Topics 2009-2010

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 2009: Unusual or Unexplained Patterns of Inheritance

Date Presenter Paper
10/7/09 Dan Clark
why do some disorders with high heritability have so little of the variance explained?
Smith et al. (2009) Genome-wide association study of bipolar disorder in European American and African American individuals. Mol. Psych. 14: 755-763.
10/21/09 Tom Cohen Nejentsev et al. (2009) Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes. Science 324: 387-389.
10/28/09 Rafael Gomez-Amaro Rangwala et al. (2006) Meiotically Stable Natural Epialleles of Sadhu, a Novel Arabidopsis Retroposon. PLoS Genetics 2: e36.
11/4/09 Stephanie Nissen Chong et al. (2007) Modifiers of epigenetic reprogramming show paternal effects in the mouse. Nature Genetics 39: 614-622.
11/11/09 Dr. Michael Kalichman Discussion - Ethics and Animals.
11/18/09 Britt Flaherty Rassoulzadegan et al. (2006) RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse. Nature 441: 469-474.
12/2/09 Morgan Pence Zhang et al. (2008) A Genome-Wide Transcription Analysis Reveals a Close Correlation of Promoter INDEL Polymorphism and Heterotic Gene Expression in Rice Hybrids. Molec. Plant 5: 720-731.
12/9/09 Taylor Bright Tonkin et al (2009) Sir2 paralogues cooperate to regulate virulence genes and antigenic variation in Plasmodium falciparum. PLoS Biol 7: e1000084.

Eveline Arnold

Du et al. (2008) Newly identified prion linked to the chromatin-remodeling factor Swi1 in Saccharomyces cerevisiae. Nature Genetics 40: 460-465.
Winter Break

Winter 2010: Non-coding RNAs

Date Presenter Paper
1/6/10 David Kochman

Figueroa-Bossi et al. (2009) Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target. Genes & Dev. 23: 2004-2015.

1/13/10 Deanna Stevens Lee et al. (2009) A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes & Dev. 23: 2639-2649.
1/20/10 Jeff Nelson Dinger et al. (2008) Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Research 18: 1433-1445.
1/27/10 Pagkapol Pongsawakul Lanford et al. (2010) Therapeutic Silencing of MicroRNA-122 in Primates with Chronic Hepatitis C Virus Infection.Science 327: 198-201.
2/3/10 Erilynn Russo Ray et al. (2009) A stress-responsive RNA switch regulates VEGFA expression. Nature 457: 915-919.
2/10/10 Julianne McCall Wayman et al. (2008) An activity-regulated microRNA controls dendritic plasticity by down-regulating p250GAP.PNAS 105: 9093-9098.
2/17/10 Emily Witham Kim et al. (2007) A MicroRNA Feedback Circuit in Midbrain Dopamine Neurons. Science 317: 1220-1224.
2/24/10 Gordon Bean Yoo et al. (2009) MicroRNA-mediated switching of chromatin-remodelling complexes in neural development.Nature 460: 642-646.
3/3/10 Anne Conway Khalil et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. PNAS 106: 11667-11672.

Dr. Fred Bonkovsky
Dr. Ted Friedmann

Ethics discussion: Gene Therapy and the Jesse Gelsinger case.
3/17/10 Mary Winn

Kishore et al. (2010) The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Hum Mol Genet
Advanced access publication - doi:10.1093/hmg/ddp585

Spring Break

Spring 2010: Host-Pathogen Interactions

Date Presenter Paper
3/31/10 Michael Lam Marraffini and Sontheimer (2010) Self versus non-self discrimination during CRISPR RNA-directed immunity.Nature 463: 568-571.
4/7/10 Mark Moyle Lacombe et al. (2010) Interfamily transfer of a plant pattern-recognition receptor confers broad-spectrum bacterial resistance. Nature Biotech. Epub ahead of print. doi:10.1038/nbt.1613
4/14/10 Chloe Rivera Carette et al. (2009) Haploid genetic screens in human cells identify host factors used by pathogens. Science 326:1231-1235.
4/21/10 Thomas Stark Arbuckle et al. (2010) The latent human herpesvirus-6A genome specifically integrates in telomeres of human chromosomes in vivo and in vitro. PNAS 107: 5563-5568.
4/28/10 Melissa Wilbert Feng et al. (2008) Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319:1096-1100.
5/5/10 Susan Zhang König et al. (2010) Human host factors required for influenza virus replication. Nature 463: 813-817.
5/12/10 Tom Cohen Horie et al. (2010) Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature 463: 84-87.
5/19/10 Morgan Pence Liu et al. (2005) Staphylococcus aureus golden pigment impairs neutrophil killing and promotes virulence through its antioxidant activity. J. Exp. Med. 202: 209-215.
5/26/10 Dr. Michael Caligiur

Human subjects in research: ethics and professional responsibilities.

  • Lo et al. (2005) A New Era in the Ethics of Human Embryonic Stem Cell Research. Stem Cells 23: 1454-1459.
  • Gruen and Grabel (2006) Concise Review: Scientific and Ethical Roadblocks to Human Embryonic Stem Cell Therapy. Stem Cells 24: 2162-2169
6/3/10 Annual Retreat
Dr. Stephen Warren, Emory University
Dr. Hamilton Smith, J.Craig Venter Institute

Faculty: Bruce Hamilton (Program Director), Richard Kolodner (Associate Director), Ted Friedmann, Trey Ideker, Jonathan Sebat, Al La Spada, Elizabeth Winzeler, Gene Yeo, Ben Yu, Michael Kalichman, Fred Bonkovsky, Michael Caligiuri