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Topics 2015-2016

Date Presenter Paper

Organizational meeting
Biomedical Research Facility II - 1104 8:00 am

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

Fall 2015: New Genetic Tools

Date Presenter Paper
10/7/15 Victoria Corey Macosko et al. (2015) Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202-1214.
10/14/15 Alexandra Buckley Newman et al. (2015) Robust enumeration of cell subsets from tissue expression profiles. Nature Methods 12, 453-457.
10/21/15 Sophia Espanola Nihongaki et al. (2015) Photoactivatable CRISPR-Cas9 for optogenetic genome editing. Nat Biotechnol. 33, 755-760.
10/28/15 Bernardo Lara Yang et al. (2015) Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index. Nature Genetics 47, 1114–1120.
11/4/15 Kevin Ross Starita et al. (2015) Massively parallel functional analysis of BRCA1 RING domain variants. Genetics 200, 413-422.
11/11/15 Genevieve Ryan Tang et al. (2015) Cell type–specific manipulation with GFP-dependent Cre recombinase. Nature Neuroscience 18, 1334-1341.
11/18/15 Sam Stoner Shi et al. (2015) Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat Biotechnol. 33, 661-667.
12/2/15 Anthony Schmitt Kind et al. (2015) Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells. Cell 161, 134-147.
12/9/15 Gene Yeo, Al La Spada Responsible Conduct of Research: The changing landscape of scientific publishing
Winter Break Selection of Winter topic.

Winter 2016: DNA Damage Response

Date Presenter Paper
1/6/16 Danny Antaki Harley et al. (2015) TRAIP promotes DNA damage response during genome replication and is mutated in primordial dwarfism. Nature Genetics 48, 36-43.
1/13/16 Daniel Chen

Kang et al. (2015) The DNA damage response induces inflammation and senescence by inhibiting autophagy of GATA4. Science 349, aaa5612.

See also Perspective by Cassidy and Narita.

1/20/16 Wilmer Del Cid Lee et al. (2012) Neurogenesis requires TopBP1 to prevent catastrophic replicative DNA damage in early progenitors. Nature Neuroscience15, 819-826.
1/27/16 Kristin Withers Wang et al. (2014) Dysregulation of gene expression as a cause of Cockayne syndrome neurological disease. PNAS 111, 14454-14459.
2/3/16 Elaine Guo Sanjiv et al. (2016) Cancer-specific synthetic lethality between ATR and CHK1 kinase activities. Cell Reports 14, 298-309.
2/10/16 Jennifer Kuo Jiang et al. (2015) Local generation of fumarate promotes DNA repair through inhibition of histone H3 demethylation. Nature Cell Biol. 17, 1158-1168.
2/17/16 Terry Solomon Cockram (2015) Quantitative genomic analysis of RecA protein binding during DNA double-strand break repair reveals RecBCD action in vivo.PNAS 112, E4735-E4742.
2/24/16 Jenhan Tao Epshtein et al. (2014) UvrD facilitates DNA repair by pulling RNA polymerase backwards. Nature 505, 372-377.
3/2/16 Tina Wang Matsumura et al. (2016) Hair follicle aging is driven by transepidermal elimination of stem cells via COL17A1 proteolysis. Science 351, DOI: 10.1126/science.aad4395.

Ted Friedmann

Responsible Conduct of Research: The International Summit on Human Gene Editing Meeting Slides and Webcasts, Meeting in Brief
Spring Break Selection of Spring topic.

Spring 2016: Epigenetics

Date Presenter Paper
3/30/16 Michael Baughn Hilton et al. (2015) Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nature Biotechnology 33, 510-517.
4/6/16 Spencer Goodman Shin et al. (2016) A RUNX2-Mediated Epigenetic Regulation of the Survival of p53 Defective Cancer Cells.PLOS Genetics 12, e1005884.
4/13/16 Samuel Lin Cohen et al. (2016) A role for the bacterial GATC methylome in antibiotic stress survival. Nature Geneticsdoi:10.1038/ng.3530
4/20/16 Alannah Miranda Hannon et al. (2016) Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci. Nature Neuroscience 19, 48-54.
4/25/16 GTP ANNUAL RETREAT Keynotes by Eric Green (NHGRI) and Sarah Tishkoff (U Penn). Research talks from J. Ecker, B. Hammerling, F. Martinez, A. Muotri, M. Parast, A. Pasquinelli, G. Pratt, M. Wilkinson, & M. Yu.
4/27/16 Shanna Newton Wang et al. (2016) SIRT6 controls hematopoietic stem cell homeostasis through epigenetic regulation of Wnt signaling.Cell Stem Cell 18, 495–507.
5/4/16 Alison Parisian Krishnakumar et al. (2016) FOXD3 Regulates Pluripotent Stem Cell Potential by Simultaneously Initiating and Repressing Enhancer Activity. Cell Stem Cell 18, 104-117
5/11/16 Brian Reilly Bintu et al. (2016) Dynamics of epigenetic regulation at the single cell level. Science351, 720-724.
5/18/16 Emily Wheeler Dominissini et al. (2016) The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA. Nature 530, 441-446.
5/25/16 Prof.s Ackerman, Field, Frazer, Ideker, Joiner, Pillus, Troemel, Winzeler Responsible Conduct of Research: How to Peer Review
Some fodder: Vale (2012) Walbot (2009)