Alumni

Kween Agba

Publications

Mike Cuoco

Publications

Toda T, Bedrosian TA, Schafer ST, Cuoco MS, Linker SB, Ghassemzadeh S, Mitchell L, Whiteley JT, Novaresi N, McDonald AH, Gallina IS, Yoon H, et al (2024) Long interspersed nuclear elements safeguard neural progenitors from precocious differentiation. Cell Rep 43:113774. PMC10948021

Amanda (AJ) Daniels

Publications

Xiaomi Du

Publications

DeForest N, Kavitha B, Hu S, Isaac R, Krohn L, Wang M, Du X, De Arruda Saldanha C, Gylys J, Merli E, Abagyan R, Najmi L, et al (2023) Human gain-of-function variants in HNF1A confer protection from diabetes but independently increase hepatic secretion of atherogenic lipoproteins. Cell Genom 3:100339. PMC10363808

Du X, DeForest N, Majithia AR (2021) Human Genetics to Identify Therapeutic Targets for NAFLD: Challenges and Opportunities. Front Endocrinol (Lausanne) 12:777075. PMC8688763

Sam Hatch

Publications

Hatch ST, Smargon AA, Yeo GW (2022) Engineered U1 snRNAs to modulate alternatively spliced exons. Methods 205:140-148. PMC11185844 

Mitchell Kong

Publications

Lawrence ES, Gu W, Bohlender RJ, Anza-Ramirez C, Cole AM, Yu JJ, Hu H, Heinrich EC, O'Brien KA, Vasquez CA, Cowan QT, Bruck PT, et al (2024) Functional EPAS1/HIF2A missense variant is associated with hematocrit in Andean highlanders. Sci Adv 10:eadj5661. PMC10857371

Brittany Leger

Publications

Leger BS, Meredith JJ, Ideker T, Sanchez-Roige S, Palmer AA (2024) Rare and common variants associated with alcohol consumption identify a conserved molecular network. Alcohol Clin Exp Res (Hoboken). 

Toikumo S, Jennings MV, Pham BK, Lee H, Mallard TT, Bianchi SB, Meredith JJ, Vilar-Ribó L, Xu H, Hatoum AS, Johnson EC, Pazdernik VK, et al (2024) Multi-ancestry meta-analysis of tobacco use disorder identifies 461 potential risk genes and reveals associations with multiple health outcomes. Nat Hum Behav 8:1177-1193. PMC11199106

Wright SN, Leger BS, Rosenthal SB, Liu SN, Jia T, Chitre AS, Polesskaya O, Holl K, Gao J, Cheng R, Garcia Martinez A, George A, et al (2023) Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks. Cell Rep 42:112873. PMC10546330  

Publications

McMillan RE, Lo MK, Zhang XQ, Beadle JR, Valiaeva N, Garretson AF, Clark AE, Freshman JE, Murphy J, Montgomery JM, Spiropoulou CF, Schooley RT, Hostetler KY, Carlin AF (2023) Enhanced broad spectrum in vitro antiviral efficacy of 3-F-4-MeO-Bn, 3-CN, and 4-CN derivatives of lipid remdesivir nucleoside monophosphate prodrugs. Antiviral Res 219:105718. PMC10790242

McMillan RE, Wang E, Carlin AF, Coufal NG (2023) Human microglial models to study host-virus interactions. Exp Neurol 363:114375. PMC10521930Branche E, Wang YT, Viramontes KM, Valls Cuevas JM, Xie J, Ana-Sosa-Batiz F, Shafee N, Duttke SH, McMillan RE, Clark AE, Nguyen MN, Garretson AF, et al (2022) SREBP2-dependent lipid gene transcription enhances the infection of human dendritic cells by Zika virus. Nat Commun 13:5341. PMC9465152

Carlin AF, Beadle JR, Clark AE, Gully KL, Moreira FR, Baric RS, Graham RL, Valiaeva N, Leibel SL, Bray W, McMillan RE, Freshman JE, et al (2023) 1-O-Octadecyl-2-O-benzyl-sn-glyceryl-3-phospho-GS-441524 (V2043). Evaluation of Oral V2043 in a Mouse Model of SARS-CoV-2 Infection and Synthesis and Antiviral Evaluation of Additional Phospholipid Esters with Enhanced Anti-SARS-CoV-2 Activity. J Med Chem 66:5802-5819. PMC10108740

Schooley RT, Carlin AF, Beadle JR, Valiaeva N, Zhang XQ, Clark AE, McMillan RE, Leibel SL, McVicar RN, Xie J, Garretson AF, Smith VI, Murphy J, Hostetler KY (2021) Rethinking Remdesivir: Synthesis, Antiviral Activity, and Pharmacokinetics of Oral Lipid Prodrugs. Antimicrob Agents Chemother 65:e0115521. PMC8448143 

Chris Balak

Publications

Fixsen BR, Han CZ, Zhou Y, Spann NJ, Saisan P, Shen Z, Balak C, Sakai M, Cobo I, Holtman IR, Warden AS, Ramirez G, Collier JG, Pasillas MP, Yu M, Hu R, Li B, Belhocine S, Gosselin D, Coufal NG, Ren B, Glass CK (2023) SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity. Nat Immunol 24: 1188-1199.

Maya Gosztyla

Publications

Correia JC, Jannig PR, Gosztyla ML, Cervenka I, Ducommun S, Præstholm SM, Dumont K, Liu Z, Liang Q, Edsgärd D, Emanuelsson O, Gregorevic P, Westerblad H, Venckunas T, Brazaitis M, Kamandulis S, Lanner JT, Yeo GW, Ruas JL (2023) Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and regeneration. bioRxiv.

Morelli KH, Wu Q, Gosztyla ML, Liu H, Yao M, Zhang C, Chen J, Marina RJ, Lee K, Jones KL, Huang MY, Li A, Smith-Geater C, Thompson LM, Duan W, Yeo GW (2023) An RNA-targeting CRISPR-Cas13d system alleviates disease-related phenotypes in Huntington's disease models. Nat Neurosci 26: 27-38.

Jin W, Brannan KW, Kapeli K, Park SS, Tan HQ, Gosztyla ML, Mujumdar M, Ahdout J, Henroid B, Rothamel K, Xiang JS, Wong L, Yeo GW (2023) HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence. Mol Cell 83: 2595-2611.e2511.

Gosztyla M (2022) How to manage your time as a researcher. Nature. DOI:10.1038/d41586-022-04364-2

Gosztyla M (2022) How to find, read and organize papers. Nature. DOI: 10.1038/d41586-022-01878-7

Gosztyla ML, Kwong L, Murray NA, Williams CE, Behnke N, Curry P, Corbett KD, KN DS, Gala de Pablo J, Gicobi J, Javidnia M, Lotay N, Prescott SM, Quinn JP, Rivera ZMG, Smith MA, Tang KTY, Venkat A, Yamoah MA (2021) Responses to 10 common criticisms of anti-racism action in STEMM. PLoS Comput Biol 17: e1009141.

Qin Y, Huttlin EL, Winsnes CF, Gosztyla ML, Wacheul L, Kelly MR, Blue SM, Zheng F, Chen M, Schaffer LV, Licon K, Bäckström A, Vaites LP, Lee JJ, Ouyang W, Liu SN, Zhang T, Silva E, Park J, Pitea A, Kreisberg JF, Gygi SP, Ma J, Harper JW, Yeo GW, Lafontaine DLJ, Lundberg E, Ideker T (2021) A multi-scale map of cell structure fusing protein images and interactions. Nature 600: 536-542. 

Alyssa Holman

Publications

Gonzalez G, Holman AR, Nelson AC, Engler AJ (2022) Engineering the niche to differentiate and deploy cardiovascular cells. Curr Opin Biotechnol 74: 122-128. 

Holman AR, Chi NC (2022) Fishing Out the Role of RBPMS2 in Cardiac Splicing. Circ Res 131: 1001-1003.

Pratibha Jagannatha

Publications

Schmok JC, Jain M, Street LA, Tankka AT, Schafer D, Her HL, Elmsaouri S, Gosztyla ML, Boyle EA, Jagannatha P, Luo EC, Kwon EJ, Jovanovic M, Yeo GW (2024) Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. Nat Biotechnol 42:1429-1441. PMC11389820

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. 

Bojing (Blair) Jia

Publications

Jia BB, Jussila A, Kern C, Zhu Q, Ren B (2023) A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. Nat Biotechnol 41: 1004-1017.

Lee L, Yu H, Jia BB, Jussila A, Zhu C, Chen J, Xie L, Hafner A, Mishra S, Wang DD, Strambio-De-Castillia C, Boettiger A, Ren B, Li Y, Hu M (2023) SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data. Nat Commun 14: 4873

Rebecca Melton

Publications

Elgamal RM, Kudtarkar P, Melton RL, Mummey HM, Benaglio P, Okino ML, Gaulton KJ (2023) An integrated map of cell type-specific gene expression in pancreatic islets. Diabetes db230130.

Zhu H, Wang G, Nguyen-Ngoc KV, Kim D, Miller M, Goss G, Kovsky J, Harrington AR, Saunders DC, Hopkirk AL, Melton R, Powers AC, Preissl S, Spagnoli FM, Gaulton KJ, Sander M (2023) Understanding cell fate acquisition in stem-cell-derived pancreatic islets using single-cell multiome-inferred regulomes. Dev Cell 58: 727-743.e711.

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

Krypton Carolino

Publications

Jado JC, Dow M, Carolino K, Klie A, Fonseca GJ, Ideker T, Carter H, Winzeler EA (2024) In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells. Sci Rep 14:13989. PMC11183241

Jiang T, Godinez-Macias KP, Collins JE, Lee JW, Wendt KL, Carolino K, Chakrabarti D, Cichewicz RH, Winzeler EA (2024) Identification of fungal natural products with potent inhibition in Toxoplasma gondii. Microbiol Spectr 12:e0414223. PMC10986609

Ottilie S, Luth MR, Hellemann E, Goldgof GM, Vigil E, Kumar P, Cheung AL, Song M, Godinez-Macias KP, Carolino K, Yang J, Lopez G, et al (2022) Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance. Commun Biol 5:128. PMC8837787

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

Carolino K, Winzeler EA (2020) The antimalarial resistome - finding new drug targets and their modes of action. Curr Opin Microbiol 57:49-55. PMC7763834

Carmine Chavez-Martinez

Publications

Kim H, Saikia J, Monte K, Ha E, Romaus-Sanjurjo D, Sanchez J, Moore A, Hernaiz-Llorens M, Chavez-Martinez C, Agba C, Li H, Lusk D, Cervantes K, Zheng B (2023) Probing regenerative heterogeneity of corticospinal neurons with scRNA-Seq. Res Sq. PMC9980198

Kim HJ, Saikia JM, Monte KMA, Ha E, Romaus-Sanjurjo D, Sanchez JJ, Moore AX, Hernaiz-Llorens M, Chavez-Martinez CL, Agba CK, Li H, Zhang J, et al (2023) Deep scRNA sequencing reveals a broadly applicable Regeneration Classifier and implicates antioxidant response in corticospinal axon regeneration. Neuron 111:3953-3969.e3955. PMC10843387

Saikia JM, Chavez-Martinez CL, Kim ND, Allibhoy S, Kim HJ, Simonyan L, Smadi S, Tsai KM, Romaus-Sanjurjo D, Jin Y, Zheng B (2022) A Critical Role for DLK and LZK in Axonal Repair in the Mammalian Spinal Cord. J Neurosci 42:3716-3732. PMC9087816

Tiffany Chu

Publications

Fitzgerald MQ, Chu T, Puppo F, Blanch R, Chillón M, Subramaniam S, Muotri AR (2024) Generation of 'semi-guided' cortical organoids with complex neural oscillations. Nat Protoc 19:2712-2738. PMC11380594

Natalie DeForest

Publications

DeForest N, Kavitha B, Hu S, Isaac R, Krohn L, Wang M, Du X, Saldanha CDA, Gylys J, Merli E, Abagyan R, Najmi L, Mohan V, Alnylam Human Genetics, AMP-T2D Consortium, Flannick, J, Peloso GM, Gordts P, Heinz S, Deaton AM, Khera AV, Olefsky J, Radha V, Majithia, AR. (2023) Human gain-of-function variants in HNF1A confer protection from diabetes but independently increase hepatic secretion of atherogenic lipoproteins. Cell Genomics 3, 100339. PMC10363808

DeForest N, Majithia AR (2022) Genetics of Type 2 Diabetes: Implications from Large-Scale Studies. Curr Diab Rep 22:227-235. PMC9072491

Du X, DeForest N, Majithia AR (2021) Human Genetics to Identify Therapeutic Targets for NAFLD: Challenges and Opportunities. Front Endocrinol (Lausanne) 12:777075. PMC8688763

Sara Elmsaouri

Publications

Schmok JC, Jain M, Street LA, Tankka AT, Schafer D, Her HL, Elmsaouri S, Gosztyla ML, Boyle EA, Jagannatha P, Luo EC, Kwon EJ, Jovanovic M, Yeo GW (2024) Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. Nat Biotechnol 42:1429-1441. PMC11389820

Elmsaouri S, Markmiller S, Yeo GW (2022) APEX Proximity Labeling of Stress Granule Proteins. Methods Mol Biol 2428:381-399.

Jenna Kovsky

Publications

Zhu H, Wang G, Nguyen-Ngoc KV, Kim D, Miller M, Goss G, Kovsky J, Harrington AR, Saunders DC, Hopkirk AL, Melton R, Powers AC, et al (2023) Understanding cell fate acquisition in stem-cell-derived pancreatic islets using single-cell multiome-inferred regulomes. Dev Cell 58:727-743.e711. PMC10175223

Eleonora Rachtman

Publications

Sarmashghi S, Balaban M, Rachtman E, Touri B, Mirarab S, Bafna V (2021) Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT. PLoS Comput Biol 17:e1009449. PMC8629397

Rachtman E, Bafna V, Mirarab S (2021) CONSULT: accurate contamination removal using locality-sensitive hashing. NAR Genom Bioinform 3:lqab071. PMC8340999

Rachtman E, Balaban M, Bafna V, Mirarab S (2020) The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters. Mol Ecol Resour 20.

Michelle Ragsac

Publications

Song BP*, Ragsac MF*, Tellez K, Jindal GA, Grudzien JL, Le SH, Farley EK (2023) Diverse logics and grammar encode notochord enhancers. Cell Reports. 42:112052.

Danielle Schafer

Publications

Xiang JS, Mueller JR, Luo EC, Yee BA, Schafer D, Schmok JC, Tan FE, Rothamel K, McVicar RN, Kwong EM, Jones KL, Her HL, et al (2022) Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions. bioRxiv. PMC8887137

James Yu

Publications

Yu JJ, Non AL, Heinrich EC, Gu W, Alcock J, Moya EA, Lawrence ES, Tift MS, O'Brien KA, Storz JF, Signore AV, Khudyakov JI, Milsom WK, Wilson SM, Beall CM, Villafuerte FC, Stobdan T, Julian CG, Moore LG, Fuster MM, Stokes JA, Milner R, West JB, Zhang J, Shyy JY, Childebayeva A, Vázquez-Medina JP, Pham LV, Mesarwi OA, Hall JE, Cheviron ZA, Sieker J, Blood AB, Yuan JX, Scott GR, Rana BK, Ponganis PJ, Malhotra A, Powell FL, Simonson TS (2022) Time Domains of Hypoxia Responses and -Omics Insights. Front Physiol. 13:885295. 

Noorsher Ahmed

Publications

Le P, Ahmed N, Yeo GW (2022) Illuminating RNA biology through imaging. Nat Cell Biol 24:815-824.

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(6):636-642. 

Melinda Beccari

Publications

Yu H, Lu S, Gasior K, Singh D, Vazquez-Sanchez S, Tapia O, Toprani D, Beccari MS, Yates JR, 3rd, Da Cruz S, Newby JM, Lafarga M, Gladfelter AS, Villa E, Cleveland DW (2021) HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells. Science 371: eabb4309. PMC8286096

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, Lin N, Wu D, Bennett CF, Rigo F, Da Cruz S, Ravits J, Lagier-Tourenne C, Cleveland DW (2019) Premature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration. Nat Neurosci 22: 180-190. PMC6348009

Jessica Bloom

Publications

Corrina Elder

Publications

Elder CR, Pasquinelli AE (2022) New Roles for MicroRNAs in Old Worms. Front Aging 3:871226. PMC9261348

Reddy KC, Dror T, Underwood RS, Osman GA, Elder CR, Desjardins CA, Cuomo CA, Barkoulas M, Troemel ER (2019) Antagonistic paralogs control a switch between growth and pathogen resistance in C. elegans. PLoS Pathog 15: e1007528. PMC6347328

Emily Ho

Publications

Ho EV, Shi C, Cassin J, He MY, Nguyen RD, Ryan GE, Tonsfeldt KJ, Mellon PL (2021) Reproductive Deficits Induced by Prenatal Antimüllerian Hormone Exposure Require Androgen Receptor in Kisspeptin Cells. Endocrinology 162. PMC8507963

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

James Hocker

Publications

Whitehead AJ, Hocker JD, Ren B, Engler AJ (2022) Improved epicardial cardiac fibroblast generation from iPSCs. J Mol Cell Cardiol 164: 58-68. PMC9048147

Hocker JD, Poirion OB, Zhu F, Buchanan J, Zhang K, Chiou J, Wang TM, Zhang Q, Hou X, Li YE, Zhang Y, Farah EN, Wang A, McCulloch AD, Gaulton KJ, Ren B, Chi NC, Preissl S (2021) Cardiac cell type-specific gene regulatory programs and disease risk association. Sci Adv 7. PMC8121433

Zhang K, Hocker JD, Miller M, Hou X, Chiou J, Poirion OB, Qiu Y, Li YE, Gaulton KJ, Wang A, Preissl S, Ren B (2021) A single-cell atlas of chromatin accessibility in the human genome. Cell 184: 5985-6001 e5919. PMC8664161

Kubo N, Ishii H, Xiong X, Bianco S, Meitinger F, Hu R, Hocker JD, Conte M, Gorkin D, Yu M, Li B, Dixon JR, Hu M, Nicodemi M, Zhao H, Ren B (2021) Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Nat Struct Mol Biol 28: 152-161. PMC7913465

Erin Ritchie

Publications

Li Y, Ritchie EM, Steinke CL, Qi C, Chen L, Zheng B, Jin Y (2021) Activation of MAP3K DLK and LZK in Purkinje cells causes rapid and slow degeneration depending on signaling strength. Elife 10: e63509. PMC7870138

Zeyang Shen

Publications

Shen Z, Li RZ, Prohaska TA, Hoeksema MA, Spann NJ, Tao J, Fonseca GJ, Le T, Stolze LK, Sakai M, Romanoski CE, Glass CK (2022) Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs. Elife 11. PMC8809895

Hoeksema MA, Shen Z, Holtman IR, Zheng A, Spann NJ, Cobo I, Gymrek M, Glass CK (2021) Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4. Sci Adv 7. PMC8208725

Shen Z, Hoeksema MA, Ouyang Z, Benner C, Glass CK (2020) MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function. Bioinformatics 36: i84-i92. PMC7355228

Nott A, Holtman IR, Coufal NG, Schlachetzki JCM, Yu M, Hu R, Han CZ, Pena M, Xiao J, Wu Y, Keulen Z, Pasillas MP, O'Connor C, Nickl CK, Schafer ST, Shen Z, Rissman RA, Brewer JB, Gosselin D, Gonda DD, Levy ML, Rosenfeld MG, McVicker G, Gage FH, Ren B, Glass CK (2019) Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Science 366: 1134-1139. PMC7028213

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

Josh Chiou

Publications

Mahajan A, Spracklen CN, Zhang W, Ng MCY, Petty LE, Kitajima H, Yu GZ, Rüeger S, Speidel L, Kim YJ, Horikoshi M, Mercader JM, et al (2022) Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation. Nat Genet 54:560-572. PMC9179018

Li YE, Preissl S, Hou X, Zhang Z, Zhang K, Qiu Y, Poirion OB, Li B, Chiou J, Liu H, Pinto-Duarte A, Kubo N, et al (2021) An atlas of gene regulatory elements in adult mouse cerebrum. Nature 598:129-136. PMC8494637

Geusz RJ, Wang A, Lam DK, Vinckier NK, Alysandratos KD, Roberts DA, Wang J, Kefalopoulou S, Ramirez A, Qiu Y, Chiou J, Gaulton KJ, et al (2021) Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors. Nat Commun 12:6636. PMC8599738

Zhang K, Hocker JD, Miller M, Hou X, Chiou J, Poirion OB, Qiu Y, Li YE, Gaulton KJ, Wang A, Preissl S, Ren B (2021) A single-cell atlas of chromatin accessibility in the human genome. Cell 184:5985-6001.e5919. PMC8664161

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

Publications

Geusz RJ, Wang A, Lam DK, Vinckier NK, Alysandratos KD, Roberts DA, Wang J, Kefalopoulou S, Ramirez A, Qiu Y, Chiou J, Gaulton KJ, Ren B, Kotton DN, Sander M (2021) Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors.
Nat Commun. 12:6636. PMC8599738

Philippi A, Heller S, Costa IG, Senée V, Breunig M, Li Z, Kwon G, Russell R, Illing A, Lin Q, Hohwieler M, Degavre A, et al (2021) Mutations and variants of ONECUT1 in diabetes. Nat Med 27:1928-1940.

Heller S, Li Z, Lin Q, Geusz R, Breunig M, Hohwieler M, Zhang X, Nair GG, Seufferlein T, Hebrok M, Sander M, Julier C, Kleger A, Costa IG (2021) Transcriptional changes and the role of ONECUT1 in hPSC pancreatic differentiation. Commun Biol. 4:1298. PMC8599846

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

Publications

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

Krystyna Kolodziej

Madeline Luth

Publications

Xie SC, Metcalfe RD, Dunn E, Morton CJ, Huang SC, Puhalovich T, Du Y, Wittlin S, Nie S, Luth MR, Ma L, Kim MS, et al (2022) Reaction hijacking of tyrosine tRNA synthetase as a new whole-of-life-cycle antimalarial strategy. Science 376:1074-1079.

Ottilie S, Luth MR, Hellemann E, Goldgof GM, Vigil E, Kumar P, Cheung AL, Song M, Godinez-Macias KP, Carolino K, Yang J, Lopez G, Abraham M, Tarsio M, LeBlanc E, Whitesell L, Schenken J, Gunawan F, Patel R, Smith J, Love MS, Williams RM, McNamara CW, Gerwick WH, Ideker T, Suzuki Y, Wirth DF, Lukens AK, Kane PM, Cowen LE, Durrant JD, Winzeler EA (2022) Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance. Commun Biol 5: 128.

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

Saugat Poudel

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

Publications

Sun X, Perl AK, Li R, Bell SM, Sajti E, Kalinichenko VV, Kalin TV, Misra RS, Deshmukh H, Clair G, Kyle J, Crotty Alexander LE, et al (2022) A census of the lung: CellCards from LungMAP. Dev Cell 57:112-145.e112. PMC9202574

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

Andrew Cooper

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

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

Publications

Gao NJ, Rodas Lima E, Nizet V (2021) Immunobiology of the Classical Lancefield Group A Streptococcal Carbohydrate Antigen. Infect Immun. 89:e0029221. PMC8594609

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

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

Ryan Marina

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

Michael Baughn

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

Publications 

Goodman S, Khan M, Sharma J, Li Z, Cano J, Castellanos C, Estrada MV, Gertsman I, Cherqui S (2021) Deficiency of the sedoheptulose kinase (Shpk) does not alter the ability of hematopoietic stem cells to rescue cystinosis in the mouse model. Mol Genet Metab 134:309-316. PMC8935660

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

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

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

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

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

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

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

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

Jacqueline Benthuysen (PhD, 2016)

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

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

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

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

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

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

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

Allen Acab

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

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

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

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

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

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

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

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

Gordon Bean

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

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

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

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

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

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

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

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

A. Taylor Bright

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

David Kochman

Julianne McCall

Jeff Nelson

Pagkapol Pongsawakul

Erilynn (Russo) Heinrichsen

Deanna Stevens

Emily (Witham) Meadows

Thomas Cohen

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

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

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

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

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

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

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

Molly Bush Lettman

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

Dan Clark

Ali Torkamani

Emily (Davis) Niederst

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

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

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

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

Madeline Lancaster

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

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

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

Wendy Alcaraz

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

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

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

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

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

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.

Minh-Ha Do

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

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

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

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

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

Harper VanSteenhouse

William Alaynick

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

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

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

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

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

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

Mike Hannon

Nate Heintzman

Nichol (Goodman) Miller

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

Alain Silk

Anne Valle

Michelle Wagner Gardinier

TJ Bowen

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

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

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

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.

Will Dolan

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

David Gold

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

Ramlah Nehring

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

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

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

Jennifer Floyd

Publications 

Jason Lam

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