African lungfish genome sheds light on the vertebrate water-to-land transition

Giant lungfish genome elucidates the conquest of land by vertebrates

(2021) Axel Meyer et al.   NATURE

Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes

(2021) Xupeng Bi et al.   CELL

The Arms Race Between KRAB–Zinc Finger Proteins and Endogenous Retroelements and Its Impact on Mammals

(2019) Melania Bruno et al.   Annual Review of Genetics

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

NextPolish: a fast and efficient genome polishing tool for long-read assembly

(2019) Jiang Hu et al.   BIOINFORMATICS

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

Arfgef1 haploinsufficiency in mice alters neuronal endosome composition and decreases membrane surface postsynaptic GABAA receptors

(2019) JiaJie Teoh et al.   NEUROBIOLOGY OF DISEASE

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Mutations in the thyroid transcription factor gene NKX2-1 result in decreased expression of SFTPB and SFTPC

(2018) Stephanie J Attarian et al.   PEDIATRIC RESEARCH

A two-million-year-long hydroclimatic context for hominin evolution in southeastern Africa

(2018) Thibaut Caley et al.   NATURE

The axolotl genome and the evolution of key tissue formation regulators

(2018) Sergej Nowoshilow et al.   NATURE

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

IgSF9b regulates anxiety behaviors through effects on centromedial amygdala inhibitory synapses

(2018) Olga Babaev et al.   Nature Communications

Genetic conflicts: the usual suspects and beyond

(2017) Richard N. McLaughlin et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

(2017) Michaël Imbeault et al.   NATURE

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

(2017) Olga Dudchenko et al.   SCIENCE

Effect of Lung Surfactant Protein SP-C and SP-C-Promoted Membrane Fragmentation on Cholesterol Dynamics

(2016) Nuria Roldan et al.   BIOPHYSICAL JOURNAL

Macroevolution of genome size in sarcopterygians during the water–land transition

(2016) Chris Organ et al.   COMPTES RENDUS PALEVOL

Reiterative expression ofpax1directs pharyngeal pouch segmentation in medaka

(2016) Kazunori Okada et al.   DEVELOPMENT

Characterization of the isoforms of type IIb sodium-dependent phosphate cotransporter (Slc34a2) in yellow catfish, Pelteobagrus fulvidraco, and their vitamin D3-regulated expression under low-phosphate conditions

(2016) Pei Chen et al.   FISH PHYSIOLOGY AND BIOCHEMISTRY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) Yacine Kherdjemil et al.   NATURE

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

Growth hormone biases amygdala network activation after fear learning

(2016) B Gisabella et al.   Translational Psychiatry

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

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

The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land

(2016) Maria Assunta Biscotti et al.   Scientific Reports

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Characterizing and evaluating the expression of the type IIb sodium-dependent phosphate cotransporter (slc34a2) gene and its potential influence on phosphorus utilization efficiency in yellow catfish (Pelteobagrus fulvidraco)

(2015) Pei Chen et al.   FISH PHYSIOLOGY AND BIOCHEMISTRY

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

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

Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection

(2015) Martin D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation

(2015) Yaping Wang et al.   NATURE GENETICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Nasal Application of Neuropeptide S Inhibits Arthritis Pain-Related Behaviors through an Action in the Amygdala

(2014) Georgina Medina et al.   Molecular Pain

A functional variant in the neuropeptide S receptor 1 gene moderates the influence of urban upbringing on stress processing in the amygdala

(2014) Fabian Streit et al.   STRESS-THE INTERNATIONAL JOURNAL ON THE BIOLOGY OF STRESS

Vertebrate Land Invasions-Past, Present, and Future: An Introduction to the Symposium

(2013) M. A. Ashley-Ross et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

The adhesion protein IgSF9b is coupled to neuroligin 2 via S-SCAM to promote inhibitory synapse development

(2013) Jooyeon Woo et al.   JOURNAL OF CELL BIOLOGY

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

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

The African coelacanth genome provides insights into tetrapod evolution

(2013) Chris T. Amemiya et al.   NATURE

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Loss of Semaphorin-Neuropilin-1 Signaling Causes Dysmorphic Vascularization Reminiscent of Alveolar Capillary Dysplasia

(2012) Stephen Joza et al.   AMERICAN JOURNAL OF PATHOLOGY

ANGES: reconstructing ANcestral GEnomeS maps

(2012) B. R. Jones et al.   BIOINFORMATICS

“Limbic associative” and “autonomic” amygdala in teleosts: A review of the evidence

(2012) Caio Maximino et al.   JOURNAL OF CHEMICAL NEUROANATOMY

Evolution of the Australian Lungfish (Neoceratodus forsteri) Genome: A Major Role for CR1 and L2 LINE Elements

(2012) C. J. Metcalfe et al.   MOLECULAR BIOLOGY AND EVOLUTION

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Chondrichthyan-like scales from the Middle Ordovician of Australia

(2012) IVAN J. SANSOM et al.   PALAEONTOLOGY

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

The earliest known stem-tetrapod from the Lower Devonian of China

(2012) Jing Lu et al.   Nature Communications

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Neuropeptide-S (NPS) Receptor Genotype Modulates Basolateral Amygdala Responsiveness to Aversive Stimuli

(2011) Udo Dannlowski et al.   NEUROPSYCHOPHARMACOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Non-syndromic Oligodontia with a Novel Mutation of PAX9

(2010) N. Suda et al.   JOURNAL OF DENTAL RESEARCH

Loss of fish actinotrichia proteins and the fin-to-limb transition

(2010) Jing Zhang et al.   NATURE

The Genome of the Western Clawed Frog Xenopus tropicalis

(2010) U. Hellsten et al.   SCIENCE

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

A new tooth-plated lungfish from the Middle Devonian of Yunnan, China, and its phylogenetic relationships

(2009) Tuo Qiao et al.   ACTA ZOOLOGICA

The Fin to Limb Transition: New Data, Interpretations, and Hypotheses from Paleontology and Developmental Biology

(2009) Jennifer A. Clack   Annual Review of Earth and Planetary Sciences

Pulmonary Surfactant Protein SP-C Counteracts the Deleterious Effects of Cholesterol on the Activity of Surfactant Films under Physiologically Relevant Compression-Expansion Dynamics

(2009) Leticia Gómez-Gil et al.   BIOPHYSICAL JOURNAL

Telencephalic Organization in the Spotted African Lungfish, Protopterus dolloi: A New Cytological Model

(2009) R. Glenn Northcutt   BRAIN BEHAVIOR AND EVOLUTION

An Immunohistochemical Approach to Lungfish Telencephalic Organization

(2009) Agustín González et al.   BRAIN BEHAVIOR AND EVOLUTION

Molecular genetics of tooth development

(2009) Marianna Bei   CURRENT OPINION IN GENETICS & DEVELOPMENT

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

The oldest articulated osteichthyan reveals mosaic gnathostome characters

(2009) Min Zhu et al.   NATURE

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

(2008) Brian J Haas et al.   GENOME BIOLOGY