Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

Avian extinction at the end of the Cretaceous: Assessing the magnitude and subsequent explosive radiation

(2014) Alan Feduccia   CRETACEOUS RESEARCH

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

(2014) Daniel J. Field et al.   EVOLUTION & DEVELOPMENT

Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds

(2014) M. S. Y. Lee et al.   SCIENCE

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

(2014) E. D. Jarvis et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

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

(2014) M. S. Y. Lee et al.   SYSTEMATIC BIOLOGY

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

(2013) B. J. Raney et al.   BIOINFORMATICS

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

(2013) Glenn Hickey 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

Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator

(2013) Qiu-Hong Wan et al.   CELL RESEARCH

Evolutionary Origin of the Turtle Shell

(2013) Tyler R. Lyson et al.   CURRENT BIOLOGY

Making the Impossible Possible: Rooting the Tree of Placental Mammals

(2013) E. C. Teeling 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

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

(2013) Zhuo Wang et al.   NATURE GENETICS

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

(2013) Felipe C. Montefeltro et al.   NATURWISSENSCHAFTEN

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

(2013) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

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

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

(2013) F. J. Vonk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

(2013) H Bradley Shaffer et al.   GENOME BIOLOGY

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

(2012) N. G. Crawford et al.   Biology Letters

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

(2012) Ylenia Chiari et al.   BMC BIOLOGY

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

(2012) Yoshihito Niimura   CURRENT GENOMICS

Reappraisal of the morphology and phylogenetic relationships of the middle Eocene alligatoroidDiplocynodon deponiae(Frey, Laemmert, and Riess, 1987) based on a three-dimensional specimen

(2012) Massimo Delfino et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

A new species ofBorealosuchus(Crocodyliformes, Eusuchia) from the Late Cretaceous–early Paleogene of New Jersey

(2012) Christopher A. Brochu et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

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

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quantifying historical trends in the completeness of the fossil record and the contributing factors: an example using Aves

(2012) Daniel T. Ksepka et al.   PALEOBIOLOGY

The first ctenosauriscid (Reptilia: Archosauromorpha) from the Lower Triassic Of Eastern Europe

(2012) A. G. Sennikov   PALEONTOLOGICAL JOURNAL

A New Eusuchian Crocodyliform with Novel Cranial Integument and Its Significance for the Origin and Evolution of Crocodylia

(2012) Casey M. Holliday et al.   PLoS One

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

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

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

(2012) M. dos Reis et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Early eusuchia crocodylomorpha from the vertebrate-rich Plattenkalk of Pietraroia (Lower Albian, southern Apennines, Italy)

(2012) ANGELA D. BUSCALIONI et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Synthesizing and databasing fossil calibrations: divergence dating and beyond

(2011) D. T. Ksepka et al.   Biology Letters

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

(2011) Sterling J. Nesbitt et al.   Earth and Environmental Science Transactions of the Royal Society of Edinburgh

A TIME-CALIBRATED SPECIES TREE OF CROCODYLIA REVEALS A RECENT RADIATION OF THE TRUE CROCODILES

(2011) Jamie R. Oaks   EVOLUTION

Significant Selective Constraint at 4-Fold Degenerate Sites in the Avian Genome and Its Consequence for Detection of Positive Selection

(2011) Axel Künstner et al.   Genome Biology and Evolution

The Anolis Lizard Genome: An Amniote Genome without Isochores

(2011) Matthew K. Fujita et al.   Genome Biology and Evolution

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

(2011) J. E. McCormack et al.   GENOME RESEARCH

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

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

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

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

(2011) Jessica Alföldi et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

(2011) Jeremy E. Martin et al.   NEUES JAHRBUCH FUR GEOLOGIE UND PALAONTOLOGIE-ABHANDLUNGEN

A New Crocodylian from the Late Maastrichtian of Spain: Implications for the Initial Radiation of Crocodyloids

(2011) Eduardo Puértolas et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

The Sail-Backed Reptile Ctenosauriscus from the Latest Early Triassic of Germany and the Timing and Biogeography of the Early Archosaur Radiation

(2011) Richard J. Butler et al.   PLoS One

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

(2011) N. R. Longrich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) R. R. Reisz et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Best Practices for Justifying Fossil Calibrations

(2011) James F. Parham et al.   SYSTEMATIC BIOLOGY

Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles

(2011) Athanasia C Tzika et al.   EvoDevo

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

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

(2010) J. Huerta-Cepas et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Transitional fossils and the origin of turtles

(2010) T. R. Lyson et al.   Biology Letters

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

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

(2010) Y. Katsu et al.   CYTOGENETIC AND GENOME RESEARCH

Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes

(2010) J. Romiguier et al.   GENOME RESEARCH

AllodaposuchusNopsca, 1928 (Crocodylia, Eusuchia), from the Late Cretaceous of southern France and its relationships to Alligatoroidea

(2010) Jeremy E. Martin   JOURNAL OF VERTEBRATE PALEONTOLOGY

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

(2010) Ignacio Medina et al.   NUCLEIC ACIDS RESEARCH

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

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

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) S. L. Brusatte et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A comparison of reptilian and avian olfactory receptor gene repertoires: Species-specific expansion of group γ genes in birds

(2009) Silke S Steiger et al.   BMC GENOMICS

Exploring Repetitive DNA Landscapes Using REPCLASS, a Tool That Automates the Classification of Transposable Elements in Eukaryotic Genomes

(2009) Cédric Feschotte et al.   Genome Biology and Evolution

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

(2009) Yoshihito Niimura   Genome Biology and Evolution

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

(2009) R. Li et al.   GENOME RESEARCH

A new neosuchian crocodylomorph (Crocodyliformes, Mesoeucrocodylia) from the Early Cretaceous of north-east Brazil

(2009) DANIEL C. FORTIER et al.   PALAEONTOLOGY

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

(2009) H. Nishihara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles

(2009) Robert C. Thomson et al.   SYSTEMATIC BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) Amarendran R Subramanian et al.   Algorithms for Molecular Biology

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

(2008) A. Wehe et al.   BIOINFORMATICS

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

(2008) Mario Stanke et al.   BIOINFORMATICS

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Genome-wide nucleotide-level mammalian ancestor reconstruction

(2008) B. Paten et al.   GENOME RESEARCH

A complete skull ofAllodaposuchus precedensNopcsa, 1928 (Eusuchia) and a reassessment of the morphology of the taxon based on the Romanian remains

(2008) Massimo Delfino et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

A Multilocus Molecular Phylogeny of the Parrots (Psittaciformes): Support for a Gondwanan Origin during the Cretaceous

(2008) Timothy F. Wright et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome analysis of the platypus reveals unique signatures of evolution

(2008) Wesley C. Warren et al.   NATURE

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

(2008) Masatoshi Nei et al.   NATURE REVIEWS GENETICS

A new species ofAcynodon(Crocodylia) from the upper cretaceous (Santonian-Campanian) of Villaggio del Pescatore, Italy

(2008) MASSIMO DELFINO et al.   PALAEONTOLOGY

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

(2008) JEREMY E. MARTIN et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

The Impact of Recombination on Nucleotide Substitutions in the Human Genome

(2008) Laurent Duret et al.   PLoS Genetics

Large-scale assignment of orthology: back to phylogenetics?

(2008) Toni Gabaldón   GENOME BIOLOGY

Large-Scale Appearance of Ultraconserved Elements in Tetrapod Genomes and Slowdown of the Molecular Clock

(2007) S. Stephen et al.   MOLECULAR BIOLOGY AND EVOLUTION