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

No abstract is available for this paper.

• Publication year

  2013

• Venue

  Science

• Publication date

  2013-10-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1126/science.1235587PMID 24092746PMCID PMC3947637
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Punctuated evolution of prostate cancer genomes.

  2013cited by this paper
• TERT Promoter Mutations in Familial and Sporadic Melanoma

  2013cited by this paper
• Identifying recent adaptations in large-scale genomic data.

  2013cited by this paper
• Interpretation of Genomic Variants Using a Unified Biological Network Approach

  2013cited by this paper
• TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal

  2013cited by this paper
• Highly Recurrent TERT Promoter Mutations in Human Melanoma

  2013cited by this paper
• Mutational Processes Molding the Genomes of 21 Breast Cancers

  2012cited by this paper
• Personal omics profiling reveals dynamic molecular and medical phenotypes.

  2012cited by this paper
• Personal and population genomics of human regulatory variation

  2012cited by this paper
• A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

  2012cited by this paper
• An integrated map of genetic variation from 1,092 human genomes

  2012influential reference
• Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations.

  2012cited by this paper
• HINT: High-quality protein interactomes and their applications in understanding human disease

  2012cited by this paper
• Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions

  2012cited by this paper
• Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma

  2012cited by this paper
• Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

  2012cited by this paper
• Supplementary materials for

  2012cited by this paper
• The accessible chromatin landscape of the human genome

  2012cited by this paper
• Architecture of the human regulatory network derived from ENCODE data

  2012cited by this paper
• The Mutational Landscape of Lethal Castrate Resistant Prostate Cancer

  2012cited by this paper
• Comprehensive molecular characterization of human colon and rectal cancer

  2012cited by this paper
• An Integrated Encyclopedia of DNA Elements in the Human Genome

  2012influential reference
• GENCODE: The reference human genome annotation for The ENCODE Project

  2012cited by this paper
• Comprehensive genomic characterization of squamous cell lung cancers

  2012cited by this paper
• VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

  2012cited by this paper
• Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer

  2012cited by this paper
• Three-dimensional reconstruction of protein networks provides insight into human genetic disease

  2012cited by this paper
• Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

  2012cited by this paper
• Interpreting non-coding variation in complex disease genetics

  2012cited by this paper
• Classic Selective Sweeps Were Rare in Recent Human Evolution

  2011cited by this paper
• A framework for variation discovery and genotyping using next-generation DNA sequencing data

  2011cited by this paper
• In-silico human genomics with GeneCards

  2011cited by this paper
• Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project

  2011cited by this paper
• AlleleSeq: analysis of allele-specific expression and binding in a network framework

  2011cited by this paper
• Demographic history and rare allele sharing among human populations

  2011cited by this paper
• CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

  2011cited by this paper
• Integrated Genomic Analyses of Ovarian Carcinoma

  2011cited by this paper
• Rare and Common Regulatory Variation in Population-Scale Sequenced Human Genomes

  2011cited by this paper
• Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets.

  2011influential reference
• Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates

  2010cited by this paper
• Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

  2010cited by this paper
• The genomic complexity of primary human prostate cancer

  2010cited by this paper
• Targeted Deletion of the 9p21 Noncoding Coronary Artery Disease Risk Interval in Mice

  2010cited by this paper
• A map of human genome variation from population-scale sequencing

  2010cited by this paper
• Mapping copy number variation by population scale genome sequencing

  2010cited by this paper
• Subsampling methods for genomic inference

  2010cited by this paper
• Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

  2010cited by this paper
• Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

  2010cited by this paper
• Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

  2010cited by this paper
• International network of cancer genome projects

  2010cited by this paper
• Edgetic perturbation models of human inherited disorders

  2009cited by this paper
• The Human Gene Mutation Database: 2008 update

  2009cited by this paper
• A census of human transcription factors: function, expression and evolution

  2009cited by this paper
• Population Differentiation as an Indicator of Recent Positive Selection in Humans: An Empirical Evaluation

  2009cited by this paper
• The promise and reality of personal genomics

  2009cited by this paper
• Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

  2009cited by this paper
• Analytical methods for inferring functional effects of single base pair substitutions in human cancers

  2009cited by this paper
• Null mutations in human and mouse orthologs frequently result in different phenotypes

  2008cited by this paper
• Natural selection has driven population differentiation in modern humans

  2008cited by this paper
• Natural selection on genes that underlie human disease susceptibility.

  2008cited by this paper
• High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

  2008cited by this paper
• Fast and flexible simulation of DNA sequence data.

  2008cited by this paper
• DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes

  2008cited by this paper
• Evo‐Devo and an Expanding Evolutionary Synthesis

  2008cited by this paper
• The Diploid Genome Sequence of an Individual Human

  2007cited by this paper
• hORFeome v3.1: A resource of human open reading frames representing over 10,000 human genes

  2007cited by this paper
• A human phenome-interactome network of protein complexes implicated in genetic disorders

  2007cited by this paper
• p31comet blocks Mad2 activation through structural mimicry.

  2007cited by this paper
• Positive selection at the protein network periphery: Evaluation in terms of structural constraints and cellular context

  2007cited by this paper
• Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution

  2007cited by this paper
• Human Genome Ultraconserved Elements Are Ultraselected

  2007cited by this paper
• Positive Natural Selection in the Human

  2006cited by this paper
• Positive Natural Selection in the Human Lineage

  2006cited by this paper
• Global variation in copy number in the human genome

  2006cited by this paper
• Mutations in lipid transporter ABCA12 in harlequin ichthyosis and functional recovery by corrective gene transfer.

  2005cited by this paper
• The MIPS mammalian protein?Cprotein interaction database

  2005cited by this paper
• iPfam: visualization of protein?Cprotein interactions in PDB at domain and amino acid resolutions

  2005cited by this paper
• Consequences of mutations in the non-coding RMRP RNA in cartilage-hair hypoplasia.

  2005cited by this paper
• Towards a proteome-scale map of the human protein–protein interaction network

  2005cited by this paper
• A novel high-throughput (HTP) cloning strategy for site-directed designed chimeragenesis and mutation using the Gateway cloning system

  2005cited by this paper
• The (1992) Bonus‐Malus System in Tunisia: An Empirical Evaluation

  2005cited by this paper
• Ultraconserved Elements in the Human Genome

  2004cited by this paper
• Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection.

  2004cited by this paper
• Self-Assembling Protein Microarrays

  2004cited by this paper
• DEG: a database of essential genes.

  2004cited by this paper
• A census of human cancer genes

  2004cited by this paper
• EG: a database of essential genes

  2004cited by this paper
• Statistical significance for genomewide studies

  2003cited by this paper
• Identification of a MAD2‐binding protein, CMT2, and its role in mitosis

  2002cited by this paper
• Evolutionary Rate in the Protein Interaction Network

  2002cited by this paper
• Uroporphyrinogen III synthase erythroid promoter mutations in adjacent GATA1 and CP2 elements cause congenital erythropoietic porphyria.

  2001cited by this paper
• Autoinhibition and activation mechanisms of the Wiskott–Aldrich syndrome protein

  2000cited by this paper
• Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus.

  2000cited by this paper
• The human gene mutation database

  1998cited by this paper
• An Empirical Evaluation

  1994cited by this paper
• Highly Recurrent TERT Promoter Mutations in Human Melanoma

  year unknowncited by this paper
• Bioinformatics Applications Note Gene Expression Rseqtools: a Modular Framework to Analyze Rna-seq Data Using Compact, Anonymized Data Summaries

  year unknowncited by this paper

• Altered benzo[a]pyrene adduct formation in nucleosomes establishes distinct mutational patterns in lung cancer.

  2026cites this paper
• Mapping transcription factor binding sites by learning UV damage fingerprints

  2025cites this paper
• The ChickenGTEx portal: a pan-tissue catalogue of regulatory variants shaping transcriptomic and phenotypic diversity

  2025cites this paper
• Long Non-Coding RNAs and RNA-Binding Proteins in Pancreatic Cancer Development and Progression

  2025cites this paper
• Advancing Targeted Therapies in Pancreatic Cancer: Leveraging Molecular Aberrations for Therapeutic Success.

  2025cites this paper
• MFDSMC: Accurate Identification of Cancer-Driver Synonymous Mutations Using Multiperspective Feature Representation Learning

  2025cites this paper
• Getting to know ovarian cancer: Focusing on the effect of LncRNAs in this cancer and the effective signaling pathways.

  2024cites this paper
• CIXG: A Comprehensive Approach to Driver Gene Identification and Causal Interpretation

  2024cites this paper
• Noncoding variation near UBE2E2 orchestrates cardiometabolic pathophenotypes through polygenic effectors

  2024cites this paper
• Oncogenic Enhancers in Leukemia.

  2024cites this paper
• Polymorphisms within autophagy‐related genes as susceptibility biomarkers for pancreatic cancer: A meta‐analysis of three large European cohorts and functional characterization

  2024cites this paper
• Melanoma-specific mutation hotspots in distal, non-coding, promoter-interacting regions implicate novel candidate driver genes

  2024cites this paper
• Identifying functional regulatory mutation blocks by integrating genome sequencing and transcriptome data

  2023cites this paper
• Integrated multi-dimensional analysis highlights DHCR7 mutations involving in cholesterol biosynthesis and contributing therapy of gastric cancer

  2023cites this paper
• WMDS.net: a network control framework for identifying key players in transcriptome programs

  2023cites this paper
• The Role of Long Noncoding Ribonucleic Acids in Glioblastoma: What the Neurosurgeon Should Know

  2023cites this paper
• Allele-specific binding (ASB) analyzer for annotation of allele-specific binding SNPs

  2023cites this paper
• Unified views on variant impact across many diseases.

  2023cites this paper
• Identification of Driver Epistatic Gene Pairs Combining Germline and Somatic Mutations in Cancer

  2023cites this paper
• Two germline mutations can serve as genetic susceptibility screening makers for a lung adenocarcinoma family

  2023cites this paper
• DIRECT-NET: An efficient method to discover cis-regulatory elements and construct regulatory networks from single-cell multiomics data

  2022cites this paper
• The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

  2022cites this paper
• Identifying driver modules based on multi‐omics biological networks in prostate cancer

  2022cites this paper
• Development of bioinformatics and multi-omics analyses in organoids

  2022cites this paper
• Interpretation of the role of germline and somatic non-coding mutations in cancer: expression and chromatin conformation informed analysis

  2022cites this paper
• Comparison of missing data handling methods for variant pathogenicity predictors

  2022cites this paper
• Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway

  2022cites this paper
• PanCancer analysis of somatic mutations in repetitive regions reveals recurrent mutations in snRNA U2

  2022cites this paper
• Somatic mutations enriched in cis-regulatory elements affect genes involved in embryonic development and immune system response in neuroblastoma.

  2022cites this paper
• Emerging role of oncogenic long noncoding RNA as cancer biomarkers

  2022cites this paper
• Molecular Mechanisms of lncRNAs in the Dependent Regulation of Cancer and Their Potential Therapeutic Use

  2022cites this paper
• Identification of a signature of evolutionarily conserved stress-induced mutagenesis in cancer

  2021cites this paper
• Robustness and evolvability in transcriptional regulation

  2021cites this paper
• Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning

  2021cites this paper
• The Expression Patterns and Prognostic Value of the Proteasome Activator Subunit Gene Family in Gastric Cancer Based on Integrated Analysis

  2021cites this paper
• Co-occurrence and mutual exclusivity: what cross-cancer mutation patterns can tell us.

  2021cites this paper
• Systematic dissection of transcriptional regulatory networks by genome-scale and single-cell CRISPR screens

  2021cites this paper
• Exploring absent protein function in yeast: assaying post translational modification and human genetic variation

  2021cites this paper
• Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway

  2021cites this paper
• Advances and challenges in quantitative delineation of the genetic architecture of complex traits

  2021cites this paper
• Multi-tissue integrative analysis of personal epigenomes

  2021cites this paper
• CTCF binding modulates UV damage formation to promote mutation hot spots in melanoma

  2021cites this paper
• A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases

  2021cites this paper
• Clonal expansion in non-cancer tissues

  2021cites this paper
• Whole-genome landscape of adult T-cell leukemia/lymphoma.

  2021cites this paper
• Mutational processes in cancer preferentially affect binding of particular transcription factors

  2021cites this paper
• Defining Breast Cancer

  2021cites this paper
• Disease-associated human genetic variation through the lens of precursor and mature RNA structure

  2021cites this paper
• High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

  2021cites this paper
• Analysis of the Batch Effect Due to Sequencing Center in Population Statistics Quantifying Rare Events in the 1000 Genomes Project

  2021cites this paper
• Computational analysis of cancer genome sequencing data

  2021cites this paper
• Multi-tissue integrative analysis of personal epigenomes

  2021cites this paper
• Optimizing Genetic Diagnosis of Neurodevelopmental Disorders in the Clinical Setting.

  2020cites this paper
• Leveraging auxiliary data from arbitrary distributions to boost GWAS discovery with Flexible cFDR

  2020cites this paper
• CNCDatabase: a database of non-coding cancer drivers

  2020cites this paper
• Functional Screening Techniques to Identify Long Non-Coding RNAs as Therapeutic Targets in Cancer

  2020cites this paper
• Rare variants discovery by extensive whole-genome sequencing of the Han Chinese population in Taiwan: Applications to cardiovascular medicine

  2020cites this paper
• Tumorigenesis-Related Long Noncoding RNAs and Their Targeting as Therapeutic Approach in Cancer

  2020cites this paper
• Genomic Characterization of Human Long Noncoding RNAs

  2020cites this paper
• LncRNAs in Cancer: From garbage to Junk

  2020cites this paper
• Prediction of genome-wide effects of single nucleotide variants on transcription factor binding

  2020cites this paper
• Development and Characterization of Near-Isogenic Lines Revealing Candidate Genes for a Major 7AL QTL Responsible for Heat Tolerance in Wheat

  2020cites this paper
• Health Data Analytics: Current Perspectives, Challenges, and Future Directions

  2020cites this paper
• Using whole-exome sequencing and protein interaction networks to prioritize candidate genes for germline cutaneous melanoma susceptibility

  2020cites this paper
• Genetics of extreme human longevity to guide drug discovery for healthy ageing

  2020cites this paper
• Colorectal Adenomas—Genetics and Searching for New Molecular Screening Biomarkers

  2020cites this paper
• Co-regularized nonnegative matrix factorization for evolving community detection in dynamic networks

  2020cites this paper
• Shaping the nebulous enhancer in the era of high-throughput assays and genome editing

  2020cites this paper
• Modeling and Simulation of Genome Evolution Using Linear Boolean Functions Associated with One Dimensional Cellular Automata

  2020cites this paper
• Nanocarriers(s) Based Approaches in Cancer Therapeutics

  2020cites this paper
• Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks.

  2020cites this paper
• Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

  2020cites this paper
• NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis

  2020cites this paper
• Mapping and characterization of structural variation in 17,795 human genomes

  2020cites this paper
• Correlated evolution of large DNA fragments in the 3D genome of Arabidopsis thaliana.

  2020cites this paper
• Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.

  2020cites this paper
• Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease

  2020cites this paper
• Lost pigs and broken genes: the search for causes of embryonic loss in the pig and the assembly of a more contiguous reference genome

  2019cites this paper
• Improving Genetic Association Analysis through Integration of Functional Annotations of the Human Genome

  2019cites this paper
• Long Noncoding RNAs and Repetitive Elements: Junk or Intimate Evolutionary Partners?

  2019cites this paper
• Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma

  2019cites this paper
• Unified inference of missense variant effects and gene constraints in the human genome

  2019cites this paper
• Horizontal transfer of mitochondria and its role in carcinogenesis

  2019cites this paper
• An Integrated Three-Long Non-coding RNA Signature Predicts Prognosis in Colorectal Cancer Patients

  2019cites this paper
• Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations

  2019cites this paper
• RegulationSpotter: annotation and interpretation of extratranscriptic DNA variants

  2019cites this paper
• Building a Hybrid Physical-Statistical Classifier for Predicting the Effect of Variants Related to Protein-Drug Interactions.

  2019cites this paper
• Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes.

  2019influential citation
• Loss-of-function tolerance of enhancers in the human genome

  2019influential citation
• Identifying Cancer Driver lncRNAs Bridged by Functional Effectors through Integrating Multi-omics Data in Human Cancers

  2019cites this paper
• A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph

  2019cites this paper
• Germline variants in cancer genes in high-risk non-BRCA patients from Puerto Rico

  2019cites this paper
• An integrative analysis of non-coding regulatory DNA variations associated with autism spectrum disorder

  2019cites this paper
• regBase: whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants

  2019influential citation
• Detecting and Annotating Rare Variants

  2019cites this paper
• A Novel approach to genome editing using Cellular automata evolutions of adjoints sequences

  2019cites this paper
• Long Noncoding RNA and Epithelial Mesenchymal Transition in Cancer

  2019cites this paper
• 1 Positional Integration of Lung Adenocarcinoma Susceptibility Loci with Primary Human Alveolar 1 Epithelial Cell

  2019influential citation
• Non-coding RNA therapy in cancer

  2019cites this paper
• Correlated evolution of large DNA fragments in the chromatin interaction network: a case study in Arabidopsis thaliana

  2019cites this paper