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.

Journal club, summer 2014

When Who What
Aug 29 Eduardo Genome-wide scan of 29,141 African Americans finds no evidence of selection since admixture. Bhatia et al. arXiv
Aug 22 Priya Recombination in the Human Pseudoautosomal Region PAR1. Hinch et al. PLoS Genetics 2014.
Aug 15 Sonal Genetics of ecological divergence during speciation. Arnegard et al. Nature 2014.
Aug 8 Daniel Hooper The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Poelstra et al. Science 2014. (Supplemental Material)
Aug 1 None Statistical Genetics seminar given by Iain Mathieson (Reich lab)
July 25 Shai Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA Huerta-Sanchez et al., Nature 2014. SOM.
June 27 Eyal Poxviruses deploy genomic accordions to adapt rapidly against host antiviral defenses Elde et al., Cell 2012.Rules of engagement: molecular insights from host-virus arms races Daugherty and Malik, Annual Reviews 2012.
June 20 none Statistical Genetics seminar given by Ilan Gronau (Siepel lab, Cornell)
June 13 Min

Precise estimates of mutation rate and spectrum in yeast. Zhu et al. PNAS 2014

Lab meetings, spring and summer 2014

LAB MEETINGS GIVEN BY:
Sept 12 Hila Sheftel, Weizmann Institute — beginning promptly at 9a

Statistical Genetics Seminar to follow

Aug 15 Daniel Hooper (Price lab, U. Chicago)
Aug 1 PJ Perry (Penn State)
July 25 Adam Auton (Einstein)
June 27 Priya
June 20 Sonal
June 13 Christina Bergey (Disotell lab, NYU)
June 6 none – NYU Annual Symposium in Genomics –
May 30 Yuri Pritykin (Singh lab, Princeton)
May 9 none – Biology of Genomes –
May 2 Eli Stahl (Mount Sinai)
April 11 Amir
April 4 Guy A. *from 10:30-12 in Fairchild 800*
Mar 28 Molly Schumer (Andolfatto lab, Princeton)
Mar 14 Amy

Journal club, spring 2014

When Who What
June 6 none – NYU Annual Symposium in Genomics –
May 30 Amy Transmission Distortion Affecting Human Noncrossover but Not Crossover Recombination: A Hidden Source of Meiotic Drive Odenthal-Hesse et al. PLoS Genet 2014.
May 9 none – Biology of Genomes –
May 2 Molly S. doublesex is a mimicry supergene Kunte et al. Nature 2014.
April 25 none Eimear Kenny (Mount Sinai) @ Statistical Genetics
April 18 Joe LD Score Regression Distinguishes Confounding from Polygenicity in Genome-Wide Association Studies Bulik-Sullivan et al. bioRxiv 2014.
April 11 Guy S. Searching for missing heritability: designing rare variant association studies. Zuk et al. PNAS 2013.
Mar 28 Amir Strong selective sweeps associated with ampliconic regions in great ape X chromosomes Nam et al. arXiv 2014.
Mar 14 Priya continued…
Mar 7 Priya

A Genetic Atlas of Human Admixture History. Hellenthal et al. 2014.

Feb 28 Eduardo

Mendelian randomization: prospects, potentials, and limitations. Smith and Ebrahin, 2004.

Causal Effects of Body Mass Index on Cardiometabolic Traits and Events: A Mendelian Randomization Analysis. Holmes et al., 2014.

Feb 7 Yuval Evaluating empirical bounds on complex disease genetic architecture. Agarwala et al. Nature Genetics 45: 1418-27.
Jan 31 Joe Joint analysis of functional genomic data and genome-wide association studies of 18 human traits. Joseph Pickrell 2013. bioRxiv. dio: 10.1101/000752.
Jan 23 Min Error-prone polymerase activity causes multinucleotide mutations in humans. Harris and Nielsen 2013.
Jan 22 Amy Practice talk

Journal club, fall 2013

When Who What
Dec 12 Molly Great ape genetic diversity and population history. Prado-Martinez et al. 2013. Nature. 499(7459):471-5.
http://www.ncbi.nlm.nih.gov/pubmed/23823723
Dec 9 Speaker: Pleuni Pennings, Postdoc with Dmitri Petrov
Dec 5 Speaker: Anand Bhaskar, Ph.D. student with Yun Song
Nov 21 Guy S. Why we are not dead one hundred times over. Charlesworth 2013. Evolution. 67(11):3354-61.
http://www.ncbi.nlm.nih.gov/pubmed/24152012
Nov 14 Guy A. Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over? Kondrashov 1995. J Theor Biol. 175(4):583-94.
http://www.ncbi.nlm.nih.gov/pubmed/7475094
Nov 7 Priya A Model-Based Analysis of GC-biased Gene Conversion in the Human and Chimpanzee Genomes. Capra et al. 2013. PLoS Genet. 9(8):e1003684.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744432/
Oct 29 Ziyue
Oct 22 Eyal

Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions. Ward and Kellis 2012. Science 337 (6102): 1675-1678.
http://www.sciencemag.org/content/337/6102/1675.long

Comment. Green and Ewing 2013. Science 340 (6133): 682.
http://www.sciencemag.org/content/340/6133/682.1.full

Response to comment. Ward and Kellis 2013. Science 340 (6133): 682.
http://www.sciencemag.org/content/340/6133/682.2.full

Oct 15 Amy Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits. Zaitlen et al. 2013. PLoS Genet. 9(5):e1003520.
http://www.ncbi.nlm.nih.gov/pubmed/23737753

Oct 8 Min Estimating human mutation rate using autozygosity in a founder population. Campbell et al. 2012. Nat Genet. 44(11): 1277–1281.
http://www.ncbi.nlm.nih.gov/pubmed/23001126

Journal club, spring 2013

When Who What
June 17 Minyoung

Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Michaelson et al. 2012. Cell 151(7):1431-42. http://www.ncbi.nlm.nih.gov/pubmed/23260136

Revising the human mutation rate: implications for understanding human evolution. Scally and Durbin 2012. Nat Rev Gen 13(10):745-753. http://www.ncbi.nlm.nih.gov/pubmed/22965354

June 10 Ellen Genetic recombination is targeted towards gene promoter regions in dogs. Auton et al. 2013. arXiv. http://arxiv.org/abs/1305.6485
June 3 Ziyue Length distributions of identity by descent reveal fine-scale demographic history. Palamara et al. 2012. Am J Hum Genet. 7;91(6):1150.
http://www.ncbi.nlm.nih.gov/pubmed/23103233
May 28 Marie Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression. Dunn et al. 2013. PLoS Genet, 9(3):e1003366.
http://www.ncbi.nlm.nih.gov/pubmed/23555283
May 20 Daniel Hybrid speciation and independent evolution in lineages of alpine butterflies. Nice et al. 2013. Evolution, 67: 1055–1068.
http://www.ncbi.nlm.nih.gov/pubmed/23550755
May 13 Amir Genomic Tests of Variation in Inbreeding Among Individuals and Among Chromosomes. Schraiber et al. 2012. Genetics. (192): 1477–1482.
http://www.ncbi.nlm.nih.gov/pubmed/23051641
May 6 Wynn Genetic Architecture of Skin and Eye Color in an African- European Admixed Population. Beleza et al. 2013. PLOS Genet. 9(3): e1003372.
PDF
May 2 Laure Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila. Bergland et al. 2013. arXiv.
http://arxiv.org/abs/1303.5044
Apr 24 Daniel A Y-like social chromosome causes alternative colony organization in fire ants. Wang et al. 2013. Nature 493, 664-668.
http://www.ncbi.nlm.nih.gov/pubmed/23334415
Apr 8 Ziyue Estimating selection coefficients in spatially structured populations from time series data of allele frequencies. Mathieson et al. 2013. Genetics 193(3), 973-984.
http://www.ncbi.nlm.nih.gov/pubmed/23307902
Apr 2 Keerthi A framework for variation discovery and genotyping using next-generation DNA sequencing data. DePristo et al. 2011. Nature Genetics 43, 491–498.
http://www.ncbi.nlm.nih.gov/pubmed/21478889

Journal club, winter 2013

When Who What
Mar 20 Amir Human aneuploidy: mechanisms and new insights into an age-old problem. Nagaoka et al. 2012. Nat Rev Genet 13(7):493-504. http://www.ncbi.nlm.nih.gov/pubmed/22705668
Mar 4 Wynn Long-term exposure to antibiotics has caused accumulation of resistance determinants in the gut microbiota of honeybees. Tian et al. 2012. MBio. Oct 30;3(6). http://www.ncbi.nlm.nih.gov/pubmed/23111871
Feb 20 Ellen / Laure A sequence-based approach demonstrates that balancing selection in classical human leukocyte antigen (HLA) loci is asymmetric. Bronson et al. 2013. HumMolGenet 22(2):252-61. http://www.ncbi.nlm.nih.gov/pubmed/23065702
Feb 4 Ellen Discrete genetic modules are responsible for complex burrow evolution in Peromyscus mice. Weber et al. 2013. Nature 493(7432):402-405. http://www.ncbi.nlm.nih.gov/pubmed/23325221
Jan 30 Amir Ancient admixture in human history. Patterson et al. 2012. Genetics 192:1065–1093 http://www.ncbi.nlm.nih.gov/pubmed/22960212
Jan 21 Daniel Practice talk.
Jan 14 Laure Genetic history of an archaic hominin group from Denisova Cave in Siberia. Reich et al. 2010. Nature 468(7327)
http://www.ncbi.nlm.nih.gov/pubmed/21179161
Jan 7 Daniel Mutations in the neverland Gene Turned Drosophila pachea into an Obligate Specialist Species. Lang et al. 2012. Science 337:1658-1661
http://www.ncbi.nlm.nih.gov/pubmed/23019649