Chimpanzee genomic diversity reveals ancient admixture with bonobos

Demographic History of the GenusPanInferred from Whole Mitochondrial Genome Reconstructions

(2016) Irene Lobon et al.   Genome Biology and Evolution

Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal

(2016) Pille Hallast et al.   GENOME RESEARCH

Ancient gene flow from early modern humans into Eastern Neanderthals

(2016) Martin Kuhlwilm et al.   NATURE

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals

(2016) B. Vernot et al.   SCIENCE

scrm: efficiently simulating long sequences using the approximated coalescent with recombination

(2015) Paul R. Staab et al.   BIOINFORMATICS

The population genetics of wild chimpanzees in Cameroon and Nigeria suggests a positive role for selection in the evolution of chimpanzee subspecies

(2015) Matthew W Mitchell et al.   BMC EVOLUTIONARY BIOLOGY

An early modern human from Romania with a recent Neanderthal ancestor

(2015) Qiaomei Fu et al.   NATURE

The fine-scale genetic structure of the British population

(2015) Stephen Leslie et al.   NATURE

The Y-chromosome point mutation rate in humans

(2015) Agnar Helgason et al.   NATURE GENETICS

Evidence for archaic adaptive introgression in humans

(2015) Fernando Racimo et al.   NATURE REVIEWS GENETICS

Genetic structure in village dogs reveals a Central Asian domestication origin

(2015) Laura M. Shannon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic assignment of large seizures of elephant ivory reveals Africa's major poaching hotspots

(2015) S. K. Wasser et al.   SCIENCE

The sampling scheme matters:Pan troglodytes troglodytesandP. t.schweinfurthiiare characterized by clinal genetic variation rather than a strong subspecies break

(2014) Tillmann Fünfstück et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

Fast and Efficient Estimation of Individual Ancestry Coefficients

(2014) Eric Frichot et al.   GENETICS

The genomic landscape of Neanderthal ancestry in present-day humans

(2014) Sriram Sankararaman et al.   NATURE

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

leeHom: adaptor trimming and merging for Illumina sequencing reads

(2014) Gabriel Renaud et al.   NUCLEIC ACIDS RESEARCH

Resurrecting Surviving Neandertal Lineages from Modern Human Genomes

(2014) B. Vernot et al.   SCIENCE

Strong male bias drives germline mutation in chimpanzees

(2014) O. Venn et al.   SCIENCE

Genome-Wide Inference of Ancestral Recombination Graphs

(2014) Matthew D. Rasmussen et al.   PLoS Genetics

DETECTING RANGE EXPANSIONS FROM GENETIC DATA

(2013) Benjamin M. Peter et al.   EVOLUTION

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

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

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

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

Great ape genetic diversity and population history

(2013) Javier Prado-Martinez et al.   NATURE

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Contrasting demographic histories of the neighboring bonobo and chimpanzee

(2013) Christina Hvilsom et al.   PRIMATES

DNA analysis of an early modern human from Tianyuan Cave, China

(2013) Q. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Ancient Structure in Africa Unlikely to Explain Neanderthal and Non-African Genetic Similarity

(2012) M. A. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution

(2012) K. E. Langergraber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Fine-Scale Chimpanzee Genetic Map from Population Sequencing

(2012) A. Auton et al.   SCIENCE

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

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

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

A linear complexity phasing method for thousands of genomes

(2011) Olivier Delaneau et al.   NATURE METHODS

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Bonobos Fall within the Genomic Variation of Chimpanzees

(2011) Anne Fischer et al.   PLoS One

Evidence from Cameroon reveals differences in the genetic structure and histories of chimpanzee populations

(2011) M. K. Gonder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hunter-gatherer genomic diversity suggests a southern African origin for modern humans

(2011) B. M. Henn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Classic Selective Sweeps Were Rare in Recent Human Evolution

(2011) R. D. Hernandez et al.   SCIENCE

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Bayesian Inference of the Demographic History of Chimpanzees

(2010) D. Wegmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content

(2010) Jennifer F. Hughes et al.   NATURE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Widespread Genomic Signatures of Natural Selection in Hominid Evolution

(2009) Graham McVicker et al.   PLoS Genetics

Genome-wide nucleotide-level mammalian ancestor reconstruction

(2008) B. Paten et al.   GENOME RESEARCH

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH

Estimation of Hominoid Ancestral Population Sizes under Bayesian Coalescent Models Incorporating Mutation Rate Variation and Sequencing Errors

(2008) Ralph Burgess et al.   MOLECULAR BIOLOGY AND EVOLUTION

Subdivision in an Ancestral Species Creates Asymmetry in Gene Trees

(2008) M. Slatkin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Linkage disequilibrium — understanding the evolutionary past and mapping the medical future

(2008) Montgomery Slatkin   NATURE REVIEWS GENETICS

Analysis of Chimpanzee History Based on Genome Sequence Alignments

(2008) Jennifer L. Caswell et al.   PLoS Genetics