Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats

Age-structure, harvesting and climate effects on population growth of Arcto-boreal fish stocks

(2017) JM Durant et al.   MARINE ECOLOGY PROGRESS SERIES

Interpreting short tandem repeat variations in humans using mutational constraint

(2017) Melissa Gymrek et al.   NATURE GENETICS

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

Linking species habitat and past palaeoclimatic events to evolution of the teleost innate immune system

(2017) Monica Hongrø Solbakken et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Novel adverse outcome pathways revealed by chemical genetics in a developing marine fish

(2017) Elin Sørhus et al.   eLife

Age-structure, harvesting and climate effects on population growth of Arcto-boreal fish stocks

(2017) JM Durant et al.   MARINE ECOLOGY PROGRESS SERIES

Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution

(2016) Richard H. Adams et al.   GENOME

Successive Losses of Central Immune Genes Characterize the Gadiformes’ Alternate Immunity

(2016) Monica H. Solbakken et al.   Genome Biology and Evolution

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo assembly and phasing of a Korean human genome

(2016) Jeong-Sun Seo et al.   NATURE

The seahorse genome and the evolution of its specialized morphology

(2016) Qiang Lin et al.   NATURE

Evolution of the immune system influences speciation rates in teleost fishes

(2016) Martin Malmstrøm et al.   NATURE GENETICS

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

(2016) Ingo Braasch et al.   NATURE GENETICS

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

(2016) Wesley C. Warren et al.   G3-Genes Genomes Genetics

Structure and evolutionary history of a large family of NLR proteins in the zebrafish

(2016) Kerstin Howe et al.   Open Biology

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

(2016) Shubha Vij et al.   PLoS Genetics

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

(2016) Alvaro Martinez Barrio et al.   eLife

A chromosome-level genome assembly of the Asian arowana, Scleropages formosus

(2016) Jia Li et al.   Scientific Data

The genome of the miiuy croaker reveals well-developed innate immune and sensory systems

(2016) Tianjun Xu et al.   Scientific Reports

Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions

(2016) Monica H. Solbakken et al.   Scientific Reports

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Variable Glutamine-Rich Repeats Modulate Transcription Factor Activity

(2015) Rita Gemayel et al.   MOLECULAR CELL

Abundant contribution of short tandem repeats to gene expression variation in humans

(2015) Melissa Gymrek et al.   NATURE GENETICS

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

NOD-Like Receptors: Versatile Cytosolic Sentinels

(2015) Vinicius Motta et al.   PHYSIOLOGICAL REVIEWS

Using optical mapping data for the improvement of vertebrate genome assemblies

(2015) Kerstin Howe et al.   GigaScience

Structure and function of Toll/interleukin-1 receptor/resistance protein (TIR) domains

(2014) Thomas Ve et al.   APOPTOSIS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

The landscape of human STR variation

(2014) Thomas Willems et al.   GENOME RESEARCH

Genome-Wide Analysis of Simple Sequence Repeats in Marine Animals—a Comparative Approach

(2014) Qun Jiang et al.   MARINE BIOTECHNOLOGY

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

(2014) Mbaye Tine et al.   Nature Communications

Spatial and temporal microsatellite variation in spawning Atlantic cod, Gadus morhua, around Iceland

(2013) Guðni Magnús Eiríksson et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

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

Unraveling the Evolution of the Atlantic Cod’s (Gadus morhua L.) Alternative Immune Strategy

(2013) Martin Malmstrøm et al.   PLoS One

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Genome-Wide Analysis of Tandem Repeats in Plants and Green Algae

(2013) Zhixin Zhao et al.   G3-Genes Genomes Genetics

A new eye on NLR proteins: focused on clarity or diffused by complexity?

(2012) Vera Bonardi et al.   CURRENT OPINION IN IMMUNOLOGY

Ras family of small GTPases in immunity and inflammation

(2012) Derek S Johnson et al.   CURRENT OPINION IN PHARMACOLOGY

Molecular evolution of vertebrate Toll-like receptors: Evolutionary rate difference between their leucine-rich repeats and their TIR domains

(2012) Tomoko Mikami et al.   GENE

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

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

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Variable Tandem Repeats Accelerate Evolution of Coding and Regulatory Sequences

(2010) Rita Gemayel et al.   Annual Review of Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach

(2010) Christoph Mayer et al.   BMC GENOMICS

Natural selection drives the accumulation of amino acid tandem repeats in human proteins

(2010) L. Mularoni et al.   GENOME RESEARCH

Defining the Origins of the NOD-Like Receptor System at the Base of Animal Evolution

(2010) C. Lange et al.   MOLECULAR BIOLOGY AND EVOLUTION

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Quantitative measures for the management and comparison of annotated genomes

(2009) Karen Eilbeck et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Cod, haddock, saithe, herring, and capelin in the Barents Sea and adjacent waters: a review of the biological value of the area

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

Population genomics of marine fishes: identifying adaptive variation in space and time

(2009) EINAR E. NIELSEN et al.   MOLECULAR ECOLOGY

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

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

(2008) Mario Stanke et al.   BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish

(2008) Kerry J Laing et al.   BMC EVOLUTIONARY BIOLOGY

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH