January 17, 2020: Kasper Munch: paper by Shchur et al. (biorXiv 2019) "On the distribution of tract lengths during adaptive introgression"
January 10, 2020: Yoann Anciaux: paper by Otto & Rosales (Am Nat 2019) "Theory in Service of Narratives in Evolution and Ecology"
November 29, 2019: Juraj Bergman - A high-resolution map of non-crossover events reveals impacts of genetic diversity on mammalian meiotic recombination
November 22, 2019: Samuele Soraggi - Bergen et al. (BiorXiv 2019) - Generalizing RNA velocity to transient cell states through dynamical modeling
November 15, 2019: Mikkel Schierup - Stern et al. (Plos Genetics 2019) - An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data
November 8, 2019: Thomas Bataillon: Fortier et al. (BiorXiv 2019) - DFEnitely different: Genome-wide characterization of differences in mutation fitness effects between populations
November 1, 2019: Marjolaine: Brevet and Lartillot (BiorXiv 2019) - Reconstructing the history of variation in effective population size along phylogenies
October 25, 2019: Moisès and Meritxell: the paper by Gao Z. et al.(PNAS 2019) entitled "Overlooked roles of DNA damage and maternal age in generating human germline mutations""
June 14: Noor: the paper by Riesselman AJ et al. (Nature Methods 2019) “Deep generative models of genetic variation capture the effects of mutations”
June 7, 2019; Meritxell: the paper by Rathje CC et al (BioRvix 2019) “Differential sperm motility mediates the sex ratio drive shaping mouse sex chromosome evolution”
May 31, 2019: Samuele: paper by Jiarui Ding et al. (bioRvix 2019) “Systematic comparative analysis of single cell RNA-sequencing methods”
May 24, 2019: Kasper: paper by Speidel et al. (BioRxiv 2019) entitled "A method for genome-wide genealogy estimation for thousands of samples”
May 10, 2019: Thomas B: paper by Ruzicka et al. (PlosBiol 2019) entitled "Genome-wide sexually antagonistic variants reveal long-standing constraints on sexual dimorphism in fruit flies"
May 3, 2019: Juraj: paper by Morgan et al. (Genetics 2019) entitled "Instability of the Pseudoautosomal Boundary in House Mice"
April 26, 2019: no journal club
April 12, 2019: Elise: paper by Corbett‐Detig et al. (Evo Letters) entitled "Bulk pollen sequencing reveals rapid evolution of segregation distortion in the male germline of Arabidopsis hybrids"
April 1, 2019: Marni: paper by Louhelainen & Miller (Jo Forensic Sciences): "Forensic Investigation of a Shawl Linked to the “Jack the Ripper” Murders"
March 29, 2019: Yoann: paper by Jones et al. (JoHeredity 2019): "The Effects of Epistasis and Pleiotropy on Genome-Wide Scans for Adaptive Outlier Loci"
March 22, 2019: Bakhtawar Noor: paper by Mondal et al. (NatCom 2019): "Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania".
March 15, 2019: no journal club (due to Novo nordisk symposium)
March 8, 2019: Meritxell: Kessler et al. (BioRxiv 2019) entitled "De novo mutations across 1,465 diverse genomes reveal novel mutational insights and reductions in the Amish founder population".
March 1, 2019: Kasper: Spence and Song (BioRxiv 2019) entitled "Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations"
February 22, 2019: Moises: Aikens et al. (MBE 2019) "Signals of variation in human mutation rate at multiple levels of sequence context".
February 15, 2019: Elise: Ruzicka et al. (bioRxiv 2018) entitled "Genome-wide sexually antagonistic variants reveal longstanding constraints on sexual dimorphism in the fruitfly".
February 8, 2019: Samuele: Green et al. (CELL 2018) entitled "A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq
February 1, 2019: Thomas B.: a paper by C. Jeong et al. (PLOS Genetics 2018) entitled "Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal".
January 25, 2019: Juraj: Rousselle et al. (MBE 2018) "Influence of recombination and GC-biased gene conversion on the adaptive and non-adaptive substitution rate in mammals vs. birds".
January 18, 2019: Mikkel: Kelleher et al. (BioRxiv 2018) entitled "Inferring the ancestry of everyone".
January 11, 2019: Yoann: a recent article from Nancy Chen et al. (2018) from PNAS called "Allele frequency dynamics in a pedigreed natural population"
December 7, 2018: no journal club (seminar)
November 30, 2018: no journal club (PhD defense)
November 23, 2018: no journal club (seminar)
November 2, 2018: Maria Izabel: "Unified single-cell analysis of testis gene regulation and pathology in 5 mouse strains".
October 19, 2018: Samuele: https://www.biorxiv.org/content/early/2018/03/20/092890
October 12, 2018: Moises: 'Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans'. https://doi.org/10.1016/j.cell.2018.08.034.
October 5, 2018: no journal club (seminar)
September 28, 2018: Juraj Bergman: paper published in Genetics this July by Bassham et al.: "Repeated Selection of Alternatively Adapted Haplotypes Creates Sweeping Genomic Remodeling in Stickleback".
September 21, 2018: no journal club
September 14, 2018: Marni: “A deep learning framework for imputing missing values in genomic data. https://www.biorxiv.org/content/early/2018/09/03/406066
September 7, 2018: no journal club (seminar)
August 17, 2018: no journal club (Mols meeting)
August 10, 2018: Kasper: Variation and constraints in hybrid genome formation.
https://www.nature.com/articles/s41559-017-0437-7
HOLIDAY BREAK
July 6, 2018: Natalia:
June 29, 2018: Elise Lucotte: “ Diverse haplotypes span human centromeres and include archaic lineages within and out of Africa” Langley et al. bioRXiv. https://www.biorxiv.org/content/early/2018/06/20/351569
June 22, 2018: Laurits Skov: “Natural selection interacts with recombination to shape the evolution of hybrid genomes” from Molly Schumer 2018. http://science.sciencemag.org/content/early/2018/04/18/science.aar3684
June 15, 2018: Doug Speed: A paper by Hillary Finucane and colleagues: https://www.nature.com/articles/s41588-018-0081-4
June 8, 2018:
June 1, 2018:
May 25, 2018: Maria Izabel: Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates Zachary Baker. https://elifesciences.org/articles/24133
May 18, 2018: no journal club (seminar Benjamin Peter)
May 11, 2018: Maria Izabel:
Physiological and Genetic Adaptations to Diving in Sea Nomads. https://www.cell.com/cell/fulltext/S0092-8674(18)30386-6
May 4, 2018: no journal club
April 27, 2018: No jounal club (holiday)
April 20, 2018: 2, 2018: Thomas Bataillon: Simons et al PLOS Biology: A population genetic interpretation of GWAS findings for human quantitative traits. http://journals.plos.org/plosbiology/article/comments?id=10.1371/journal.pbio.2002985
April 13, 2018: no journal club (seminar)
April 6, 2018: David Castellano: Understanding the factors that shape patterns of nucleotide diversity in the house mouse genome”, bioRxiv 2018. https://www.biorxiv.org/content/early/2018/03/02/275610
March 30, 2018: no journal club (holiday)
March 23, 2018: no journal club (Maéva's PhD defense)
March 16, 2018: Moises
March 9, 2018: Svend Nielsen: I will present the attached paper 'A Spatial Framework for Understanding Population Structure and Admixture'(2016).
March 2, 2018: Thomas Bataillon: Bay et al.: Genomic signals of selection predict climate-driven population declines in a migratory bird (Science 2018)
February 23, 2018: Matthew Hartfield: Murray et al.: Natural selection shaped the rise and fall of passenger pigeon genomic diversity. DOI: 10.1126/science.aao0960
Dec 8, 2017: Asger Hobolth: 'Analysis of Population Structure: A Unifying Framework and Novel Methods Based on Sparse Facor Analysis' by B. Engelhardt & M. Stephens.
Nov 1st: Thomas Bataillon: 'Faster Evolving Primate Genes are more Likely to Dublicate' by O'Toole, Hurst & McLysaght,
Nov 24, 2017: David Castallano: 'Deleterious variation mimics signatures of genomic incompatibility and adaptive introgression' - https://www.biorxiv.org/content/early/2017/11/17/221705
Nov 17, 2017: No club
Nov 10, 2017: No club (Tanja Slotte seminar)
Nov 3, 2017: Mikkel Schierup: 'Loci associated with skin pigmentation identified in African populations' by Crawford et al, http://science.sciencemag.org/content/early/2017/10/11/science.aan8433
Oct 27, 2017: No club (school holidays)
Oct 20, 2017: Kasper Munch: ' Signatures of long-term balancing selection in human genomes',
https://www.biorxiv.org/content/early/2017/07/24/119529
Oct 13, 2017: No club (Kai Zeng seminar)
Oct 6, 2017: Svend Nielsen: I will present Minimal-assumption inference from population-genomic data by Weissman and Hallatschek (2017). It is a new method for estimating the distribution of coalescence times - which they then use to estimate population parameters.
Sept 29, 2017: Elise Lucotte: "Sex-biased gene expression resolves sexual conflict through the evolution of sex-specific genetic architecture”, by Wright et al. 2017 (on bioRxiv). Find it here: https://www.biorxiv.org/content/early/2017/08/16/176990
Sept 22, 2017: Cancelled due to ProbGen17
Sept 15, 2017: Matthew Hartfield: "Negative selection in humans and fruit flies involves synergistic epistasis" (http://science.sciencemag.org/content/356/6337/539).
----
May 5, 2017: Maria Simonsen: Park et al. (2011): “Distribution of allele frequencies and effect sizes and their interrelationships for common genetic susceptibility variants”
April 28, 2017: Cancelled
April 21, 2017: Marni Tausen: Metagenomic Predictions: From Microbiome to Complex Health and Environmental Phenotypes in Humans and Cattle.
March 31, 2017: Kasper Munch: Ancient hybridization and strong adaptation to viruses across African
vervet monkey populations. http://dx.doi.org/10.1101/088989
March 17, 2017: Maria Izabel Alves: The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection (in nature genetics). doi:10.1038/ng.3657
March 10, 2017 David Castellano: Evidence that Adaptation in Drosophila Is Not Limited by Mutation at Single Sites. http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000924
March 3, 2017 Matthew Hartfield: Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster: http://www.nature.com/articles/s41559-016-0025
Feb 10, 2017 Elise Lucotte: Innocenti & Morrow PLOS Biology 2010
Feb 3, 2017 Laurits Skov: Detecting ancient positive selection in humans using extended lineage sorting. http://biorxiv.org/content/biorxiv/early/2016/10/26/083634.full.pdf
Jan 27, 2017 Thomas B: Detection of human adaptation during the past 2,000 years:
http://biorxiv.org/content/early/2016/05/07/052084
Dec 9, 2016: Maria Simonsen, Xmas special : Fst @STR loci & human forensics. doi: 10.1111/ahg.12081
http://onlinelibrary.wiley.com/doi/10.1111/ahg.12081/epdf
Nov 25, 2016: Jonas Berglund: Companion paper.
http://www.cell.com/cell-systems/fulltext/S2405-4712(16)30183-1
Nov 18, 2016: Kalle Leppälä: (TO BE CONFIRMED): Inference of ancestral recombination graphs through topological data analysis" by P. G. Cámara, A. J. Levine and R. Rabadán.
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005071
Nov 11, 2016: Matthew Hartfield:
Nov 4, 2016: Asger: Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach, By Boitard et al, PLOS Genetics 2016 http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005877
Oct 28, 2016: Thomas Bataillon:Sex Specific Selection and Sex biased gene expression in humans and flies by Cheng & Kirkpatrick, PLOS Genetics 2016
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006170
Oct 14, 2016: Miguel: A genomic history of Aboriginal Australia, Nature. doi:10.1038/nature18299
Oct 7, 2016: Maria Izabel: The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection, Nature Genetics
Sept 23, 2016: Kasper Munch: The Simons Diversity Project,Nature doi:10.1038/nature18964
Sept 16, 2016: Thomas Bataillon: Determining the factors driving selective effects of new nonsynonymous mutations,bioRxiv preprint first posted online Aug. 23, 2016;
