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Topics 2011-2012

Date Presenter Paper

Organizational meeting
Leichtag 3A05 - 8 am

Introductions, GTP Student Advising Committee, Choose Fall topic, How to choose and critique a paper.

Fall 2011: Cancer Genetics

Date Presenter Paper
10/5/11 Gordon Bean The Cancer Genome Atlas Research Network. (2011) Integrated genomic analyses of ovarian carcinoma. Nature 474, 609–615.
10/12/11 Anne Conway Iliopoulos et al. (2011) Inhibition of miR-193a expression by Max and RXRa activates K-Ras and PLAU to mediate distinct aspects of cellular transformation. Cancer Res. 71, 5144-53.
10/19/11 Michael Kalichman Ethics discussion: Patient-derived research materials
10/26/11 Mark Moyle Hahn et al. (2011) Heritable GATA2 mutations associated with familial myelodysplastic syndrome and acute myeloid leukemia. Nature Genetics 43, 1012-1017.
11/2/11 Chloe Rivera Tay et al. (2011) Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs. Cell 147, 344-357.
11/9/11 Tom Stark Soroceanu et al. (2011) Human Cytomegalovirus US28 Found in Glioblastoma Promotes an Invasive and Angiogenic Phenotype. Cancer Res. 71, 6643-6653.
11/16/11 Melissa Wilbert Campbell et al. (2010) The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 467, 1109-1113.
11/30/11 Susan Zhang Prickett et al. (2011) Exon capture analysis of G protein-coupled receptors identifies activating mutations in GRM3 in melanoma. Nature Genetics 43, 1119-1126.
12/7/11 Allan Acab Zhu et al. (2011) BRCA1 tumour suppression occurs via heterochromatin-mediated silencing. Nature 477, 179-184.

Tiffany Taylor

Mulholland et al. (2011) Cell Autonomous Role of PTEN in Regulating Castration-Resistant Prostate Cancer Growth.Cancer Cell 19, 792-804.
Winter Break

Winter 2012: Genetics of Domestication

Date Presenter Paper
1/11/12 Jennifer Higginbotham

Brown et al. (2011) Distinct Genetic Architectures for Male and Female Inflorescence Traits of Maize. PLoS Genetics 7, e1002383.

1/18/12 Jason Lehman Dunn and Sherlock (2008) Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus . Genome Research 18, 1610-1623.
1/25/12 Sol Reyna Kukekova et al. (2011) Mapping Loci for Fox Domestication: Deconstruction/Reconstruction of a Behavioral Phenotype.Behav Genet 41, 593-606.
2/1/12 Suzy Szumowski Cong et al. (2008) Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nature Genetics 40, 800-804.
2/8/12 Dawn Zhang Vonholdt et al. (2010) Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464, 898-902.
2/15/12 Alexa Clemmons Rubin et al. (2010) Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464, 587-593.
2/22/12 Grace Woodruff Christie et al. (2012) Genetic adaptation to captivity can occur in a single generation. PNAS 109, 238-242.
2/29/12 Chris DeBoever Kijas et al. (2012) Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection. PLoS Biology 10: e1001258.
3/7/12 Jacqueline Benthuysen Studer et al. (2011) Identification of a functional transposon insertion in the maize domestication gene tb1 . Nature Genetics 43, 1160-1163.

Shannon Muir

Plantinga et al. (2012) Low prevalence of lactase persistence in Neolithic South-West Europe. Eur. J. Hum. Genet. [advance online publication] doi: 10.1038/ejhg.2011.254

Program Retreat 8:30-5:30
Medical Education and Telemedicine Auditorium

Guest Speakers: Hank Greely (Stanford Law School & Dept. of Genetics), Eric Lander (Broad Institute).

Spring Break

Spring 2012: Classic Papers in Gene Regulation

Date Presenter Paper
4/4/12 Larry Du Brenner, Jacob, and Meselson (1961) An Unstable Intermediate Carrying Information from Genes to Ribosomes for Protein Synthesis. Nature 190: 576-581.
4/11/12 Lauren Fong Fire et al. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811.
4/18/12 Panid Sharifnia Nüsslein-Volhard and Wieschaus (1980) Mutations affecting segment number and polarity in Drosophila. Nature 287, 795-801.
4/25/12 Sidney Kuo Elowitz et al. (2002) Stochastic Gene Expression in a Single Cell. Science 297, 1183-1186.
5/2/12 Danjuma Quarless Chee et al. (1996) Accessing Genetic Information with High-Density DNA Arrays. Science 274, 610-614.
5/9/12 Amanda Mason Watson and Crick (1953) Molecular stucture of Nucleic Acids, a structure for Deoxyribose nucleic acid. Nature 171, 737-738. [pdf]
5/16/12 Arjana Pradhan Avery, Macleod, and McCarty (1944) Studies of the chemical nature of the substance inducing transformation of pneumococcal types. J. Exp. Med. 79, 137-158. [pdf]
5/23/12 Fred Bonkovsky Responsible Conduct of Research.
Responsibilities of authorship. Errors, mistakes and misconduct. Rise in retractions (NY Times coverage).
5/30/12 Jonathan Grinstein

A classic controversy:
Sutcliffe et al. (1984) Identifier sequences are transcribed specifically in brain. Nature 308, 237 - 241 . [pdf]

Owens et al. (1985) Brain "identifier sequence" is not restricted to brain: similar abundance in nuclear RNA of other organs. Science 229, 1263-1265 .

6/6/12 Micah Manary Berget, Moore, and Sharp (1977) Spliced segments at the 5' terminus of adenovirus 2 late mRNA. Proc. Natl. Acad. Sci USA 74, 3171-3175. [pdf]

Faculty: Bruce Hamilton (Program Director), Richard Kolodner (Associate Director), Web Cavenee, X. D. Fu, Frank Furnari, Alysson Muotri, Scott Rifkin, Joe Vinetz, Steven Wasserman, Elizabeth Winzeler, Ben Yu, Fred Bonkovsky, Michael Kalichman, Dena Plemmons (Research Ethics Program).