Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species’ Phenotypic and Genomic Differences

“Reverse Genomics” Predicts Function of Human Conserved Noncoding Elements

(2016) Amir Marcovitz et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of animal genomes

(2015) Casey W Dunn et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution

(2015) Prashanti Manda et al.   GENESIS

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

(2015) Richard C. Edmunds et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-cell analysis reveals transcriptional heterogeneity of neural progenitors in human cortex

(2015) Matthew B Johnson et al.   NATURE NEUROSCIENCE

Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies

(2015) T. Alexander Dececchi et al.   SYSTEMATIC BIOLOGY

Finding Our Way through Phenotypes

(2015) Andrew R. Deans et al.   PLOS BIOLOGY

The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets

(2015) Takaya Saito et al.   PLoS One

Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution

(2014) Melissa J Hubisz et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Light propagation in burrows of subterranean rodents: tunnel system architecture but not photoreceptor sensitivity limits light sensation range

(2014) O. Kott et al.   JOURNAL OF ZOOLOGY

Parallel Sites Implicate Functional Convergence of the Hearing Gene Prestin among Echolocating Mammals

(2014) Zhen Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Evidence for a single loss of mineralized teeth in the common avian ancestor

(2014) R. W. Meredith et al.   SCIENCE

Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax

(2014) Xiaodong Fang et al.   Nature Communications

Genomics and the Evolution of Phenotypic Traits

(2013) Gregory A. Wray   Annual Review of Ecology Evolution and Systematics

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Heterogeneous Models Place the Root of the Placental Mammal Phylogeny

(2013) Claire C. Morgan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals

(2013) Jonathan Romiguier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish

(2013) Michael Hiller et al.   NUCLEIC ACIDS RESEARCH

Many human accelerated regions are developmental enhancers

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

The Placental Mammal Ancestor and the Post-K-Pg Radiation of Placentals

(2013) M. A. O'Leary et al.   SCIENCE

A Recent Evolutionary Change Affects a Regulatory Element in the Human FOXP2 Gene

(2012) Tomislav Maricic et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hundreds of conserved non-coding genomic regions are independently lost in mammals

(2012) Michael Hiller et al.   NUCLEIC ACIDS RESEARCH

A “Forward Genomics” Approach Links Genotype to Phenotype using Independent Phenotypic Losses among Related Species

(2012) Michael Hiller et al.   Cell Reports

Parallel Evolution of Auditory Genes for Echolocation in Bats and Toothed Whales

(2012) Yong-Yi Shen et al.   PLoS Genetics

MorphoBank: phylophenomics in the “cloud”

(2011) Maureen A. O’Leary et al.   CLADISTICS

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

(2011) Cory Y. McLean et al.   NATURE

Genome sequencing reveals insights into physiology and longevity of the naked mole rat

(2011) Eun Bae Kim et al.   NATURE

Recent Loss of Vitamin C Biosynthesis Ability in Bats

(2011) Jie Cui et al.   PLoS One

Creating a Buzz About Insect Genomes

(2011) G. E. Robinson et al.   SCIENCE

Time to change how we describe biodiversity

(2011) Andrew R. Deans et al.   TRENDS IN ECOLOGY & EVOLUTION

Convergent sequence evolution between echolocating bats and dolphins

(2010) Yang Liu et al.   CURRENT BIOLOGY

Progressive Pseudogenization: Vitamin C Synthesis and Its Loss in Bats

(2010) Jie Cui et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature

(2010) Wasila M. Dahdul et al.   PLoS One

Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales

(2010) R. W. Meredith et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

A Humanized Version of Foxp2 Affects Cortico-Basal Ganglia Circuits in Mice

(2009) Wolfgang Enard et al.   CELL

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

The hearing gene Prestin reunites echolocating bats

(2008) G. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human-Specific Gain of Function in a Developmental Enhancer

(2008) S. Prabhakar et al.   SCIENCE

The Vestigial Olfactory Receptor Subgenome of Odontocete Whales: Phylogenetic Congruence between Gene-Tree Reconciliation and Supermatrix Methods

(2008) Michael R. McGowen et al.   SYSTEMATIC BIOLOGY

Loss of Egg Yolk Genes in Mammals and the Origin of Lactation and Placentation

(2008) David Brawand et al.   PLOS BIOLOGY