Journal Club

Fall 2016 - Analysis of Failure

What can we learn about best practices from acknowledged errors?

September 28: Organizational Meeting.
Introductions, GTP advising committee, how to critique a paper, selection of Fall topic.

October 5: Danny Antaki
Overview: Casadevall (2016) A Framework for Improving the Quality of Research in the Biological Sciences. mBio 7, e01256-16. http://mbio.asm.org/content/7/4/e01256-16.full
Paper: Identification of gene ontologies linked to prefrontal–hippocampal functional coupling in the human brain. PNAS (2014) http://dx.doi.org/10.1073/pnas.1404082111. Retracted.

October 12: Daniel Chen
DNA methylation age of human tissues and cell types. Genome Biology (2015) http://dx.doi.org/10.1186/gb-2013-14-10-r115. Published erratum.

October 19: Kristin Withers
Genetic Signatures of Exceptional Longevity in Humans. Science (2010) http://dx.doi.org/10.1126/science.1190532. Retracted.

October 26: Jennifer Kuo
Alternative splicing produces high levels of noncoding isoforms of bHLH transcription factors during development. Genes & Development (2010) http://dx.doi.org/10.1101/gad.1847110. Retracted in light of later data:
A Critical Analysis of Atoh7 (Math5) mRNA Splicing in the Developing Mouse Retina. PLOS One (2010) http://dx.doi.org/10.1371/journal.pone.0012315

November 2: Terry Solomon
Identification of a Novel Gammaretrovirus in Prostate Tumors of Patients Homozygous for R462Q RNASEL Variant. PLOS Pathogens (2006) http://dx.doi.org/10.1371/journal.ppat.0020025. Retracted.

November 9: Jenhan Tao
Structure of MsbA from E. coli: A Homolog of the Multidrug Resistance ATP Binding Cassette (ABC) Transporters. Science (2001) http://dx.doi.org/10.1126/science.293.5536.1793. Retracted. See also.

November 16: Tina Wang
Cellular APOBEC3G restricts HIV-1 infection in resting CD4+ T cells. Nature (2005) https://dx.doi.org/10.1038/nature03493. Retracted.

November 23: No class - Happy Thanksgiving.

November 30: Responsible Conduct of Research Discussion
Find your failures faster - design, validation, and review practices to minimize publication errors.
Professors Chi, Glass, Hamilton, Jin, and Wasserman.


Winter 2017 - Personal Genomes

January 11: Michael Baughn
Hoch et al. (2017) XRCC1 mutation is associated with PARP1 hyperactivation and cerebellar ataxia. Nature 541, 87-91.

January 18: Spencer Goodman
Jones et al. (2015) Personalized genomic analyses for cancer mutation discovery and interpretation. Science Translational Medicine 7, 283ra53.

January 25: Samuel Lin
Minikel et al. (2016) Quantifying prion disease penetrance using large population control cohorts. Science Translational Medicine 8, 322ra9.

February 1: Alannah Miranda
Chen et al. (2016) Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases. Nature Biotech 34, 531-538.

February 8: Shanna Newton
Chong et al. (2016) Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features. Genetics in Medicine 18, 788-795.

February 15: Alison Parisian
Zanoni et al. (2016) Rare variant in scavenger receptor BI raises HDL cholesterol and increases risk of coronary heart disease. Science 351, 1166-1171.

February 22: Brian Reilly
Abraham et al. (2014) Accurate and Robust Genomic Prediction of Celiac Disease Using Statistical Learning. PLOS Genetics 10, e1004137.

March 1: Emily Wheeler
Reuter et al. (2016) Simul-seq: combined DNA and RNA sequencing for whole-genome and transcriptome profiling. Nature Methods 13, 953–958.

March 8: Responsible Conduct of Research Discussion
Julie Cakici, Project Manager, Rady Children’s Institute for Genomic Medicine.

March 15: Carolina Galarreta
Bodian et al. (2016) Utility of whole-genome sequencing for detection of newborn screening disorders in a population cohort of 1,696 neonates. Genetics in Medicine 18, 221–230.

 

Spring 2017 - Genetics of Infectious Disease

April 5: Andrew Cooper
Rawat et al. (2016) Wheat Fhb1 encodes a chimeric lectin with agglutinin domains and a pore-forming toxin-like domain conferring resistance to Fusarium head blight. Nature Genetics 48, 1576-1580.

April 12: Elie Farah
Marvig et al. (2015) Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis. Nature Genetics 47, 57–64.

April 19: Nina Gao
Maury et al. (2016) Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity. Nature Genetics 48, 308-313.

April 26: Shereen Georges
Seshadri et al. (2017) Transcriptional networks are associated with resistance to Mycobacterium tuberculosis infection. PLoS ONE 12, e0175844.

May 3: Natalie Hollingsworth
Dudas et al. (2017) Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature 544, 309-315.

May 10: Ryan Marina
Painter et al. (2017) Capturing in vivo RNA transcriptional dynamics from the malaria parasite Plasmodium falciparum. Genome Research (AOP

May 17: Caroline Sferrazza
Ansari et al. (2017) Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus. Nature Genetics 49, 666–673.

May 24: Mike Vaill
Weyrich et al. (2017) Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus Nature 544, 357-361.

May 31: Krystyna Kolodziej
Zhang et al. (2016) Molecular signatures associated with ZIKV exposure in human cortical neural progenitors. Nucleic Acids Research 44, 8610-8620.

June 7: Responsible Conduct of Research Discussion
Faculty Panel on Authorship: Professors Hamilton, Schroeder, and Varki
See: McNutt et al. (2017) Transparency In Authors' Contributions And Responsibilities To Promote Integrity In Scientific Publication. BioRxiv