pharmacy
Advisor: Fred Levine
Next position: Intern, Pfizer
Current position: Pharmacy Supervisor, CVS Health 
 

Publications

Lee SH, Athavankar S, Cohen T, Piran R, Kiselyuk A, Levine F (2013) Identification of alverine and benfluorex as HNF4alpha activators. ACS Chem Biol 8:1730-1736. PMC3922238

Kiselyuk A, Lee SH, Farber-Katz S, Zhang M, Athavankar S, Cohen T, Pinkerton AB, Ye M, Bushway P, Richardson AD, Hostetler HA, Rodriguez-Lee M, et al (2012) HNF4alpha antagonists discovered by a high-throughput screen for modulators of the human insulin promoter. Chem Biol 19:806-818. PMC3447631

Lee SH, Hao E, Kiselyuk A, Shapiro J, Shields DJ, Lowy A, Levine F, Itkin-Ansari P (2011) The Id3/E47 axis mediates cell-cycle control in human pancreatic ducts and adenocarcinoma. Mol Cancer Res 9:782-790. PMC3954712

Kiselyuk A, Farber-Katz S, Cohen T, Lee SH, Geron I, Azimi B, Heynen-Genel S, Singer O, Price J, Mercola M, Itkin-Ansari P, Levine F (2010) Phenothiazine neuroleptics signal to the human insulin promoter as revealed by a novel high-throughput screen. J Biomol Screen 15:663-670. PMC3374493

Dawson MI, Ye M, Cao X, Farhana L, Hu QY, Zhao Y, Xu LP, Kiselyuk A, Correa RG, Yang L, Hou T, Reed JC, et al (2009) Derivation of a retinoid X receptor scaffold from peroxisome proliferator-activated receptor gamma ligand 1-Di(1H-indol-3-yl)methyl-4-trifluoromethylbenzene. ChemMedChem 4:1106-1119. PMC3031428

 

Kelly Lagor

Entry program: Biological Sciences
Advisor: Steven Briggs
Next position: Senior Inside Sales Representative, Life Technologies
Current position: Senior Field Applications Scientist, Illumina
 
 

Madeline Lancaster

Entry program: Biomedical Sciences
Advisor: Joseph Gleeson
Next position: Postdoc, Jurgen Knoblich lab, Institute of Molecular Biology, Vienna
Current position: Group Leader, MRC Laboratory of Molecular Biology, Cambridge
 

Publications 

Lancaster MA, Gopal DJ, Kim J, Saleem SN, Silhavy JL, Louie CM, Thacker BE, Williams Y, Zaki MS, Gleeson JG (2011) Defective Wnt-dependent cerebellar midline fusion in a mouse model of Joubert syndrome. Nat Med 17:726-731. PMC3110639

Lancaster MA, Schroth J, Gleeson JG (2011) Subcellular spatial regulation of canonical Wnt signalling at the primary cilium. Nat Cell Biol 13:700-707. PMC3107376

Lancaster MA, Gleeson JG (2010) Cystic kidney disease: the role of Wnt signaling. Trends Mol Med 16:349-360. PMC2919646

Louie CM, Caridi G, Lopes VS, Brancati F, Kispert A, Lancaster MA, Schlossman AM, Otto EA, Leitges M, Grone HJ, Lopez I, Gudiseva HV, et al (2010) AHI1 is required for photoreceptor outer segment development and is a modifier for retinal degeneration in nephronophthisis. Nat Genet 42:175-180. PMC2884967

Lancaster MA, Gleeson JG (2009) The primary cilium as a cellular signaling center: lessons from disease. Curr Opin Genet Dev 19:220-229. PMC2953615

Lancaster MA, Louie CM, Silhavy JL, Sintasath L, Decambre M, Nigam SK, Willert K, Gleeson JG (2009) Impaired Wnt-beta-catenin signaling disrupts adult renal homeostasis and leads to cystic kidney ciliopathy. Nat Med 15:1046-1054. PMC2895985

Valente EM, Silhavy JL, Brancati F, Barrano G, Krishnaswami SR, Castori M, Lancaster MA, Boltshauser E, Boccone L, Al-Gazali L, Fazzi E, Signorini S, et al (2006) Mutations in CEP290, which encodes a centrosomal protein, cause pleiotropic forms of Joubert syndrome. Nat Genet 38:623-625.

 

Janine Low-Marchelli

Entry program: Biomedical Sciences
Advisor: Jing Yang
Next position: IRACDA Postdoc, Catriona Jamieson lab, Sanford Consortium for Regenerative Medicine
Current position: Manager, Technical Information Services, The Jackson Laboratory
 

Publications 

Low-Marchelli JM, Ardi VC, Vizcarra EA, van Rooijen N, Quigley JP, Yang J (2013) Twist1 induces CCL2 and recruits macrophages to promote angiogenesis. Cancer Res 73:662-671. PMC3566985

Navratil AM, Song H, Hernandez JB, Cherrington BD, Santos SJ, Low JM, Do MH, Lawson MA (2009) Insulin augments gonadotropin-releasing hormone induction of translation in LbetaT2 cells. Mol Cell Endocrinol 311:47-54. PMC2739255

 

Dustin Wakeman

Entry program: Biomedical Sciences
Advisor: Evan Snyder
Next position: Instructor, Rush University Medical Center
Current position: Director, Translational Science, Aspen Neuroscience
  

Publications 

Hartman RE, Nathan NH, Ghosh N, Pernia CD, Law J, Nuryyev R, Plaia A, Yusof A, Tone B, Dulcich M, Wakeman DR, Dilmac N, et al (2020) A Biomarker for Predicting Responsiveness to Stem Cell Therapy Based on Mechanism-of-Action: Evidence from Cerebral Injury. Cell Rep 31:107622.

Lee JP, Zhang R, Yan M, Duggineni S, Wakeman DR, Niles WL, Feng Y, Chen J, Hamblin MH, Han EB, Gonzalez R, Fang X, et al (2020) Chemical mutagenesis of a GPCR ligand: Detoxifying "inflammo-attraction" to direct therapeutic stem cell migration. Proc Natl Acad Sci U S A 117:31177-31188. PMC7733796

Goncharova V, Das S, Niles W, Schraufstatter I, Wong AK, Povaly T, Wakeman D, Miller L, Snyder EY, Khaldoyanidi SK (2014) Homing of neural stem cells from the venous compartment into a brain infarct does not involve conventional interactions with vascular endothelium. Stem Cells Transl Med 3:229-240. PMC3925049

Wakeman DR, Redmond DE, Jr., Dodiya HB, Sladek JR, Jr., Leranth C, Teng YD, Samulski RJ, Snyder EY (2014) Human neural stem cells survive long term in the midbrain of dopamine-depleted monkeys after GDNF overexpression and project neurites toward an appropriate target. Stem Cells Transl Med 3:692-701. PMC4039459

Chernov AV, Baranovskaya S, Golubkov VS, Wakeman DR, Snyder EY, Williams R, Strongin AY (2010) Microarray-based transcriptional and epigenetic profiling of matrix metalloproteinases, collagens, and related genes in cancer. J Biol Chem 285:19647-19659. PMC2885243

Wakeman DR, Hofmann MR, Redmond DE, Jr., Teng YD, Snyder EY (2009) Long-term multilayer adherent network (MAN) expansion, maintenance, and characterization, chemical and genetic manipulation, and transplantation of human fetal forebrain neural stem cells. Curr Protoc Stem Cell Biol Chapter 2:Unit2D 3.

Mueller FJ, Serobyan N, Schraufstatter IU, DiScipio R, Wakeman D, Loring JF, Snyder EY, Khaldoyanidi SK (2006) Adhesive interactions between human neural stem cells and inflamed human vascular endothelium are mediated by integrins. Stem Cells 24:2367-2372. PMC2885956

  

2004 Trainees

Wendy Alcaraz

Entry program: Biomedical Sciences
Advisor: Bruce Hamilton
Next position: Postdoc, Baylor College of Medicine
Current position: Laboratory Director, Ambry Genetics
 

Publications 

Alcaraz WA, Liu Z, Valdes P, Chen E, Valdovino Gonzalez AG, Wade S, Wong C, Kim E, Chen HM, Ponn A, Concepcion D, Hamilton BA (2020) Strain-Dependent Modifier Genes Determine Survival in Zfp423 Mice. G3 (Bethesda) 10:4241-4247. PMC7642944

Alcaraz WA, Chen E, Valdes P, Kim E, Lo YH, Vo J, Hamilton BA (2011) Modifier genes and non-genetic factors reshape anatomical deficits in Zfp423-deficient mice. Hum Mol Genet 20:3822-3830. PMC3168291

Alcaraz WA, Gold DA, Raponi E, Gent PM, Concepcion D, Hamilton BA (2006) Zfp423 controls proliferation and differentiation of neural precursors in cerebellar vermis formation. Proc Natl Acad Sci U S A 103:19424-19429. PMC1748242

 

Anthony Essex

Entry program: Biomedical Sciences
Advisor: Arshad Desai
Next position: Postdoc, Salk Institute
Current position: Chief Scientific Officer, PhenoVista Biosciences
 

Publications 

Gassmann R, Rechtsteiner A, Yuen KW, Muroyama A, Egelhofer T, Gaydos L, Barron F, Maddox P, Essex A, Monen J, Ercan S, Lieb JD, et al (2012) An inverse relationship to germline transcription defines centromeric chromatin in C. elegans. Nature 484:534-537. PMC3538161

Essex A, Dammermann A, Lewellyn L, Oegema K, Desai A (2009) Systematic analysis in Caenorhabditis elegans reveals that the spindle checkpoint is composed of two largely independent branches. Mol Biol Cell 20:1252-1267. PMC2642744

Gassmann R, Essex A, Hu JS, Maddox PS, Motegi F, Sugimoto A, O'Rourke SM, Bowerman B, McLeod I, Yates JR, 3rd, Oegema K, Cheeseman IM, Desai A (2008) A new mechanism controlling kinetochore-microtubule interactions revealed by comparison of two dynein-targeting components: SPDL-1 and the Rod/Zwilch/Zw10 complex. Genes Dev 22:2385-2399. PMC2532926

 

Jason Goode

Entry program: Biomedical Sciences
Advisor: Marc Montminy
Next position: Associate Product Manager, Illumina
Current position: Vice President of Business Development and Product Strategy, Vivid Genomics
  

Publications  

Wang Y, Li G, Goode J, Paz JC, Ouyang K, Screaton R, Fischer WH, Chen J, Tabas I, Montminy M (2012) Inositol-1,4,5-trisphosphate receptor regulates hepatic gluconeogenesis in fasting and diabetes. Nature 485:128-132. PMC3343222

Song Y, Altarejos J, Goodarzi MO, Inoue H, Guo X, Berdeaux R, Kim JH, Goode J, Igata M, Paz JC, Hogan MF, Singh PK, et al (2010) CRTC3 links catecholamine signalling to energy balance. Nature 468:933-939. PMC3025711

Wang B, Goode J, Best J, Meltzer J, Schilman PE, Chen J, Garza D, Thomas JB, Montminy M (2008) The insulin-regulated CREB coactivator TORC promotes stress resistance in Drosophila. Cell Metab 7:434-444. PMC3704161

 

Linsey Lewellyn

Entry program: Biomedical Sciences
Advisor: Karen Oegema
Next position: Postdoc, Sally Horne-Badovinac lab, University of Chicago
Current position: Associate Professor of Biological Sciences, Butler University

Publications 

Green RA, Mayers JR, Wang S, Lewellyn L, Desai A, Audhya A, Oegema K (2013) The midbody ring scaffolds the abscission machinery in the absence of midbody microtubules. J Cell Biol 203:505-520. PMC3824018

Lewellyn L, Carvalho A, Desai A, Maddox AS, Oegema K (2011) The chromosomal passenger complex and centralspindlin independently contribute to contractile ring assembly. J Cell Biol 193:155-169. PMC3082186

Lewellyn L, Dumont J, Desai A, Oegema K (2010) Analyzing the effects of delaying aster separation on furrow formation during cytokinesis in the Caenorhabditis elegans embryo. Mol Biol Cell 21:50-62. PMC2801719

Essex A, Dammermann A, Lewellyn L, Oegema K, Desai A (2009) Systematic analysis in Caenorhabditis elegans reveals that the spindle checkpoint is composed of two largely independent branches. Mol Biol Cell 20:1252-1267. PMC2642744

Canman JC, Lewellyn L, Laband K, Smerdon SJ, Desai A, Bowerman B, Oegema K (2008) Inhibition of Rac by the GAP activity of centralspindlin is essential for cytokinesis. Science 322:1543-1546. PMC2736296

Maddox AS, Lewellyn L, Desai A, Oegema K (2007) Anillin and the septins promote asymmetric ingression of the cytokinetic furrow. Dev Cell 12:827-835.

  

Carrie Louie

Entry program: Biomedical Sciences
Advisor: Joseph Gleeson
Next position: Postdoc, Clinical Molecular Genetics, UCLA
Current position: Technical Director, Molecular Genetics, Southern California Permanente Medical Group
 

Publications 

Lee JE, Silhavy JL, Zaki MS, Schroth J, Bielas SL, Marsh SE, Olvera J, Brancati F, Iannicelli M, Ikegami K, Schlossman AM, Merriman B, et al (2012) CEP41 is mutated in Joubert syndrome and is required for tubulin glutamylation at the cilium. Nat Genet 44:193-199. PMC3267856

Lancaster MA, Gopal DJ, Kim J, Saleem SN, Silhavy JL, Louie CM, Thacker BE, Williams Y, Zaki MS, Gleeson JG (2011) Defective Wnt-dependent cerebellar midline fusion in a mouse model of Joubert syndrome. Nat Med 17:726-731. PMC3110639

Louie CM, Caridi G, Lopes VS, Brancati F, Kispert A, Lancaster MA, Schlossman AM, Otto EA, Leitges M, Grone HJ, Lopez I, Gudiseva HV, et al (2010) AHI1 is required for photoreceptor outer segment development and is a modifier for retinal degeneration in nephronophthisis. Nat Genet 42:175-180. PMC2884967

Lancaster MA, Louie CM, Silhavy JL, Sintasath L, Decambre M, Nigam SK, Willert K, Gleeson JG (2009) Impaired Wnt-beta-catenin signaling disrupts adult renal homeostasis and leads to cystic kidney ciliopathy. Nat Med 15:1046-1054. PMC2895985

Valente EM, Silhavy JL, Brancati F, Barrano G, Krishnaswami SR, Castori M, Lancaster MA, Boltshauser E, Boccone L, Al-Gazali L, Fazzi E, Signorini S, et al (2006) Mutations in CEP290, which encodes a centrosomal protein, cause pleiotropic forms of Joubert syndrome. Nat Genet 38:623-625.

Louie CM, Gleeson JG (2005) Genetic basis of Joubert syndrome and related disorders of cerebellar development. Hum Mol Genet 14 Spec No. 2:R235-242.

Dixon-Salazar T, Silhavy JL, Marsh SE, Louie CM, Scott LC, Gururaj A, Al-Gazali L, Al-Tawari AA, Kayserili H, Sztriha L, Gleeson JG (2004) Mutations in the AHI1 gene, encoding jouberin, cause Joubert syndrome with cortical polymicrogyria. Am J Hum Genet 75:979-987. PMC1182159

 

Rany Salem

Entry program: Public Health Epidemiology
Advisor: Daniel O'Connor
Next position: Postdoc, Joel Hirschhorn lab, Broad Institute and Boston Children's Hospital
Current position: Assistant Professor, UC San Diego
 

Publications 

Friese RS, Altshuler AE, Zhang K, Miramontes-Gonzalez JP, Hightower CM, Jirout ML, Salem RM, Gayen JR, Mahapatra NR, Biswas N, Cale M, Vaingankar SM, et al (2013) MicroRNA-22 and promoter motif polymorphisms at the Chga locus in genetic hypertension: functional and therapeutic implications for gene expression and the pathogenesis of hypertension. Hum Mol Genet 22:3624-3640. PMC3749858

Fung MM, Salem RM, Lipkowitz MS, Bhatnagar V, Pandey B, Schork NJ, O'Connor DT, Investigators AS (2012) Methylenetetrahydrofolate reductase (MTHFR) polymorphism A1298C (Glu429Ala) predicts decline in renal function over time in the African-American Study of Kidney Disease and Hypertension (AASK) Trial and Veterans Affairs Hypertension Cohort (VAHC). Nephrol Dial Transplant 27:197-205. PMC3350339

Chen Y, Lipkowitz MS, Salem RM, Fung MM, Bhatnagar V, Mahata M, Nievergelt CM, Rao F, Mahata SK, Schork NJ, Hicks PJ, Bowden DW, et al (2010) Progression of chronic kidney disease: Adrenergic genetic influence on glomerular filtration rate decline in hypertensive nephrosclerosis. Am J Nephrol 32:23-30. PMC2914391

Chen Y, Rao F, Wen G, Gayen JR, Zhang K, Vaingankar SM, Biswas N, Mahata M, Friese RS, Fung MM, Salem RM, Nievergelt C, et al (2010) Naturally occurring genetic variants in human chromogranin A (CHGA) associated with hypertension as well as hypertensive renal disease. Cell Mol Neurobiol 30:1395-1400. PMC3008929

Chen Y, Salem RM, Rao F, Fung MM, Bhatnagar V, Pandey B, Mahata M, Waalen J, Nievergelt CM, Lipkowitz MS, Hamilton BA, Mahata SK, O'Connor DT (2010) Common charge-shift mutation Glu65Lys in K+ channel beta(1)-Subunit KCNMB1: pleiotropic consequences for glomerular filtration rate and progressive renal disease. Am J Nephrol 32:414-424. PMC2975731

Fung MM, Salem RM, Mehtani P, Thomas B, Lu CF, Perez B, Rao F, Stridsberg M, Ziegler MG, Mahata SK, O'Connor DT (2010) Direct vasoactive effects of the chromogranin A (CHGA) peptide catestatin in humans in vivo. Clin Exp Hypertens 32:278-287. PMC3109075

Salem RM, O'Connor DT, Schork NJ (2010) Curve-based multivariate distance matrix regression analysis: application to genetic association analyses involving repeated measures. Physiol Genomics 42:236-247. PMC3032281

Salem RM, Pandey B, Richard E, Fung MM, Garcia EP, Brophy VH, Schork NJ, O'Connor DT, Bhatnagar V (2010) The VA Hypertension Primary Care Longitudinal Cohort: Electronic medical records in the post-genomic era. Health Informatics J 16:274-286. PMC3099595

Zhang K, Rao F, Wang L, Rana BK, Ghosh S, Mahata M, Salem RM, Rodriguez-Flores JL, Fung MM, Waalen J, Tayo B, Taupenot L, Mahata SK, O'Connor DT (2010) Common functional genetic variants in catecholamine storage vesicle protein promoter motifs interact to trigger systemic hypertension. J Am Coll Cardiol 55:1463-1475. PMC2889490

Bhatnagar V, O'Connor DT, Brophy VH, Schork NJ, Richard E, Salem RM, Nievergelt CM, Bakris GL, Middleton JP, Norris KC, Wright J, Hiremath L, et al (2009) G-protein-coupled receptor kinase 4 polymorphisms and blood pressure response to metoprolol among African Americans: sex-specificity and interactions. Am J Hypertens 22:332-338. PMC2715837

Fung MM, Chen Y, Lipkowitz MS, Salem RM, Bhatnagar V, Mahata M, Nievergelt CM, Rao F, Mahata SK, Schork NJ, Brophy VH, O'Connor DT, Co-Investigators A (2009) Adrenergic beta-1 receptor genetic variation predicts longitudinal rate of GFR decline in hypertensive nephrosclerosis. Nephrol Dial Transplant 24:3677-3686. PMC2790952

Fung MM, Rana BK, Tang CM, Shiina T, Nievergelt CM, Rao F, Salem RM, Waalen J, Ziegler MG, Insel PA, O'Connor DT (2009) Dopamine D1 receptor (DRD1) genetic polymorphism: pleiotropic effects on heritable renal traits. Kidney Int 76:1070-1080. PMC2803094

Zhang K, Rao F, Rana BK, Gayen JR, Calegari F, King A, Rosa P, Huttner WB, Stridsberg M, Mahata M, Vaingankar S, Mahboubi V, et al (2009) Autonomic function in hypertension; role of genetic variation at the catecholamine storage vesicle protein chromogranin B. Circ Cardiovasc Genet 2:46-56. PMC2792940

Chen Y, Rao F, Rodriguez-Flores JL, Mahapatra NR, Mahata M, Wen G, Salem RM, Shih PA, Das M, Schork NJ, Ziegler MG, Hamilton BA, Mahata SK, O'Connor DT (2008) Common genetic variants in the chromogranin A promoter alter autonomic activity and blood pressure. Kidney Int 74:115-125. PMC2576285

Chen Y, Rao F, Rodriguez-Flores JL, Mahata M, Fung MM, Stridsberg M, Vaingankar SM, Wen G, Salem RM, Das M, Cockburn MG, Schork NJ, et al (2008) Naturally occurring human genetic variation in the 3'-untranslated region of the secretory protein chromogranin A is associated with autonomic blood pressure regulation and hypertension in a sex-dependent fashion. J Am Coll Cardiol 52:1468-1481. PMC2659417

Fung MM, Nguyen C, Mehtani P, Salem RM, Perez B, Thomas B, Das M, Schork NJ, Mahata SK, Ziegler MG, O'Connor DT (2008) Genetic variation within adrenergic pathways determines in vivo effects of presynaptic stimulation in humans. Circulation 117:517-525. PMC2628716

Rao F, Zhang L, Wessel J, Zhang K, Wen G, Kennedy BP, Rana BK, Das M, Rodriguez-Flores JL, Smith DW, Cadman PE, Salem RM, et al (2008) Adrenergic polymorphism and the human stress response. Ann N Y Acad Sci 1148:282-296. PMC2743085

Salem RM, Cadman PE, Chen Y, Rao F, Wen G, Hamilton BA, Rana BK, Smith DW, Stridsberg M, Ward HJ, Mahata M, Mahata SK, et al (2008) Chromogranin A polymorphisms are associated with hypertensive renal disease. J Am Soc Nephrol 19:600-614. PMC2391050

Bhatnagar V, O'Connor DT, Schork NJ, Salem RM, Nievergelt CM, Rana BK, Smith DW, Bakris GL, Middleton JP, Norris KC, Wright JT, Cheek D, et al (2007) Angiotensin-converting enzyme gene polymorphism predicts the time-course of blood pressure response to angiotensin converting enzyme inhibition in the AASK trial. J Hypertens 25:2082-2092. PMC2792638

Rao F, Wen G, Gayen JR, Das M, Vaingankar SM, Rana BK, Mahata M, Kennedy BP, Salem RM, Stridsberg M, Abel K, Smith DW, et al (2007) Catecholamine release-inhibitory peptide catestatin (chromogranin A(352-372)): naturally occurring amino acid variant Gly364Ser causes profound changes in human autonomic activity and alters risk for hypertension. Circulation 115:2271-2281.

Rao F, Wessel J, Wen G, Zhang L, Rana BK, Kennedy BP, Greenwood TA, Salem RM, Chen Y, Khandrika S, Hamilton BA, Smith DW, et al (2007) Renal albumin excretion: twin studies identify influences of heredity, environment, and adrenergic pathway polymorphism. Hypertension 49:1015-1031.

Rao F, Zhang L, Wessel J, Zhang K, Wen G, Kennedy BP, Rana BK, Das M, Rodriguez-Flores JL, Smith DW, Cadman PE, Salem RM, et al (2007) Tyrosine hydroxylase, the rate-limiting enzyme in catecholamine biosynthesis: discovery of common human genetic variants governing transcription, autonomic activity, and blood pressure in vivo. Circulation 116:993-1006.

Zhang L, Rao F, Zhang K, Khandrika S, Das M, Vaingankar SM, Bao X, Rana BK, Smith DW, Wessel J, Salem RM, Rodriguez-Flores JL, et al (2007) Discovery of common human genetic variants of GTP cyclohydrolase 1 (GCH1) governing nitric oxide, autonomic activity, and cardiovascular risk. J Clin Invest 117:2658-2671. PMC1950457

Zhang K, Rao F, Wen G, Salem RM, Vaingankar S, Mahata M, Mahapatra NR, Lillie EO, Cadman PE, Friese RS, Hamilton BA, Hook VY, et al (2006) Catecholamine storage vesicles and the metabolic syndrome: The role of the chromogranin A fragment pancreastatin. Diabetes Obes Metab 8:621-633.

O'Connor DT, Cadman PE, Smiley C, Salem RM, Rao F, Smith J, Funk SD, Mahata SK, Mahata M, Wen G, Taupenot L, Gonzalez-Yanes C, et al (2005) Pancreastatin: multiple actions on human intermediary metabolism in vivo, variation in disease, and naturally occurring functional genetic polymorphism. J Clin Endocrinol Metab 90:5414-5425.

 

2003 Trainees

Minh-Ha Do

Entry program: Biomedical Sciences
Advisor: Mark Lawson
Next position: Scientist, aTyr Pharma
Current position: Director Preclinical Innovation, Luos Pharma
 

Publications 

Do MT, Kim T, He F, Dave H, Intriago RE, Astorga UA, Jain S, Lawson MA (2014) Polyribosome and ribonucleoprotein complex redistribution of mRNA induced by GnRH involves both EIF2AK3 and MAPK signaling. Mol Cell Endocrinol 382:346-357. PMC4042833

Kim T, Do MH, Lawson MA (2014) Translational control of gene expression in the gonadotrope. Mol Cell Endocrinol 385:78-87. PMC4009948

Do MH, Santos SJ, Lawson MA (2009) GNRH induces the unfolded protein response in the LbetaT2 pituitary gonadotrope cell line. Mol Endocrinol 23:100-112. PMC2646596

Navratil AM, Song H, Hernandez JB, Cherrington BD, Santos SJ, Low JM, Do MH, Lawson MA (2009) Insulin augments gonadotropin-releasing hormone induction of translation in LbetaT2 cells. Mol Cell Endocrinol 311:47-54. PMC2739255

  

Edmund Hollis

Entry program: Biomedical Sciences
Advisor: Mark Tuszynski
Next position: Postdoc, Yimin Zou lab, UC San Diego
Current position: Director, Circuit Repair Laboratory, Burke Neurological Institute
 

Publications 

Hollis ER, 2nd, Tuszynski MH (2011) Neurotrophins: potential therapeutic tools for the treatment of spinal cord injury. Neurotherapeutics 8:694-703. PMC3250295

Giger RJ, Hollis ER, 2nd, Tuszynski MH (2010) Guidance molecules in axon regeneration. Cold Spring Harb Perspect Biol 2:a001867. PMC2890195

Hollis ER, 2nd, Jamshidi P, Lorenzana AO, Lee JK, Gray SJ, Samulski RJ, Zheng B, Tuszynski MH (2010) Transient demyelination increases the efficiency of retrograde AAV transduction. Mol Ther 18:1496-1500. PMC2927074

Alto LT, Havton LA, Conner JM, Hollis ER, 2nd, Blesch A, Tuszynski MH (2009) Chemotropic guidance facilitates axonal regeneration and synapse formation after spinal cord injury. Nat Neurosci 12:1106-1113. PMC2753201

Hollis ER, 2nd, Jamshidi P, Low K, Blesch A, Tuszynski MH (2009) Induction of corticospinal regeneration by lentiviral trkB-induced Erk activation. Proc Natl Acad Sci U S A 106:7215-7220. PMC2678459

Hollis ER, 2nd, Lu P, Blesch A, Tuszynski MH (2009) IGF-I gene delivery promotes corticospinal neuronal survival but not regeneration after adult CNS injury. Exp Neurol 215:53-59. PMC2632606

Hollis ER, 2nd, Kadoya K, Hirsch M, Samulski RJ, Tuszynski MH (2008) Efficient retrograde neuronal transduction utilizing self-complementary AAV1. Mol Ther 16:296-301.

  

Michelle Mendoza

Entry program: Biomedical Sciences
Advisor: Richard Firtel
Next position: Postdoc, John Blenis lab, Harvard Medical School
Current position: Assistant Professor, Huntsman Cancer Institute, University of Utah
email: michelle.mendoza@hci.utah.edu
  

Publications  

Mendoza MC, Booth EO, Shaulsky G, Firtel RA (2007) MEK1 and protein phosphatase 4 coordinate Dictyostelium development and chemotaxis. Mol Cell Biol 27:3817-3827. PMC1899987

Mendoza MC, Firtel RA (2006) Assaying chemotaxis of Dictyostelium cells. Methods Mol Biol 346:393-405.

Mendoza MC, Du F, Iranfar N, Tang N, Ma H, Loomis WF, Firtel RA (2005) Loss of SMEK, a novel, conserved protein, suppresses MEK1 null cell polarity, chemotaxis, and gene expression defects. Mol Cell Biol 25:7839-7853. PMC1190274

  

Joost Monen

Entry program: Biomedical Sciences
Advisor: Karen Oegema
Next position: Postdoc, Cornell University
Current position: Associate Professor, Ramapo College of New Jersey
  

Publications 

de Groot C, Houston J, Davis B, Gerson-Gurwitz A, Monen J, Lara-Gonzalez P, Oegema K, Shiau AK, Desai A (2021) The N-terminal tail of C. elegans CENP-A interacts with KNL-2 and is essential for centromeric chromatin assembly. Mol Biol Cell 32:1193-1201. PMC8351560

Monen J, Hattersley N, Muroyama A, Stevens D, Oegema K, Desai A (2015) Separase Cleaves the N-Tail of the CENP-A Related Protein CPAR-1 at the Meiosis I Metaphase-Anaphase Transition in C. elegans. PLoS One 10:e0125382. PMC4412405

Gassmann R, Rechtsteiner A, Yuen KW, Muroyama A, Egelhofer T, Gaydos L, Barron F, Maddox P, Essex A, Monen J, Ercan S, Lieb JD, et al (2012) An inverse relationship to germline transcription defines centromeric chromatin in C. elegans. Nature 484:534-537. PMC3538161

Green RA, Audhya A, Pozniakovsky A, Dammermann A, Pemble H, Monen J, Portier N, Hyman A, Desai A, Oegema K (2008) Expression and imaging of fluorescent proteins in the C. elegans gonad and early embryo. Methods Cell Biol 85:179-218.

Maddox PS, Hyndman F, Monen J, Oegema K, Desai A (2007) Functional genomics identifies a Myb domain-containing protein family required for assembly of CENP-A chromatin. J Cell Biol 176:757-763. PMC2064049

Monen J, Maddox PS, Hyndman F, Oegema K, Desai A (2005) Differential role of CENP-A in the segregation of holocentric C. elegans chromosomes during meiosis and mitosis. Nat Cell Biol 7:1248-1255.

 

Scarlet Shell

Entry program: Biomedical Sciences
Advisor: Richard Kolodner
Next position: Postdoc, Harvard T. H. Chan School of Public Health, lab of Sarah Fortune
Current position: Associate Professor, Worcester Polytechnic Institute
email: sshell@wpi.edu
LinkedIn profile: 
https://www.linkedin.com/in/scarlet-shell-71b3b23/
"The 8am journal clubs were worth it!"
"My training at UCSD gave me a critical foundation that allowed me to find my way to my dream job, where I just got tenure."

Publications 

Hargreaves VV, Shell SS, Mazur DJ, Hess MT, Kolodner RD (2010) Interaction between the Msh2 and Msh6 nucleotide-binding sites in the Saccharomyces cerevisiae Msh2-Msh6 complex. J Biol Chem 285:9301-9310. PMC2838348

Shell SS, Putnam CD, Kolodner RD (2007) Chimeric Saccharomyces cerevisiae Msh6 protein with an Msh3 mispair-binding domain combines properties of both proteins. Proc Natl Acad Sci U S A 104:10956-10961. PMC1904149

Shell SS, Putnam CD, Kolodner RD (2007) The N terminus of Saccharomyces cerevisiae Msh6 is an unstructured tether to PCNA. Mol Cell 26:565-578. PMC2001284

Yang G, Scherer SJ, Shell SS, Yang K, Kim M, Lipkin M, Kucherlapati R, Kolodner RD, Edelmann W (2004) Dominant effects of an Msh6 missense mutation on DNA repair and cancer susceptibility. Cancer Cell 6:139-150.

  

Ambika Sundarasan

Entry program: Biological Sciences
Advisor: Jospeh Ecker
Next position: Bioinformatics Scientist, Illumina
Current position: Senior Data Scientist, Denali Therapeutics
 

Harper VanSteenhouse

Entry program: Neurosciences
Advisor: Barbara Ranscht
Next position: Science Marketing Writer, Illumina
Current position: President, BioClavis Ltd

Publications 

Ciatto C, Bahna F, Zampieri N, VanSteenhouse HC, Katsamba PS, Ahlsen G, Harrison OJ, Brasch J, Jin X, Posy S, Vendome J, Ranscht B, et al (2010) T-cadherin structures reveal a novel adhesive binding mechanism. Nat Struct Mol Biol 17:339-347. PMC2873897

  

2002 Trainees

William Alaynick

Entry program: Biomedical Sciences
Advisor: Ron Evans
Next position: Postdoc, Sam Pfaff lab, Salk Institute
Current position: Founder, VP International at NanoCellect Biomedical, Inc.
 

Publications 

Berry R, Harewood L, Pei L, Fisher M, Brownstein D, Ross A, Alaynick WA, Moss J, Hastie ND, Hohenstein P, Davies JA, Evans RM, FitzPatrick DR (2011) Esrrg functions in early branch generation of the ureteric bud and is essential for normal development of the renal papilla. Hum Mol Genet 20:917-926. PMC3033182

Narkar VA, Fan W, Downes M, Yu RT, Jonker JW, Alaynick WA, Banayo E, Karunasiri MS, Lorca S, Evans RM (2011) Exercise and PGC-1alpha-independent synchronization of type I muscle metabolism and vasculature by ERRgamma. Cell Metab 13:283-293. PMC3084588

Alaynick WA, Way JM, Wilson SA, Benson WG, Pei L, Downes M, Yu R, Jonker JW, Holt JA, Rajpal DK, Li H, Stuart J, et al (2010) ERRgamma regulates cardiac, gastric, and renal potassium homeostasis. Mol Endocrinol 24:299-309. PMC2817599

Alaynick WA, Way JM, Wilson SA, Benson WG, Pei L, Downes M, Yu R, Jonker JW, Holt JA, Rajpal DK, Li H, Stuart J, et al (2009) ERRgamma Regulates Cardiac, Gastric, and Renal Potassium Homeostasis. Endocr Rev 30:931.

Alaynick WA, Kondo RP, Xie W, He W, Dufour CR, Downes M, Jonker JW, Giles W, Naviaux RK, Giguere V, Evans RM (2007) ERRgamma directs and maintains the transition to oxidative metabolism in the postnatal heart. Cell Metab 6:13-24.

Dufour CR, Wilson BJ, Huss JM, Kelly DP, Alaynick WA, Downes M, Evans RM, Blanchette M, Giguere V (2007) Genome-wide orchestration of cardiac functions by the orphan nuclear receptors ERRalpha and gamma. Cell Metab 5:345-356.

Lee CH, Kang K, Mehl IR, Nofsinger R, Alaynick WA, Chong LW, Rosenfeld JM, Evans RM (2006) Peroxisome proliferator-activated receptor delta promotes very low-density lipoprotein-derived fatty acid catabolism in the macrophage. Proc Natl Acad Sci U S A 103:2434-2439. PMC1413732

Barish GD, Downes M, Alaynick WA, Yu RT, Ocampo CB, Bookout AL, Mangelsdorf DJ, Evans RM (2005) A Nuclear Receptor Atlas: macrophage activation. Mol Endocrinol 19:2466-2477.

  

Steffan Aung

Entry program: Biological Sciences
Advisor: Kit Pogliano
Next position: 
Current position: 
LinkedIn profile: 
 

Publications 

Aung S, Shum J, Abanes-De Mello A, Broder DH, Fredlund-Gutierrez J, Chiba S, Pogliano K (2007) Dual localization pathways for the engulfment proteins during Bacillus subtilis sporulation. Mol Microbiol 65:1534-1546. PMC2885130

Abanes-De Mello A, Sun YL, Aung S, Pogliano K (2002) A cytoskeleton-like role for the bacterial cell wall during engulfment of the Bacillus subtilis forespore. Genes Dev 16:3253-3264. PMC187501

  

Stephanie Bielas

Entry program: Biological Sciences
Advisor: Joseph Gleeson
Next position: Postdoc, Joseph Gleeson lab, UC San Diego
Current position: Associate Professor of Human Genetics, University of Michigan

Publications 

Baek ST, Kerjan G, Bielas SL, Lee JE, Fenstermaker AG, Novarino G, Gleeson JG (2014) Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous microRNA dysregulation. Neuron 82:1255-1262. PMC4086250

Dixon-Salazar TJ, Silhavy JL, Udpa N, Schroth J, Bielas S, Schaffer AE, Olvera J, Bafna V, Zaki MS, Abdel-Salam GH, Mansour LA, Selim L, et al (2012) Exome sequencing can improve diagnosis and alter patient management. Sci Transl Med 4:138ra178. PMC4442637

Lee JE, Silhavy JL, Zaki MS, Schroth J, Bielas SL, Marsh SE, Olvera J, Brancati F, Iannicelli M, Ikegami K, Schlossman AM, Merriman B, et al (2012) CEP41 is mutated in Joubert syndrome and is required for tubulin glutamylation at the cilium. Nat Genet 44:193-199. PMC3267856

Lee JH, Silhavy JL, Lee JE, Al-Gazali L, Thomas S, Davis EE, Bielas SL, Hill KJ, Iannicelli M, Brancati F, Gabriel SB, Russ C, et al (2012) Evolutionarily assembled cis-regulatory module at a human ciliopathy locus. Science 335:966-969. PMC3671610

Abdel Aleem A, Abu-Shahba N, Swistun D, Silhavy J, Bielas SL, Sattar S, Gleeson JG, Zaki MS (2011) Expanding the clinical spectrum of SPG11 gene mutations in recessive hereditary spastic paraplegia with thin corpus callosum. Eur J Med Genet 54:82-85. PMC3073376

Cantagrel V, Lefeber DJ, Ng BG, Guan Z, Silhavy JL, Bielas SL, Lehle L, Hombauer H, Adamowicz M, Swiezewska E, De Brouwer AP, Blumel P, et al (2010) SRD5A3 is required for converting polyprenol to dolichol and is mutated in a congenital glycosylation disorder. Cell 142:203-217. PMC2940322

Bielas SL, Silhavy JL, Brancati F, Kisseleva MV, Al-Gazali L, Sztriha L, Bayoumi RA, Zaki MS, Abdel-Aleem A, Rosti RO, Kayserili H, Swistun D, et al (2009) Mutations in INPP5E, encoding inositol polyphosphate-5-phosphatase E, link phosphatidyl inositol signaling to the ciliopathies. Nat Genet 41:1032-1036. PMC2746682

Cantagrel V, Silhavy JL, Bielas SL, Swistun D, Marsh SE, Bertrand JY, Audollent S, Attie-Bitach T, Holden KR, Dobyns WB, Traver D, Al-Gazali L, et al (2008) Mutations in the cilia gene ARL13B lead to the classical form of Joubert syndrome. Am J Hum Genet 83:170-179. PMC2495072

Bielas SL, Serneo FF, Chechlacz M, Deerinck TJ, Perkins GA, Allen PB, Ellisman MH, Gleeson JG (2007) Spinophilin facilitates dephosphorylation of doublecortin by PP1 to mediate microtubule bundling at the axonal wrist. Cell 129:579-591. PMC1920181

Brancati F, Barrano G, Silhavy JL, Marsh SE, Travaglini L, Bielas SL, Amorini M, Zablocka D, Kayserili H, Al-Gazali L, Bertini E, Boltshauser E, et al (2007) CEP290 mutations are frequently identified in the oculo-renal form of Joubert syndrome-related disorders. Am J Hum Genet 81:104-113. PMC1950920

Bielas S, Higginbotham H, Koizumi H, Tanaka T, Gleeson JG (2004) Cortical neuronal migration mutants suggest separate but intersecting pathways. Annu Rev Cell Dev Biol 20:593-618.

Bielas SL, Gleeson JG (2004) Cytoskeletal-associated proteins in the migration of cortical neurons. J Neurobiol 58:149-159.

Higginbotham H, Bielas S, Tanaka T, Gleeson JG (2004) Transgenic mouse line with green-fluorescent protein-labeled Centrin 2 allows visualization of the centrosome in living cells. Transgenic Res 13:155-164.

  

Adam Boutin

Entry program: Biological Sciences
Advisor: Randy Johnson
Next position: Postdoc, Harvard Medical School
Current position: Principal Scientist and Head of Translational Biology, Glympse Bio

Publications 

Cowburn AS, Takeda N, Boutin AT, Kim JW, Sterling JC, Nakasaki M, Southwood M, Goldrath AW, Jamora C, Nizet V, Chilvers ER, Johnson RS (2013) HIF isoforms in the skin differentially regulate systemic arterial pressure. Proc Natl Acad Sci U S A 110:17570-17575. PMC3808605

Weidemann A, Kerdiles YM, Knaup KX, Rafie CA, Boutin AT, Stockmann C, Takeda N, Scadeng M, Shih AY, Haase VH, Simon MC, Kleinfeld D, Johnson RS (2009) The glial cell response is an essential component of hypoxia-induced erythropoiesis in mice. J Clin Invest 119:3373-3383. PMC2769183

Boutin AT, Weidemann A, Fu Z, Mesropian L, Gradin K, Jamora C, Wiesener M, Eckardt KU, Koch CJ, Ellies LG, Haddad G, Haase VH, et al (2008) Epidermal sensing of oxygen is essential for systemic hypoxic response. Cell 133:223-234. PMC2849644

Peyssonnaux C, Boutin AT, Zinkernagel AS, Datta V, Nizet V, Johnson RS (2008) Critical role of HIF-1alpha in keratinocyte defense against bacterial infection. J Invest Dermatol 128:1964-1968.

Boutin AT, Johnson RS (2007) Waiting to inhale: HIF-1 modulates aerobic respiration. Cell 129:29-30.

 

Richard Brusch

Entry program: Biomedical Sciences
Advisor: Larry Goldstein 

Publications

Haghnia M, Cavalli V, Shah SB, Schimmelpfeng K, Brusch R, Yang G, Herrera C, Pilling A, Goldstein LS (2007) Dynactin is required for coordinated bidirectional motility, but not for dynein membrane attachment. Mol Biol Cell 18:2081-2089. PMC1877108

Stokin GB, Lillo C, Falzone TL, Brusch RG, Rockenstein E, Mount SL, Raman R, Davies P, Masliah E, Williams DS, Goldstein LS (2005) Axonopathy and transport deficits early in the pathogenesis of Alzheimer's disease. Science 307:1282-1288.

Gunawardena S, Her LS, Brusch RG, Laymon RA, Niesman IR, Gordesky-Gold B, Sintasath L, Bonini NM, Goldstein LS (2003) Disruption of axonal transport by loss of huntingtin or expression of pathogenic polyQ proteins in Drosophila. Neuron 40:25-40.

  

Matthew Busse

Entry program: Biological Sciences
Advisor: Steven Wasserman
Next position: Freelance Science Writer
Current position: Freelance Science Writer
 

Publications 

Busse MS, Arnold CP, Towb P, Katrivesis J, Wasserman SA (2007) A kappaB sequence code for pathway-specific innate immune responses. EMBO J 26:3826-3835. PMC1952218

  

Xochitl Cortez-Gonzalez

Entry program: Biomedical Sciences
Advisor: Mauricio Zanetti
Next position: Postdoc, UC San Diego
Current position: Clinical Pharmacist, Yavapai Regional Medical Center
  

Publications 

Almanza G, Fernandez A, Volinia S, Cortez-Gonzalez X, Croce CM, Zanetti M (2010) Selected microRNAs define cell fate determination of murine central memory CD8 T cells. PLoS One 5:e11243. PMC2889817

Cortez-Gonzalez X, Zanetti M (2010) Identification of immunogenic peptides of the self-tumor antigen: our experience with telomerase reverse transcriptase. Methods Mol Biol 651:211-225.

Pellicciotta I, Cortez-Gonzalez X, Sasik R, Reiter Y, Hardiman G, Langlade-Demoyen P, Zanetti M (2008) Presentation of telomerase reverse transcriptase, a self-tumor antigen, is down-regulated by histone deacetylase inhibition. Cancer Res 68:8085-8093.

Cortez-Gonzalez X, Zanetti M (2007) Telomerase immunity from bench to bedside: round one. J Transl Med 5:12. PMC1839079

Cortez-Gonzalez X, Pellicciotta I, Gerloni M, Wheeler MC, Castiglioni P, Lenert P, Zanetti M (2006) TLR9-independent activation of B lymphocytes by bacterial DNA. DNA Cell Biol 25:253-261.

Cortez-Gonzalez X, Sidney J, Adotevi O, Sette A, Millard F, Lemonnier F, Langlade-Demoyen P, Zanetti M (2006) Immunogenic HLA-B7-restricted peptides of hTRT. Int Immunol 18:1707-1718.

Wheeler M, Cortez-Gonzalez X, Frazzi R, Zanetti M (2006) Ex vivo programming of antigen-presenting B lymphocytes: considerations on DNA uptake and cell activation. Int Rev Immunol 25:83-97.

Castiglioni P, Gerloni M, Cortez-Gonzalez X, Zanetti M (2005) CD8 T cell priming by B lymphocytes is CD4 help dependent. Eur J Immunol 35:1360-1370.

  

Mike Hannon

Entry program: Biological Sciences
Advisor: Jeff Long
Next position: Postdoc, UC San Diego
Current position: Frontend Engineer at Amazon Web Services

Publications 

Hsia CC, Pare AC, Hannon M, Ronshaugen M, McGinnis W (2010) Silencing of an abdominal Hox gene during early development is correlated with limb development in a crustacean trunk. Evol Dev 12:131-143. PMC2893884

Szemenyei H, Hannon M, Long JA (2008) TOPLESS mediates auxin-dependent transcriptional repression during Arabidopsis embryogenesis. Science 319:1384-1386.

 

Nate Heintzman

Entry program: Biomedical Sciences
Advisor: Bing Ren
Next position: Postdoc, Ludwig Institute for Cancer Research
Current position: Director Data Science, Dexcom
LinkedIn profile: https://www.linkedin.com/in/nateheintzman/
  

Publications 

Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, et al (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459:108-112. PMC2910248

Heintzman ND, Ren B (2009) Finding distal regulatory elements in the human genome. Curr Opin Genet Dev 19:541-549. PMC3321269

Consortium EP, Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, et al (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816. PMC2212820

Heintzman ND, Ren B (2007) The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome. Cell Mol Life Sci 64:386-400.

Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, et al (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39:311-318.

    

Nichol (Goodman) Miller

Entry program: Biomedical Sciences
Advisor: Pamela Mellon
Next position: Postdoc, David Schlaepfer lab, UCSD Moores Cancer Center
Current position: Director of Translational & Discovery Biology at Kinnate Biopharma Inc.
 

Publications 

Larder R, Clark DD, Miller NL, Mellon PL (2011) Hypothalamic dysregulation and infertility in mice lacking the homeodomain protein Six6. J Neurosci 31:426-438. PMC3103738

Iyer AK, Miller NL, Yip K, Tran BH, Mellon PL (2010) Enhancers of GnRH transcription embedded in an upstream gene use homeodomain proteins to specify hypothalamic expression. Mol Endocrinol 24:1949-1964. PMC2954641

Miller NL, Wevrick R, Mellon PL (2009) Necdin, a Prader-Willi syndrome candidate gene, regulates gonadotropin-releasing hormone neurons during development. Hum Mol Genet 18:248-260. PMC2638776

Rave-Harel N, Miller NL, Givens ML, Mellon PL (2005) The Groucho-related gene family regulates the gonadotropin-releasing hormone gene through interaction with the homeodomain proteins MSX1 and OCT1. J Biol Chem 280:30975-30983. PMC2773698

Givens ML, Kurotani R, Rave-Harel N, Miller NL, Mellon PL (2004) Phylogenetic footprinting reveals evolutionarily conserved regions of the gonadotropin-releasing hormone gene that enhance cell-specific expression. Mol Endocrinol 18:2950-2966. PMC2932476

   

Steven Miller

Entry program: Biological Sciences
Advisor: James Posakony
Next position: Postdoc, UC San Diego
Current position: University Lecturer, UC San Diego and Adjunct Faculty, San Diego Mesa College
 

Publications 

Miller SW, Rebeiz M, Atanasov JE, Posakony JW (2014) Neural precursor-specific expression of multiple Drosophila genes is driven by dual enhancer modules with overlapping function. Proc Natl Acad Sci U S A 111:17194-17199. PMC4260543

Negre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, et al (2011) A cis-regulatory map of the Drosophila genome. Nature 471:527-531. PMC3179250

Rebeiz M, Miller SW, Posakony JW (2011) Notch regulates numb: integration of conditional and autonomous cell fate specification. Development 138:215-225. PMC3005598

Miller SW, Avidor-Reiss T, Polyanovsky A, Posakony JW (2009) Complex interplay of three transcription factors in controlling the tormogen differentiation program of Drosophila mechanoreceptors. Dev Biol 329:386-399. PMC2762865

   

Alain Silk

Entry program: Biomedical Sciences
Advisor: Don Cleveland
Next position: Postdoc, Oregon Health & Sciences University
Current position: Director of Regulatory Affairs, Tempus Labs, Inc.
 

Publications 

Silk AD, Zasadil LM, Holland AJ, Vitre B, Cleveland DW, Weaver BA (2013) Chromosome missegregation rate predicts whether aneuploidy will promote or suppress tumors. Proc Natl Acad Sci U S A 110:E4134-4141. PMC3816416

Kolano A, Brunet S, Silk AD, Cleveland DW, Verlhac MH (2012) Error-prone mammalian female meiosis from silencing the spindle assembly checkpoint without normal interkinetochore tension. Proc Natl Acad Sci U S A 109:E1858-1867. PMC3390881

Silk AD, Holland AJ, Cleveland DW (2009) Requirements for NuMA in maintenance and establishment of mammalian spindle poles. J Cell Biol 184:677-690. PMC2686415

Weaver BA, Silk AD, Cleveland DW (2008) Low rates of aneuploidy promote tumorigenesis while high rates of aneuploidy cause cell death and tumor suppression. Cell Oncol 30:453. PMC4618964

Weaver BA, Silk AD, Montagna C, Verdier-Pinard P, Cleveland DW (2007) Aneuploidy acts both oncogenically and as a tumor suppressor. Cancer Cell 11:25-36.

Weaver BA, Silk AD, Cleveland DW (2006) Cell biology: nondisjunction, aneuploidy and tetraploidy. Nature 442:E9-10; discussion E10.

Weaver BA, Bonday ZQ, Putkey FR, Kops GJ, Silk AD, Cleveland DW (2003) Centromere-associated protein-E is essential for the mammalian mitotic checkpoint to prevent aneuploidy due to single chromosome loss. J Cell Biol 162:551-563. PMC2173788

Putkey FR, Cramer T, Morphew MK, Silk AD, Johnson RS, McIntosh JR, Cleveland DW (2002) Unstable kinetochore-microtubule capture and chromosomal instability following deletion of CENP-E. Dev Cell 3:351-365.

Anne Valle

Entry program: Biomedical Sciences
Advisor: Palmer Taylor
Next position: 
Current position: Professor, El Camino College
 

Publications 

Valle AM, Radic Z, Rana BK, Mahboubi V, Wessel J, Shih PA, Rao F, O'Connor DT, Taylor P (2011) Naturally occurring variations in the human cholinesterase genes: heritability and association with cardiovascular and metabolic traits. J Pharmacol Exp Ther 338:125-133. PMC3126649

Kucukkilinc T, Cochran R, Kalisiak J, Garcia E, Valle A, Amitai G, Radic Z, Taylor P (2010) Investigating the structural influence of surface mutations on acetylcholinesterase inhibition by organophosphorus compounds and oxime reactivation. Chem Biol Interact 187:238-240. PMC2933076

Rana BK, Wessel J, Mahboubi V, Rao F, Haeller J, Gayen JR, Eskin E, Valle AM, Das M, Mahata SK, Taupenot L, Stridsberg M, et al (2009) Natural variation within the neuronal nicotinic acetylcholine receptor cluster on human chromosome 15q24: influence on heritable autonomic traits in twin pairs. J Pharmacol Exp Ther 331:419-428. PMC2775266

Valle AM, Radic Z, Rana BK, Whitfield JB, O'Connor DT, Martin NG, Taylor P (2008) The cholinesterases: analysis by pharmacogenomics in man. Chem Biol Interact 175:343-345. PMC2585411

Valle A, O'Connor DT, Taylor P, Zhu G, Montgomery GW, Slagboom PE, Martin NG, Whitfield JB (2006) Butyrylcholinesterase: association with the metabolic syndrome and identification of 2 gene loci affecting activity. Clin Chem 52:1014-1020.

  

 

Michelle Wagner Gardinier

Entry program: Biomedical Sciences
Advisor: Steven Dowdy
Next position: Senior Scientist, Calmune Corporation
Current position: Principal Scientist, Pfizer
 

Publications 

Wagner MV, Smolka MB, de Bruin RA, Zhou H, Wittenberg C, Dowdy SF (2009) Whi5 regulation by site specific CDK-phosphorylation in Saccharomyces cerevisiae. PLoS One 4:e4300. PMC2627923

Wadia JS, Wagner MV, Ezhevsky SA, Dowdy SF (2004) Apoptin/VP3 contains a concentration-dependent nuclear localization signal (NLS), not a tumorigenic selective NLS. J Virol 78:6077-6078. PMC415785

  

2001 Trainees

TJ Bowen

Entry program: Biomedical Sciences
Advisor: Anthony Wynshaw-Boris
Next position: Consultant, L.E.K. Consulting
Current position: Chief Scientist and Co-Founder, Deep Lens
  

Publications  

Toyo-oka K, Bowen TJ, Hirotsune S, Li Z, Jain S, Ota S, Escoubet-Lozach L, Garcia-Bassets I, Lozach J, Rosenfeld MG, Glass CK, Eisenman R, et al (2006) Mnt-deficient mammary glands exhibit impaired involution and tumors with characteristics of myc overexpression. Cancer Res 66:5565-5573.

Bowen TJ, Yakushiji H, Montagna C, Jain S, Ried T, Wynshaw-Boris A (2005) Atm heterozygosity cooperates with loss of Brca1 to increase the severity of mammary gland cancer and reduce ductal branching. Cancer Res 65:8736-8746.

Winrow CJ, Pankratz DG, Vibat CR, Bowen TJ, Callahan MA, Warren AJ, Hilbush BS, Wynshaw-Boris A, Hasel KW, Weaver Z, Lockhart DJ, Barlow C (2005) Aberrant recombination involving the granzyme locus occurs in Atm-/- T-cell lymphomas. Hum Mol Genet 14:2671-2684.

Resor L, Bowen TJ, Wynshaw-Boris A (2001) Unraveling human cancer in the mouse: recent refinements to modeling and analysis. Hum Mol Genet 10:669-675.

 

Christine Federovitch

Entry program: Biological Sciences
Advisor: Randolph Hampton
Next position: Program Consultant, Rady School of Management, UC San Diego
Current position: Director Operations and Manufacturing, Navigate BioPharma
 

Publications 

Federovitch CM, Jones YZ, Tong AH, Boone C, Prinz WA, Hampton RY (2008) Genetic and structural analysis of Hmg2p-induced endoplasmic reticulum remodeling in Saccharomyces cerevisiae. Mol Biol Cell 19:4506-4520. PMC2555956

Federovitch CM, Ron D, Hampton RY (2005) The dynamic ER: experimental approaches and current questions. Curr Opin Cell Biol 17:409-414.

 

Danielle Huffman

Entry program: Biological Sciences
Advisor: Raffi Aroian
Next position: Technical Writer, Stratagene
Current position: Technical Writer, Agilent Technologies 
  

Publications 

Kao CY, Los FC, Huffman DL, Wachi S, Kloft N, Husmann M, Karabrahimi V, Schwartz JL, Bellier A, Ha C, Sagong Y, Fan H, et al (2011) Global functional analyses of cellular responses to pore-forming toxins. PLoS Pathog 7:e1001314. PMC3048360

Bischof LJ, Huffman DL, Aroian RV (2006) Assays for toxicity studies in C. elegans with Bt crystal proteins. Methods Mol Biol 351:139-154.

Huffman DL, Abrami L, Sasik R, Corbeil J, van der Goot FG, Aroian RV (2004) Mitogen-activated protein kinase pathways defend against bacterial pore-forming toxins. Proc Natl Acad Sci U S A 101:10995-11000. PMC503732

Huffman DL, Bischof LJ, Griffitts JS, Aroian RV (2004) Pore worms: using Caenorhabditis elegans to study how bacterial toxins interact with their target host. Int J Med Microbiol 293:599-607.

Griffitts JS, Huffman DL, Whitacre JL, Barrows BD, Marroquin LD, Muller R, Brown JR, Hennet T, Esko JD, Aroian RV (2003) Resistance to a bacterial toxin is mediated by removal of a conserved glycosylation pathway required for toxin-host interactions. J Biol Chem 278:45594-45602.

   

Katie Kindt

Entry program: Biomedical Sciences
Advisor: William Shafer
Next position: Postdoc, Teresa Nicholson lab, Oregon Health Sciences University
Current position: Investigator, NIDCD
  

Publications 

Chatzigeorgiou M, Grundy L, Kindt KS, Lee WH, Driscoll M, Schafer WR (2010) Spatial asymmetry in the mechanosensory phenotypes of the C. elegans DEG/ENaC gene mec-10. J Neurophysiol 104:3334-3344. PMC3007656

Chatzigeorgiou M, Yoo S, Watson JD, Lee WH, Spencer WC, Kindt KS, Hwang SW, Miller DM, 3rd, Treinin M, Driscoll M, Schafer WR (2010) Specific roles for DEG/ENaC and TRP channels in touch and thermosensation in C. elegans nociceptors. Nat Neurosci 13:861-868. PMC2975101

Kindt KS, Quast KB, Giles AC, De S, Hendrey D, Nicastro I, Rankin CH, Schafer WR (2007) Dopamine mediates context-dependent modulation of sensory plasticity in C. elegans. Neuron 55:662-676.

Kindt KS, Viswanath V, Macpherson L, Quast K, Hu H, Patapoutian A, Schafer WR (2007) Caenorhabditis elegans TRPA-1 functions in mechanosensation. Nat Neurosci 10:568-577.

Frokjaer-Jensen C, Kindt KS, Kerr RA, Suzuki H, Melnik-Martinez K, Gerstbreih B, Driscol M, Schafer WR (2006) Effects of voltage-gated calcium channel subunit genes on calcium influx in cultured C. elegans mechanosensory neurons. J Neurobiol 66:1125-1139.

Sanyal S, Wintle RF, Kindt KS, Nuttley WM, Arvan R, Fitzmaurice P, Bigras E, Merz DC, Hebert TE, van der Kooy D, Schafer WR, Culotti JG, Van Tol HH (2004) Dopamine modulates the plasticity of mechanosensory responses in Caenorhabditis elegans. EMBO J 23:473-482. PMC1271763

Kindt KS, Tam T, Whiteman S, Schafer WR (2002) Serotonin promotes G(o)-dependent neuronal migration in Caenorhabditis elegans. Curr Biol 12:1738-1747.

 

2000 Trainees

Will Dolan

Entry program: Biological Sciences
Advisor: Susan Forsburg
Next position: Associate, McKinsey & Company
Current position: Vice President Corporate Strategy, Seres Therapeutics
 

Publications 

Dolan WP, Le AH, Schmidt H, Yuan JP, Green M, Forsburg SL (2010) Fission yeast Hsk1 (Cdc7) kinase is required after replication initiation for induced mutagenesis and proper response to DNA alkylation damage. Genetics 185:39-53. PMC2870973

Dolan WP, Sherman DA, Forsburg SL (2004) Schizosaccharomyces pombe replication protein Cdc45/Sna41 requires Hsk1/Cdc7 and Rad4/Cut5 for chromatin binding. Chromosoma 113:145-156.

Siam R, Dolan WP, Forsburg SL (2004) Choosing and using Schizosaccharomyces pombe plasmids. Methods 33:189-198.

 

Laura (Resor) Erker

Entry program: Biomedical Sciences
Advisor: Anthony Wynshaw-Boris
Next position: Postdoc, Joel Rothman lab, UC Santa Barbara
Current position: Director Of Strategic Partnerships, Oregon Health and Science University
 

Publications 

Erker L, Schubert R, Elchuri S, Huang TT, Tarin D, Mueller K, Zielen S, Epstein CJ, Wynshaw-Boris A (2006) Effect of the reduction of superoxide dismutase 1 and 2 or treatment with alpha-tocopherol on tumorigenesis in Atm-deficient mice. Free Radic Biol Med 41:590-600.

Erker L, Schubert R, Yakushiji H, Barlow C, Larson D, Mitchell JB, Wynshaw-Boris A (2005) Cancer chemoprevention by the antioxidant tempol acts partially via the p53 tumor suppressor. Hum Mol Genet 14:1699-1708.

Schubert R, Erker L, Barlow C, Yakushiji H, Larson D, Russo A, Mitchell JB, Wynshaw-Boris A (2004) Cancer chemoprevention by the antioxidant tempol in Atm-deficient mice. Hum Mol Genet 13:1793-1802.

Resor L, Bowen TJ, Wynshaw-Boris A (2001) Unraveling human cancer in the mouse: recent refinements to modeling and analysis. Hum Mol Genet 10:669-675.

 

David Gold

Entry program: Biomedical Sciences
Advisor: Bruce Hamilton
Next position: Postdoc, Ron Evans Lab, Salk Institute
Current position: Senior Director, Strategic Alliances, Regeneron Pharmaceuticals
 

Publications  

Gold DA, Gent PM, Hamilton BA (2007) ROR alpha in genetic control of cerebellum development: 50 staggering years. Brain Res 1140:19-25.

Alcaraz WA, Gold DA, Raponi E, Gent PM, Concepcion D, Hamilton BA (2006) Zfp423 controls proliferation and differentiation of neural precursors in cerebellar vermis formation. Proc Natl Acad Sci U S A 103:19424-19429. PMC1748242

Floyd JA, Gold DA, Concepcion D, Poon TH, Wang X, Keithley E, Chen D, Ward EJ, Chinn SB, Friedman RA, Yu HT, Moriwaki K, Shiroishi T, Hamilton BA (2003) A natural allele of Nxf1 suppresses retrovirus insertional mutations. Nat Genet 35:221-228. PMC2756099

Gold DA, Baek SH, Schork NJ, Rose DW, Larsen DD, Sachs BD, Rosenfeld MG, Hamilton BA (2003) RORalpha coordinates reciprocal signaling in cerebellar development through sonic hedgehog and calcium-dependent pathways. Neuron 40:1119-1131. PMC2717708

 

Kelly Hester

Entry program: Biomedical Sciences
Advisor: Chris Glass
Next position: Postdoc, Torrey Pines Institute for Molecular Studies
Current position: Principal Scientist, Triphase Accelerator Corporation
  

Publications  

Hester KD, Verhelle D, Escoubet-Lozach L, Luna R, Rose DW, Glass CK (2007) Differential repression of c-myc and cdc2 gene expression by ERF and PE-1/METS. Cell Cycle 6:1594-1604.

Sawka-Verhelle D, Escoubet-Lozach L, Fong AL, Hester KD, Herzig S, Lebrun P, Glass CK (2004) PE-1/METS, an antiproliferative Ets repressor factor, is induced by CREB-1/CREM-1 during macrophage differentiation. J Biol Chem 279:17772-17784.

  

Ramlah Nehring

Entry program: Biological Sciences
Advisor: Joseph Ecker
Next position: Lecturer, Division of Biological Sciences, UC San Diego
Current position: Global Head of Strategy and Transactions, Roche Diagnostics
email: ramlah.nehring@gmail.com
 
I'm glad to see the alumni of this group being brought together, we have quite a few accomplished members."
  
Publications  

Zander M, Willige BC, He Y, Nguyen TA, Langford AE, Nehring R, Howell E, McGrath R, Bartlett A, Castanon R, Nery JR, Chen H, et al (2019) Epigenetic silencing of a multifunctional plant stress regulator. Elife 8. PMC6739875

Maloof JN, Borevitz JO, Dabi T, Lutes J, Nehring RB, Redfern JL, Trainer GT, Wilson JM, Asami T, Berry CC, Weigel D, Chory J (2001) Natural variation in light sensitivity of Arabidopsis. Nat Genet 29:441-446.

 

Sara Olson

Entry program: Biomedical Sciences
Advisor: Jeff Esko
Next position: Postdoc, Karen Oegema lab, Ludwig Institute for Cancer Research
Current position: Associate Professor of Biology, Pomona College
email: sara.olson@pomona.edu
"I remember feeling out of my depth at the journal clubs my first year on the training grant. Everyone else seemed so much smarter than me, and I felt like I didn't belong there. But things got better - I gained skills, expertise, and confidence. And now I'm a professor at a top-tier college with 2 NSF grants. So hang in there if you also feel like you're out of your depth - you're not, you belong there, you've got ideas to contribute, and some of us just take a bit more time and effort to get there. But we all make it. Trust yourself."
 

Publications 

Lawrence R, Olson SK, Steele RE, Wang L, Warrior R, Cummings RD, Esko JD (2008) Evolutionary differences in glycosaminoglycan fine structure detected by quantitative glycan reductive isotope labeling. J Biol Chem 283:33674-33684. PMC2586254

Bender AM, Kirienko NV, Olson SK, Esko JD, Fay DS (2007) lin-35/Rb and the CoREST ortholog spr-1 coordinately regulate vulval morphogenesis and gonad development in C. elegans. Dev Biol 302:448-462. PMC1933485

Olson SK, Bishop JR, Yates JR, Oegema K, Esko JD (2006) Identification of novel chondroitin proteoglycans in Caenorhabditis elegans: embryonic cell division depends on CPG-1 and CPG-2. J Cell Biol 173:985-994. PMC2063922

Hwang HY, Olson SK, Brown JR, Esko JD, Horvitz HR (2003) The Caenorhabditis elegans genes sqv-2 and sqv-6, which are required for vulval morphogenesis, encode glycosaminoglycan galactosyltransferase II and xylosyltransferase. J Biol Chem 278:11735-11738.

Hwang HY, Olson SK, Esko JD, Horvitz HR (2003) Caenorhabditis elegans early embryogenesis and vulval morphogenesis require chondroitin biosynthesis. Nature 423:439-443.

Crawford BE, Olson SK, Esko JD, Pinhal MA (2001) Cloning, Golgi localization, and enzyme activity of the full-length heparin/heparan sulfate-glucuronic acid C5-epimerase. J Biol Chem 276:21538-21543.

Pinhal MA, Smith B, Olson S, Aikawa J, Kimata K, Esko JD (2001) Enzyme interactions in heparan sulfate biosynthesis: uronosyl 5-epimerase and 2-O-sulfotransferase interact in vivo. Proc Natl Acad Sci U S A 98:12984-12989. PMC60811

 

Nick Reeves

Entry program: Biological Sciences
Advisor: Jim Posakony
Next position: Visiting Assistant Professor, W.M. Keck Science Department, Claremont Colleges
Current position: Associate Professor and Chair, Biological Sciences Department, Mt. San Jacinto College - Menifee Valley Campus
"I entered graduate school at UCSD with the goal to pursue a career in teaching at the college level. I discovered opportunities to develop my skills in teaching while I completed my graduate research including being a teaching assistant for undergraduate courses and participating in undergraduate teaching workshops provided by the Graduate Student Association. The journal club for the Genetics Training Program also helped prepare me for the honors seminar courses that I teach in my current position. By sharing my career plans with my graduate advisor, I received invaluable support when I applied for positions in teaching after I graduated. Near the end of my degree, I secured a temporary position as a Visiting Assistant Professor teaching introductory biology courses by networking with an UCSD alumnus in the W.M. Keck Science Department at the Claremont Colleges. My experiences and the personal network I formed during graduate school at UCSD made my transition into a career much easier."
  

Publications 

Ocorr K, Reeves NL, Wessells RJ, Fink M, Chen HS, Akasaka T, Yasuda S, Metzger JM, Giles W, Posakony JW, Bodmer R (2007) KCNQ potassium channel mutations cause cardiac arrhythmias in Drosophila that mimic the effects of aging. Proc Natl Acad Sci U S A 104:3943-3948. PMC1820688

Reeves N, Posakony JW (2005) Genetic programs activated by proneural proteins in the developing Drosophila PNS. Dev Cell 8:413-425.

Rebeiz M, Reeves NL, Posakony JW (2002) SCORE: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. Site clustering over random expectation. Proc Natl Acad Sci U S A 99:9888-9893. PMC125053

  

1999 Trainees

Jennifer Floyd

Entry program: Biomedical Sciences
Advisor: Bruce Hamilton
Next position: Postdoc, Steve McIntire lab, Ernest Gallo Clinic and Research Center-UCSF
Current position: Patent Agent, Wilson Sonsini
"Spend the time to think about life after grad school with an open mind, even if you think you know what you want to do after. You never know where life will take you and there are lots of great careers out there for folks with your background."
 

Publications 

Floyd JA, Gold DA, Concepcion D, Poon TH, Wang X, Keithley E, Chen D, Ward EJ, Chinn SB, Friedman RA, Yu HT, Moriwaki K, Shiroishi T, Hamilton BA (2003) A natural allele of Nxf1 suppresses retrovirus insertional mutations. Nat Genet 35:221-228. PMC2756099

Floyd JA, Hamilton BA (1999) Intranuclear inclusions and the ubiquitin-proteasome pathway: digestion of a red herring? Neuron 24:765-766.

  

Jason Lam

Entry program: Biomedical Sciences
Advisor: Kenneth Chien
Next position: Postdoc, Alessandra Moretti lab, Technischen Universität München
Current position: Senior Scientist, Orachard Therapeutics 
 

Publications 

Moretti A, Caron L, Nakano A, Lam JT, Bernshausen A, Chen Y, Qyang Y, Bu L, Sasaki M, Martin-Puig S, Sun Y, Evans SM, Laugwitz KL, Chien KR (2006) Multipotent embryonic isl1+ progenitor cells lead to cardiac, smooth muscle, and endothelial cell diversification. Cell 127:1151-1165.

Wang J, Hoshijima M, Lam J, Zhou Z, Jokiel A, Dalton ND, Hultenby K, Ruiz-Lozano P, Ross J, Jr., Tryggvason K, Chien KR (2006) Cardiomyopathy associated with microcirculation dysfunction in laminin alpha4 chain-deficient mice. J Biol Chem 281:213-220.

Kaliman P, Catalucci D, Lam JT, Kondo R, Gutierrez JC, Reddy S, Palacin M, Zorzano A, Chien KR, Ruiz-Lozano P (2005) Myotonic dystrophy protein kinase phosphorylates phospholamban and regulates calcium uptake in cardiomyocyte sarcoplasmic reticulum. J Biol Chem 280:8016-8021.

Laugwitz KL, Moretti A, Lam J, Gruber P, Chen Y, Woodard S, Lin LZ, Cai CL, Lu MM, Reth M, Platoshyn O, Yuan JX, Evans S, Chien KR (2005) Postnatal isl1+ cardioblasts enter fully differentiated cardiomyocyte lineages. Nature 433:647-653. PMC5578466

 

1998 Trainees

Sherri Goode-Liang

Entry program: Biomedical Sciences
Advisor: John Kelsoe
 

Publications 

McCarthy MJ, Liang S, Spadoni AD, Kelsoe JR, Simmons AN (2014) Whole brain expression of bipolar disorder associated genes: structural and genetic analyses. PLoS One 9:e100204. PMC4062532

Nissen S, Liang S, Shehktman T, Kelsoe JR, Bipolar Genome S, Greenwood TA, Nievergelt CM, McKinney R, Shilling PD, Smith EN, Schork NJ, Bloss CS, et al (2012) Evidence for association of bipolar disorder to haplotypes in the 22q12.3 region near the genes stargazin, IFT27 and parvalbumin. Am J Med Genet B Neuropsychiatr Genet 159B:941-950. PMC3665332

Barrett TB, Emberton JE, Nievergelt CM, Liang SG, Hauger RL, Eskin E, Schork NJ, Kelsoe JR (2007) Further evidence for association of GRK3 to bipolar disorder suggests a second disease mutation. Psychiatr Genet 17:315-322.

Liang SG, Sadovnick AD, Remick RA, Keck PE, McElroy SL, Kelsoe JR (2002) A linkage disequilibrium study of bipolar disorder and microsatellite markers on 22q13. Psychiatr Genet 12:231-235.

  

Marjan Haghnia

Entry program: Biochemistry
Advisor: Larry Goldstein
Next position: Senior Research Scientist, Nanogen
Current position: Senior Director, Product Technical Support, GenMark Diagnostics
email: mhaghnia@hotmail.com
 

Publications 

Haghnia M, Cavalli V, Shah SB, Schimmelpfeng K, Brusch R, Yang G, Herrera C, Pilling A, Goldstein LS (2007) Dynactin is required for coordinated bidirectional motility, but not for dynein membrane attachment. Mol Biol Cell 18:2081-2089. PMC1877108

Ji JY, Haghnia M, Trusty C, Goldstein LS, Schubiger G (2002) A genetic screen for suppressors and enhancers of the Drosophila cdk1-cyclin B identifies maternal factors that regulate microtubule and microfilament stability. Genetics 162:1179-1195. PMC1462342

  

Robin Truelove

Entry program: Biological Sciences
Advisor: Gary Karpen
Next position: Scientist, ScienceMedia
Current position: Independent Accelrys Pipeline Pilot Consultant

1997 Trainees

J. Suzie Bailey

Entry program: Biomedical Sciences
Advisor: Pamela Mellon
Next position: Faculty Fellow, UC San Diego; Postdoc, Genomics Institute of the Novartis Foundation
Current position: Professor, Mira Costa College
 

Publications 

Cherrington BD, Bailey JS, Diaz AL, Mellon PL (2008) NeuroD1 and Mash1 temporally regulate GnRH receptor gene expression in immortalized mouse gonadotrope cells. Mol Cell Endocrinol 295:106-114. PMC2640340

Zhang H, Bailey JS, Coss D, Lin B, Tsutsumi R, Lawson MA, Mellon PL, Webster NJ (2006) Activin modulates the transcriptional response of LbetaT2 cells to gonadotropin-releasing hormone and alters cellular proliferation. Mol Endocrinol 20:2909-2930. PMC2673912

McGillivray SM, Bailey JS, Ramezani R, Kirkwood BJ, Mellon PL (2005) Mouse GnRH receptor gene expression is mediated by the LHX3 homeodomain protein. Endocrinology 146:2180-2185. PMC2930620

Bailey JS, Rave-Harel N, McGillivray SM, Coss D, Mellon PL (2004) Activin regulation of the follicle-stimulating hormone beta-subunit gene involves Smads and the TALE homeodomain proteins Pbx1 and Prep1. Mol Endocrinol 18:1158-1170. PMC2935796

Spady TJ, Shayya R, Thackray VG, Ehrensberger L, Bailey JS, Mellon PL (2004) Androgen regulates follicle-stimulating hormone beta gene expression in an activin-dependent manner in immortalized gonadotropes. Mol Endocrinol 18:925-940. PMC2932479

Pernasetti F, Vasilyev VV, Rosenberg SB, Bailey JS, Huang HJ, Miller WL, Mellon PL (2001) Cell-specific transcriptional regulation of follicle-stimulating hormone-beta by activin and gonadotropin-releasing hormone in the LbetaT2 pituitary gonadotrope cell model. Endocrinology 142:2284-2295.

  

Justin Borevitz

Entry program: Biological Sciences
Advisor: Joanne Chory
Next position: Postdoc, Joseph Ecker lab, Salk Institute
Current position: Professor of Biology, Australian National University
 

Publications 

Balasubramanian S, Schwartz C, Singh A, Warthmann N, Kim MC, Maloof JN, Loudet O, Trainer GT, Dabi T, Borevitz JO, Chory J, Weigel D (2009) QTL mapping in new Arabidopsis thaliana advanced intercross-recombinant inbred lines. PLoS One 4:e4318. PMC2629843

Schwartz C, Balasubramanian S, Warthmann N, Michael TP, Lempe J, Sureshkumar S, Kobayashi Y, Maloof JN, Borevitz JO, Chory J, Weigel D (2009) Cis-regulatory changes at FLOWERING LOCUS T mediate natural variation in flowering responses of Arabidopsis thaliana. Genetics 183:723-732, 721SI-727SI. PMC2766330

Filiault DL, Wessinger CA, Dinneny JR, Lutes J, Borevitz JO, Weigel D, Chory J, Maloof JN (2008) Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light. Proc Natl Acad Sci U S A 105:3157-3162. PMC2268601

Borevitz JO, Hazen SP, Michael TP, Morris GP, Baxter IR, Hu TT, Chen H, Werner JD, Nordborg M, Salt DE, Kay SA, Chory J, et al (2007) Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc Natl Acad Sci U S A 104:12057-12062. PMC1914337

Werner JD, Borevitz JO, Uhlenhaut NH, Ecker JR, Chory J, Weigel D (2005) FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions. Genetics 170:1197-1207. PMC1451178

Werner JD, Borevitz JO, Warthmann N, Trainer GT, Ecker JR, Chory J, Weigel D (2005) Quantitative trait locus mapping and DNA array hybridization identify an FLM deletion as a cause for natural flowering-time variation. Proc Natl Acad Sci U S A 102:2460-2465. PMC548991

Borevitz JO, Chory J (2004) Genomics tools for QTL analysis and gene discovery. Curr Opin Plant Biol 7:132-136.

Wolyn DJ, Borevitz JO, Loudet O, Schwartz C, Maloof J, Ecker JR, Berry CC, Chory J (2004) Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana. Genetics 167:907-917. PMC1470895

Borevitz JO, Liang D, Plouffe D, Chang HS, Zhu T, Weigel D, Berry CC, Winzeler E, Chory J (2003) Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res 13:513-523. PMC430246

Borevitz JO, Maloof JN, Lutes J, Dabi T, Redfern JL, Trainer GT, Werner JD, Asami T, Berry CC, Weigel D, Chory J (2002) Quantitative trait loci controlling light and hormone response in two accessions of Arabidopsis thaliana. Genetics 160:683-696. PMC1461994

Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D (2002) The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet 30:190-193.

Maloof JN, Borevitz JO, Dabi T, Lutes J, Nehring RB, Redfern JL, Trainer GT, Wilson JM, Asami T, Berry CC, Weigel D, Chory J (2001) Natural variation in light sensitivity of Arabidopsis. Nat Genet 29:441-446.

Maloof JN, Borevitz JO, Weigel D, Chory J (2000) Natural variation in phytochrome signaling. Semin Cell Dev Biol 11:523-530.

Weigel D, Ahn JH, Blazquez MA, Borevitz JO, Christensen SK, Fankhauser C, Ferrandiz C, Kardailsky I, Malancharuvil EJ, Neff MM, Nguyen JT, Sato S, et al (2000) Activation tagging in Arabidopsis. Plant Physiol 122:1003-1013. PMC1539247

 

Tiffany Greenwood

Entry program: Biomedical Sciences
Advisor: John Kelsoe
Next position: 
Current position: Associate Professor of Psychiatry, Director of the Laboratory for Psychiatric Spectrum Research, UC San Diego
LinkedIn profile: https://www.linkedin.com/in/tiffany-greenwood-455b267/
  

Publications 

Nissen S, Liang S, Shehktman T, Kelsoe JR, Bipolar Genome S, Greenwood TA, Nievergelt CM, McKinney R, Shilling PD, Smith EN, Schork NJ, Bloss CS, et al (2012) Evidence for association of bipolar disorder to haplotypes in the 22q12.3 region near the genes stargazin, IFT27 and parvalbumin. Am J Med Genet B Neuropsychiatr Genet 159B:941-950. PMC3665332

Greenwood TA, Alexander M, Keck PE, McElroy S, Sadovnick AD, Remick RA, Shaw SH, Kelsoe JR (2002) Segmental linkage disequilibrium within the dopamine transporter gene. Mol Psychiatry 7:165-173.

Greenwood TA, Alexander M, Keck PE, McElroy S, Sadovnick AD, Remick RA, Kelsoe JR (2001) Evidence for linkage disequilibrium between the dopamine transporter and bipolar disorder. Am J Med Genet 105:145-151.

  

Rex Kerr

Entry program: Biological Sciences
Advisor: William Schafer
Next position: Fellow, HHMI Janelia Farm Research Campus
Current position: Associate Scientist, CalicoLabs
 

Publications 

Yemini E, Kerr RA, Schafer WR (2011) Preparation of samples for single-worm tracking. Cold Spring Harb Protoc 2011:1475-1479. PMC4886831

Yemini E, Kerr RA, Schafer WR (2011) Illumination for worm tracking and behavioral imaging. Cold Spring Harb Protoc 2011:1480-1482. PMC4874461

Yemini E, Kerr RA, Schafer WR (2011) Tracking movement behavior of multiple worms on food. Cold Spring Harb Protoc 2011:1483-1487. PMC4874462

Zhang M, Chung SH, Fang-Yen C, Craig C, Kerr RA, Suzuki H, Samuel AD, Mazur E, Schafer WR (2008) A self-regulating feed-forward circuit controlling C. elegans egg-laying behavior. Curr Biol 18:1445-1455. PMC2621019

Frokjaer-Jensen C, Kindt KS, Kerr RA, Suzuki H, Melnik-Martinez K, Gerstbreih B, Driscol M, Schafer WR (2006) Effects of voltage-gated calcium channel subunit genes on calcium influx in cultured C. elegans mechanosensory neurons. J Neurobiol 66:1125-1139.

Kerr RA, Schafer WR (2006) Intracellular Ca2+ imaging in C. elegans. Methods Mol Biol 351:253-264.

Hilliard MA, Apicella AJ, Kerr R, Suzuki H, Bazzicalupo P, Schafer WR (2005) In vivo imaging of C. elegans ASH neurons: cellular response and adaptation to chemical repellents. EMBO J 24:63-72. PMC544906

Shyn SI, Kerr R, Schafer WR (2003) Serotonin and Go modulate functional states of neurons and muscles controlling C. elegans egg-laying behavior. Curr Biol 13:1910-1915.

Suzuki H, Kerr R, Bianchi L, Frokjaer-Jensen C, Slone D, Xue J, Gerstbrein B, Driscoll M, Schafer WR (2003) In vivo imaging of C. elegans mechanosensory neurons demonstrates a specific role for the MEC-4 channel in the process of gentle touch sensation. Neuron 39:1005-1017.

Hardaker LA, Singer E, Kerr R, Zhou G, Schafer WR (2001) Serotonin modulates locomotory behavior and coordinates egg-laying and movement in Caenorhabditis elegans. J Neurobiol 49:303-313.

Kerr R, Lev-Ram V, Baird G, Vincent P, Tsien RY, Schafer WR (2000) Optical imaging of calcium transients in neurons and pharyngeal muscle of C. elegans. Neuron 26:583-594.

   

Felix Tinkov

Entry program: Biomedical Sciences
Advisor: Ted Friedmann
Next position: Law Student, University of San Diego
Current position: Principal, Law Office of Felix Tinkov
Last update: September 20, 2021