Genetic variants and their interactions in disease risk prediction – machine learning and network perspectives

Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations

(2012) Tapio Pahikkala et al.   Algorithms for Molecular Biology

Optimal Unified Approach for Rare-Variant Association Testing with Application to Small-Sample Case-Control Whole-Exome Sequencing Studies

(2012) Seunggeun Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A scalable and portable framework for massively parallel variable selection in genetic association studies

(2012) Gary K. Chen   BIOINFORMATICS

A Lasso multi-marker mixed model for association mapping with population structure correction

(2012) Barbara Rakitsch et al.   BIOINFORMATICS

Learning from our GWAS mistakes: from experimental design to scientific method

(2012) C. G. Lambert et al.   BIOSTATISTICS

Interaction among apoptosis-associated sequence variants and joint effects on aggressive prostate cancer

(2012) Nicole A Lavender et al.   BMC Medical Genomics

Network biology methods integrating biological data for translational science

(2012) G. Bebek et al.   BRIEFINGS IN BIOINFORMATICS

Achieving the Promise of Personalized Medicine

(2012) K S Reynolds   CLINICAL PHARMACOLOGY & THERAPEUTICS

Risk estimation and risk prediction using machine-learning methods

(2012) Jochen Kruppa et al.   HUMAN GENETICS

Network-Induced Classification Kernels for Gene Expression Profile Analysis

(2012) Ofer Lavi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

(2012) Andrea Califano et al.   NATURE GENETICS

BiForce Toolbox: powerful high-throughput computational analysis of gene-gene interactions in genome-wide association studies

(2012) A. Gyenesei et al.   NUCLEIC ACIDS RESEARCH

The rocky road to personalized medicine: computational and statistical challenges

(2012) Jukka Corander et al.   Personalized Medicine

Bayesian Variable Selection in Searching for Additive and Dominant Effects in Genome-Wide Data

(2012) Tomi Peltola et al.   PLoS One

Genetic Signatures of Exceptional Longevity in Humans

(2012) Paola Sebastiani et al.   PLoS One

Epistasis dominates the genetic architecture of Drosophila quantitative traits

(2012) W. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The mystery of missing heritability: Genetic interactions create phantom heritability

(2012) O. Zuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cancer heterogeneity: origins and implications for genetic association studies

(2012) Davnah Urbach et al.   TRENDS IN GENETICS

Pathway analysis of genomic data: concepts, methods, and prospects for future development

(2012) Vijay K. Ramanan et al.   TRENDS IN GENETICS

Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction

(2012) Magali Michaut et al.   PLoS Computational Biology

Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes

(2012) Christof Winter et al.   PLoS Computational Biology

The Empirical Power of Rare Variant Association Methods: Results from Sanger Sequencing in 1,998 Individuals

(2012) Martin Ladouceur et al.   PLoS Genetics

Using Whole-Genome Sequence Data to Predict Quantitative Trait Phenotypes in Drosophila melanogaster

(2012) Ulrike Ober et al.   PLoS Genetics

Mining high-throughput screens for cancer drug targets-lessons from yeast chemical-genomic profiling and synthetic lethality

(2012) Marja A. Heiskanen et al.   Wiley Interdisciplinary Reviews-Data Mining and Knowledge Discovery

A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization

(2012) Johannes Tuikkala et al.   BioData Mining

Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms

(2012) Fredrik Barrenäs et al.   GENOME BIOLOGY

Six Degrees of Epistasis: Statistical Network Models for GWAS

(2012) B. A. McKinney et al.   Frontiers in Genetics

Bayesian Methods for Multivariate Modeling of Pleiotropic SNP Associations and Genetic Risk Prediction

(2012) Stephen W. Hartley et al.   Frontiers in Genetics

eCEO: an efficient Cloud Epistasis cOmputing model in genome-wide association study

(2011) Z. Wang et al.   BIOINFORMATICS

Characterizing genetic interactions in human disease association studies using statistical epistasis networks

(2011) Ting Hu et al.   BMC BIOINFORMATICS

Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis

(2011) Rolf O Lindén et al.   BMC Systems Biology

An empirical assessment of validation practices for molecular classifiers

(2011) P. J. Castaldi et al.   BRIEFINGS IN BIOINFORMATICS

Validation in Genetic Association Studies

(2011) I. R. Konig   BRIEFINGS IN BIOINFORMATICS

Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power

(2011) Trey Ideker et al.   CELL

Genetic Interactions in Cancer Progression and Treatment

(2011) Alan Ashworth et al.   CELL

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Predicting Genetic Values: A Kernel-Based Best Linear Unbiased Prediction With Genomic Data

(2011) Ulrike Ober et al.   GENETICS

The GA and the GWAS: Using Genetic Algorithms to Search for Multilocus Associations

(2011) M. A. Mooney et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Initial impact of the sequencing of the human genome

(2011) Eric S. Lander   NATURE

Predicting mutation outcome from early stochastic variation in genetic interaction partners

(2011) Alejandro Burga et al.   NATURE

Predicting phenotypic variation in yeast from individual genome sequences

(2011) Rob Jelier et al.   NATURE GENETICS

A rare variant in MYH6 is associated with high risk of sick sinus syndrome

(2011) Hilma Holm et al.   NATURE GENETICS

Basic statistical analysis in genetic case-control studies

(2011) Geraldine M Clarke et al.   Nature Protocols

Molecular mechanisms of epistasis within and between genes

(2011) Ben Lehner   TRENDS IN GENETICS

Beyond Missing Heritability: Prediction of Complex Traits

(2011) Robert Makowsky et al.   PLoS Genetics

Pathways of Distinction Analysis: A New Technique for Multi–SNP Analysis of GWAS Data

(2011) Rosemary Braun et al.   PLoS Genetics

Integrating Pathway Analysis and Genetics of Gene Expression for Genome-wide Association Studies

(2010) Hua Zhong et al.   AMERICAN JOURNAL OF HUMAN GENETICS

FastEpistasis: a high performance computing solution for quantitative trait epistasis

(2010) Thierry Schüpbach et al.   BIOINFORMATICS

Bioinformatics challenges for genome-wide association studies

(2010) J. H. Moore et al.   BIOINFORMATICS

A variable selection method for genome-wide association studies

(2010) Qianchuan He et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

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

Quantitative Genetic Interactions Reveal Biological Modularity

(2010) Pedro Beltrao et al.   CELL

Genome-wide gene and pathway analysis

(2010) Li Luo et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Risk prediction using genome-wide association studies

(2010) Charles Kooperberg et al.   GENETIC EPIDEMIOLOGY

Founder population-specific HapMap panel increases power in GWA studies through improved imputation accuracy and CNV tagging

(2010) I. Surakka et al.   GENOME RESEARCH

A multilocus genetic risk score for coronary heart disease: case-control and prospective cohort analyses

(2010) Samuli Ripatti et al.   LANCET

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

Hints of hidden heritability in GWAS

(2010) Greg Gibson   NATURE GENETICS

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

Analysing biological pathways in genome-wide association studies

(2010) Kai Wang et al.   NATURE REVIEWS GENETICS

Statistical analysis strategies for association studies involving rare variants

(2010) Vikas Bansal et al.   NATURE REVIEWS GENETICS

Missing heritability and strategies for finding the underlying causes of complex disease

(2010) Evan E. Eichler et al.   NATURE REVIEWS GENETICS

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Genomewide Association Studies and Assessment of the Risk of Disease

(2010) Teri A. Manolio   NEW ENGLAND JOURNAL OF MEDICINE

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Mathematical Modeling of Molecular Data in Translational Medicine: Theoretical Considerations

(2010) N. F. Marko et al.   Science Translational Medicine

Beyond genome-wide association studies: genetic heterogeneity and individual predisposition to cancer

(2010) Antonella Galvan et al.   TRENDS IN GENETICS

Genetic Variants and Their Interactions in the Prediction of Increased Pre-Clinical Carotid Atherosclerosis: The Cardiovascular Risk in Young Finns Study

(2010) Sebastian Okser et al.   PLoS Genetics

Epistasis and Its Implications for Personal Genetics

(2009) Jason H. Moore et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Pitfalls of supervised feature selection

(2009) Pawel Smialowski et al.   BIOINFORMATICS

Genome-wide association analysis by lasso penalized logistic regression

(2009) Tong Tong Wu et al.   BIOINFORMATICS

Gene and pathway-based second-wave analysis of genome-wide association studies

(2009) Gang Peng et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Harnessing the information contained within genome-wide association studies to improve individual prediction of complex disease risk

(2009) David M. Evans et al.   HUMAN MOLECULAR GENETICS

Pathway and network-based analysis of genome-wide association studies in multiple sclerosis

(2009) S. E. Baranzini et al.   HUMAN MOLECULAR GENETICS

Personalizing medicine: a systems biology perspective

(2009) Thomas S Deisboeck   Molecular Systems Biology

Molecular networks as sensors and drivers of common human diseases

(2009) Eric E. Schadt   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Beyond odds ratios — communicating disease risk based on genetic profiles

(2009) Peter Kraft et al.   NATURE REVIEWS GENETICS

Detecting gene–gene interactions that underlie human diseases

(2009) Heather J Cordell   NATURE REVIEWS GENETICS

Synthetic Lethality — A New Direction in Cancer-Drug Development

(2009) J. Dirk Iglehart et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

Pathway Analysis of GWAS Provides New Insights into Genetic Susceptibility to 3 Inflammatory Diseases

(2009) Hariklia Eleftherohorinou et al.   PLoS One

Genome-Wide Association Data Reveal a Global Map of Genetic Interactions among Protein Complexes

(2009) Gregory Hannum et al.   PLoS Genetics

Capturing the Spectrum of Interaction Effects in Genetic Association Studies by Simulated Evaporative Cooling Network Analysis

(2009) Brett A. McKinney et al.   PLoS Genetics

Interpretation of Genetic Association Studies: Markers with Replicated Highly Significant Odds Ratios May Be Poor Classifiers

(2009) Johanna Jakobsdottir et al.   PLoS Genetics

From Disease Association to Risk Assessment: An Optimistic View from Genome-Wide Association Studies on Type 1 Diabetes

(2009) Zhi Wei et al.   PLoS Genetics

Systematic Mapping of Genetic Interaction Networks

(2008) Scott J. Dixon et al.   Annual Review of Genetics

A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification

(2008) Alexander Statnikov et al.   BMC BIOINFORMATICS

Pathway analysis of seven common diseases assessed by genome-wide association

(2008) Ali Torkamani et al.   GENOMICS

Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseases

(2008) Kristine A. Pattin et al.   HUMAN GENETICS

Pathways-based analyses of whole-genome association study data in bipolar disorder reveal genes mediating ion channel activity and synaptic neurotransmission

(2008) Kathleen Askland et al.   HUMAN GENETICS

Detecting Interactions in Association Studies by Using Simple Allele Recoding

(2008) Mikko J. Sillanpää   HUMAN HEREDITY

Accounting for ancestry: population substructure and genome-wide association studies

(2008) C. Tian et al.   HUMAN MOLECULAR GENETICS

Whole genome survey of coding SNPs reveals a reproducible pathway determinant of Parkinson disease

(2008) Balaji S. Srinivasan et al.   HUMAN MUTATION

Personal genomes: The case of the missing heritability

(2008) Brendan Maher   NATURE

Progress and challenges in genome-wide association studies in humans

(2008) Peter Donnelly   NATURE

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology

Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems

(2008) Patrick C. Phillips   NATURE REVIEWS GENETICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Network properties of genes harboring inherited disease mutations

(2008) I. Feldman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology