Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

Punctuated Evolution of Prostate Cancer Genomes

(2013) Sylvan C. Baca et al.   CELL

Identifying Recent Adaptations in Large-Scale Genomic Data

(2013) Sharon R. Grossman et al.   CELL

TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal

(2013) P. J. Killela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TERT Promoter Mutations in Familial and Sporadic Melanoma

(2013) S. Horn et al.   SCIENCE

Highly Recurrent TERT Promoter Mutations in Human Melanoma

(2013) F. W. Huang et al.   SCIENCE

Interpretation of Genomic Variants Using a Unified Biological Network Approach

(2013) Ekta Khurana et al.   PLoS Computational Biology

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

(2012) Lukas Habegger et al.   BIOINFORMATICS

HINT: High-quality protein interactomes and their applications in understanding human disease

(2012) Jishnu Das et al.   BMC Systems Biology

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations

(2012) Tobias Rausch et al.   CELL

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Personal and population genomics of human regulatory variation

(2012) B. Vernot et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

The mutational landscape of lethal castration-resistant prostate cancer

(2012) Catherine S. Grasso et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

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

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer

(2012) Christopher E Barbieri et al.   NATURE GENETICS

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma

(2012) Michael Krauthammer et al.   NATURE GENETICS

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

(2012) L. D. Ward et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

Subsampling methods for genomic inference

(2011) Peter J. Bickel et al.   Annals of Applied Statistics

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

(2011) Wing Chung Wong et al.   BIOINFORMATICS

AlleleSeq: analysis of allele-specific expression and binding in a network framework

(2011) J. Rozowsky et al.   Molecular Systems Biology

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

The genomic complexity of primary human prostate cancer

(2011) Michael F. Berger et al.   NATURE

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project

(2011) Xinmeng Jasmine Mu et al.   NUCLEIC ACIDS RESEARCH

Demographic history and rare allele sharing among human populations

(2011) S. Gravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Classic Selective Sweeps Were Rare in Recent Human Evolution

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

Molecular Characterization of Neuroendocrine Prostate Cancer and Identification of New Drug Targets

(2011) H. Beltran et al.   Cancer Discovery

Rare and Common Regulatory Variation in Population-Scale Sequenced Human Genomes

(2011) Stephen B. Montgomery et al.   PLoS Genetics

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries

(2010) Lukas Habegger et al.   BIOINFORMATICS

Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice

(2010) Axel Visel et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

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

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

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates

(2010) Zhengdong D Zhang et al.   GENOME BIOLOGY

Population Differentiation as an Indicator of Recent Positive Selection in Humans: An Empirical Evaluation

(2009) Y. Xue et al.   GENETICS

Analytical methods for inferring functional effects of single base pair substitutions in human cancers

(2009) William Lee et al.   HUMAN GENETICS

Edgetic perturbation models of human inherited disorders

(2009) Quan Zhong et al.   Molecular Systems Biology

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

(2009) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

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

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

The Human Gene Mutation Database: 2008 update

(2009) Peter D Stenson et al.   Genome Medicine

The promise and reality of personal genomics

(2009) Bryndis Yngvadottir et al.   GENOME BIOLOGY

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Natural Selection on Genes that Underlie Human Disease Susceptibility

(2008) Ran Blekhman et al.   CURRENT BIOLOGY

Fast and flexible simulation of DNA sequence data

(2008) G. K. Chen et al.   GENOME RESEARCH

Natural selection has driven population differentiation in modern humans

(2008) Luis B Barreiro et al.   NATURE GENETICS

DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes

(2008) R. Zhang et al.   NUCLEIC ACIDS RESEARCH

Null mutations in human and mouse orthologs frequently result in different phenotypes

(2008) B.-Y. Liao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE