Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates

Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes

(2018) Yuichiro Hara et al.   BMC BIOLOGY

A staging table for the embryonic development of the brownbanded bamboo shark (Chiloscyllium punctatum )

(2018) Koh Onimaru et al.   DEVELOPMENTAL DYNAMICS

Leptin and the maintenance of elevated body weight

(2018) Warren W. Pan et al.   NATURE REVIEWS NEUROSCIENCE

Global priorities for conserving the evolutionary history of sharks, rays and chimaeras

(2018) R. William Stein et al.   Nature Ecology & Evolution

Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates

(2017) Julien Roux et al.   MOLECULAR BIOLOGY AND EVOLUTION

The long noncoding RNA Malat1: Its physiological and pathophysiological functions

(2017) Xuejing Zhang et al.   RNA Biology

Regulation of clustered protocadherin genes in individual neurons

(2017) Teruyoshi Hirayama et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Identification and Characterization of a Class of MALAT1 -like Genomic Loci

(2017) Bin Zhang et al.   Cell Reports

CTCF binding landscape in jawless fish with reference to Hox cluster evolution

(2017) Mitsutaka Kadota et al.   Scientific Reports

CTCF-mediated topological boundaries during development foster appropriate gene regulation

(2016) Varun Narendra et al.   GENES & DEVELOPMENT

CTCF: making the right connections

(2016) Rodolfo Ghirlando et al.   GENES & DEVELOPMENT

Evolution of Hoxa11 regulation in vertebrates is linked to the pentadactyl state

(2016) Yacine Kherdjemil et al.   NATURE

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Eye lens radiocarbon reveals centuries of longevity in the Greenland shark (Somniosus microcephalus)

(2016) J. Nielsen et al.   SCIENCE

Molecular developmental mechanism in polypterid fish provides insight into the origin of vertebrate lungs

(2016) Norifumi Tatsumi et al.   Scientific Reports

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing

(2015) Kaori Tatsumi et al.   BIOTECHNIQUES

Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

(2015) Yuichiro Hara et al.   BMC GENOMICS

Colour vision in marine organisms

(2015) Justin Marshall et al.   CURRENT OPINION IN NEUROBIOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

New insights in prolactin: pathological implications

(2015) Valérie Bernard et al.   Nature Reviews Endocrinology

Ghrelin and motilin receptors as drug targets for gastrointestinal disorders

(2015) Gareth J. Sanger et al.   Nature Reviews Gastroenterology & Hepatology

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

Split-alignment of genomes finds orthologies more accurately

(2015) Martin C Frith et al.   GENOME BIOLOGY

Vertical Movements and Patterns in Diving Behavior of Whale Sharks as Revealed by Pop-Up Satellite Tags in the Eastern Gulf of Mexico

(2015) John P. Tyminski et al.   PLoS One

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Elephant shark genome provides unique insights into gnathostome evolution

(2014) Byrappa Venkatesh et al.   NATURE

SMART: recent updates, new developments and status in 2015

(2014) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Discovery of the Elusive Leptin in Birds: Identification of Several ‘Missing Links’ in the Evolution of Leptin and Its Receptor

(2014) Jeremy W. Prokop et al.   PLoS One

Genomic evidence for rod monochromacy in sloths and armadillos suggests early subterranean history for Xenarthra

(2014) C. A. Emerling et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

(2013) Richard M. Leggett et al.   BIOINFORMATICS

Clustered protocadherins

(2013) W. V. Chen et al.   DEVELOPMENT

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity

(2013) Shigehiro Kuraku et al.   NUCLEIC ACIDS RESEARCH

Chromatin organization and global regulation of Hox gene clusters

(2013) T. Montavon et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Rod Monochromacy and the Coevolution of Cetacean Retinal Opsins

(2013) Robert W. Meredith et al.   PLoS Genetics

A Fox stops the Wnt: implications for forebrain development and diseases

(2012) Catherine Danesin et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Horizontal Transfers of Tc1 Elements between Teleost Fishes and Their Vertebrate Parasites, Lampreys

(2012) Shigehiro Kuraku et al.   Genome Biology and Evolution

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

UCNEbase—a database of ultraconserved non-coding elements and genomic regulatory blocks

(2012) Slavica Dimitrieva et al.   NUCLEIC ACIDS RESEARCH

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A Natural Deletion of the HoxC Cluster in Elasmobranch Fishes

(2011) B. L. King et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Identification and characterization of visual pigments in caecilians (Amphibia: Gymnophiona), an order of limbless vertebrates with rudimentary eyes

(2010) S. M. Mohun et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Evolution of Hox Gene Clusters in Gnathostomes: Insights from a Survey of a Shark (Scyliorhinus canicula) Transcriptome

(2010) S. Oulion et al.   MOLECULAR BIOLOGY AND EVOLUTION

Leptin: The Weight-reducing Plasma Protein Encoded by the Obese Gene

(2010) George Wolf   NUTRITION REVIEWS

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

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

On the Origin and Evolution of Vertebrate Olfactory Receptor Genes: Comparative Genome Analysis Among 23 Chordate Species

(2009) Yoshihito Niimura   Genome Biology and Evolution

Into the blue: Gene duplication and loss underlie color vision adaptations in a deep-sea chimaera, the elephant shark Callorhinchus milii

(2009) W. L. Davies et al.   GENOME RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

A Conserved SET Domain Methyltransferase, Set11, Modifies Ribosomal Protein Rpl12 in Fission Yeast

(2008) Mahito Sadaie et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Timing of Genome Duplications Relative to the Origin of the Vertebrates: Did Cyclostomes Diverge before or after?

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

Hormones of the gut–brain axis as targets for the treatment of upper gastrointestinal disorders

(2008) Gareth J. Sanger et al.   NATURE REVIEWS DRUG DISCOVERY

The genetics of early telencephalon patterning: some assembly required

(2008) Jean M. Hébert et al.   NATURE REVIEWS NEUROSCIENCE

Elephant shark sequence reveals unique insights into the evolutionary history of vertebrate genes: A comparative analysis of the protocadherin cluster

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

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates

(2008) S. Yokoyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY