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 (@1:30pm) |
Nitin Phadnis | The molecular basis of speciation in Drosophila |
| February 16th | Journal Club (@12:00pm) | 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 (@10:00am) | 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 | Tom 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 (@2:30pm) | 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 (@1:45pm) | 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. |
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 (@10:00am) |
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 (@9:45am) |
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.
| 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. |
| 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.
| 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” |
| 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” |
| When | Who | What |
|---|---|---|
| Dec 7 | Yuval | Lodato et al., 2015. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science. |
| Nov 30 | Alva | Paper TBA |
| Nov 23 | Chen | Lodato et al., 2015. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science. |
| Nov 16 | Priya | Paper TBA |
| Nov 9 | Guy A | Francioli et al., 2015. Genome-wide patterns and properties of de novo mutations in humans. Nature Genetics. |
| Nov 2 | Laura | Bhatia et al., 2015. Haplotypes of common SNPs can explain missing heritability of complex diseases. BioRxiv. |
| Oct 5 | Eduardo | Fumagalli et al., 2015. Greenlandic Inuit show genetic signatures of diet and climate adaptation. Science. |
| 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 Analysis. PLoS Medicine. |
| 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 Age. PLoS Genetics. |
| Feb 9 | Eduardo | Foll et al. 2014. Widespread signals of convergent adaptation to high altitude in Asia and America. AJHG. |
| Feb 16 | Joe | Tomasetti and Vogelstein. 2015. Variation in cancer risk among tissues can be explained by the number of stem cell divisions. Science. Suppl Info. |
| Feb 23 | Yuval | Yuen et al. 2015. Whole-genome sequencing of quartet families with autism spectrum disorder. Nature Medicine. Suppl Info. |
| March 2 | Sonal | Barber and Elde. 2014. Escape from bacterial iron piracy through rapid evolution of transferrin. Science. Suppl Info. |
| March 9 & 16 | No meetings for spring break. | |
| March 23 | Priya | Mathieson et al. 2015. Eight thousand years of natural selection in Europe. bioRxiv. |
| 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 populations. PNAS. |
| 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. 2015. The genetic architecture of gene expression levels in wild baboons. Elife. |
| 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 Species. PLoS 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. |
| 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 |