Phylogenetics/Stochastic Processes Journal Club
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Phylogenetics/Stochastic Processes Journal Club

Shim Lab, Rao Lab, and He Lab are reading papers related to phylogenetics, comparative genomics, applications of stochastic processes to those fields, etc. Feel free to email us if you'd like to join (even for a particular paper) or you have any suggestions.

Date Paper
July 6 2018 Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data, Yang et al, 2018
June 6 2018 Birth/birth-death processes and their computable transition probabilities with biological applications, Ho et al, 2018
May 17 2018 A genome-wide association study identifies a horizontally transferred bacterial surface adhesin gene associated with antimicrobial resistant strains, Suzuki et al, 2016
May 17 2018 Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota, Iraola et al, 2017
April 4 2018 Estimating the tempo and mode of gene family evolution from comparative genomic data, Hahn et al, 2005
July 7 2017 Punctuated evolution shaped modern vertebrate diversity, Landis and Schraiber, 2017
April 12 2017 Inference of Evolutionary Jumps in Large Phylogenies using Lévy Processes, Duchen et al, 2017
April 5 2017 Phylogenetic Analysis Using Lévy Processes: Finding Jumps in the Evolution of Continuous Traits, LANDIS et al, 2013
March 8 2017 Bridging Inter- and Intraspecific Trait Evolution with a Hierarchical Bayesian Approach, Kostikova et al, 2016
March 1 2017 Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree, Ansari and Didelot, 2016
February 15 2017 Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution, Hubisz and Pollard,2014 and An RNA gene expressed during cortical development evolved rapidly in humans, Pollard et al, 2006
January 11 2017, 2pm A high-resolution map of human evolutionary constraint using 29 mammals, Lindblad-Toh et al, 2011
December 14 2016, 3pm Genome sequencing reveals insights into physiology and longevity of the naked mole rat, Kim et al, 2011
December 1 2016, 2pm Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic, Lynch et al, 2015
August 18 2016, 2pm Chapter 11 of Molecular Evolution: A Statistical Approach, Ziheng Yang
July 11 2016 New Methods for Detecting Lineage-Specific Selection, Siepel et al, 2006
June 30 2016 Detection of nonneutral substitution rates on mammalian phylogenies, Pollard et al, 2010
May 26 2016 Gene finding with a hidden Markov model of genome structure and evolution, Pedersen and Hein, 2003 and Multiple-sequence functional annotation and the generalized hidden Markov phylogeny, McAuliffe et al, 2004
May 12 2016 Combining phylogenetic and hidden Markov models in biosequence analysis, Siepel and Haussler, 2004