4.7 Review

Methods of integrating data to uncover genotype-phenotype interactions

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemical Research Methods

ATHENA: the analysis tool for heritable and environmental network associations

Emily R. Holzinger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

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

Jeffrey G. Reid et al.

BMC BIOINFORMATICS (2014)

Article Computer Science, Information Systems

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

Allison P. Heath et al.

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION (2014)

Article Biochemical Research Methods

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

Xiang Zhou et al.

NATURE METHODS (2014)

Article Biochemical Research Methods

Bayesian consensus clustering

Eric F. Lock et al.

BIOINFORMATICS (2013)

Article Multidisciplinary Sciences

Transcriptome and genome sequencing uncovers functional variation in humans

Tuuli Lappalainen et al.

NATURE (2013)

Article Genetics & Heredity

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

Montserrat Garcia-Closas et al.

NATURE GENETICS (2013)

Article Genetics & Heredity

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

Kyriaki Michailidou et al.

NATURE GENETICS (2013)

Editorial Material Genetics & Heredity

The nature of confounding in genome-wide association studies

Bjarni J. Vilhjalmsson et al.

NATURE REVIEWS GENETICS (2013)

Review Genetics & Heredity

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

A. F. Maarten Altelaar et al.

NATURE REVIEWS GENETICS (2013)

Review Genetics & Heredity

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

Ehud Shapiro et al.

NATURE REVIEWS GENETICS (2013)

Article Multidisciplinary Sciences

Extensive Variation in Chromatin States Across Humans

Maya Kasowski et al.

SCIENCE (2013)

Article Multidisciplinary Sciences

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

Graham McVicker et al.

SCIENCE (2013)

Article Genetics & Heredity

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

Xiaoxing Wei et al.

GENOMICS PROTEOMICS & BIOINFORMATICS (2013)

Article Mathematical & Computational Biology

PathAct: a novel method for pathway analysis using gene expression profiles

Kaoru Mogushi et al.

BIOINFORMATION (2013)

Article Biochemical Research Methods

Bayesian correlated clustering to integrate multiple datasets

Paul Kirk et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

Andrey A. Shabalin

BIOINFORMATICS (2012)

Article Genetics & Heredity

A Bayesian Integrative Genomic Model for Pathway Analysis of Complex Traits

Brooke L. Fridley et al.

GENETIC EPIDEMIOLOGY (2012)

Article Biochemistry & Molecular Biology

Annotation of functional variation in personal genomes using RegulomeDB

Alan P. Boyle et al.

GENOME RESEARCH (2012)

Article Computer Science, Interdisciplinary Applications

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

Dokyoon Kim et al.

JOURNAL OF BIOMEDICAL INFORMATICS (2012)

Article Biochemistry & Molecular Biology

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

Zia Khan et al.

MOLECULAR SYSTEMS BIOLOGY (2012)

Article Multidisciplinary Sciences

Integrative Subtype Discovery in Glioblastoma Using iCluster

Ronglai Shen et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

A Two-Stage Random Forest-Based Pathway Analysis Method

Ren-Hua Chung et al.

PLOS ONE (2012)

Article Biochemistry & Molecular Biology

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

Joel Rozowsky et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Review Genetics & Heredity

RNA sequencing: advances, challenges and opportunities

Fatih Ozsolak et al.

NATURE REVIEWS GENETICS (2011)

Article Biotechnology & Applied Microbiology

Next generation sequencing based approaches to epigenomics

Martin Hirst et al.

BRIEFINGS IN FUNCTIONAL GENOMICS (2010)

Article Biochemistry & Molecular Biology

An Integrated Approach to Uncover Drivers of Cancer

Uri David Akavia et al.

Review Biochemistry & Molecular Biology

RNA-seq: from technology to biology

Samuel Marguerat et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2010)

Article Genetics & Heredity

Quality Control and Quality Assurance in Genotypic Data for Genome-Wide Association Studies

Cathy C. Laurie et al.

GENETIC EPIDEMIOLOGY (2010)

Article Biochemistry & Molecular Biology

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

Aaron McKenna et al.

GENOME RESEARCH (2010)

Review Genetics & Heredity

APPLICATIONS OF NEXT-GENERATION SEQUENCING Sequencing technologies - the next generation

Michael L. Metzker

NATURE REVIEWS GENETICS (2010)

Review Genetics & Heredity

Next-generation genomics: an integrative approach

R. David Hawkins et al.

NATURE REVIEWS GENETICS (2010)

Review Genetics & Heredity

Principles and challenges of genome-wide DNA methylation analysis

Peter W. Laird

NATURE REVIEWS GENETICS (2010)

Article Biochemistry & Molecular Biology

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

Kai Wang et al.

NUCLEIC ACIDS RESEARCH (2010)

Review Biotechnology & Applied Microbiology

The case for cloud computing in genome informatics

Lincoln D. Stein

GENOME BIOLOGY (2010)

Review Genetics & Heredity

RNA-Seq: a revolutionary tool for transcriptomics

Zhong Wang et al.

NATURE REVIEWS GENETICS (2009)

Review Genetics & Heredity

ChIP-seq: advantages and challenges of a maturing technology

Peter J. Park

NATURE REVIEWS GENETICS (2009)

Article Multidisciplinary Sciences

Selective inference in complex research

Yoav Benjamini et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2009)

Article Mathematical & Computational Biology

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

Casey S Greene et al.

BioData Mining (2009)

Article Oncology

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

R. Stephanie Huang et al.

MOLECULAR CANCER THERAPEUTICS (2008)

Article Multidisciplinary Sciences

Genetics of gene expression and its effect on disease

Valur Emilsson et al.

NATURE (2008)

Article Biochemical Research Methods

Graph sharpening plus graph integration: a synergy that improves protein functional classification

Hyunjung Shin et al.

BIOINFORMATICS (2007)

Article Genetics & Heredity

Capturing heterogeneity in gene expression studies by surrogate variable analysis

Jeffrey T. Leek et al.

PLOS GENETICS (2007)

Review Biochemistry & Molecular Biology

Moving toward a system genetics view of disease

Solveig K. Sieberts et al.

MAMMALIAN GENOME (2007)

Article Multidisciplinary Sciences

Replicating genotype-phenotype associations

Stephen J. Chanock et al.

NATURE (2007)

Article Multidisciplinary Sciences

A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity

R. Stephanie Huang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Oncology

Estrogens, enzyme variants, and breast cancer: A risk model

Philip S. Crooke et al.

CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION (2006)

Article Biochemical Research Methods

Ensemble classifier for protein fold pattern recognition

Hong-Bin Shen et al.

BIOINFORMATICS (2006)

Article Statistics & Probability

Sparse principal component analysis

Hui Zou et al.

JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS (2006)

Review Biochemical Research Methods

Metabolomics technology and bioinformatics

Vladimir Shulaev

BRIEFINGS IN BIOINFORMATICS (2006)

Article Computer Science, Artificial Intelligence

An introduction to ROC analysis

Tom Fawcett

PATTERN RECOGNITION LETTERS (2006)

Article Biochemical Research Methods

Fast protein classification with multiple networks

K Tsuda et al.

BIOINFORMATICS (2005)

Article Biochemical Research Methods

Protein function prediction via graph kernels

KM Borgwardt et al.

BIOINFORMATICS (2005)

Review Biochemical Research Methods

Integrated analysis of genetic, genomic and proteomic data

DM Reif et al.

EXPERT REVIEW OF PROTEOMICS (2004)

Article Biochemical Research Methods

A statistical framework for genomic data fusion

GRG Lanckriet et al.

BIOINFORMATICS (2004)

Article Biochemical Research Methods

Predicting HIV drug resistance with neural networks

S Draghici et al.

BIOINFORMATICS (2003)

Review Genetics & Heredity

Unbiased methods for population-based association studies

B Devlin et al.

GENETIC EPIDEMIOLOGY (2001)

Article Biochemistry & Molecular Biology

The family based association test method: strategies for studying general genotype-phenotype associations

S Horvath et al.

EUROPEAN JOURNAL OF HUMAN GENETICS (2001)

Article Biotechnology & Applied Microbiology

Molecular epidemiology of breast cancer: genetic variation in steroid hormone metabolism

VN Kristensen et al.

MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH (2000)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)

Article Genetics & Heredity

A general test of association for quantitative traits in nuclear families

GR Abecasis et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2000)