Topics 2011-2012

Date	Presenter	Paper
9/28/11	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.
Thanksgiving
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.
12/14/11	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.
3/14/12	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
3/22/12		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).