The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization

Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification

(2019) Pavel Neumann et al.   Mobile DNA

Antarctic blackfin icefish genome reveals adaptations to extreme environments

(2019) Bo-Mi Kim et al.   Nature Ecology & Evolution

De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication

(2019) Zelin Chen et al.   Science Advances

Draft Genome and Complete Hox-Cluster Characterization of the Sterlet (Acipenser ruthenus)

(2019) Peilin Cheng et al.   Frontiers in Genetics

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

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(2018)   BIOINFORMATICS

Transposable elements: genome innovation, chromosome diversity, and centromere conflict

(2018) Savannah J. Klein et al.   CHROMOSOME RESEARCH

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

(2018) Lily C. Hughes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FishTEDB: a collective database of transposable elements identified in the complete genomes of fish

(2018) Feng Shao et al.   Database-The Journal of Biological Databases and Curation

Sturgeon genetics and cytogenetics: a review related to ploidy levels and interspecific hybridization

(2018) Miloš Havelka et al.   FOLIA ZOOLOGICA

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Comparison of Egg Envelope Thickness in Teleosts and its Relationship to the Sites of ZP Protein Synthesis

(2017) Kaori Sano et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads

(2017) Petr Novák et al.   NUCLEIC ACIDS RESEARCH

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Next Generation Sequencing of Chromosome-Specific Libraries Sheds Light on Genome Evolution in Paleotetraploid Sterlet (Acipenser ruthenus)

(2017) Daria Andreyushkova et al.   Genes

Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection

(2016) Erik Kjærner-Semb et al.   BMC GENOMICS

B chromosomes: from cytogenetics to systems biology

(2016) Guilherme T. Valente et al.   CHROMOSOMA

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

(2016) Peter Edge et al.   GENOME RESEARCH

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

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

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

The seahorse genome and the evolution of its specialized morphology

(2016) Qiang Lin et al.   NATURE

Genome evolution in the allotetraploid frog Xenopus laevis

(2016) Adam M. Session et al.   NATURE

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

(2016) Ingo Braasch et al.   NATURE GENETICS

Neofunctionalization of zona pellucida proteins enhances freeze-prevention in the eggs of Antarctic notothenioids

(2016) Lixue Cao et al.   Nature Communications

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

(2015) Domitille Chalopin et al.   Genome Biology and Evolution

Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting

(2015) Svetlana A. Romanenko et al.   Molecular Cytogenetics

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time

(2014) Gavin C Conant et al.   CURRENT OPINION IN PLANT BIOLOGY

Evolution of Polyploidy and Functional Diploidization in Sturgeons: Microsatellite Analysis in 10 Sturgeon Species

(2014) J. Rajkov et al.   JOURNAL OF HEREDITY

Enigmatic Orthology Relationships between Hox Clusters of the African Butterfly Fish and Other Teleosts Following Ancient Whole-Genome Duplication

(2014) Kyle J. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Origin And Migration Of Primordial Germ Cells In Sturgeons

(2014) Taiju Saito et al.   PLoS One

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

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

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

(2014) Camille Berthelot et al.   Nature Communications

Conservation and Divergence of Regulatory Strategies at Hox Loci and the Origin of Tetrapod Digits

(2014) Joost M. Woltering et al.   PLOS BIOLOGY

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Polyploidy in Animals: Effects of Gene Expression on Sex Determination, Evolution and Ecology

(2013) B. Wertheim et al.   CYTOGENETIC AND GENOME RESEARCH

Typology of historical sources and the reconstruction of long-term historical changes of riverine fish: a case study of the Austrian Danube and northern Russian rivers

(2013) Gertrud Haidvogl et al.   ECOLOGY OF FRESHWATER FISH

Extensive genome duplications in sturgeons: new evidence from microsatellite data

(2013) M. Havelka et al.   JOURNAL OF APPLIED ICHTHYOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

The African coelacanth genome provides insights into tetrapod evolution

(2013) Chris T. Amemiya et al.   NATURE

The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits

(2013) Manfred Schartl et al.   NATURE GENETICS

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

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

(2013) R. De Smet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation

(2013) Daniel L. Rabosky et al.   Nature Communications

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference

(2012) Karen D. Crow et al.   Genome Biology and Evolution

Positionally biased gene loss after whole genome duplication: Evidence from human, yeast, and plant

(2012) T. Makino et al.   GENOME RESEARCH

Use of Feulgen image analysis densitometry to study the effect of genome size on nuclear size in polyploid sturgeons

(2012) D. Bytyutskyy et al.   JOURNAL OF APPLIED ICHTHYOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines

(2012) J. A. Birchler 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

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Positional orthology: putting genomic evolutionary relationships into context

(2011) C. N. Dewey   BRIEFINGS IN BIOINFORMATICS

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

A review of sex determination and searches for sex-specific markers in sturgeon

(2010) Saeed Keyvanshokooh et al.   AQUACULTURE RESEARCH

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition

(2009) Michael Freeling   Annual Review of Plant Biology

bioDBnet: the biological database network

(2009) Uma Mudunuri et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The evolution and maintenance of Hox gene clusters in vertebrates and the teleost-specific genome duplication

(2009) Shigehiro Kuraku et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Mechanisms of seawater acclimation in a primitive, anadromous fish, the green sturgeon

(2009) Peter J. Allen et al.   JOURNAL OF COMPARATIVE PHYSIOLOGY B-BIOCHEMICAL SYSTEMIC AND ENVIRONMENTAL PHYSIOLOGY

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

genBlastA: Enabling BLAST to identify homologous gene sequences

(2008) R. She et al.   GENOME RESEARCH

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

Zona Pellucida Glycoproteins

(2008) Paul M. Wassarman   JOURNAL OF BIOLOGICAL CHEMISTRY

Differential Evolution of the 13 Atlantic Salmon Hox Clusters

(2008) S. Mungpakdee et al.   MOLECULAR BIOLOGY AND EVOLUTION

Synteny and Collinearity in Plant Genomes

(2008) H. Tang et al.   SCIENCE

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY