Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes

The transcriptome of the bowhead whale Balaena mysticetus reveals adaptations of the longest-lived mammal

(2016) Inge Seim et al.   Aging-US

Naked but Not Hairless: The Pitfalls of Analyses of Molecular Adaptation Based on Few Genome Sequence Comparisons

(2015) Frédéric Delsuc et al.   Genome Biology and Evolution

Convergent evolution of the genomes of marine mammals

(2015) Andrew D Foote et al.   NATURE GENETICS

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

(2014) Shiping Liu et al.   CELL

Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories

(2014) Mark J. Statham et al.   MOLECULAR ECOLOGY

A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes)

(2013) Verena E Kutschera et al.   BMC EVOLUTIONARY BIOLOGY

The Branch-Site Test of Positive Selection Is Surprisingly Robust but Lacks Power under Synonymous Substitution Saturation and Variation in GC

(2013) Walid H. Gharib et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular and clinical characterization of the myopathic form of mitochondrial DNA depletion syndrome caused by mutations in the thymidine kinase (TK2) gene

(2013) Sirisak Chanprasert et al.   MOLECULAR GENETICS AND METABOLISM

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

The genetic causes of convergent evolution

(2013) David L. Stern   NATURE REVIEWS GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants

(2012) Nicole Gruenheit et al.   BMC GENOMICS

Identification of differentially expressed genes and pathways for intramuscular fat deposition in pectoralis major tissues of fast-and slow-growing chickens

(2012) Huan-Xian Cui et al.   BMC GENOMICS

The RGD finger of Del-1 is a unique structural feature critical for integrin binding

(2012) Thomas Schürpf et al.   FASEB JOURNAL

V-AKT murine thymoma viral oncogene homolog/mammalian target of rapamycin activation induces a module of metabolic changes contributing to growth in insulin-induced hepatocarcinogenesis

(2012) Matthias Evert et al.   HEPATOLOGY

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Kretzoiarctos gen. nov., the Oldest Member of the Giant Panda Clade

(2012) Juan Abella et al.   PLoS One

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

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

Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage

(2012) F. Hailer et al.   SCIENCE

Protein Interactions among Fe65, the Low-Density Lipoprotein Receptor-Related Protein, and the Amyloid Precursor Protein

(2011) Melinda M. Mulvihill et al.   BIOCHEMISTRY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

(2011) Qiong-Yi Zhao et al.   BMC BIOINFORMATICS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Sequence comparison of prefrontal cortical brain transcriptome from a tame and an aggressive silver fox (Vulpes vulpes)

(2011) Anna V Kukekova et al.   BMC GENOMICS

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Global Gene Expression Analysis of Murine Limb Development

(2011) Leila Taher et al.   PLoS One

The real cost of sequencing: higher than you think!

(2011) Andrea Sboner et al.   GENOME BIOLOGY

Normalization of genomic DNA using duplex-specific nuclease

(2010) Irina Shagina et al.   BIOTECHNIQUES

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

(2010) A. McKenna et al.   GENOME RESEARCH

A Genome-wide Survey of the Prevalence and Evolutionary Forces Acting on Human Nonsense SNPs

(2009) Bryndis Yngvadottir et al.   AMERICAN JOURNAL OF HUMAN GENETICS

TagDust--a program to eliminate artifacts from next generation sequencing data

(2009) T. Lassmann et al.   BIOINFORMATICS

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) P. Librado et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment

(2009) Adrian Schneider et al.   Genome Biology and Evolution

A novel missense mutation in theSLC6A19gene in a Chinese family with Hartnup disorder

(2009) Yanhong Zheng et al.   INTERNATIONAL JOURNAL OF DERMATOLOGY

The evolution of South American endemic canids: a history of rapid diversification and morphological parallelism

(2009) F. A. PERINI et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gnathostome Phylogenomics Utilizing Lungfish EST Sequences

(2008) B. M. Hallstrom et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic analysis of 1.5 Mbp and platypus EST data refute the Marsupionta hypothesis and unequivocally support Monotremata as sister group to Marsupialia/Placentalia

(2008) Morgan Kullberg et al.   ZOOLOGICA SCRIPTA