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Topics 2013-2014

Date Presenter Paper
10/2/13

Organizational meeting
Leichtag 3A05 - 8 am

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

Fall 2013: Regeneration

Date Presenter Paper
10/9/13 Jackie Benthuysen Takeo et al. (2013) Wnt activation in nail epithelium couples nail growth to digit regeneration. Nature 499, 228-232.
10/16/13 Gregory Goldgof Lopez-Garcia et al. (2010) Intestinal Stem Cell Replacement Follows a Pattern of Neutral Drift. Science 330, 822-825.
10/23/13 Larry Du Zhu et al. (2012) Activation of germline-specific genes is required for limb regeneration in the Mexican axolotl. Dev. Biol. 370, 42–51.
10/30/13 Lauren Fong Chen et al. (2012) An RNA interference screen uncovers a new molecule in stem cell self-renewal and long-term regeneration. Nature 485, 104-108.
11/6/13 Jonathan Grinstein Zhang et al. (2013) In vivo cardiac reprogramming contributes to zebrafish heart regeneration. Nature 498, 497-501.
11/13/13 Amanda Mason Liu et al. (2013) Reactivating head regrowth in a regeneration-deficient planarian species. Nature 500, 81-84.
11/21/13 Panid Sharifnia Zou et al. (2013) Developmental Decline in Neuronal Regeneration by the Progressive Change of Two Intrinsic Timers. Science 340, 372-376.
Thanksgiving
12/4/13 Chris DeBoever Paige et al. (2012) A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Regulators of Cardiac Development. Cell 151, 221-232.
12/11/13 Larry Goldstein, Elizabeth Winzeler, Gene Yeo Responsible Conduct Panel Discussion: Reading, Writing and Refereeing papers in an era of online supplements.
Winter Break Selection of Winter topic.

Winter 2014: Single Cell Anaylses

Date Presenter Paper
1/8/14 Bruce Hamilton, Elizabeth Winzeler

Responsible Conduct Panel Discussion: Reproducibility

Background Reading:

  • Park (2013) Modeling the effects of subjective and objective decision making in peer review. Nature Published online 04 December 2013
  • Phil Bourne (2013) I Cannot Reproduce the Work From My Own Laboratory (9 slides)
  • Ülo Palm (2012) Lack of Reproducibility in Biomedical Research (22 slides)
  • Begley & Ellis (2012) Raise standards for preclinical cancer research. Nature483, 531-533 and Editor's note
  • Naik (2011) Scientists' Elusive Goal: Reproducing Study Results Wall Street Journal
  • Ioannidis (2005) Why most published research findings are false. PLoS Med2(8): e124.
1/15/14 Naomi Frank

Moignard et al. (2013) Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis. Nature Cell Biology 4, 363-372.
1/22/14 Babette Hamerling Gole et al. (2013) Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nature Biotechnology31, 1126–1132.
1/29/14 Fernando Martinez Lovatt et al. (2014) Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue. Nature Methods doi:10.1038/nmeth.2804
2/5/14

Micah Manary
This date only – meet in Leichtag 107

 Pamp et al. (2012) Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). Genome Research 22, 1107-1119.
2/12/14 Cynthia Hsu Navin et al. (2011) Tumour evolution inferred by single-cell sequencing.Nature 472, 90–94.
2/19/14

Gabriel Pratt

 Deng et al. (2014) Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells. Science 343, 193-196.
2/26/14 Eric Scott McConnell et al. (2013) Mosaic Copy Number Variation in Human Neurons.Science 342, 632-637.
3/5/14 Michael Yu Jaitin et al. (2014) Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types. Science 343, 776-779.
3/12/14

Anthony Schmitt

 Nagano et al. (2013) Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502, 59–64.
3/19/14

Sophia Española

 Wu et al. (2014) Quantitative assessment of single-cell RNA-sequencing methods. Nature Methods 11, 41-46.
Spring Break

Spring 2014: Genetics of Aging

Date Presenter Paper
4/2/14 Bernardo Lara Carnemolla et al. (2014) Contesting the dogma of an age-related heat shock response impairment: implications for cardiac-specific age-related disorders.Human Molecular Genetics online ahead of print, doi: 10.1093/hmg/ddu073
4/9/14 Kevin Ross Lu et al. (2014) REST and stress resistance in ageing and Alzheimer’s disease. Nature 507, 448-454.
4/16/14 Alexandra Buckley Ross et al. (2013) Germline mitochondrial DNA mutations aggravate ageing and can impair brain development. Nature 501, 412-415.
4/23/14 Megan Chu Zhang et al. (2013) Direct and Indirect Gene Regulation by a Life-Extending FOXO Protein in C. elegans: Roles for GATA Factors and Lipid Gene Regulators. Cell Metabolism 17, 85-100.
4/30/14 Asa Gustafsson and Richard Kolodner

Responsible Conduct Panel Discussion: Mentor and Trainee Responsibilities
5/2/14 GTP RETREAT Sanford Consortium for Regenerative Medicine Auditorium
5/7/14
 Victoria Doroski Bernardes de Jesus et al. (2012) Telomerase gene therapy in adult and old mice delays aging and increases longevity without increasing cancer. EMBO Molec. Med. 4, 691-704.
5/14/14 Genevieve Ryan Chang and Guarente (2013) SIRT1 Mediates Central Circadian Control in the SCN by a Mechanism that Decays with Aging. Cell 153, 1448–1460.
5/21/14
 Sam Stoner Florian et al. (2013) A canonical to non-canonical Wnt signalling switch in haematopoietic stem-cell ageing. Nature 503, 392-396.
5/28/14 Bruce Hamilton Career planning: Implementing the Individual Development Plan
NIH Guide Notice / Sally Rockey's blog / UCSD Prototype (docx)
myIDP website

Faculty: Bruce Hamilton (Program Director), Richard Kolodner (Associate Director), Elizabeth Winzeler, Ben Yu, Neil Chi, Larry Goldstein, Bing Ren, Maike Sander, Gene Yeo, Asa Gustafsson.