Topics 2012-2013
Date | Presenter | Paper |
10/3/12 |
Organizational meeting |
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. |
Thanksgiving | ||
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. |
12/19/12 |
Mary Devereaux, |
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. |
3/13/13 |
Xiang-Dong Fu, Bing Ren |
Discussion: Data management and authorship issues in consortium papers |
3/20/13 |
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).