An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

Allele frequency dynamics in a pedigreed natural population

(2019) Nancy Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Why structure matters

(2019) Nick Barton et al.   eLife

Artificial selection sheds light on developmental mechanisms of limb elongation

(2018) Marta Marchini et al.   EVOLUTION

Limb development: a paradigm of gene regulation

(2017) Florence Petit et al.   NATURE REVIEWS GENETICS

Automated Phenotyping Indicates Pupal Size in Drosophila Is a Highly Heritable Trait with an Apparent Polygenic Basis

(2017) R. Guy Reeves et al.   G3-Genes Genomes Genetics

Genotype Imputation with Millions of Reference Samples

(2016) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The mouse Gene Expression Database (GXD): 2017 update

(2016) Jacqueline H. Finger et al.   NUCLEIC ACIDS RESEARCH

Rapid evolutionary response to a transmissible cancer in Tasmanian devils

(2016) Brendan Epstein et al.   Nature Communications

Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells

(2016) Pamela Milani et al.   Scientific Reports

Power Analysis of Artificial Selection Experiments Using Efficient Whole Genome Simulation of Quantitative Traits

(2015) Darren Kessner et al.   GENETICS

Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation inDrosophila melanogaster

(2015) Aashish R. Jha et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sall4-Gli3system in early limb progenitors is essential for the development of limb skeletal elements

(2015) Ryutaro Akiyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular mechanisms underlying the exceptional adaptations of batoid fins

(2015) Tetsuya Nakamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Power Analysis of Artificial Selection Experiments Using Efficient Whole Genome Simulation of Quantitative Traits

(2015) Darren Kessner et al.   GENETICS

MCMC Methods for Multi-Response Generalized Linear Mixed Models: TheMCMCglmmRPackage

(2015) Jarrod D. Hadfield   Journal of Statistical Software

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Impacts of genetic correlation on the independent evolution of body mass and skeletal size in mammals

(2014) Marta Marchini et al.   BMC EVOLUTIONARY BIOLOGY

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

A promoter-level mammalian expression atlas

(2014)   NATURE

Defining the role of common variation in the genomic and biological architecture of adult human height

(2014) Andrew R Wood et al.   NATURE GENETICS

Evolutionary rates for multivariate traits: the role of selection and genetic variation

(2014) W. Pitchers et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Population Genetic Signal of Polygenic Adaptation

(2014) Jeremy J. Berg et al.   PLoS Genetics

THE LOCI OF REPEATED EVOLUTION: A CATALOG OF GENETIC HOTSPOTS OF PHENOTYPIC VARIATION

(2013) Arnaud Martin et al.   EVOLUTION

LIMITS TO BEHAVIORAL EVOLUTION: THE QUANTITATIVE GENETICS OF A COMPLEX TRAIT UNDER DIRECTIONAL SELECTION

(2013) Vincent Careau et al.   EVOLUTION

Derived variants at six genes explain nearly half of size reduction in dog breeds

(2013) M. Rimbault et al.   GENOME RESEARCH

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Dynamics of Adaptive Alleles in Divergently Selected Body Weight Lines of Chickens

(2013) Mats E. Pettersson et al.   G3-Genes Genomes Genetics

Parallel Selection Mapping Using Artificially Selected Mice Reveals Body Weight Control Loci

(2012) Yingguang Frank Chan et al.   CURRENT BIOLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

A Test for Selection Employing Quantitative Trait Locus and Mutation Accumulation Data

(2012) D. P. Rice et al.   GENETICS

On the Pleiotropic Structure of the Genotype-Phenotype Map and the Evolvability of Complex Organisms

(2012) W. G. Hill et al.   GENETICS

Adaptation ofDrosophilato a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles

(2012) PABLO OROZCO-terWENGEL et al.   MOLECULAR ECOLOGY

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Evidence of widespread selection on standing variation in Europe at height-associated SNPs

(2012) Michael C Turchin et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Sensitive detection of chromatin coassociations using enhanced chromosome conformation capture on chip

(2012) Tom Sexton et al.   Nature Protocols

Four Loci Explain 83% of Size Variation in the Horse

(2012) Shokouh Makvandi-Nejad et al.   PLoS One

Limits to the Rate of Adaptive Substitution in Sexual Populations

(2012) Daniel B. Weissman et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Growth of limb muscle is dependent on skeletal-derived Indian hedgehog

(2011) Yvette Bren-Mattison et al.   DEVELOPMENTAL BIOLOGY

New Bapx1Cre-EGFP mouse lines for lineage tracing and conditional knockout studies

(2011) V. Sivakamasundari et al.   GENESIS

Climate change and evolutionary adaptation

(2011) Ary A. Hoffmann et al.   NATURE

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster

(2011) Thomas L. Turner et al.   PLoS Genetics

Adaptations to Climate-Mediated Selective Pressures in Humans

(2011) Angela M. Hancock et al.   PLoS Genetics

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

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

Genome-wide analysis of a long-term evolution experiment with Drosophila

(2010) Molly K. Burke et al.   NATURE

Commercially Available Outbred Mice for Genome-Wide Association Studies

(2010) Binnaz Yalcin et al.   PLoS Genetics

Homozygous Inactivating Mutations in the NKX3-2 Gene Result in Spondylo-Megaepiphyseal-Metaphyseal Dysplasia

(2009) Jan Hellemans et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genetic analysis of an F2 intercross between two chicken lines divergently selected for body-weight

(2009) Per Wahlberg et al.   BMC GENOMICS

A New Standard Genetic Map for the Laboratory Mouse

(2009) Allison Cox et al.   GENETICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Data and Theory Point to Mainly Additive Genetic Variance for Complex Traits

(2008) William G. Hill et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY