Pervasive introgression facilitated domestication and adaptation in the Bos species complex

Tracing the peopling of the world through genomics

(2017) Rasmus Nielsen et al.   NATURE

Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks

(2017) Ivica Medugorac et al.   NATURE GENETICS

Deciphering the Wisent Demographic and Adaptive Histories from Individual Whole-Genome Sequences

(2016) Mathieu Gautier et al.   MOLECULAR BIOLOGY AND EVOLUTION

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Tree of Life Reveals Clock-Like Speciation and Diversification

(2015) S. Blair Hedges et al.   MOLECULAR BIOLOGY AND EVOLUTION

Increased prevalence of EPAS1 variant in cattle with high-altitude pulmonary hypertension

(2015) John H. Newman et al.   Nature Communications

The roles of microphthalmia-associated transcription factor and pigmentation in melanoma

(2014) Jennifer J. Hsiao et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Human high-altitude adaptation: forward genetics meets the HIF pathway

(2014) Abigail W. Bigham et al.   GENES & DEVELOPMENT

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

(2014) Emilia Huerta-Sánchez et al.   NATURE

Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle

(2014) Hans D Daetwyler et al.   NATURE GENETICS

A genetic mechanism for Tibetan high-altitude adaptation

(2014) Felipe R Lorenzo et al.   NATURE GENETICS

Agriculture facilitated permanent human occupation of the Tibetan Plateau after 3600 B.P.

(2014) F. H. Chen et al.   SCIENCE

Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression

(2014) Mirte Bosse et al.   Nature Communications

The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit

(2014) Miguel Carneiro et al.   PLoS Genetics

Behavior Genetics and the Domestication of Animals

(2014) Per Jensen   Annual Review of Animal Biosciences

RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference

(2013) Brian K. Maples et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data

(2013) B. L. Browning et al.   GENETICS

Artificial Selection on Brain-Expressed Genes during the Domestication of Dog

(2013) Yan Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R

(2012) Andrei-Alin Popescu et al.   BIOINFORMATICS

Combining multiple autosomal introns for studying shallow phylogeny and taxonomy of Laurasiatherian mammals: Application to the tribe Bovini (Cetartiodactyla, Bovidae)

(2012) Alexandre Hassanin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The yak genome and adaptation to life at high altitude

(2012) Qiang Qiu et al.   NATURE GENETICS

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species

(2012) Thomas Mailund et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies

(2011) Yong Kong   GENOMICS

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model

(2011) Thomas Mailund et al.   PLoS Genetics

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Genetic diversity and origin of Gayal and cattle in Yunnan revealed by mtDNA control region andSRYgene sequence variation

(2010) X. Gou et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Phenotypic plasticity and genetic adaptation to high-altitude hypoxia in vertebrates

(2010) J. F. Storz et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Genetic Architecture of Complex Traits and Accuracy of Genomic Prediction: Coat Colour, Milk-Fat Percentage, and Type in Holstein Cattle as Contrasting Model Traits

(2010) Ben J. Hayes et al.   PLoS Genetics

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Mice lacking synapsin III show abnormalities in explicit memory and conditioned fear

(2009) B. Porton et al.   GENES BRAIN AND BEHAVIOR

Sept5 deficiency exerts pleiotropic influence on affective behaviors and cognitive functions in mice

(2009) G. Suzuki et al.   HUMAN MOLECULAR GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics

(2009) J. E. Decker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From wild animals to domestic pets, an evolutionary view of domestication

(2009) C. A. Driscoll et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

(2009) et al.   SCIENCE