Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards

Immune genes are hotspots of shared positive selection across birds and mammals

(2019) Allison J Shultz et al.   eLife

Shared Ancient Sex Chromosomes in Varanids, Beaded Lizards, and Alligator Lizards

(2019) Michail Rovatsos et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chronic captopril treatment reveals the role of ANG II in cardiovascular function of embryonic American alligators (Alligator mississippiensis)

(2018) Casey A. Mueller et al.   JOURNAL OF COMPARATIVE PHYSIOLOGY B-BIOCHEMICAL SYSTEMIC AND ENVIRONMENTAL PHYSIOLOGY

Dynamic sex chromosomes in Old World chameleons (Squamata: Chamaeleonidae)

(2018) S. V. Nielsen et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Angiotensin II Signal Transduction: An Update on Mechanisms of Physiology and Pathophysiology

(2018) Steven J. Forrester et al.   PHYSIOLOGICAL REVIEWS

Identification of the sex-determining locus in grass puffer (Takifugu niphobles) provides evidence for sex-chromosome turnover in a subset of Takifugu species

(2018) Risa Ieda et al.   PLoS One

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

(2018) Stephen A. Smith et al.   PLoS One

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Sexual selection and the chemical signal design of lacertid lizards

(2017) Simon Baeckens et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

A Duplicated, Truncated amh Gene Is Involved in Male Sex Determination in an Old World Silverside

(2017) Dilip Kumar Bej et al.   G3-Genes Genomes Genetics

Enter the Dragon: The Dynamic and Multifunctional Evolution of Anguimorpha Lizard Venoms

(2017) Ivan Koludarov et al.   Toxins

Vomeronasal Receptors in Vertebrates and the Evolution of Pheromone Detection

(2017) Liliana Silva et al.   Annual Review of Animal Biosciences

Transcriptome analysis of the response of Burmese python to digestion

(2017) Jinjie Duan et al.   GigaScience

Contrasting origin of B chromosomes in two cervids (Siberian roe deer and grey brocket deer) unravelled by chromosome-specific DNA sequencing

(2016) Alexey I. Makunin et al.   BMC GENOMICS

First Description of the Karyotype and Sex Chromosomes in the Komodo Dragon (Varanus komodoensis)

(2016) Martina Johnson Pokorná et al.   CYTOGENETIC AND GENOME RESEARCH

Perm1 enhances mitochondrial biogenesis, oxidative capacity, and fatigue resistance in adult skeletal muscle

(2016) Yoshitake Cho et al.   FASEB JOURNAL

Evolutionary dynamics of Anolis sex chromosomes revealed by sequencing of flow sorting-derived microchromosome-specific DNA

(2016) Ilya G. Kichigin et al.   MOLECULAR GENETICS AND GENOMICS

Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species

(2016) Yuchi Zheng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Ecological allometries and niche use dynamics across Komodo dragon ontogeny

(2016) Deni Purwandana et al.   NATURWISSENSCHAFTEN

Giraffe genome sequence reveals clues to its unique morphology and physiology

(2016) Morris Agaba et al.   Nature Communications

Draft genome of the leopard gecko, Eublepharis macularius

(2016) Zijun Xiong et al.   GigaScience

Ecological allometries and niche use dynamics across Komodo dragon ontogeny

(2016) Deni Purwandana et al.   Science of Nature

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record

(2015) Allison Y Hsiang et al.   BMC EVOLUTIONARY BIOLOGY

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

Restriction Site-Associated DNA Sequencing (RAD-seq) Reveals an Extraordinary Number of Transitions among Gecko Sex-Determining Systems

(2015) Tony Gamble et al.   MOLECULAR BIOLOGY AND EVOLUTION

Do missing data influence the accuracy of divergence-time estimation with BEAST?

(2015) Yuchi Zheng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Exploring genome characteristics and sequence quality without a reference

(2014) Jared T. Simpson   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Cretaceous park of sex determination: sex chromosomes are conserved across iguanas

(2014) M. Rovatsos et al.   Biology Letters

CONSERVED SEX CHROMOSOMES ACROSS ADAPTIVELY RADIATEDANOLISLIZARDS

(2014) Michail Rovatsos et al.   EVOLUTION

Assignment of 2′-O-Methyltransferases to Modification Sites on the Mammalian Mitochondrial Large Subunit 16 S Ribosomal RNA (rRNA)

(2014) Ken-Wing Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Origins and functional evolution of Y chromosomes across mammals

(2014) Diego Cortez et al.   NATURE

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

(2014) R. E. Green et al.   SCIENCE

Integrative taxonomy and phylogeny-based species delimitation of Philippine water monitor lizards (Varanus salvator Complex) with descriptions of two new cryptic species

(2014) Luke J. Welton et al.   ZOOTAXA

Infernal 1.1: 100-fold faster RNA homology searches

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

Integration of molecules and new fossils supports a Triassic origin for Lepidosauria (lizards, snakes, and tuatara)

(2013) Marc EH Jones et al.   BMC EVOLUTIONARY BIOLOGY

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

(2013) R Pyron et al.   BMC EVOLUTIONARY BIOLOGY

Contrasted Evolution of the Vomeronasal Receptor Repertoires in Mammals and Squamate Reptiles

(2013) Urszula Brykczynska et al.   Genome Biology and Evolution

Peroxisome Proliferator-activated Receptor γ Coactivator 1 (PGC-1)- and Estrogen-related Receptor (ERR)-induced Regulator in Muscle 1 (PERM1) Is a Tissue-specific Regulator of Oxidative Capacity in Skeletal Muscle Cells

(2013) Yoshitake Cho et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

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

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

(2013) T. A. Castoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale phylogeny of chameleons suggests African origins and Eocene diversification

(2013) K. A. Tolley et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolution and development of the building plan of the vertebrate heart

(2012) Bjarke Jensen et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Molecular evidence for an Asian origin of monitor lizards followed by Tertiary dispersals to Africa and Australasia

(2012) N. Vidal et al.   Biology Letters

Emergence and evolution of the renin–angiotensin–aldosterone system

(2012) David Fournier et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

A Y-linked anti-Mullerian hormone duplication takes over a critical role in sex determination

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

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

EVOLUTION OF EXTREME BODY SIZE DISPARITY IN MONITOR LIZARDS (VARANUS)

(2011) David C. Collar et al.   EVOLUTION

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation

(2011) Ted M. Townsend et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Monitors cross the Red Sea: The biogeographic history of Varanus yemenensis

(2011) Daniel M. Portik et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The genome of the green anole lizard and a comparative analysis with birds and mammals

(2011) Jessica Alföldi et al.   NATURE

Evaluation of the gene encoding calcium and diacylglycerol regulated guanine nucleotide exchange factor I (CalDAG-GEFI) in human patients with congenital qualitative platelet disorders

(2011) John Puetz et al.   PLATELETS

Involvement of human ELAC2 gene product in 3' end processing of mitochondrial tRNAs

(2011) Lien K. Brzezniak et al.   RNA Biology

Fatty Acids Identified in the Burmese Python Promote Beneficial Cardiac Growth

(2011) C. A. Riquelme et al.   SCIENCE

Tandem evolution of diet and chemosensory responses in snakes

(2010) William Cooper   AMPHIBIA-REPTILIA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Dynamic Nucleotide Mutation Gradients and Control Region Usage in Squamate Reptile Mitochondrial Genomes

(2010) T.A. Castoe et al.   CYTOGENETIC AND GENOME RESEARCH

Regulation of Cellular Metabolism by Protein Lysine Acetylation

(2010) S. Zhao et al.   SCIENCE

Combining Phylogenomics and Fossils in Higher-Level Squamate Reptile Phylogeny: Molecular Data Change the Placement of Fossil Taxa

(2010) John J. Wiens et al.   SYSTEMATIC BIOLOGY

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

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

Elucidation of separate, but collaborative functions of the rRNA methyltransferase-related human mitochondrial transcription factors B1 and B2 in mitochondrial biogenesis reveals new insight into maternally inherited deafness

(2009) Justin Cotney et al.   HUMAN MOLECULAR GENETICS

Hidden support from unpromising data sets strongly unites snakes with anguimorph ‘lizards’

(2009) M. S. Y. LEE   JOURNAL OF EVOLUTIONARY BIOLOGY

Conservation phylogenetics of helodermatid lizards using multiple molecular markers and a supertree approach

(2009) Michael E. Douglas et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A central role for venom in predation by Varanus komodoensis (Komodo Dragon) and the extinct giant Varanus (Megalania) priscus

(2009) B. G. Fry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates

(2009) M. E. Alfaro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Likelihood Method for Assessing Molecular Divergence Time Estimates and the Placement of Fossil Calibrations

(2009) R. Alexander Pyron   SYSTEMATIC BIOLOGY

Phylogeny of sex-determining mechanisms in squamate reptiles: are sex chromosomes an evolutionary trap?

(2009) MARTINA POKORNÁ et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

RNase P without RNA: Identification and Functional Reconstitution of the Human Mitochondrial tRNA Processing Enzyme

(2008) Johann Holzmann et al.   CELL

Mitogenomic perspectives into iguanid phylogeny and biogeography: Gondwanan vicariance for the origin of Madagascan oplurines

(2008) Yasuhisa Okajima et al.   GENE

Requirements of SLP76 tyrosines in ITAM and integrin receptor signaling and in platelet function in vivo

(2008) Natalie A. Bezman et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Molecular evidence for a rapid late-Miocene radiation of Australasian venomous snakes (Elapidae, Colubroidea)

(2007) Kate L. Sanders et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION