The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

Estrogen receptor signaling during vertebrate development

(2015) Maria Bondesson et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

Effects of Spring Temperatures on the Strength of Selection on Timing of Reproduction in a Long-Distance Migratory Bird

(2015) Marcel E. Visser et al.   PLOS BIOLOGY

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Comparative genomics reveals tissue-specific regulation of prolactin receptor gene expression

(2014) Anke Schennink et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

Whole-genome duplication in teleost fishes and its evolutionary consequences

(2014) Stella M. K. Glasauer et al.   MOLECULAR GENETICS AND GENOMICS

Whole-genome haplotyping using long reads and statistical methods

(2014) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

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

(2014) Andrew R Wood et al.   NATURE GENETICS

Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

(2014) Rajiv C. McCoy et al.   PLoS One

Pan-vertebrate comparative genomics unmasks retrovirus macroevolution

(2014) Alexander Hayward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

(2014) M. Carneiro et al.   SCIENCE

Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension

(2014) Gang Wang et al.   Frontiers in Genetics

Molecular consequences of animal breeding

(2013) Leif Andersson   CURRENT OPINION IN GENETICS & DEVELOPMENT

Estimating Variable Effective Population Sizes from Multiple Genomes: A Sequentially Markov Conditional Sampling Distribution Approach

(2013) S. Sheehan et al.   GENETICS

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Adaptive evolution of fish hatching enzyme: one amino acid substitution results in differential salt dependency of the enzyme

(2013) M. Kawaguchi et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

The African coelacanth genome provides insights into tetrapod evolution

(2013) Chris T. Amemiya et al.   NATURE

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The saccus vasculosus of fish is a sensor of seasonal changes in day length

(2013) Yusuke Nakane et al.   Nature Communications

Accelerating Improvement of Livestock with Genomic Selection

(2013) Theo Meuwissen et al.   Annual Review of Animal Biosciences

The genome sequence of the colonial chordate, Botryllus schlosseri

(2013) Ayelet Voskoboynik et al.   eLife

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values

(2012) B. S. Pedersen et al.   BIOINFORMATICS

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

Gonadotrophin-Releasing Hormone Signalling Downstream of Calmodulin

(2012) P. Melamed et al.   JOURNAL OF NEUROENDOCRINOLOGY

Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)

(2012) MORTEN T. LIMBORG et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring

(2012) S. Lamichhaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolution of ray-finned fish phylogeny and timing of diversification

(2012) T. J. Near et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection

(2012) James W. Kijas et al.   PLOS BIOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Class-C SOX Transcription Factors ControlGnRHGene Expression via the Intronic Transcriptional Enhancer

(2011) Hee-Dae Kim et al.   MOLECULAR ENDOCRINOLOGY

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter 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

MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus

(2010) Gregory Ewing et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Lessons learned from stock collapse and recovery of North Sea herring: a review

(2010) M. Dickey-Collas et al.   ICES JOURNAL OF MARINE SCIENCE

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Evidence that Adaptation in Drosophila Is Not Limited by Mutation at Single Sites

(2010) Talia Karasov et al.   PLoS Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Genetic variability in Atlantic herring (Clupea harengus harengus): description of protein loci and population data

(2009) LEIF ANDERSSON et al.   HEREDITAS

Temporally stable genetic structure of heavily exploited Atlantic herring (Clupea harengus) in Swedish waters

(2009) L C Larsson et al.   HEREDITY

Spatial diversity of Pacific herring (Clupea pallasi) spawning areas

(2009) D. E. Hay et al.   ICES JOURNAL OF MARINE SCIENCE

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

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

(2008) Mario Stanke et al.   BIOINFORMATICS

Ancestral TSH Mechanism Signals Summer in a Photoperiodic Mammal

(2008) Elodie A. Hanon et al.   CURRENT BIOLOGY

Geological Dates and Molecular Rates: Fish DNA Sheds Light on Time Dependency

(2008) C. P. Burridge et al.   MOLECULAR BIOLOGY AND EVOLUTION

Thyrotrophin in the pars tuberalis triggers photoperiodic response

(2008) Nobuhiro Nakao et al.   NATURE

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

Involvement of thyrotropin in photoperiodic signal transduction in mice

(2008) H. Ono et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA