Spring 2017

When What Who Details
January 6th Journal Club David Murphy Campos et al. 2016 Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion.
January 13th Lab Meeting Fernando Racimo Detecting polygenic adaptation in an admixture graph
Journal Club Zachary Baker Larson et al. 2016 The composite regulatory basis of the large X-effect in mouse speciation. Mol Bio Evol.
January 27th Lab Meeting Joe Pickrell Methods for scaling genome-wide association studies using ultra-low-coverage sequencing and mobile phenotyping
February 10th Lab Meeting Diego Hartasanchez Modeling and simulation of interlocus gene conversion
Journal Club Ipsita Agarwal Lynch et al. 2016 Genetic drift, selection and the evolution of the mutation rate. Nature Review Genetics.
February 17th Lab Meeting Jeremy Berg How Natural Selection has Impacted the Evolution of Anthropometric Traits
Journal Club Yuki Haba Miles et al. 2016 Natural diversity of the malaria vector Anopheles gambiae. BioRxiv.
March 3rd Symposium Public symposium on Social Evolution and Genome Complexity
March 20th (Monday @2:30pm) Lab Meeting Claude Bhérer
March 24th Journal Club Fernando Racimo Robinson et al. 2016 Genetic evidence of assortative mating in humans. Nature Human Behavior.
April 7th (@3:00pm) Lab Meeting Molly Schumer
April 14th Journal Club Jeremy Berg Cassa et al. 2017 Estimating the selective effects of heterozygous protein-truncating variants from human exome data. Nature Genetics.
April 26th (Wednesday @10:00am) Lab Meeting Ana Pinharanda Speciation in two sympatric species of neo-tropical butterflies
April 28th Symposium Precision Medicine symposium
May 5th Journal Club Practice talks for Biology of Genomes
May 8th (Monday @12:00pm) Lab Meeting Thanasis Kousathanas The demographic history and mutational load of African hunter-gatherers and farmers
May 26th Lab Meeting Felix Wu TBD
Journal Club Hakhamanesh Mostafavi Kong et al. 2016 Selection against variants in the genome associated with educational attainment. PNAS.
June 2nd Lab Meeting Li Zhao Evolution of de novo genes in Drosophila melanogaster.
June 6th (Tuesday) Lab Meeting Arbel Harpak The high rate of non-allelic gene conversion in humans and its effect on the divergence of gene duplicates
June 10th Journal Club Guy Sella Malinsky et al. 2017 Whole Genome Sequences Of Malawi Cichlids Reveal Multiple Radiations Interconnected By Gene Flow. BioRxiv.

Fall 2016

When What Who Details
Sept 16 Journal Club Molly Schumer Fu et al. 2016  The genetic history of Ice Age Europe. Nature.
Sept 23 Lab Meeting Avi Flamholz (UC Berkeley) Mangan and Flamholz et al. 2016  pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism. PNAS.
Oct 7 Lab Meeting Zachary Baker The evolutionary history of PRDM9 in vertebrates: implications for recombination mechanisms.
Journal Club Fernando Racimo Aeschbacher et al. 2016  Population-genomic inference of the strength and timing of selection against gene flow. bioRxiv.
Oct 21 Lab Meeting Molly Schumer Recombination patterns in fish reveal evolutionary conservation of recombination mechanisms across the vertebrate phylogeny.
Journal Club Zachary Baker Halldorsson et al. 2016  The rate of meiotic gene conversion varies by sex and age. Nature Genetics.
Nov 4 Journal Club Jeremy Halldorsson et al. 2016  Linkage disequilibrium dependent architecture of human complex traits reveals action of negative selection. BioRxiv.
Nov 18 Lab Meeting Ipsita Agarwal Comparing mutational patterns on the X chromosome and Autosomes using ExAC data.
Journal Club Chen Chen Lindsay et al. 2016  Striking differences in patterns of germline mutation between mice and humans. BioRXiv.
Dec 2 Lab Meeting Michel Georges Insights in the de novo mutation process from sequencing cows: frequency of mosaicism points towards mutation prone early cleavage cell divisions.
Dec 13 (Tuesday) Lab Meeting Zachary Fuller Evolutionary mechanisms that shape chromosome structure in Drosophila pseudoobscura

For examples of topics previously discussed by our lab, please view schedules from previous semesters.

Lab Meeting, Spring 2016

When Who
Aug 8 Jason O’Rawe (CSHL): “Toward Reliable Analysis of Individual Genomes”
July 18 Linda Boettger (The Broad Institute): “Utilizing comparative genomics to identify the targets of balancing selection in mammals”
June 13 Eduardo
May 16 Luke Jostins (Wellcome Trust for Human Genetics at Oxford)
May 9 Laure Ségurel (Musée de l’Homme), “Influence of diet, parasitism and host genetics on the biodiversity of the human gut microbiota in rural populations from Cameroon”
April 25 Champak Reddy (City College of NY), “Approximate likelihood inference of complex population histories and recombination using multiple whole genome sequences”
April 18 Jeremy Berg (Coop Lab, UC Davis)
March 30 (Wed)
At 2:30pm
Yun Song (UPenn), “New methods for inferring population demographic history and fine-scale recombination rates”
March 21 Jimmy (NYGC)
March 7 David
February 1 Zach
January 11 Cyril
January 4 Andrew Taverner, Andolfatto Lab, Princeton University, “Clustering of Non-Synonymous Substitutions Provides Evidence of Epistasis and Positive Selection in Drosophila, Primates, and Arabidopsis”

Journal Club, Spring 2016

When Who What
Jun 13 Claude Galinsky et al. 2016  Population structure of UK Biobank and ancient Eurasians reveals adaptation at genes influencing blood pressure.. bioRxiv.
May 23 Hakhamanesh Smith et al. 2016, Modeling linkage disequilibrium and mutation to estimate time to the common ancestor for a beneficial allele.
Apr 25 Guy S. TBA
Apr 18 Guy A. Harpak et al. 2016 Effects of variable mutation rates and epistasis on the distribution of allele frequencies in humans. bioRxiv.
Apr 11 David Goodrich et al. 2014 Human Genetics Shape the Gut Microbiome. Cell.
April 4 Zach

&

Priya

Kuhlwilm et al. 2016 Ancient gene flow from early modern humans into Eastern Neanderthals. Nature.

Vernot et al. 2016 Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science.

March 28 Laura Matuszewski et al. 2015  Catch Me if You Can: Adaptation from Standing Genetic Variation to a Moving Phenotypic Optimum. Genetics.

Mar 21 Molly S. Davies et al. 2016 Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice. Nature.
Feb 22 Guy A. Narasimhan et al. 2015 Health and population effects of rare gene knockouts in adult humans with related parents. BioRXiv.

Saleheen et al. 2015 Human knockouts in a cohort with a high rate of consanguinity . BioRXiv.

Feb 8 Eduardo ExAC 2015 Analysis of protein-coding genetic variation in 60,706 humans . BioRXiv.
At 10 am
Jan 25 Alva Rabhari et al. 2015. Timing, rates and spectra of human germline mutation . Nature Genetics.
At 10 am

Lab Meeting, Fall 2015

When Who
Dec 7 – 3:45pm Fernando Racimo, Slatkin Lab, UC Berkeley
November 30 Anna Di Rienzo, University of Chicago
November 23 Hakhamanesh
November 16 Chen
October 5 Molly Schumer, Andolfatto lab, Princeton
September 14 Duncan Palmer, McVean Group, University of Oxford, “Estimating HLA associated selection in HIV-1: The great escape”
August 21 Sharon Greenblum, University of Washington, “Metagenomic Systems Biology: Frameworks for Modeling a Community of Genomes”
July 27 Daniel Rosenbloom, Columbia, “Tumorclocky: Inferring tumor evolution from static samples”

Journal Club, Fall 2015

When Who What
Dec 7 Yuval Lodato et al., 2015. Somatic mutation in single human neurons tracks developmental and transcriptional historyScience.
Nov 30 Alva Paper TBA
Nov 23 Chen Lodato et al., 2015. Somatic mutation in single human neurons tracks developmental and transcriptional historyScience.
Nov 16 Priya Paper TBA
Nov 9 Guy A Francioli et al., 2015. Genome-wide patterns and properties of de novo mutations in humansNature Genetics.
Nov 2 Laura Bhatia et al., 2015. Haplotypes of common SNPs can explain missing heritability of complex diseasesBioRxiv.
Oct 5 Eduardo Fumagalli et al., 2015. Greenlandic Inuit show genetic signatures of diet and climate adaptationScience.
Sept 28 Joe Zhang et al., 2015. Assessing the Causal Relationship of Maternal Height on Birth Size and Gestational Age at Birth: A Mendelian Randomization AnalysisPLoS Medicine.