4.8 Article

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

Brian J. Raney et al.

BIOINFORMATICS (2014)

Article Evolutionary Biology

Selecting optimal partitioning schemes for phylogenomic datasets

Robert Lanfear et al.

BMC EVOLUTIONARY BIOLOGY (2014)

Article Evolutionary Biology

Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles

Daniel J. Field et al.

EVOLUTION & DEVELOPMENT (2014)

Article Biochemistry & Molecular Biology

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

Jaime Huerta-Cepas et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds

Michael S. Y. Lee et al.

SCIENCE (2014)

Article Multidisciplinary Sciences

Whole-genome analyses resolve early branches in the tree of life of modern birds

Erich D. Jarvis et al.

SCIENCE (2014)

Article Multidisciplinary Sciences

Comparative genomics reveals insights into avian genome evolution and adaptation

Guojie Zhang et al.

SCIENCE (2014)

Article Evolutionary Biology

Morphological Clocks in Paleontology, and a Mid-Cretaceous Origin of Crown Aves

Michael S. Y. Lee et al.

SYSTEMATIC BIOLOGY (2014)

Article Biochemical Research Methods

HAL: a hierarchical format for storing and analyzing multiple genome alignments

Glenn Hickey et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Evolutionary Origin of the Turtle Shell

Tyler R. Lyson et al.

CURRENT BIOLOGY (2013)

Editorial Material Biochemistry & Molecular Biology

Making the Impossible Possible: Rooting the Tree of Placental Mammals

Emma C. Teeling et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemistry & Molecular Biology

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

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Multidisciplinary Sciences

A new neosuchian with Asian affinities from the Jurassic of northeastern Brazil

Felipe C. Montefeltro et al.

NATURWISSENSCHAFTEN (2013)

Article Multidisciplinary Sciences

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

Todd A. Castoe et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

Freek J. Vonk et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biotechnology & Applied Microbiology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Daehwan Kim et al.

GENOME BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Olfactory Receptor Multigene Family in Vertebrates: From the Viewpoint of Evolutionary Genomics

Yoshihito Niimura

CURRENT GENOMICS (2012)

Article Paleontology

A NEW SPECIES OF BOREALOSUCHUS (CROCODYLIFORMES, EUSUCHIA) FROM THE LATE CRETACEOUS-EARLY PALEOGENE OF NEW JERSEY

Christopher A. Brochu et al.

JOURNAL OF VERTEBRATE PALEONTOLOGY (2012)

Article Biochemistry & Molecular Biology

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

Robert Lanfear et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Article Multidisciplinary Sciences

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

Sen Song et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biology

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

Mario dos Reis et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2012)

Article Evolutionary Biology

Best Practices for Justifying Fossil Calibrations

James F. Parham et al.

SYSTEMATIC BIOLOGY (2012)

Article Evolutionary Biology

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

Brant C. Faircloth et al.

SYSTEMATIC BIOLOGY (2012)

Article Biochemical Research Methods

Assigning duplication events to relative temporal scales in genome-wide studies

Jaime Huerta-Cepas et al.

BIOINFORMATICS (2011)

Editorial Material Biology

Synthesizing and databasing fossil calibrations: divergence dating and beyond

Daniel T. Ksepka et al.

BIOLOGY LETTERS (2011)

Article Biochemical Research Methods

PHAST and RPHAST: phylogenetic analysis with space/time models

Melissa J. Hubisz et al.

BRIEFINGS IN BIOINFORMATICS (2011)

Article Evolutionary Biology

The Anolis Lizard Genome: An Amniote Genome without Isochores

Matthew K. Fujita et al.

GENOME BIOLOGY AND EVOLUTION (2011)

Article Biochemistry & Molecular Biology

Cactus: Algorithms for genome multiple sequence alignment

Benedict Paten et al.

GENOME RESEARCH (2011)

Article Biochemistry & Molecular Biology

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

Koichiro Tamura et al.

MOLECULAR BIOLOGY AND EVOLUTION (2011)

Article Multidisciplinary Sciences

Inference of human population history from individual whole-genome sequences

Heng Li et al.

NATURE (2011)

Article Multidisciplinary Sciences

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

Jessica Alfoeldi et al.

NATURE (2011)

Article Biotechnology & Applied Microbiology

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

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Article Paleontology

Taxonomic clarification of Diplocynodon POMEL, 1847 (Crocodilia) from the Miocene of Styria, Austria

Jeremy E. Martin et al.

NEUES JAHRBUCH FUR GEOLOGIE UND PALAONTOLOGIE-ABHANDLUNGEN (2011)

Article Multidisciplinary Sciences

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

Fran Supek et al.

PLOS ONE (2011)

Article Multidisciplinary Sciences

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

Sante Gnerre et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Mass extinction of birds at the Cretaceous-Paleogene (K-Pg) boundary

Nicholas R. Longrich et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biology

Footprints pull origin and diversification of dinosaur stem lineage deep into Early Triassic

Stephen L. Brusatte et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2011)

Article Biology

A new Early Permian reptile and its significance in early diapsid evolution

Robert R. Reisz et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2011)

Article Biochemical Research Methods

Accelerated Profile HMM Searches

Sean R. Eddy

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Geosciences, Multidisciplinary

Reconstruction of a continuous high-resolution CO2 record over the past 20 million years

R. S. W. van de Wal et al.

CLIMATE OF THE PAST (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biology

Transitional fossils and the origin of turtles

Tyler R. Lyson et al.

BIOLOGY LETTERS (2010)

Article Biochemical Research Methods

ETE: a python Environment for Tree Exploration

Jaime Huerta-Cepas et al.

BMC BIOINFORMATICS (2010)

Article Geosciences, Multidisciplinary

A sail-backed suchian from the Heshanggou Formation (Early Triassic: Olenekian) of China

Sterling J. Nesbitt et al.

EARTH AND ENVIRONMENTAL SCIENCE TRANSACTIONS OF THE ROYAL SOCIETY OF EDINBURGH (2010)

Article Biochemistry & Molecular Biology

De novo assembly of human genomes with massively parallel short read sequencing

Ruiqiang Li et al.

GENOME RESEARCH (2010)

Article Multidisciplinary Sciences

The genome of a songbird

Wesley C. Warren et al.

NATURE (2010)

Article Biochemical Research Methods

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

Salvador Capella-Gutierrez et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Cell Biology

From Reptilian Phylogenomics to Reptilian Genomes: Analyses of c-Jun and DJ-1 Proto-Oncogenes

Y. Katsu et al.

CYTOGENETIC AND GENOME RESEARCH (2009)

Article Multidisciplinary Sciences

Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals

Hidenori Nishihara et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biotechnology & Applied Microbiology

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

Ben Langmead et al.

GENOME BIOLOGY (2009)

Article Biochemical Research Methods

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

Amarendran R. Subramanian et al.

ALGORITHMS FOR MOLECULAR BIOLOGY (2008)

Article Biochemical Research Methods

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony

Andre Wehe et al.

BIOINFORMATICS (2008)

Article Biochemical Research Methods

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

Mario Stanke et al.

BIOINFORMATICS (2008)

Article Biochemical Research Methods

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

David Ellinghaus et al.

BMC BIOINFORMATICS (2008)

Review Biochemical Research Methods

Recent developments in the MAFFT multiple sequence alignment program

Kazutaka Katoh et al.

BRIEFINGS IN BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

Genome-wide nucleotide-level mammalian ancestor reconstruction

Benedict Paten et al.

GENOME RESEARCH (2008)

Review Biochemistry & Molecular Biology

A multilocus molecular phylogeny of the parrots (Psittaciformes): Support for a Gondwanan origin during the Cretaceous

Timothy F. Wright et al.

MOLECULAR BIOLOGY AND EVOLUTION (2008)

Article Biochemistry & Molecular Biology

Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock

Stuart Stephen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2008)

Article Multidisciplinary Sciences

Genome analysis of the platypus reveals unique signatures of evolution

Wesley C. Warren et al.

NATURE (2008)

Review Genetics & Heredity

The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity

Masatoshi Nei et al.

NATURE REVIEWS GENETICS (2008)

Article Zoology

Crocodilus affuvelensis Matheron, 1869 from the Late Cretaceous of southern France:: a reassessment

Jeremy E. Martin et al.

ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY (2008)

Article Genetics & Heredity

The impact of recombination on nucleotide substitutions in the human genome

Laurent Duret et al.

PLOS GENETICS (2008)

Review Biotechnology & Applied Microbiology

Large-scale assignment of orthology: back to phylogenetics?

Toni Gabaldon

GENOME BIOLOGY (2008)

Article Biochemistry & Molecular Biology

PhylomeDB: a database for genome-wide collections of gene phylogenies

Jaime Huerta-Cepas et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Multidisciplinary Sciences

Extensive Gains and Losses of Olfactory Receptor Genes in Mammalian Evolution

Yoshihito Niimura et al.

PLOS ONE (2007)

Article Biochemistry & Molecular Biology

Heads or tails: A simple reliability check for multiple sequence alignments

Giddy Landan et al.

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Multidisciplinary Sciences

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genorne

Andrew M. Shedlock et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Paleontology

First report on a new basal eusuchian crocodyliform with multicusped teeth from the Upper Cretaceous (Santonian) of Hungary

Attila Osi et al.

NEUES JAHRBUCH FUR GEOLOGIE UND PALAONTOLOGIE-ABHANDLUNGEN (2007)

Review Biochemistry & Molecular Biology

Paleontological evidence to date the tree of life

Michael J. Benton et al.

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biochemical Research Methods

RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Alexandros Stamatakis

BIOINFORMATICS (2006)

Article Biochemical Research Methods

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor

Oleksiy Kohany et al.

BMC BIOINFORMATICS (2006)

Article Biology

The origin of modern crocodyliforms: new evidence from the Cretaceous of Australia

Steven W. Salisbury et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2006)

Review Genetics & Heredity

Hearing silence: non-neutral evolution at synonymous sites in mammals

JV Chamary et al.

NATURE REVIEWS GENETICS (2006)

Article Biochemistry & Molecular Biology

M-Coffee: combining multiple sequence alignment methods with T-Coffee

IM Wallace et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Evolutionary Biology

Efficient likelihood computations with nonreversible models of evolution

Bastien Boussau et al.

SYSTEMATIC BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

A Siepel et al.

GENOME RESEARCH (2005)

Article Biochemical Research Methods

De novo identification of repeat families in large genomes

AL Price et al.

BIOINFORMATICS (2005)

Article Biochemical Research Methods

PILER: identification and classification of genomic repeats

RC Edgar et al.

BIOINFORMATICS (2005)

Article Multidisciplinary Sciences

Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods

Y Niimura et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Multidisciplinary Sciences

The rate of DNA evolution: Effects of body size and temperature on the molecular clock

JF Gillooly et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Multidisciplinary Sciences

Definitive fossil evidence for the extant avian radiation in the Cretaceous

JA Clarke et al.

NATURE (2005)

Article Multidisciplinary Sciences

The rate of DNA evolution: Effects of body size and temperature on the molecular clock

JF Gillooly et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemistry & Molecular Biology

MAFFT version 5: improvement in accuracy of multiple sequence alignment

K Katoh et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Ecology

Effects of body size and temperature on population growth

VM Savage et al.

AMERICAN NATURALIST (2004)

Article Biochemical Research Methods

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

RC Edgar

BMC BIOINFORMATICS (2004)

Article Multidisciplinary Sciences

Phylogeny and diversification of the largest avian radiation

FK Barker et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biochemistry & Molecular Biology

Reconstructing large regions of an ancestral mammalian genome in silico

M Blanchette et al.

GENOME RESEARCH (2004)

Article Multidisciplinary Sciences

Ultraconserved elements in the human genome

G Bejerano et al.

SCIENCE (2004)

Article Biotechnology & Applied Microbiology

Versatile and open software for comparing large genomes

S Kurtz et al.

GENOME BIOLOGY (2004)

Article Evolutionary Biology

True and false gharials: A nuclear gene phylogeny of Crocodylia

J Harshman et al.

SYSTEMATIC BIOLOGY (2003)

Review Evolutionary Biology

Combined support for wholesale taxic atavism in gavialine crocodylians

J Gatesy et al.

SYSTEMATIC BIOLOGY (2003)

Article Biochemistry & Molecular Biology

Estimation of divergence times for major lineages of primate species

GV Glazko et al.

MOLECULAR BIOLOGY AND EVOLUTION (2003)

Review Multidisciplinary Sciences

Initial sequencing and comparative analysis of the mouse genome

RH Waterston et al.

NATURE (2002)

Article Biochemistry & Molecular Biology

Automated de novo identification of repeat sequence families in sequenced genomes

ZR Bao et al.

GENOME RESEARCH (2002)

Article Biochemical Research Methods

CONSEL: for assessing the confidence of phylogenetic tree selection

H Shimodaira et al.

BIOINFORMATICS (2001)

Letter Biochemistry & Molecular Biology

Local rates of recombination are positively correlated with GC content in the human genome

SM Fullerton et al.

MOLECULAR BIOLOGY AND EVOLUTION (2001)

Review Multidisciplinary Sciences

Initial sequencing and analysis of the human genome

ES Lander et al.

NATURE (2001)

Article Biochemistry & Molecular Biology

A phylogenomic approach to microbial evolution

T Sicheritz-Pontén et al.

NUCLEIC ACIDS RESEARCH (2001)