Repeat associated mechanisms of genome evolution and function revealed by theMus caroliandMus paharigenomes

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

(2017) Valerie A. Schneider et al.   GENOME RESEARCH

Integration site selection by retroviruses and transposable elements in eukaryotes

(2017) Tania Sultana et al.   NATURE REVIEWS GENETICS

Identification of critical base pairs required for CTCF binding in motif M1 and M2

(2017) Wufeng Li et al.   Protein & Cell

Simultaneous gene finding in multiple genomes

(2016) Stefanie König et al.   BIOINFORMATICS

How retrotransposons shape genome regulation

(2016) Paolo Mita et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes

(2016) Václav Janoušek et al.   Genome Biology and Evolution

Ensembl 2017

(2016) Bronwen L. Aken et al.   NUCLEIC ACIDS RESEARCH

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

Ensembl comparative genomics resources

(2016) Javier Herrero et al.   Database-The Journal of Biological Databases and Curation

Chromosomal polymorphism in mammals: an evolutionary perspective

(2015) Gauthier Dobigny et al.   BIOLOGICAL REVIEWS

A Genome-Wide Landscape of Retrocopies in Primate Genomes

(2015) Fábio C.P. Navarro et al.   Genome Biology and Evolution

Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice

(2015) Arikuni Uchimura et al.   GENOME RESEARCH

Convergent evolution of the genomes of marine mammals

(2015) Andrew D Foote et al.   NATURE GENETICS

Genome-wide analyses of LINE–LINE-mediated nonallelic homologous recombination

(2015) Michał Startek et al.   NUCLEIC ACIDS RESEARCH

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

The Genome 10K Project: A Way Forward

(2015) Klaus-Peter Koepfli et al.   Annual Review of Animal Biosciences

Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

(2014) Shiping Liu et al.   CELL

The Robertsonian phenomenon in the house mouse: mutation, meiosis and speciation

(2014) Silvia Garagna et al.   CHROMOSOMA

Gibbon genome and the fast karyotype evolution of small apes

(2014) Lucia Carbone et al.   NATURE

A Phylogeographic Survey of the Pygmy Mouse Mus minutoides in South Africa: Taxonomic and Karyotypic Inference from Cytochrome b Sequences of Museum Specimens

(2014) Pascale Chevret et al.   PLoS One

Comparative analysis of pseudogenes across three phyla

(2014) Cristina Sisu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Camelid genomes reveal evolution and adaptation to desert environments

(2014) Huiguang Wu et al.   Nature Communications

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes

(2014) Petra C Schwalie et al.   GENOME BIOLOGY

RCPedia: a database of retrocopied genes

(2013) Fábio C. P. Navarro et al.   BIOINFORMATICS

The role of retrotransposons in gene family expansions: insights from the mouse Abp gene family

(2013) Václav Janoušek et al.   BMC EVOLUTIONARY BIOLOGY

Genome Sequencing Reveals Loci under Artificial Selection that Underlie Disease Phenotypes in the Laboratory Rat

(2013) Santosh S. Atanur et al.   CELL

The Effective Population Sizes of the Anthropoid Ancestors of the Human-Chimpanzee Lineage Provide Insights on the Historical Biogeography of the Great Apes

(2013) C. G. Schrago   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

(2013) Pierre-Étienne Jacques et al.   PLoS Genetics

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations

(2012) C. Robberecht et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

Analyses of pig genomes provide insight into porcine demography and evolution

(2012) Martien A. M. Groenen et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FastML: a web server for probabilistic reconstruction of ancestral sequences

(2012) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

(2012) Mikhail Pachkov et al.   NUCLEIC ACIDS RESEARCH

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

The genomic landscape shaped by selection on transposable elements across 18 mouse strains

(2012) Christoffer Nellåker et al.   GENOME BIOLOGY

The GENCODE pseudogene resource

(2012) Baikang Pei et al.   GENOME BIOLOGY

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

(2011) E. Gazave et al.   GENOME RESEARCH

Higher differentiation among subspecies of the house mouse (Mus musculus) in genomic regions with low recombination

(2011) A. GERALDES et al.   MOLECULAR ECOLOGY

Reinforcement selection acting on the European house mouse hybrid zone

(2011) BARBORA VOŠLAJEROVÁ BÍMOVÁ et al.   MOLECULAR ECOLOGY

Comparative and demographic analysis of orang-utan genomes

(2011) Devin P. Locke et al.   NATURE

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Genome sequencing reveals insights into physiology and longevity of the naked mole rat

(2011) Eun Bae Kim et al.   NATURE

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

(2010) Ari Löytynoja et al.   BMC BIOINFORMATICS

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Why do species vary in their rate of molecular evolution?

(2009) L. Bromham   Biology Letters

Comparative analysis of Alu repeats in primate genomes

(2009) G. E. Liu et al.   GENOME RESEARCH

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

A burst of segmental duplications in the genome of the African great ape ancestor

(2009) Tomas Marques-Bonet et al.   NATURE

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

(2009) et al.   SCIENCE

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms

(2008) W. Lai et al.   BIOINFORMATICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals

(2008) Christina M Laukaitis et al.   BMC EVOLUTIONARY BIOLOGY

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues

(2008) Lan Lin et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY