Methods of integrating data to uncover genotype–phenotype interactions

Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline

(2014) Jeffrey G Reid et al.   BMC BIOINFORMATICS

Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets

(2014) Allison P Heath et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Efficient multivariate linear mixed model algorithms for genome-wide association studies

(2014) Xiang Zhou et al.   NATURE METHODS

Diverse convergent evidence in the genetic analysis of complex disease: coordinating omic, informatic, and experimental evidence to better identify and validate risk factors

(2014) Timothy H Ciesielski et al.   BioData Mining

ATHENA: the analysis tool for heritable and environmental network associations

(2013) Emily R. Holzinger et al.   BIOINFORMATICS

Bayesian consensus clustering

(2013) Eric F. Lock et al.   BIOINFORMATICS

Common genetic determinants of breast-cancer risk in East Asian women: a collaborative study of 23 637 breast cancer cases and 25 579 controls

(2013) Wei Zheng et al.   HUMAN MOLECULAR GENETICS

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis

(2013) Yun Liu et al.   NATURE BIOTECHNOLOGY

Genome-wide association studies identify four ER negative–specific breast cancer risk loci

(2013) Montserrat Garcia-Closas et al.   NATURE GENETICS

Large-scale genotyping identifies 41 new loci associated with breast cancer risk

(2013) Kyriaki Michailidou et al.   NATURE GENETICS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

GobyWeb: Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data

(2013) Kevin C. Dorff et al.   PLoS One

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

(2013) G. McVicker et al.   SCIENCE

ATHENA: Identifying interactions between different levels of genomic data associated with cancer clinical outcomes using grammatical evolution neural network

(2013) Dokyoon Kim et al.   BioData Mining

A Computational Workflow to Identify Allele-specific Expression and Epigenetic Modification in Maize

(2013) Xiaoxing Wei et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Bayesian correlated clustering to integrate multiple datasets

(2012) Paul Kirk et al.   BIOINFORMATICS

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

A Bayesian Integrative Genomic Model for Pathway Analysis of Complex Traits

(2012) Brooke L. Fridley et al.   GENETIC EPIDEMIOLOGY

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

Synergistic effect of different levels of genomic data for cancer clinical outcome prediction

(2012) Dokyoon Kim et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS

(2012) Zia Khan et al.   Molecular Systems Biology

The nature of confounding in genome-wide association studies

(2012) Bjarni J. Vilhjálmsson et al.   NATURE REVIEWS GENETICS

Next-generation proteomics: towards an integrative view of proteome dynamics

(2012) A. F. Maarten Altelaar et al.   NATURE REVIEWS GENETICS

Experimental validation of in silico predicted KCNA1, KCNA2, KCNA6 and KCNQ2 genes for association studies of peripheral nerve hyperexcitability syndrome in Jack Russell Terriers

(2012) Mario Van Poucke et al.   NEUROMUSCULAR DISORDERS

Integrating heterogeneous high-throughput data for meta-dimensional pharmacogenomics and disease-related studies

(2012) Emily R Holzinger et al.   PHARMACOGENOMICS

Integrative Subtype Discovery in Glioblastoma Using iCluster

(2012) Ronglai Shen et al.   PLoS One

A Two-Stage Random Forest-Based Pathway Analysis Method

(2012) Ren-Hua Chung et al.   PLoS One

Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation

(2012) Jun Zhu et al.   PLOS BIOLOGY

Computational prediction and experimental validation associating FABP-1 and pancreatic adenocarcinoma with diabetes

(2011) Ravi N Sharaf et al.   BMC GASTROENTEROLOGY

Next generation sequencing based approaches to epigenomics

(2011) M. Hirst et al.   Briefings in Functional Genomics

Pitfalls of merging GWAS data: lessons learned in the eMERGE network and quality control procedures to maintain high data quality

(2011) Rebecca L. Zuvich et al.   GENETIC EPIDEMIOLOGY

A genome-wide association study identifies locus at 10q22 associated with clinical outcomes of adjuvant tamoxifen therapy for breast cancer patients in Japanese

(2011) Kazuma Kiyotani et al.   HUMAN MOLECULAR GENETICS

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

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

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

Time to Recurrence and Survival in Serous Ovarian Tumors Predicted from Integrated Genomic Profiles

(2011) Parminder K. Mankoo et al.   PLoS One

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

Quality control and quality assurance in genotypic data for genome-wide association studies

(2010) Cathy C. Laurie et al.   GENETIC EPIDEMIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Next-generation genomics: an integrative approach

(2010) R. David Hawkins et al.   NATURE REVIEWS GENETICS

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

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

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

ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci

(2010) Stephen D Turner et al.   BioData Mining

The case for cloud computing in genome informatics

(2010) Lincoln D Stein   GENOME BIOLOGY

RNA-seq: from technology to biology

(2009) Samuel Marguerat et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Selective inference in complex research

(2009) Y. Benjamini et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Failure to Replicate a Genetic Association May Provide Important Clues About Genetic Architecture

(2009) Casey S. Greene et al.   PLoS One

Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions

(2009) Soumya Raychaudhuri et al.   PLoS Genetics

Spatially Uniform ReliefF (SURF) for computationally-efficient filtering of gene-gene interactions

(2009) Casey S Greene et al.   BioData Mining

Population-specific genetic variants important in susceptibility to cytarabine arabinoside cytotoxicity

(2008) C. M. Hartford et al.   BLOOD

Genetic variants associated with carboplatin-induced cytotoxicity in cell lines derived from Africans

(2008) R. S. Huang et al.   MOLECULAR CANCER THERAPEUTICS

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS