Adaptive Evolution as a Predictor of Species-Specific Innate Immune Response

Differences in the repertoire, regulation and function of Toll-like Receptors and inflammasome-forming Nod-like Receptors between human and mouse

(2013) Juliana K Ariffin et al.   CURRENT OPINION IN MICROBIOLOGY

Structural dynamics flexibility informs function and evolution at a proteome scale

(2013) Zeynep Nevin Gerek et al.   Evolutionary Applications

Synthetic Biology of Phenotypic Adaptation in Vertebrates: The Next Frontier

(2013) S. Yokoyama   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for Polygenic Adaptation to Pathogens in the Human Genome

(2013) Josephine T. Daub et al.   MOLECULAR BIOLOGY AND EVOLUTION

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Genomic responses in mouse models poorly mimic human inflammatory diseases

(2013) Junhee Seok et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Consequence of Positive Selection Revealed through Rational Mutagenesis of Human Myeloperoxidase

(2012) Noeleen B. Loughran et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequence Evolution Correlates with Structural Dynamics

(2012) Ying Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Revising the human mutation rate: implications for understanding human evolution

(2012) Aylwyn Scally et al.   NATURE REVIEWS GENETICS

Measuring the distance between multiple sequence alignments

(2011) B. P. Blackburne et al.   BIOINFORMATICS

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Human-specific loss of regulatory DNA and the evolution of human-specific traits

(2011) Cory Y. McLean et al.   NATURE

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Revised age of late Neanderthal occupation and the end of the Middle Paleolithic in the northern Caucasus

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

The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans

(2011) L. Abi-Rached et al.   SCIENCE

Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations

(2011) Sudhir Kumar et al.   TRENDS IN GENETICS

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

RDP3: a flexible and fast computer program for analyzing recombination

(2010) D. P. Martin et al.   BIOINFORMATICS

Manipulation of Conformational Change in Proteins by Single-Residue Perturbations

(2010) C. Atilgan et al.   BIOPHYSICAL JOURNAL

Binding to complement factors and activation of the alternative pathway by Acanthamoeba

(2010) Wilawan Pumidonming et al.   IMMUNOBIOLOGY

Adaptation and Constraint at Toll-Like Receptors in Primates

(2010) G. Wlasiuk et al.   MOLECULAR BIOLOGY AND EVOLUTION

Statistical Properties of the Branch-Site Test of Positive Selection

(2010) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Antagonistic coevolution accelerates molecular evolution

(2010) Steve Paterson et al.   NATURE

Crucial role for human Toll-like receptor 4 in the development of contact allergy to nickel

(2010) Marc Schmidt et al.   NATURE IMMUNOLOGY

Genetic Evidence for High-Altitude Adaptation in Tibet

(2010) T. S. Simonson et al.   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment

(2009) Adrian Schneider et al.   Genome Biology and Evolution

Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes

(2009) D. Alvarez-Ponce et al.   GENOME RESEARCH

The Correlation of Evolutionary Rate with Pathway Position in Plant Terpenoid Biosynthesis

(2009) Heather Ramsay et al.   MOLECULAR BIOLOGY AND EVOLUTION

Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein

(2009) Canan Atilgan et al.   PLoS Computational Biology

InnateDB: facilitating systems-level analyses of the mammalian innate immune response

(2008) David J Lynn et al.   Molecular Systems Biology

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates

(2008) S. Yokoyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics