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

Prioritization of pathogenic mutations in the protein kinase superfamily

(2012) Jose MG Izarzugaza et al.   BMC GENOMICS

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

(2012) Yana Bromberg et al.   BMC GENOMICS

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

(2012) Sanne Nygaard et al.   BMC Medical Genomics

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

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

(2012) D. R. Parkinson et al.   CLINICAL CANCER RESEARCH

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

(2012) M. Frenkel-Morgenstern et al.   GENOME RESEARCH

Sequencing set to alter clinical landscape

(2012) Erika Check Hayden   NATURE

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

Postzygotic HRAS and KRAS mutations cause nevus sebaceous and Schimmelpenning syndrome

(2012) Leopold Groesser et al.   NATURE GENETICS

Detectable clonal mosaicism and its relationship to aging and cancer

(2012) Kevin B Jacobs et al.   NATURE GENETICS

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

(2012) Cathy C Laurie et al.   NATURE GENETICS

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

(2012) Sarah Djebali et al.   PLoS One

Whole-Genome Sequencing: The New Standard of Care?

(2012) L. R. Brunham et al.   SCIENCE

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

(2012) Ido Goldstein et al.   TRENDS IN MOLECULAR MEDICINE

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

(2012) Elizabeth T Cirulli et al.   GENOME BIOLOGY

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

(2011) Abel González-Pérez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2011) T. Muth et al.   BIOINFORMATICS

Bioinformatics challenges for personalized medicine

(2011) Guy Haskin Fernald et al.   BIOINFORMATICS

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

(2011) Enrico Glaab et al.   BMC BIOINFORMATICS

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

(2011) Alexandre Riazanov et al.   BMC BIOINFORMATICS

Exploiting drug-disease relationships for computational drug repositioning

(2011) J. T. Dudley et al.   BRIEFINGS IN BIOINFORMATICS

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

(2011) Philip J. Stephens et al.   CELL

Identification of a Novel TP53 Cancer Susceptibility Mutation Through Whole-Genome Sequencing of a Patient With Therapy-Related AML

(2011) Daniel C. Link   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

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

(2011) M. Hidalgo et al.   MOLECULAR CANCER THERAPEUTICS

Secrets of the human genome disclosed

(2011) Erika Check Hayden   NATURE

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

(2011) Ignacio Varela et al.   NATURE

Initial genome sequencing and analysis of multiple myeloma

(2011) Michael A. Chapman 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

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

(2011) Xose S. Puente et al.   NATURE

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

(2011) Yingrui Li et al.   NATURE BIOTECHNOLOGY

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

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

(2011) Yaoting Gui et al.   NATURE GENETICS

High-resolution characterization of a hepatocellular carcinoma genome

(2011) Yasushi Totoki et al.   NATURE GENETICS

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

(2011) Xiao-Jing Yan et al.   NATURE GENETICS

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

(2011) Jianmin Wang et al.   NATURE METHODS

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

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Ma'n H. Zawati et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

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

(2011) K. Kannan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Personalized Cancer Diagnostics

(2011) C. L. Corless   SCIENCE

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

(2011) N. Agrawal et al.   SCIENCE

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

(2011) E. B. Bookman et al.   Science Translational Medicine

Future medical applications of single-cell sequencing in cancer

(2011) Nicholas Navin et al.   Genome Medicine

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

(2010) Emily Doughty et al.   BIOINFORMATICS

Mutated genes, pathways and processes in tumours

(2010) Anaïs Baudot et al.   EMBO REPORTS

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

(2010) C. J. David et al.   GENES & DEVELOPMENT

Ethical challenges in genotype-driven research recruitment

(2010) L. M. Beskow et al.   GENOME RESEARCH

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

(2010) Daniel Summerer et al.   GENOMICS

Challenges in the clinical application of whole-genome sequencing

(2010) Kelly E Ormond et al.   LANCET

Cancer-gene testing ramps up

(2010) Ewen Callaway   NATURE

Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes

(2010) Gillian L. Dalgliesh et al.   NATURE

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

The FEBS Letters/BioCreative II.5 experiment: making biological information accessible

(2010) Florian Leitner et al.   NATURE BIOTECHNOLOGY

Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

Individual Genomes on the Horizon

(2010) Richard P. Lifton   NEW ENGLAND JOURNAL OF MEDICINE

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

(2010) James R. Lupski et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2010) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

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

(2010) A. Rausell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) F. Iorio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) J. C. Roach et al.   SCIENCE

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

(2010) I. S. Kohane et al.   Science Translational Medicine

Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks

(2010) Karine Audouze et al.   PLoS Computational Biology

The Characterization of Twenty Sequenced Human Genomes

(2010) Kimberly Pelak et al.   PLoS Genetics

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

(2009) R. Matthew Ward et al.   BIOINFORMATICS

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

(2009) Kevin Nagel et al.   BMC BIOINFORMATICS

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

(2009) Jose MG Izarzugaza et al.   BMC BIOINFORMATICS

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

(2009) Martin Krallinger et al.   BMC BIOINFORMATICS

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

(2009) Yael Garten et al.   BMC BIOINFORMATICS

PALB2 Links BRCA1 and BRCA2 in the DNA-Damage Response

(2009) Feng Zhang et al.   CURRENT BIOLOGY

From cancer genomes to cancer models: bridging the gaps

(2009) Anaïs Baudot et al.   EMBO REPORTS

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

(2009) F. Hormozdiari et al.   GENOME RESEARCH

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

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

(2009) Ken Chen et al.   NATURE METHODS

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

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

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

Common Genetic Variation and Human Traits

(2009) David B. Goldstein   NEW ENGLAND JOURNAL OF MEDICINE

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

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Stacia K. Wyman et al.   PLoS One

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

(2009) Tamar Uziel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2009) Jose M. G. Izarzugaza et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Exomic Sequencing Identifies PALB2 as a Pancreatic Cancer Susceptibility Gene

(2009) S. Jones et al.   SCIENCE

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

(2008) J. C. Marioni et al.   GENOME RESEARCH

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

(2008) Brian T. Wilhelm et al.   NATURE

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

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

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

(2008) S. Jones et al.   SCIENCE

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

(2008) M. Sultan et al.   SCIENCE