Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations

Climate change, adaptation, and phenotypic plasticity: the problem and the evidence

(2014) Juha Merilä et al.   Evolutionary Applications

Fast and Efficient Estimation of Individual Ancestry Coefficients

(2014) Eric Frichot et al.   GENETICS

Landscape models for nuclear genetic diversity and genetic structure in white-footed mice (Peromyscus leucopus)

(2014) Z S Taylor et al.   HEREDITY

A genetic map of Peromyscus with chromosomal assignment of linkage groups (a Peromyscus genetic map)

(2014) Jane Kenney-Hunt et al.   MAMMALIAN GENOME

Prevention, diagnosis and treatment of high-throughput sequencing data pathologies

(2014) Xiaofan Zhou et al.   MOLECULAR ECOLOGY

Recent novel approaches for population genomics data analysis

(2014) Kimberly R. Andrews et al.   MOLECULAR ECOLOGY

First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species,Pinus halepensisMill

(2014) S. Pinosio et al.   Molecular Ecology Resources

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

Urban park characteristics, genetic variation, and historical demography of white-footed mouse (Peromyscus leucopus) populations in New York City

(2014) Jason Munshi-South et al.   PeerJ

On the optimal trimming of high-throughput mRNA sequence data

(2014) Matthew D. MacManes   Frontiers in Genetics

Detecting Natural Selection in Genomic Data

(2013) Joseph J. Vitti et al.   Annual Review of Genetics

FUNCTIONAL GENOMICS OF ADAPTATION TO HYPOXIC COLD-STRESS IN HIGH-ALTITUDE DEER MICE: TRANSCRIPTOMIC PLASTICITY AND THERMOGENIC PERFORMANCE

(2013) Zachary A. Cheviron et al.   EVOLUTION

Genomic Divergence during Speciation Driven by Adaptation to Altitude

(2013) Mark A. Chapman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic inference accurately predicts the timing and severity of a recent bottleneck in a nonmodel insect population

(2013) Rajiv C. McCoy et al.   MOLECULAR ECOLOGY

Accuracy of allele frequency estimation using pooled RNA-Seq

(2013) M. Konczal et al.   Molecular Ecology Resources

Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial

(2013) Jochen B. W. Wolf   Molecular Ecology Resources

Discrete genetic modules are responsible for complex burrow evolution in Peromyscus mice

(2013) Jesse N. Weber et al.   NATURE

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

Signatures of Rapid Evolution in Urban and Rural Transcriptomes of White-Footed Mice (Peromyscus leucopus) in the New York Metropolitan Area

(2013) Stephen E. Harris et al.   PLoS One

Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin

(2013) C. Natarajan et al.   SCIENCE

Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene

(2013) C. R. Linnen et al.   SCIENCE

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Genetic structure of the white-footed mouse in the context of the emergence of Lyme disease in southern Québec

(2013) Anita Rogic et al.   Ecology and Evolution

Improving transcriptome assembly through error correction of high-throughput sequence reads

(2013) Matthew D. MacManes et al.   PeerJ

Targeted sequence capture as a powerful tool for evolutionary analysis1

(2012) Corrinne E. Grover et al.   AMERICAN JOURNAL OF BOTANY

The Noncoding RNA MALAT1 Is a Critical Regulator of the Metastasis Phenotype of Lung Cancer Cells

(2012) T. Gutschner et al.   CANCER RESEARCH

Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome-wide digital gene expression analysis

(2012) Tobias L. Lenz et al.   MOLECULAR ECOLOGY

Urban landscape genetics: canopy cover predicts gene flow between white-footed mouse (Peromyscus leucopus) populations in New York City

(2012) JASON MUNSHI-SOUTH   MOLECULAR ECOLOGY

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments

(2012) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis

(2012) Pierre De Wit et al.   Molecular Ecology Resources

Reference-free transcriptome assembly in non-model animals from next-generation sequencing data

(2012) V. CAHAIS et al.   Molecular Ecology Resources

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Regulatory changes contribute to the adaptive enhancement of thermogenic capacity in high-altitude deer mice

(2012) Z. A. Cheviron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

What is needed for next-generation ecological and evolutionary genomics?

(2012) Scott A. Pavey et al.   TRENDS IN ECOLOGY & EVOLUTION

De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity

(2011) Massimo Iorizzo et al.   BMC GENOMICS

Investigating niche and lineage diversification in widely distributed taxa: phylogeography and ecological niche modeling of thePeromyscus maniculatusspecies group

(2011) Håkon M. Kalkvik et al.   ECOGRAPHY

Evolution and behavioural responses to human-induced rapid environmental change

(2011) Andrew Sih et al.   Evolutionary Applications

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Molecular spandrels: tests of adaptation at the genetic level

(2011) Rowan D. H. Barrett et al.   NATURE REVIEWS GENETICS

BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata

(2011) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Using Population Genomics to Detect Selection in Natural Populations: Key Concepts and Methodological Considerations

(2010)   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Genetic differences in hemoglobin function between highland and lowland deer mice

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

Rapid, pervasive genetic differentiation of urban white-footed mouse (Peromyscus leucopus) populations in New York City

(2010) JASON MUNSHI-SOUTH et al.   MOLECULAR ECOLOGY

Ecological genomics-changing perspectives on Darwin’s basic concerns

(2010) SUZY C. P. RENN et al.   MOLECULAR ECOLOGY

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Constructing genomic maps of positive selection in humans: Where do we go from here?

(2009) J. M. Akey   GENOME RESEARCH

Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin

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

Hosts as ecological traps for the vector of Lyme disease

(2009) F. Keesing et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

On the Origin and Spread of an Adaptive Allele in Deer Mice

(2009) C. R. Linnen et al.   SCIENCE

Comparative genome mapping of the deer mouse (Peromyscus maniculatus) reveals greater similarity to rat (Rattus norvegicus) than to the lab mouse (Mus musculus)

(2008) Clifton M Ramsdell et al.   BMC EVOLUTIONARY BIOLOGY

NATURAL SELECTION ALONG AN ENVIRONMENTAL GRADIENT: A CLASSIC CLINE IN MOUSE PIGMENTATION

(2008) Lynne M. Mullen et al.   EVOLUTION

Molecular evolution of cytochrome b in high- and low-altitude deer mice (genus Peromyscus)

(2008) E J Gering et al.   HEREDITY

Rapid morphological and genetic change in Chicago-areaPeromyscus

(2007) OLIVER R. W. PERGAMS et al.   MOLECULAR ECOLOGY

msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design

(2007) BRANT C. FAIRCLOTH   Molecular Ecology Resources