Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain

Soft Shoulders Ahead: Spurious Signatures of Soft and Partial Selective Sweeps Result from Linked Hard Sweeps

(2015) D. R. Schrider et al.   GENETICS

A method for calculating probabilities of fitness consequences for point mutations across the human genome

(2015) Brad Gulko et al.   NATURE GENETICS

Discovering Functional DNA Elements Using Population Genomic Information: A Proof of Concept Using Human mtDNA

(2014) Daniel R. Schrider et al.   Genome Biology and Evolution

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

(2013) Justin Cotney et al.   CELL

A Study of GluK1 Kainate Receptor Polymorphisms in Down Syndrome Reveals Allelic Non-Disjunction at 1173(C/T)

(2013) Debarati Ghosh et al.   DISEASE MARKERS

Learning Natural Selection from the Site Frequency Spectrum

(2013) R. Ronen et al.   GENETICS

On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

(2013) D. Graur et al.   Genome Biology and Evolution

A Homozygous Deletion in GRID2 Causes a Human Phenotype With Cerebellar Ataxia and Atrophy

(2013) G. Eda Utine et al.   JOURNAL OF CHILD NEUROLOGY

A Scan for Human-Specific Relaxation of Negative Selection Reveals Unexpected Polymorphism in Proteasome Genes

(2013) Mehmet Somel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Deletions in GRID2 lead to a recessive syndrome of cerebellar ataxia and tonic upgaze in humans

(2013) L. B. Hills et al.   NEUROLOGY

Comment on "Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions"

(2013) P. Green et al.   SCIENCE

Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees

(2013) E. M. Leffler et al.   SCIENCE

Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques

(2012) X. Liu et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Current relaxation of selection on the human genome: Tolerance of deleterious mutations on olfactory receptors

(2012) Denis Pierron et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012)   NATURE

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions

(2012) L. D. Ward et al.   SCIENCE

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Accurate and comprehensive sequencing of personal genomes

(2011) S. S. Ajay et al.   GENOME RESEARCH

The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome

(2011) D. Kostka et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2011) Cory Y. McLean et al.   NATURE

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Classic Selective Sweeps Were Rare in Recent Human Evolution

(2011) R. D. Hernandez et al.   SCIENCE

Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome

(2011) Kirk E. Lohmueller et al.   PLoS Genetics

Distinguishing Positive Selection From Neutral Evolution: Boosting the Performance of Summary Statistics

(2010) K. Lin et al.   GENETICS

Searching for Footprints of Positive Selection in Whole-Genome SNP Data From Nonequilibrium Populations

(2010) P. Pavlidis et al.   GENETICS

Fine-scale recombination rate differences between sexes, populations and individuals

(2010) Augustine Kong et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

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 de novo 8.8-Mb deletion of 21q21.1-q21.3 in an autistic male with a complex rearrangement involving chromosomes 6, 10, and 21

(2009) Chad R. Haldeman-Englert et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Recent de novo origin of human protein-coding genes

(2009) D. G. Knowles et al.   GENOME RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

All Human-Specific Gene Losses Are Present in the Genome as Pseudogenes

(2009) Daniel R. Schrider et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Overlapping Function of Lmx1a and Lmx1b in Anterior Hindbrain Roof Plate Formation and Cerebellar Growth

(2009) Y. Mishima et al.   JOURNAL OF NEUROSCIENCE

Correcting the Site Frequency Spectrum for Divergence-Based Ascertainment

(2009) Andrew D. Kern   PLoS One

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread Genomic Signatures of Natural Selection in Hominid Evolution

(2009) Graham McVicker et al.   PLoS Genetics

Hyperglycosylation and Reduced GABA Currents of Mutated GABRB3 Polypeptide in Remitting Childhood Absence Epilepsy

(2008) Miyabi Tanaka et al.   AMERICAN JOURNAL OF HUMAN GENETICS

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome

(2008) Adam R. Boyko et al.   PLoS Genetics