Bioinformatics for personal genome interpretation

A Genome-wide Comparison of the Functional Properties of Rare and Common Genetic Variants in Humans

(2011) Qianqian Zhu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Bioinformatics challenges for personalized medicine

(2011) Guy Haskin Fernald et al.   BIOINFORMATICS

SVA: software for annotating and visualizing sequenced human genomes

(2011) Dongliang Ge et al.   BIOINFORMATICS

KvSNP: accurately predicting the effect of genetic variants in voltage-gated potassium channels

(2011) L. F. Stead et al.   BIOINFORMATICS

DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases

(2011) Wangshu Zhang et al.   BMC Systems Biology

A probabilistic disease-gene finder for personal genomes

(2011) M. Yandell et al.   GENOME RESEARCH

A new disease-specific machine learning approach for the prediction of cancer-causing missense variants

(2011) Emidio Capriotti et al.   GENOMICS

Prediction of functional regulatory SNPs in monogenic and complex disease

(2011) Yiqiang Zhao et al.   HUMAN MUTATION

Performance of mutation pathogenicity prediction methods on missense variants

(2011) Janita Thusberg et al.   HUMAN MUTATION

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

Epigenome-wide association studies for common human diseases

(2011) Vardhman K. Rakyan et al.   NATURE REVIEWS GENETICS

PINTA: a web server for network-based gene prioritization from expression data

(2011) D. Nitsch et al.   NUCLEIC ACIDS RESEARCH

Génie: literature-based gene prioritization at multi genomic scale

(2011) Jean-Fred Fontaine et al.   NUCLEIC ACIDS RESEARCH

Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations

(2011) Sudhir Kumar et al.   TRENDS IN GENETICS

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

(2011) Nathan L. Nehrt et al.   PLoS Computational Biology

Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence

(2011) Frederick E. Dewey et al.   PLoS Genetics

DA DA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization

(2011) Sinan Erten et al.   BioData Mining

Easy retrieval of single amino-acid polymorphisms and phenotype information using SwissVar

(2010) Anaïs Mottaz et al.   BIOINFORMATICS

Improving disease gene prioritization using the semantic similarity of Gene Ontology terms

(2010) Andreas Schlicker et al.   BIOINFORMATICS

DMDM: domain mapping of disease mutations

(2010) T. A. Peterson et al.   BIOINFORMATICS

Using bioinformatics to predict the functional impact of SNVs

(2010) M. S. Cline et al.   BIOINFORMATICS

GAMES identifies and annotates mutations in next-generation sequencing projects

(2010) M. E. Sana et al.   BIOINFORMATICS

is-rSNP: a novel technique for in silico regulatory SNP detection

(2010) Geoff Macintyre et al.   BIOINFORMATICS

The power of protein interaction networks for associating genes with diseases

(2010) Saket Navlakha et al.   BIOINFORMATICS

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

SeqAnt: A web service to rapidly identify and annotate DNA sequence variations

(2010) Amol Shetty et al.   BMC BIOINFORMATICS

Algorithms and semantic infrastructure for mutation impact extraction and grounding

(2010) Jonas B Laurila et al.   BMC GENOMICS

A guide to web tools to prioritize candidate genes

(2010) L.-C. Tranchevent et al.   BRIEFINGS IN BIOINFORMATICS

Locus-specific database domain and data content analysis: evolution and content maturation toward clinical usea

(2010) Christina Mitropoulou et al.   HUMAN MUTATION

Performance of protein stability predictors

(2010) Sofia Khan et al.   HUMAN MUTATION

Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)

(2010) S. N. Murphy et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Clinical assessment incorporating a personal genome

(2010) Euan A Ashley et al.   LANCET

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

Tackling the epigenome: challenges and opportunities for collaboration

(2010) John S Satterlee et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Public data archives for genomic structural variation

(2010) Deanna M Church et al.   NATURE GENETICS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The RCSB Protein Data Bank: redesigned web site and web services

(2010) P. W. Rose et al.   NUCLEIC ACIDS RESEARCH

Pharmacogenomics and bioinformatics: PharmGKB

(2010) Caroline F Thorn et al.   PHARMACOGENOMICS

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

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

Associating Genes and Protein Complexes with Disease via Network Propagation

(2010) Oron Vanunu et al.   PLoS Computational Biology

Genomic features defining exonic variants that modulate splicing

(2010) Adam Woolfe et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures

(2009) Michael Ryan et al.   BIOINFORMATICS

Automated inference of molecular mechanisms of disease from amino acid substitutions

(2009) B. Li et al.   BIOINFORMATICS

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0

(2009) Yves Dehouck et al.   BIOINFORMATICS

Next generation tools for the annotation of human SNPs

(2009) Rachel Karchin   BRIEFINGS IN BIOINFORMATICS

Cancer-Specific High-Throughput Annotation of Somatic Mutations: Computational Prediction of Driver Missense Mutations

(2009) H. Carter et al.   CANCER RESEARCH

Gene Clusters, Molecular Evolution and Disease: A Speculation

(2009) Leah Elizondo et al.   CURRENT GENOMICS

The SAAPdb web resource: A large-scale structural analysis of mutant proteins

(2009) Jacob M. Hurst et al.   HUMAN MUTATION

Functional annotations improve the predictive score of human disease-related mutations in proteins

(2009) Remo Calabrese et al.   HUMAN MUTATION

Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods

(2009) Janita Thusberg et al.   HUMAN MUTATION

Two Distinct Pathways for Metabolism of Theophylline and Caffeine Are Coexpressed in Pseudomonas putida CBB5

(2009) C. L. Yu et al.   JOURNAL OF BACTERIOLOGY

An agenda for personalized medicine

(2009) Pauline C. Ng et al.   NATURE

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Human genetic variation and its contribution to complex traits

(2009) Kelly A. Frazer et al.   NATURE REVIEWS GENETICS

The Gene Wiki: community intelligence applied to human gene annotation

(2009) Jon W. Huss et al.   NUCLEIC ACIDS RESEARCH

PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning

(2009) Y. Yoshida et al.   NUCLEIC ACIDS RESEARCH

COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer

(2009) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

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

The Human Gene Mutation Database: 2008 update

(2009) Peter D Stenson et al.   Genome Medicine

Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation

(2009) Nicole L. Washington et al.   PLOS BIOLOGY

Walking the Interactome for Prioritization of Candidate Disease Genes

(2008) Sebastian Köhler et al.   AMERICAN JOURNAL OF HUMAN GENETICS

PGMapper: a web-based tool linking phenotype to genes

(2008) Q. Xiong et al.   BIOINFORMATICS

Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis

(2008) M. Masso et al.   BIOINFORMATICS

SNAP predicts effect of mutations on protein function

(2008) Yana Bromberg et al.   BIOINFORMATICS

Defining functional distances over Gene Ontology

(2008) Angela del Pozo et al.   BMC BIOINFORMATICS

Gene Prospector: An evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases

(2008) Wei Yu et al.   BMC BIOINFORMATICS

CANDID: a flexible method for prioritizing candidate genes for complex human traits

(2008) Janna E. Hutz et al.   GENETIC EPIDEMIOLOGY

In silico analysis of missense substitutions using sequence-alignment based methods

(2008) Sean V. Tavtigian et al.   HUMAN MUTATION

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

A wiki for the life sciences where authorship matters

(2008) Robert Hoffmann   NATURE GENETICS

ENDEAVOUR update: a web resource for gene prioritization in multiple species

(2008) L.-C. Tranchevent et al.   NUCLEIC ACIDS RESEARCH

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites

(2008) D. Cheng et al.   NUCLEIC ACIDS RESEARCH

McKusick's Online Mendelian Inheritance in Man (OMIM(R))

(2008) J. Amberger et al.   NUCLEIC ACIDS RESEARCH

In Silico Detection of Sequence Variations Modifying Transcriptional Regulation

(2008) Malin C. Andersen et al.   PLoS Computational Biology

GeneDistiller—Distilling Candidate Genes from Linkage Intervals

(2008) Dominik Seelow et al.   PLoS One

An integrated approach to inferring gene-disease associations in humans

(2008) Predrag Radivojac et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function

(2008) Marco Punta et al.   PLoS Computational Biology

Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis

(2008) Ugo Ala et al.   PLoS Computational Biology

Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes

(2007) Pawel Michalak   GENOMICS

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE