Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences

Genomic Locations of Conserved Noncoding Sequences and Their Proximal Protein-Coding Genes in Mammalian Expression Dynamics

(2016) Isaac Adeyemi Babarinde et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tree of Life Reveals Clock-Like Speciation and Diversification

(2015) S. Blair Hedges et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Lineage-Specific Conserved Noncoding Sequences of Plant Genomes: Their Possible Role in Nucleosome Positioning

(2014) Nilmini Hettiarachchi et al.   Genome Biology and Evolution

Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution

(2014) B. A. Moyers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gibbon genome and the fast karyotype evolution of small apes

(2014) Lucia Carbone et al.   NATURE

8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage

(2014) Chris M. Rands et al.   PLoS Genetics

Heterogeneous Tempo and Mode of Conserved Noncoding Sequence Evolution among Four Mammalian Orders

(2013) Isaac Adeyemi Babarinde et al.   Genome Biology and Evolution

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Great ape genetic diversity and population history

(2013) Javier Prado-Martinez et al.   NATURE

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

New genes as drivers of phenotypic evolution

(2013) Sidi Chen et al.   NATURE REVIEWS GENETICS

1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans

(2013) Marc Pybus et al.   NUCLEIC ACIDS RESEARCH

TreeFam v9: a new website, more species and orthology-on-the-fly

(2013) Fabian Schreiber et al.   NUCLEIC ACIDS RESEARCH

From remote enhancers to gene regulation: charting the genome's regulatory landscapes

(2013) O. Symmons et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Drosophila Functional Elements Are Embedded in Structurally Constrained Sequences

(2013) Ephraim Kenigsberg et al.   PLoS Genetics

Problem solving in great apes (Pan paniscus, Pan troglodytes, Gorilla gorilla, and Pongo abelii): the effect of visual feedback

(2012) Christoph J. Völter et al.   ANIMAL COGNITION

Identification and Characterization of Lineage-Specific Highly Conserved Noncoding Sequences in Mammalian Genomes

(2012) M. Takahashi et al.   Genome Biology and Evolution

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

INSL4 Pseudogenes Help Define the Relaxin Family Repertoire in the Common Ancestor of Placental Mammals

(2012) José Ignacio Arroyo et al.   JOURNAL OF MOLECULAR EVOLUTION

Structure of a force-conveying cadherin bond essential for inner-ear mechanotransduction

(2012) Marcos Sotomayor et al.   NATURE

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

(2012) Michael Hiller et al.   NUCLEIC ACIDS RESEARCH

Dfam: a database of repetitive DNA based on profile hidden Markov models

(2012) Travis J. Wheeler et al.   NUCLEIC ACIDS RESEARCH

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

(2012) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Identification of Novel Cholesteatoma-Related Gene Expression Signatures Using Full-Genome Microarrays

(2012) Christin Klenke et al.   PLoS One

Assembly of an Evolutionarily New Pathway for  -Pyrone Biosynthesis in Arabidopsis

(2012) J.-K. Weng et al.   SCIENCE

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Frequent Recent Origination of Brain Genes Shaped the Evolution of Foraging Behavior in Drosophila

(2012) Sidi Chen et al.   Cell Reports

Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs

(2012) Chen Xie et al.   PLoS Genetics

Loss-of-Function Mutation in a Repressor Module of Human-Specifically Activated Enhancer HACNS1

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

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Deletion of a remote enhancer near ATOH7 disrupts retinal neurogenesis, causing NCRNA disease

(2011) Noor M Ghiasvand et al.   NATURE NEUROSCIENCE

Hypomethylated DSCR4 is a placenta-derived epigenetic marker for trisomy 21

(2011) Yingying Du et al.   PRENATAL DIAGNOSIS

MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data

(2010) Kirill Kryukov et al.   BMC BIOINFORMATICS

Human functional genetic studies are biased against the medically most relevant primate-specific genes

(2010) Lili Hao et al.   BMC EVOLUTIONARY BIOLOGY

Relaxed Purifying Selection and Possibly High Rate of Adaptation in Primate Lineage-Specific Genes

(2010) James J. Cai et al.   Genome Biology and Evolution

Reptiles and Mammals Have Differentially Retained Long Conserved Noncoding Sequences from the Amniote Ancestor

(2010) D.E. Janes et al.   Genome Biology and Evolution

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME 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

Gene regulation by nucleosome positioning

(2010) Lu Bai et al.   TRENDS IN GENETICS

Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome

(2010) Yong E. Zhang et al.   PLOS BIOLOGY

Cerebellum and Nonmotor Function

(2009) Peter L. Strick et al.   Annual Review of Neuroscience

A burst of segmental duplications in the genome of the African great ape ancestor

(2009) Tomas Marques-Bonet et al.   NATURE

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

The evolution of Fox genes and their role in development and disease

(2009) Sridhar Hannenhalli et al.   NATURE REVIEWS GENETICS

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

(2009) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Global discovery of primate-specific genes in the human genome

(2009) S.-K. Tay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

(2009) Y. I. Wolf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Y. F. Chan et al.   SCIENCE

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Association Between the Catechol-O-Methyltransferase Val158Met Polymorphism and Cocaine Dependence

(2008) Falk W Lohoff et al.   NEUROPSYCHOPHARMACOLOGY

DNA physical properties determine nucleosome occupancy from yeast to fly

(2008) Vincent Miele et al.   NUCLEIC ACIDS RESEARCH

Positive Selection in East Asians for an EDAR Allele that Enhances NF-κB Activation

(2008) Jarosław Bryk et al.   PLoS One

Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures

(2008) Ran Blekhman et al.   PLoS Genetics

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics