Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics

Inference of Macromolecular Assemblies from Crystalline State

2007 • 9,346 citations

A map of human genome variation from population-scale sequencing

2010 • 7,765 citations

Integrated genomic analyses of ovarian carcinoma

2011 • 7,228 citations

dbSNP: the NCBI database of genetic variation

2001 • 6,995 citations

SIFT: predicting amino acid changes that affect protein function

2003 • 5,952 citations

Table S2: Trans-factors and trinucleotide repeat instability Trans-factor

2010 • 5,471 citations

Long non-coding RNAs: insights into functions

2009 • 5,356 citations

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

2009 • 4,036 citations

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

2008 • 3,870 citations

A census of human cancer genes

2004 • 3,190 citations

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders

2004 • 3,142 citations

Clonal evolution in cancer

2012 • 2,892 citations

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

2008 • 2,860 citations

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

2008 • 2,741 citations

Tumour evolution inferred by single-cell sequencing

2011 • 2,478 citations

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

2011 • 2,254 citations

KEGG for representation and analysis of molecular networks involving diseases and drugs

2009 • 2,253 citations

Targeted capture and massively parallel sequencing of 12 human exomes

2009 • 1,986 citations

Exome sequencing identifies the cause of a mendelian disorder

2009 • 1,909 citations

Predicting the functional impact of protein mutations: application to cancer genomics

2011 • 1,871 citations

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

2010 • 1,770 citations

JASPAR: an open-access database for eukaryotic transcription factor binding profiles

2003 • 1,718 citations

Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1

2011 • 1,619 citations

Reactome: a database of reactions, pathways and biological processes

2010 • 1,553 citations

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

2009 • 1,496 citations

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

2011 • 1,469 citations

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

2009 • 1,447 citations

Initial genome sequencing and analysis of multiple myeloma

2011 • 1,394 citations

Understanding mechanisms underlying human gene expression variation with RNA sequencing

2010 • 1,303 citations

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

2008 • 1,270 citations

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

2012 • 1,242 citations

Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma

2011 • 1,218 citations

The genomic complexity of primary human prostate cancer

2011 • 1,209 citations

DNA breaks and chromosome pulverization from errors in mitosis

2012 • 1,163 citations

Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome

2007 • 1,150 citations

Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes

2010 • 1,149 citations

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

2010 • 1,096 citations

TRANSFAC: a database on transcription factors and their DNA binding sites

1996 • 1,057 citations

Increased methylation variation in epigenetic domains across cancer types

2011 • 1,022 citations

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia

2011 • 975 citations

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

2008 • 956 citations

Bioinformatics: The Machine Learning Approach

1998 • 942 citations

Common Genetic Variation and Human Traits

2009 • 941 citations

The Catalogue of Somatic Mutations in Cancer (COSMIC)

2008 • 886 citations

A side effect resource to capture phenotypic effects of drugs

2010 • 858 citations

Transcriptome genetics using second generation sequencing in a Caucasian population

2010 • 826 citations

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

2012 • 823 citations

Discovery of drug mode of action and drug repositioning from transcriptional responses

2010 • 803 citations

Exomic Sequencing Identifies PALB2 as a Pancreatic Cancer Susceptibility Gene

2009 • 798 citations

Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia

2011 • 784 citations

Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged

2010 • 766 citations

Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, Condel

2011 • 760 citations

Whole-Genome Sequencing in a Patient with Charcot–Marie–Tooth Neuropathy

2010 • 758 citations

Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder

2011 • 683 citations

UniProtKB/Swiss-Prot

2007 • 679 citations

Critical assessment of methods of protein structure prediction (CASP) — round x

2013 • 675 citations

Ensembl 2007

2006 • 622 citations

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

2003 • 611 citations

Detectable clonal mosaicism and its relationship to aging and cancer

2012 • 563 citations

Detectable clonal mosaicism from birth to old age and its relationship to cancer

2012 • 553 citations

Overview of BioCreAtIvE: critical assessment of information extraction for biology

2005 • 552 citations

Computational methods for discovering structural variation with next-generation sequencing

2009 • 543 citations

microRNAs join the p53 network — another piece in the tumour-suppression puzzle

2007 • 535 citations

PALB2 Links BRCA1 and BRCA2 in the DNA-Damage Response

2009 • 516 citations

Exploiting drug-disease relationships for computational drug repositioning

2011 • 502 citations

CREST maps somatic structural variation in cancer genomes with base-pair resolution

2011 • 486 citations

PMUT: a web-based tool for the annotation of pathological mutations on proteins

2005 • 478 citations

PharmGKB: the Pharmacogenetics Knowledge Base

2002 • 417 citations

A Pilot Clinical Study of Treatment Guided by Personalized Tumorgrafts in Patients with Advanced Cancer

2011 • 383 citations

Critical assessment of methods of protein structure prediction-Round VII.

2007 • 321 citations

Determinants of protein function revealed by combinatorial entropy optimization

2007 • 308 citations

Alternative expression analysis by RNA sequencing

2010 • 303 citations

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes

2009 • 301 citations

Postzygotic HRAS and KRAS mutations cause nevus sebaceous and Schimmelpenning syndrome

2012 • 292 citations

High-resolution characterization of a hepatocellular carcinoma genome

2011 • 282 citations

The miR-17 ∼ 92 cluster collaborates with the Sonic Hedgehog pathway in medulloblastoma

2009 • 272 citations

Bioinformatics challenges for personalized medicine

2011 • 241 citations

Repertoire of microRNAs in Epithelial Ovarian Cancer as Determined by Next Generation Sequencing of Small RNA cDNA Libraries

2009 • 237 citations

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

2012 • 233 citations

Challenges in the clinical application of whole-genome sequencing

2010 • 228 citations

2020 Vision

1991 • 198 citations

Future medical applications of single-cell sequencing in cancer

2011 • 194 citations

Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing

2011 • 178 citations

Critical assessment of methods of protein structure prediction—Round VIII

2009 • 172 citations

MutationFinder: a high-performance system for extracting point mutation mentions from text

2007 • 167 citations

The Characterization of Twenty Sequenced Human Genomes

2010 • 162 citations

Identification of a Novel <emph type="ital">TP53</emph> Cancer Susceptibility Mutation Through Whole-Genome Sequencing of a Patient With Therapy-Related AML

2011 • 157 citations

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing

2010 • 150 citations

iHOP web services

2007 • 147 citations

Protein interactions and ligand binding: From protein subfamilies to functional specificity

2010 • 146 citations

Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly

2011 • 133 citations

Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

2012 • 133 citations

Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text

2009 • 130 citations

ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation

2006 • 121 citations

Automatic annotation of protein function

2005 • 120 citations

Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature

2010 • 101 citations

The CATH database

2010 • 95 citations

GeneQuiz: a workbench for sequence analysis.

1994 • 90 citations

Automatic extraction of mutations from Medline and cross-validation with OMIM

2004 • 87 citations

Making Personalized Cancer Medicine a Reality: Challenges and Opportunities in the Development of Biomarkers and Companion Diagnostics

2012 • 72 citations

Multidimensional Results Reporting to Participants in Genomic Studies: Getting It Right

2010 • 71 citations

Whole-Genome Sequencing: The New Standard of Care?

2012 • 66 citations

FireDB--a database of functionally important residues from proteins of known structure

2006 • 56 citations

Profiling Epigenetic Alterations in Disease

2011 • 55 citations

Computational protein function prediction: Are we making progress?

2007 • 51 citations

Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks

2010 • 50 citations

Extending pathways and processes using molecular interaction networks to analyse cancer genome data

2010 • 49 citations

Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing

2009 • 48 citations

Extraction of human kinase mutations from literature, databases and genotyping studies

2009 • 41 citations

The Complex Epidemiology of Respiratory Virus Infections

1964 • 39 citations

Ethical challenges in genotype-driven research recruitment: Box 1.

2010 • 37 citations

From cancer genomes to cancer models: bridging the gaps

2009 • 37 citations

Mutated genes, pathways and processes in tumours

2010 • 36 citations

Targeted high throughput sequencing of a cancer-related exome subset by specific sequence capture with a fully automated microarray platform

2010 • 32 citations

Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb

2009 • 31 citations

Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates

2009 • 31 citations

Distribution analysis of nonsynonymous polymorphisms within the human kinase gene family

2007 • 30 citations

Personalized Cancer Diagnostics

2011 • 27 citations

Cancer‐associated mutations are preferentially distributed in protein kinase functional sites

2009 • 27 citations

Prioritization of pathogenic mutations in the protein kinase superfamily

2012 • 25 citations

JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures

2011 • 24 citations

Sequencing set to alter clinical landscape

2012 • 21 citations

The changes that count

2012 • 18 citations

Deploying mutation impact text-mining software with the SADI Semantic Web Services framework

2011 • 18 citations

Cancer research, a field on the verge of a paradigm shift?

2012 • 13 citations

Between proteins and phenotypes: annotation and interpretation of mutations

2009 • 13 citations

A mutation-centric approach to identifying pharmacogenomic relations in text

2012 • 13 citations

Interpretation of the Consequences of Mutations in Protein Kinases: Combined Use of Bioinformatics and Text Mining

2012 • 12 citations

Cancer Systems Biology, Bioinformatics and Medicine: Research and Clinical Applications

2011 • 11 citations

An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D

2009 • 11 citations

SNP-SIG Meeting 2011: Identification and annotation of SNPs in the context of structure, function, and disease

2012 • 9 citations

Cancer-gene testing ramps up

2010 • 9 citations

Mutation-prediction software rewarded

2010 • 6 citations

Secrets of the human genome disclosed

2011 • 6 citations

Incidental Findings in Data-Intensive Postgenomics Science and Legal Liability of Clinician–Researchers: Ready for Vaccinomics?

2011 • 5 citations

Incidental Findings in Data-Intensive Postgenomics Science and Legal Liability of Clinician-Researchers: Ready for Vaccinomics?

2011 • 4 citations

Norway to bring cancer-gene tests to the clinic

2012 • 3 citations

Education and Research Infrastructures

2011 • 3 citations