Convergent regulatory evolution and loss of flight in paleognathous birds

DNA fragility in the parallel evolution of pelvic reduction in stickleback fish

(2019) Kathleen T. Xie et al.   SCIENCE

Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees

(2019) Zhirui Hu et al.   MOLECULAR BIOLOGY AND EVOLUTION

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages

(2018) Dennis Kostka et al.   MOLECULAR BIOLOGY AND EVOLUTION

A genomics approach reveals insights into the importance of gene losses for mammalian adaptations

(2018) Virag Sharma et al.   Nature Communications

Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals

(2018) Mark J Berger et al.   NUCLEIC ACIDS RESEARCH

Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals

(2018) Wynn K. Meyer et al.   SCIENCE

Genome-Wide Convergence during Evolution of Mangroves from Woody Plants

(2017) Shaohua Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird ( Aepyornis sp.) eggshell

(2017) Alicia Grealy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A genetic signature of the evolution of loss of flight in the Galapagos cormorant

(2017) Alejandro Burga et al.   SCIENCE

Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics

(2017) Scott V. Edwards et al.   SYSTEMATIC BIOLOGY

Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features

(2017) Ryohei Seki et al.   Nature Communications

Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling

(2017) Raghavendran Partha et al.   eLife

A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes

(2016) Nicole E. Wheeler et al.   BIOINFORMATICS

The Anatomy and Taxonomy of the Exquisitely Preserved Green River Formation (Early Eocene) Lithornithids (Aves) and the Relationships of Lithornithidae

(2016) Sterling J. Nesbitt et al.   BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY

Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals

(2016) Maria Chikina et al.   MOLECULAR BIOLOGY AND EVOLUTION

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Causes of molecular convergence and parallelism in protein evolution

(2016) Jay F. Storz   NATURE REVIEWS GENETICS

Convergent local adaptation to climate in distantly related conifers

(2016) S. Yeaman et al.   SCIENCE

Gene Tree Discordance Causes Apparent Substitution Rate Variation

(2016) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus

(2016) Betty M. Booker et al.   PLoS Genetics

ExaML version 3: a tool for phylogenomic analyses on supercomputers

(2015) Alexey M. Kozlov et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

A shift in anterior–posterior positional information underlies the fin-to-limb evolution

(2015) Koh Onimaru et al.   eLife

Kiwi genome provides insights into evolution of a nocturnal lifestyle

(2015) Diana Le Duc et al.   GENOME BIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Formation of Proximal and Anterior Limb Skeleton Requires Early Function of Irx3 and Irx5 and Is Negatively Regulated by Shh Signaling

(2014) Danyi Li et al.   DEVELOPMENTAL CELL

Genomic Support for a Moa–Tinamou Clade and Adaptive Morphological Convergence in Flightless Ratites

(2014) Allan J. Baker et al.   MOLECULAR BIOLOGY AND EVOLUTION

RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

(2014) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

Patterning and post-patterning modes of evolutionary digit loss in mammals

(2014) Kimberly L. Cooper et al.   NATURE

Regulatory modulation of the T-box geneTbx5links development, evolution, and adaptation of the sternum

(2014) Sorrel R. B. Bickley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep conservation of wrist and digit enhancers in fish

(2014) Andrew R. Gehrke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

(2014) R. E. Green et al.   SCIENCE

Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution

(2014) K. J. Mitchell 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

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

(2013) Glenn Hickey et al.   BIOINFORMATICS

GAT: a simulation framework for testing the association of genomic intervals

(2013) A. Heger et al.   BIOINFORMATICS

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

THE LOCI OF REPEATED EVOLUTION: A CATALOG OF GENETIC HOTSPOTS OF PHENOTYPIC VARIATION

(2013) Arnaud Martin et al.   EVOLUTION

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

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

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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 genetic causes of convergent evolution

(2013) David L. Stern   NATURE REVIEWS GENETICS

Many human accelerated regions are developmental enhancers

(2013) J. A. Capra et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs

(2013) Adrian M. Altenhoff et al.   PLoS One

Sex-biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution

(2013) B. Vicoso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Parallel Molecular Evolution in an Herbivore Community

(2012) Y. Zhen et al.   SCIENCE

Evolution of a tissue-specific silencer underlies divergence in the expression of pax2 and pax8 paralogues

(2012) Haruki Ochi et al.   Nature Communications

Setting the stage – Building and working in an ancient DNA laboratory

(2011) Michael Knapp et al.   ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

CONVERGENCE, ADAPTATION, AND CONSTRAINT

(2011) Jonathan B. Losos   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

Neurofibromin (Nf1) is required for skeletal muscle development

(2011) Nadine Kossler et al.   HUMAN MOLECULAR GENETICS

A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection

(2011) Sergei L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

PHAST and RPHAST: phylogenetic analysis with space/time models

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

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

TEAD Transcription Factors Mediate the Function of TAZ in Cell Growth and Epithelial-Mesenchymal Transition

(2009) Heng Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Regulating Evolution

(2009) Sean B. Carroll et al.   SCIENTIFIC AMERICAN

Tinamous and Moa Flock Together: Mitochondrial Genome Sequence Analysis Reveals Independent Losses of Flight among Ratites

(2009) Matthew J. Phillips et al.   SYSTEMATIC BIOLOGY

Congenic method in the chick limb buds by electroporation

(2008) Takayuki Suzuki et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

TEAD mediates YAP-dependent gene induction and growth control

(2008) B. Zhao et al.   GENES & DEVELOPMENT

PHYLOGENY AND EVOLUTION OF THE RATITE BIRDS

(2008) Joel Cracraft   IBIS

Redundant Roles of Tead1 and Tead2 in Notochord Development and the Regulation of Cell Proliferation and Survival

(2008) A. Sawada et al.   MOLECULAR AND CELLULAR BIOLOGY

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

(2008) Axel Visel et al.   NATURE GENETICS

Phylogenomic evidence for multiple losses of flight in ratite birds

(2008) J. Harshman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA