Topics 2013-2014

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 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.
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

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.

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.

Anthony Schmitt

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

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
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.
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.