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Topics 2012-2013

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 2012: Paleogenetics / Ancient DNA

Date Presenter Paper
10/10/12 Jason Lehman Green et al. (2009) The Neandertal genome and ancient DNA authenticity.EMBO J.28, 2494–2502.
10/17/12 Alexa Clemmons Serre et al. (2004) No Evidence of Neandertal mtDNA Contribution to Early Modern Humans. PLoS Biology 2, e57.
10/24/12 Jennifer Higginbotham Meyer et al. (2012) A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science 338, 222-622.
10/31/12 Allan Acab Bos et al. (2011) A draft genome of Yersinia pestis from victims of the Black Death. Nature 478, 506-510.
11/7/12 Sol Reyna Green et al. (2010) A Draft Sequence of the Neandertal Genome. Science 328, 710-722.
11/14/12 Grace Woodruff Rasmussen et al. (2010) Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757-762.
12/5/12 Tiffany Taylor Knapp et al. (2012) Complete mitochondrial DNA genome sequences from the first New Zealanders. PNAS 109, 18350–18354.
12/12/12 Suzy Szumowski Campbell et al. (2010) Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance. Nature Genetics 42, 536-540.

Mary Devereaux,
Biomedical Ethics Program

Juengst et al. (2012) Personalized Genomic Medicine and Rhetoric of Empowerment. Hastings Center Report 42, 34-40. [pdf]
Winter Break

Winter 2013: ENCODE - What have we learned?

Date Presenter Paper
1/9/13 Jackie Benthuysen

Neph et al. (2012) An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489, 83–90.

1/16/13 Chris DeBoever Djebali et al. (2012) Landscape of transcription in human cells. Nature 489, 101-108.
1/23/13 Gregory Goldgof Vernot et al. (2012) Personal and population genomics of human regulatory variation. Genome Research 22, 1689-1697.
1/30/13 Larry Du Sanyal et al. (2012) The long-range interaction landscape of gene promoters Nature 489, 109–113.
2/6/13 Jonathan Grinstein Bánfai et al. (2012) Long noncoding RNAs are rarely translated in two human cell lines.Genome Research 22, 1646-57.
2/13/13 Lauren Fong Thurman et al. (2012) The accessible chromatin landscape of the human genome. Nature 489, 75-82.
2/20/13 Amanda Mason Gerstein et al. (2012) Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91–100.
2/27/13 Panid Sharifnia Maurano et al. (2012) Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190-1195.
3/6/13 Karmel Allison Yip et al. (2012) Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biology 13, R48.

Xiang-Dong Fu, Bing Ren

Discussion: Data management and authorship issues in consortium papers

Naomi Frank

Wang (2012) Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Research 22, 1680-1688.
Spring Break

Spring 2013: Genome Engineering and Gene Therapy

Date Presenter Paper
4/3/13 Babette Hamerling Le Cong et al. (2013) Multiplex Genome Engineering Using CRISPR/Cas Systems. Science 339, 819-823.
4/10/13 Cynthia Hsu Wheeler et al. (2012) Targeting nuclear RNA for in vivo correction of myotonic dystrophy.. Nature 448, 111-115.
4/17/13 Micah Manary Brentjens et al. (2013) CD19-Targeted T Cells Rapidly Induce Molecular Remissions in Adults with Chemotherapy-Refractory Acute Lymphoblastic Leukemia. Science Transl. Med. 5, 177ra38.
4/24/13 Ted Friedmann Responsible Conduct in Gene Therapy
5/1/13 Fernando Martinez

Ding et al. (2012) A TALEN Genome-Editing System for Generating Human Stem Cell-Based Disease Models. Cell Stem Cell 12, 238-251.

5/8/13 Gabriel Pratt Nathwani et al. (2006) Self-complementary adeno-associated virus vectors containing a novel liver-specific human factor IX expression cassette enable highly efficient transduction of murine and nonhuman primate liver. Blood 107, 2653-2661.
5/15/13 Eric Scott Gaspar et al. (2011) Hematopoietic Stem Cell Gene Therapy for Adenosine Deaminase–Deficient Severe Combined Immunodeficiency Leads to Long-Term Immunological Recovery and Metabolic Correction. Sci Transl Med 3, 97ra80.
5/24/13 ANNUAL RETREAT Andrew Fire, Herb Boyer and more!
5/29/13 Michael Yu Wang et al. (2013) One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering. Cell 153, 910-918.
6/5/13 Larry Du Mali et al. (2013) RNA-guided human genome engineering vai Cas9. Science 339, 823-826.

Faculty: Bruce Hamilton (Program Director), Richard Kolodner (Associate Director), Elizabeth Winzeler, Ben Yu, Neil Chi, Xiang-Dong Fu, Bing Ren, Maike Sander, Ted Friedmann, Mary Devereaux (Research Ethics Program).