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Journal Club

Fall 2019 - Genetics of typical trait variation

October 2: Organizational Meeting
Introductions, GTP advising committee, Program expectations, How to critique a paper, Selection of Fall topic.

October 9: Joshua Chiou (Gaulton Lab)
Yoshiura et al. (2006) A SNP in the ABCC11 gene is the determinant of human earwax type. Nature Genetics 38, 324-330. [link]

October 16: Ryan Geusz (Sander Lab)
Ilardo et al. (2018) Physiological and Genetic Adaptations to Diving in Sea Nomads. Cell 173, 569-580. [link]

October 23: Emily Griffin (Ackerman Lab)
Labrie et al. (2016) Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging. Nat Struct Mol Biol. 23, 566-573. [link] [PMC]

October 30: Madeline Luth (Winzeler Lab)
Karim et al. (2011) Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nature Genetics 43, 405-413. [link]

November 6: Professors Majithia, Ren, Sun, Winzeler, and Zheng
Responsible Conduct of Research Discussion: Experimental design for rigor and reproducibility.

November 20: Saugat Poudel (Nizet Lab)
Marouli et al. (2017) Rare and low-frequency coding variants alter human adult height. Nature 542, 186-190. [link] [PMC]

November 27: Thanksgiving Holiday

December 4: Mike Valdez (Sun Lab)
Guenther et al. (2014) A molecular basis for classic blond hair color in Europeans. Nature Genetics  46, 748-752. [link] [PMC]

December 11: James Yu (Simonson Lab)
Barrett et al. (2019) Linking a mutation to survival in wild mice. Science 363, 499-504. [link] [preprint]

Select Winter topic.

Winter 2020 - Sex-biased traits

January 8: Noorsher Ahmed (Yeo Lab)
Thion et al. (2018) Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner. Cell 172, 500-516.e16. [link] [PMC]

January 15: Melinda Beccari (Cleveland Lab)
Naqvi et al. (2019) Conservation, acquisition and functional impact of sex-biased gene expression in mammals. Science 365, eaaw7317 [link] [PMC]

January 22: Jessica Bloom (Rifkin Lab)
Hilbert and Kim (2017) Sexually dimorphic control of gene expression in sensory neurons regulates decision-making behavior in C. elegans. eLife 6, e21166. Open access [link]

January 29: Professors Dowdy, Hamilton, and Winzeler
Responsible Conduct of Research Discussion: Conflicts of Interest

February 5: Corrina Elder (Pasquinelli Lab)
Regan et al. (2016) Sex difference in pathology of the ageing gut mediates the greater response of female lifespan to dietary restriction. eLife 5, e10956. Open access [link]

February 12: Emily Ho (Mellon Lab)
van Nas et al. (2009) Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks. Endocrinology 150, 1235-1249. [link] [PMC]

February 19: James Hocker (Ren Lab)
Barson et al. (2015) Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon. Nature 528, 405-408. [link] [preprint]

February 26: Erin Ritchie (Jin Lab)
McNairn et al. (2019) Female-biased embryonic death from inflammation induced by genomic instability. Nature 567, 105-108. [link] [PMC] [preprint]

March 4: Zeyang Shen (Glass Lab)
Small et al. (2018) Regulatory variants at KLF14 influence type 2 diabetes risk via a female-specific effect on adipocyte size and body composition. Nature Genetics 05, 572-580. [link] [PMC]

March 11: Carmine Chavez-Martinez (Zheng Lab)
van der Linden et al. (2018) Sex separation induces differences in the olfactory sensory receptor repertoires of male and female mice. Nature Communications 9, 5081. Open access [link]

Select Spring quarter topic.

Spring 2020 - Genetics & Epidemiology of Infectious Disease

April 1: Patrick Bruck (Muotri Lab)
Enard et al. (2016) Viruses are a dominant driver of protein adaptation in mammals. eLife 5:e12469 [link]

April 8: Krypton Carolino (Winzeler Lab)
Park et al. (2017) A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors. Nature Genetics 49, 193-203. [link] [PMC]

April 15: Tiffany Chu (Muotri Lab)
Manson et al. (2017) Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nature Genetics 49, 395–402. [link] [PMC]

April 22: Natalie DeForest (Majithia Lab)
Grifoni et al. (2020) A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2. Cell Host & Microbe (ahead of print) [link]

April 29: Sara Elmasaouri (Yeo Lab)
Monteil et al. (2020) Inhibition of SARS-CoV-2 Infections in Engineered Human Tissues Using Clinical-Grade Soluble Human ACE2. Cell (ahead of print) Open access [link]

May 6: Jenna Kovsky (Sander Lab)
Raymond et al. (2019) Antisense oligonucleotides extend survival of prion-infected mice. JCI Insight 4, e131175. [link] [PMC] Backstory coverage in Wired

May 13: Mengdan Liu (Zhang Lab)
Harrison et al. (2019) Natural selection contributed to immunological differences between hunter-gatherers and agriculturalists. Nature Ecology & Evolution 3, 1253-1264. [link] [PMC]

May 20: Clarence Mah (Carter Lab)
Pereyra et al. (2010) The Major Genetic Determinants of HIV-1 Control Affect HLA Class 1 Peptide Presentation. Science 330, 1551-1557. [link] [PMC]

May 27: Michelle Ragsac (Farley Lab)
Uhlemann et al. (2014) Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community. PNAS 111, 6738-43. [link] [PMC]

June 3: Danielle Schafer (Yeo Lab)
Brann et al. (2020) Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia. bioRxiv 2020.03.25.009084. [link]

June 10: Eleanora Rachtman (Bafna Lab)
Mühlemann et al. (2018) Ancient hepatitis B viruses from the Bronze Age to the Medieval period. Nature 557, 418-423. [link] [EuropePMC]

June 17: Professors Nizet, Schooley, and Winzeler
Responsible Conduct of Research Discussion: Conduct during a crisis.

Summer Book Club: How to be an Anti-Racist (Kendi)