Spring 2018

Full Schedule:

When What Who Details
January 19th Lab Meeting Jeremy Berg Practice Job Talk
January 26th Lab Meeting (@11:30am) Hakhamanesh Mostafavi Viability selection in contemporary humans
February 2nd Conference NY Genome Center NY Human Genetics in NYC Conference
February 9th Lab Meeting
Nitin Phadnis The molecular basis of speciation in Drosophila
February 16th Journal Club
Felix Wu Liggett et al 2017 Conserved patterns of somatic mutations in human peripheral blood cells. bioRxiv.
February 23rd Journal Club Jeremy Berg Stephens 2017 False Discovery Rates: A New Deal. Biostatistics.
March 2nd Lab Meeting Zachary Fuller A population genetics perspective on the intolerance to mutation
March 9th Lab Meeting Felix Wu Estimating De Novo Mutation Rates in Humans and Baboons by Deep Sequencing of Family Units
March 23rd Journal Club Laura Hayward Chan et al 2018 A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks. bioRxiv.
March 30th Lab Meeting Iain Mathieson Watching evolution with ancient DNA
Journal Club Hakhamanesh Mostafavi Kong et al 2018 The nature of nurture: Effects of parental genotypes. Science.
April 5th Lab Meeting
Yoav Benjamini The replicability problems in science: it’s not the p-value’s fault
April 6th Lab Meeting Felix Wu Estimating De Novo Mutation Rates in Humans and Baboons by Deep Sequencing of Family Units
Journal Club Carla Hoge Murray et al 2018 Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Science.
April 13th Journal Club Yuval Simons Nelson and Cresko 2018 Ancient genomic variation underlies repeated ecological adaptation in young stickleback populations. Evolution Letters.
April 26th Lab Meeting T​om DiPrete Genetic Instrumental Variable (GIV) regression: Explaining socioeconomic and health outcomes in non-experimental data
April 27th Journal Club Zachary Fuller Meiklejohn et al 2018 Gene flow mediates the role of sex chromosome meiotic drive during complex speciation. BioRxiv.
May 4th Lab Meeting
Carla Hoge and
Xiaoting Li
Rotation Project Overviews
May 11th Conference Cold Spring Harbor Laboratories Biology of Genomes
May 18th Lab Meeting Zachary Baker The story of PRDM9
Lab Meeting
Molly Schumer Searching for adaptive introgression with linked deleterious sites
May 25th Lab Meeting Guy Amster Life history effects on X-to-autosomes polymorphism ratios
Journal Club Zachary Baker Brand et al 2018 Molecular Evolution at a Meiosis Gene Mediates Species Differences in the Rate and Patterning of Recombination. Current Biology.
June 8th Lab Meeting Jeremy Berg All of the empirical results from my PhD thesis are wrong!
Journal Club Hakhamanesh Mostafavi Haworth et al 2018 Common genetic variants and health outcomes appear geographically structured in the UK Biobank sample: Old concerns returning and their implications. BioRxiv.
Yengo et al 2018 Meta-analysis of genome-wide association studies for height and body mass index in ~700,000 individuals of European ancestry. BioRxiv.

Fall 2017

Full Schedule:

When What Who Details
July 21st Lab Meeting (@2:00pm) Magnus Nordborg Epigenetic Variation in Arabidopsis
Journal Club Guy Amster Pelletier et al. 2017 Eco-evolutionary dynamics in a contemporary human population. Nature.
July 28th Journal Club Hakhamanesh Mostafavi Ge et al. 2017 Phenome-wide heritability analysis of the UK Biobank. Plos Genetics.
August 4th Lab Meeting Jeremy Berg Population genetic models for the evolution of human complex disease
August 18th Lab Meeting Yuki Haba The genomics of behavioral adaptation to photoperiodism in an Asian burying beetle
Journal Club Laura Hayward Fernando et al. 2009 Additive Genetic Variability and the Bayesian Alphabet. Genetics.
August 25th Lab Meeting Zach Fuller Genetic variation associated with heat tolerance in corals
September 8th Lab Meeting Laura Hayward A model for selection on a polygenic trait after a sudden change in environment
Journal Club David Murphy Lunter et al. 2014 8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage.GeneticsPlos Genetics
September 22nd Journal Club Felix Wu Niederhuber et al. 2017 Germline De Novo Mutation Clusters Arise During Oocyte Aging In Genomic Regions With Increased Double-Strand Break Incidence. BioRxiv.
September 29th Lab Meeting Andy Kern Putting the HAL in Haldane: leveraging machine learning for population genetics
Journal Club Jeremy Berg Cherry et al. 1998 Should We Expect Substitution Rate to Depend on Population Size?. Genetics.
October 6th Lab Meeting Kristen Lee Detecting signatures of convergent adaptation in population genomic data
Journal Club Hakhamanesh Mostafavi Tahmasbi et al. 2017 Testing the moderation of quantitative gene by environment interactions in unrelated individuals. BioRxiv.
October 20th Journal Club Laura Hayward Lello et al. 2017 Accurate Genomic Prediction Of Human Height. BioRxiv.
October 27th Lab Meeting
Ipsita Agarwal Sex differences in the mutation spectrum
Journal Club Zach Fuller Prince et al. 2017 The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation. ScienceAdvances.
November 10th Lab Meeting
Parul Johri Population genomics reveals evolutionary constraints across the genomes of Paramecium species
Journal Club Yuval Simons Crawford et al. 2017 Loci associated with skin pigmentation identified in African populations. Science.
November 17th Lab Meeting Noah Reid Rapid repeated evolution of extreme pollution tolerance in killfishes (Fundulus)
Journal Club Guy Amster Lynch et al. 2008 The Cellular, Developmental and Population-Genetic Determinants of Mutation-Rate Evolution. Genetics.
December 1st Lab Meeting Eduardo Amorim Barbarian migrations and social organization in 6th century Europe
Journal Club Zach Baker Latrille et al. 2017 The Red Queen model of recombination hot-spot evolution: a theoretical investigation. Philos Trans R Soc Lond.
December 8th Lab Meeting Molly Schumer Breakdown of population structure and hybrid incompatibility in a swordtail population
Journal Club Ipsita Agarwal Ju et al. 2017 Somatic mutations reveal asymmetric cellular dynamics in the early human embryo. Nature.

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

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



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.

Journal Club, Spring 2015

When Who What
Jan 12 cancelled due to Biology seminar
Jan 19 MLK Jr Holiday
Jan 26 cancelled
Feb 2 Shai MacArthur et al., 2014. The Rate of Nonallelic Homologous Recombination in Males Is Highly Variable, Correlated between Monozygotic Twins and Independent of AgePLoS Genetics.
 Feb 9  Eduardo Foll et al. 2014. Widespread signals of convergent adaptation to high altitude in Asia and AmericaAJHG.
 Feb 16 Joe Tomasetti and Vogelstein. 2015. Variation in cancer risk among tissues can be explained by the number of stem cell divisionsScience. Suppl Info.
Feb 23 Yuval Yuen et al. 2015. Whole-genome sequencing of quartet families with autism spectrum disorderNature Medicine. Suppl Info.
March 2 Sonal Barber and Elde. 2014. Escape from bacterial iron piracy through rapid evolution of transferrinScience.  Suppl Info.
March 9 & 16 No meetings for spring break.
March 23 Priya Mathieson et al. 2015. Eight thousand years of natural selection in EuropebioRxiv.
March 30 Harold de Vladar; Parmenides Foundation. He will be giving a talk in lieu of journal club.
April 6 Chen Polak et al. 2015. Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature.Note: we will meet at 10 am.
April 13 Guy S. Charlesworth. 2015. Causes of natural variation in fitness: Evidence from studies of Drosophila populationsPNAS.
April 20 Guy S Continuation of last week; will be at 10 am, bc of Stats talk at 4
April 27 Alva Tung et al. 2015The genetic architecture of gene expression levels in wild baboonsElife.
May 4 Priya Helgason et al. 2015. The Y-chromosome point mutation rate in humans.  Nat Genet.
May 11 Sonal Corbett-Detig et al. 2015. Natural Selection Constrains Neutral Diversity across A Wide Range of SpeciesPLoS Biology
May 18 David Lan and Pritchard. 2015. Long-term survival of duplicate genes despite absence of subfunctionalized expression. bioRxiv.
 May 25 No journal club; Memorial Day
June 1 lab meeting in lieu of journal club; Daniel Jordan, Harvard
June 8 Guy A. Dutheil et al. 2009 Ancestral Population Genomics: The Coalescent Hidden Markov Model Approach  Genetics.

Lab Meeting, Spring 2015

When Who
 Jan 12 Mark Lipson, Harvard (Note: lab meeting is exceptionally at 3:45 pm, in lieu of journal club.)
Jan 19 MLK Jr Holiday
Jan 26 Lavanya Kannan, AMNH
Feb 2 Tuuli Lappalainen, New York Genome Center & Columbia
Feb 16 Elliot Aguilar, “”Evolution of Cultural Systems”, CUNY
March 2 Tomaz
March 23 Joe
March 30 Mike Hickerson, CUNY
April 13 Yaniv Erlich, Columbia & New York Genome Center – CANCELLED
April 20 Guy S [journal club instead of lab meeting; continuation of last week]
May 11 Laurent Excoffier, Bern
May 25 No lab meeting; Memorial Day

Lab Meetings, Fall 2014

When Who
Sept 15th Molly
Sept 22nd Chris Nasrallah (NC State)
Oct 13th Yuval
Oct 27th Judy Cho MD (Mt Sinai)
Nov 3 Shai (Pe’er Lab)
Nov 24 Minyoung
Dec 1 Ziyue
Dec 15 Sonal

Journal Club, Fall 2014

When Who What
 Sept 15 Guy A. Inferring human population size and separation history from multiple genome sequences. Nature Gen. Schiffels and Durbin, 2014.
 Sept 22 Joe

Common genetic variants associated with cognitive performance identified using the proxy-phenotype method. PNAS 2014 

 Sept 29 Sonal Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature. Romiguier et al., 2014. Suppl. Info.
 Oct 13 David Probabilities of Fitness Consequences for Point Mutations across the Human Genome. bioRxiv. Gulko et al., 2014.
Oct 20 Priya Highly variable recessive lethal or nearly lethal mutation rates during germ-line development of Drosophila melanogaster. PNAS. Gao et al. 2011.
Oct 27 Eduardo The genetics of monarch butterfly migration and warning colorationNature. Zhan et al., 2014. Suppl Info.
Nov 3 Guy S  (Please see Guy’s email for preprint.)
Nov 10 Alva  Mouse tetrad analysis provides insights into recombination mechanisms and hotspot evolutionary dynamics. Nat gen. Cole et al. 2014. Supplementary Information.
Nov 17 Priya Genomic structure in Europeans dating back to at least 36,200 years. Science. Seguin-Orlando et al. 2014. Supplementary Information
Nov 24 Yuval Characteristics of Neutral and Deleterious Protein-Coding Variation among Individuals and Populations. AJHG. Fu et al. 2014.
Dec 1 Guy A  Rate and cost of adaptation in the Drosophila genomebioRxiv. Schiffels et al.
Dec 15 Molly The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes. PLoS Genet. Lesecque et al. 2014.