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

Candidate gene polymorphisms for behavioural adaptations during urbanization in blackbirds

(2013) J. C. Mueller et al.   MOLECULAR ECOLOGY

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

(2013) Jesse N. Weber et al.   NATURE

Digging the New York City Skyline: Soil Fungal Communities in Green Roofs and City Parks

(2013) Krista L. McGuire et al.   PLoS One

Analysis of a native whitefly transcriptome and its sequence divergence with two invasive whitefly species

(2012) Xiao-Wei Wang et al.   BMC GENOMICS

Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies

(2012) Robert Ekblom et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

Mapping where ecologists work: biases in the global distribution of terrestrial ecological observations

(2012) Laura J Martin et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae)

(2012) J Ferreira de Carvalho et al.   HEREDITY

A beginners guide to SNP calling from high-throughput DNA-sequencing data

(2012) André Altmann et al.   HUMAN GENETICS

Detecting Selective Sweeps from Pooled Next-Generation Sequencing Samples

(2012) S. Boitard et al.   MOLECULAR BIOLOGY AND EVOLUTION

Looking for Darwin in Genomic Sequences—Validity and Success of Statistical Methods

(2012) Weiwei Zhai et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

De novoassembly of the transcriptome of an invasive snail and its multiple ecological applications

(2012) J. Sun 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

Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever

(2012) K. G. Andersen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data: A Simulation Approach

(2012) Marvin Mundry et al.   PLoS One

The Social Brain: Transcriptome Assembly and Characterization of the Hippocampus from a Social Subterranean Rodent, the Colonial Tuco-Tuco (Ctenomys sociabilis)

(2012) Matthew D. MacManes et al.   PLoS One

Transcriptome Sequencing and Annotation for the Jamaican Fruit Bat (Artibeus jamaicensis)

(2012) Timothy I. Shaw et al.   PLoS One

Rapid Evolutionary Change and the Coexistence of Species

(2011) Richard A. Lankau   Annual Review of Ecology Evolution and Systematics

Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing

(2011) Anna W Santure et al.   BMC GENOMICS

The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus

(2011) Ben Ewen-Campen et al.   BMC GENOMICS

Newly rare or newly common: evolutionary feedbacks through changes in population density and relative species abundance, and their management implications

(2011) Richard A. Lankau et al.   Evolutionary Applications

Evolution and behavioural responses to human-induced rapid environmental change

(2011) Andrew Sih et al.   Evolutionary Applications

A Hierarchical Bayesian Model for Next-Generation Population Genomics

(2011) Z. Gompert et al.   GENETICS

Comparative Transcriptomics of Eastern African Cichlid Fishes Shows Signs of Positive Selection and a Large Contribution of Untranslated Regions to Genetic Diversity

(2011) Laura Baldo et al.   Genome Biology and Evolution

Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing

(2011) Jennifer Becker et al.   JOURNAL OF BIOTECHNOLOGY

Guidelines of the American Society of Mammalogists for the use of wild mammals in research

(2011) Robert S. Sikes et al.   JOURNAL OF MAMMALOGY

Joint analysis of demography and selection in population genetics: where do we stand and where could we go?

(2011) JUNRUI LI et al.   MOLECULAR ECOLOGY

De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae)

(2011) DANIEL B. SLOAN et al.   Molecular Ecology Resources

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Applications of next-generation sequencing to phylogeography and phylogenetics

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

The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

Patterns of Positive Selection and Neutral Evolution in the Protein-Coding Genes of Tetraodon and Takifugu

(2011) Juan I. Montoya-Burgos   PLoS One

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Transcriptome Sequencing of the Blind Subterranean Mole Rat, Spalax galili: Utility and Potential for the Discovery of Novel Evolutionary Patterns

(2011) Assaf Malik et al.   PLoS One

A Novel Approach for Mining Polymorphic Microsatellite Markers In Silico

(2011) Joseph I. Hoffman et al.   PLoS One

Mechanistic Basis of Resistance to PCBs in Atlantic Tomcod from the Hudson River

(2011) I. Wirgin et al.   SCIENCE

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate

(2010) Wiesław Babik et al.   BMC GENOMICS

A guide to the genomics of ecological speciation in natural animal populations

(2010) Amber M. Rice et al.   ECOLOGY LETTERS

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

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

(2010)   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Urban ecological systems: Scientific foundations and a decade of progress

(2010) S.T.A. Pickett et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

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

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

Comparative transcriptomics implicates mechanisms of evolved pollution tolerance in a killifish population

(2010) A. WHITEHEAD et al.   MOLECULAR ECOLOGY

Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonusspp. Salmonidae)

(2010) SÉBASTIEN RENAUT et al.   MOLECULAR ECOLOGY

Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes

(2010) K. R. ELMER et al.   MOLECULAR ECOLOGY

A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection

(2010) S. R. Grossman et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Genetic differentiation in the urban habitat: the great tits (Parus major) of the parks of Barcelona city

(2009) MATS BJÖRKLUND et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx

(2009) Eli Meyer et al.   BMC GENOMICS

Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila

(2009) Chengjie Fu et al.   BMC GENOMICS

Air pollution and mutations in the germline: are humans at risk?

(2009) Christopher M. Somers et al.   HUMAN GENETICS

Molecular mechanisms of heavy metal tolerance and evolution in invertebrates

(2009) Thierry K. S. Janssens et al.   Insect Science

Divergent patterns of breakpoint reuse in Muroid rodents

(2009) E. E. Mlynarski et al.   MAMMALIAN GENOME

Nuclear and mitochondrial DNA reveal contrasting evolutionary processes in populations of deer mice (Peromyscus maniculatus)

(2009) DOU-SHUAN YANG et al.   MOLECULAR ECOLOGY

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Genome-wide scans for footprints of natural selection

(2009) T. K. Oleksyk et al.   PHILOSOPHICAL TRANSACTIONS 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

Testing hypotheses of aging in long-lived mice of the genus Peromyscus: association between longevity and mitochondrial stress resistance, ROS detoxification pathways, and DNA repair efficiency

(2008) Zoltan Ungvari et al.   AGE

Adaptive phenotypic plasticity in an island songbird exposed to a novel predation risk

(2008) Susana I. Peluc et al.   BEHAVIORAL ECOLOGY

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

Expressed sequence tags from Peromyscus testis and placenta tissue: Analysis, annotation, and utility for mapping

(2008) Julie Glenn et al.   BMC GENOMICS

New York's nature: a review of the status and trends in species richness across the metropolitan region

(2008) Linda M. Puth et al.   DIVERSITY AND DISTRIBUTIONS

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

(2008) Lynne M. Mullen et al.   EVOLUTION

Comparative Analysis of Testis Protein Evolution in Rodents

(2008) L. M. Turner et al.   GENETICS

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

(2008) J. CRISTOBAL VERA et al.   MOLECULAR ECOLOGY

Population genomics: a new generation of genome scans to bridge the gap with functional genomics

(2008) AURÉLIE BONIN   MOLECULAR ECOLOGY

Sequencing goes 454 and takes large-scale genomics into the wild

(2008) HANS ELLEGREN   MOLECULAR ECOLOGY

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Comparative population dynamics of Peromyscus leucopus in North America: influences of climate, food, and density dependence

(2008) Guiming Wang et al.   POPULATION ECOLOGY

Germ-line mutations, DNA damage, and global hypermethylation in mice exposed to particulate air pollution in an urban/industrial location

(2008) C. Yauk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid evolution of seed dispersal in an urban environment in the weed Crepis sancta

(2008) P.-O. Cheptou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Change and the Ecology of Cities

(2008) N. B. Grimm et al.   SCIENCE

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics