Regularized Machine Learning in the Genetic Prediction of Complex Traits

Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression

(2014) Pekka Marttinen et al.   BIOINFORMATICS

Prediction of Fetal Hemoglobin in Sickle Cell Anemia Using an Ensemble of Genetic Risk Prediction Models

(2014) J. N. Milton et al.   Circulation-Cardiovascular Genetics

MultiBLUP: improved SNP-based prediction for complex traits

(2014) Doug Speed et al.   GENOME RESEARCH

Advantages and pitfalls in the application of mixed-model association methods

(2014) Jian Yang et al.   NATURE GENETICS

Improving the Accuracy of Whole Genome Prediction for Complex Traits Using the Results of Genome Wide Association Studies

(2014) Zhe Zhang et al.   PLoS One

Exploiting SNP Correlations within Random Forest for Genome-Wide Association Studies

(2014) Vincent Botta et al.   PLoS One

Genome-wide Association Analysis for Multiple Continuous Secondary Phenotypes

(2013) Elizabeth D. Schifano et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Large Sample Size, Wide Variant Spectrum, and Advanced Machine-Learning Technique Boost Risk Prediction for Inflammatory Bowel Disease

(2013) Zhi Wei et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Network-guided sparse regression modeling for detection of gene-by-gene interactions

(2013) Chen Lu et al.   BIOINFORMATICS

PleioGRiP: genetic risk prediction with pleiotropy

(2013) S. W. Hartley et al.   BIOINFORMATICS

ETHNOPRED: a novel machine learning method for accurate continental and sub-continental ancestry identification and population stratification correction

(2013) Mohsen Hajiloo et al.   BMC BIOINFORMATICS

Predicting phenotypic variation from genotypes, phenotypes and a combination of the two

(2013) Alejandro Burga et al.   CURRENT OPINION IN BIOTECHNOLOGY

Strategies for Developing Prediction Models From Genome-Wide Association Studies

(2013) Jincao Wu et al.   GENETIC EPIDEMIOLOGY

Genetic Prediction of Quantitative Lipid Traits: Comparing Shrinkage Models to Gene Scores

(2013) Helen Warren et al.   GENETIC EPIDEMIOLOGY

Genetic and Nongenetic Variation Revealed for the Principal Components of Human Gene Expression

(2013) Anita Goldinger et al.   GENETICS

Genome-Wide Prediction of Traits with Different Genetic Architecture Through Efficient Variable Selection

(2013) V. Wimmer et al.   GENETICS

Building a Genome Analysis Pipeline to Predict Disease Risk and Prevent Disease

(2013) Y. Bromberg   JOURNAL OF MOLECULAR BIOLOGY

Epigenetic epistatic interactions constrain the evolution of gene expression

(2013) S. Park et al.   Molecular Systems Biology

Negligible impact of rare autoimmune-locus coding-region variants on missing heritability

(2013) Karen A. Hunt et al.   NATURE

Finding the sources of missing heritability in a yeast cross

(2013) Joshua S. Bloom et al.   NATURE

Combined sequence-based and genetic mapping analysis of complex traits in outbred rats

(2013) Amelie Baud et al.   NATURE GENETICS

Projecting the performance of risk prediction based on polygenic analyses of genome-wide association studies

(2013) Nilanjan Chatterjee et al.   NATURE GENETICS

Genotype to phenotype: lessons from model organisms for human genetics

(2013) Ben Lehner   NATURE REVIEWS GENETICS

Integrative approaches for finding modular structure in biological networks

(2013) Koyel Mitra et al.   NATURE REVIEWS GENETICS

Pleiotropy in complex traits: challenges and strategies

(2013) Nadia Solovieff et al.   NATURE REVIEWS GENETICS

Bringing genome-wide association findings into clinical use

(2013) Teri A. Manolio   NATURE REVIEWS GENETICS

Pitfalls of predicting complex traits from SNPs

(2013) Naomi R. Wray et al.   NATURE REVIEWS GENETICS

Genome-wide association studies with high-dimensional phenotypes

(2013) Pekka Marttinen et al.   Statistical Applications in Genetics and Molecular Biology

From personalized to public health genomics

(2013) Greg Gibson et al.   Genome Medicine

Incremental value of rare genetic variants for the prediction of multifactorial diseases

(2013) Raluca Mihaescu et al.   Genome Medicine

PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data

(2013) Gabriel E. Hoffman et al.   PLoS Computational Biology

Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms

(2013) Ohad Manor et al.   PLoS Computational Biology

Robust Prediction of Expression Differences among Human Individuals Using Only Genotype Information

(2013) Ohad Manor et al.   PLoS Genetics

Pathways-Driven Sparse Regression Identifies Pathways and Genes Associated with High-Density Lipoprotein Cholesterol in Two Asian Cohorts

(2013) Matt Silver et al.   PLoS Genetics

Prediction of Complex Human Traits Using the Genomic Best Linear Unbiased Predictor

(2013) Gustavo de los Campos et al.   PLoS Genetics

Low Frequency Variants, Collapsed Based on Biological Knowledge, Uncover Complexity of Population Stratification in 1000 Genomes Project Data

(2013) Carrie B. Moore et al.   PLoS Genetics

Power and Predictive Accuracy of Polygenic Risk Scores

(2013) Frank Dudbridge   PLoS Genetics

Polygenic Modeling with Bayesian Sparse Linear Mixed Models

(2013) Xiang Zhou et al.   PLoS Genetics

GUESS-ing Polygenic Associations with Multiple Phenotypes Using a GPU-Based Evolutionary Stochastic Search Algorithm

(2013) Leonardo Bottolo et al.   PLoS Genetics

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

(2013) Sebastian Okser et al.   BioData Mining

Using Bayesian networks to discover relations between genes, environment, and disease

(2013) Chengwei Su et al.   BioData Mining

eQTL Epistasis – Challenges and Computational Approaches

(2013) Yang Huang et al.   Frontiers in Genetics

Evaluation of the lasso and the elastic net in genome-wide association studies

(2013) Patrik Waldmann et al.   Frontiers in Genetics

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

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

synbreed: a framework for the analysis of genomic prediction data using R

(2012) Valentin Wimmer et al.   BIOINFORMATICS

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

SparSNP: Fast and memory-efficient analysis of all SNPs for phenotype prediction

(2012) Gad Abraham et al.   BMC BIOINFORMATICS

Network biology methods integrating biological data for translational science

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

Machine learning approaches for the discovery of gene-gene interactions in disease data

(2012) R. Upstill-Goddard et al.   BRIEFINGS IN BIOINFORMATICS

Beyond genotype to phenotype: why the phenotype of an individual cannot always be predicted from their genome sequence and the environment that they experience

(2012) Alejandro Burga et al.   FEBS Journal

Performance and Robustness of Penalized and Unpenalized Methods for Genetic Prediction of Complex Human Disease

(2012) Gad Abraham et al.   GENETIC EPIDEMIOLOGY

Risk estimation and risk prediction using machine-learning methods

(2012) Jochen Kruppa et al.   HUMAN GENETICS

Improving the Prediction of Clinical Outcomes from Genomic Data Using Multiresolution Analysis

(2012) Pablo H. Hennings-Yeomans et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Correction for population stratification in random forest analysis

(2012) Yang Zhao et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Rare and common variants: twenty arguments

(2012) Greg Gibson   NATURE REVIEWS GENETICS

Identification of gene pathways implicated in Alzheimer's disease using longitudinal imaging phenotypes with sparse regression

(2012) Matt Silver et al.   NEUROIMAGE

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

(2012) Tomi Peltola et al.   PLoS One

Cancer heterogeneity: origins and implications for genetic association studies

(2012) Davnah Urbach et al.   TRENDS IN GENETICS

Chapter 11: Genome-Wide Association Studies

(2012) William S. Bush et al.   PLoS Computational Biology

Use of Pleiotropy to Model Genetic Interactions in a Population

(2012) Gregory W. Carter et al.   PLoS Genetics

Comparison of Family History and SNPs for Predicting Risk of Complex Disease

(2012) Chuong B. Do et al.   PLoS Genetics

Lessons from Model Organisms: Phenotypic Robustness and Missing Heritability in Complex Disease

(2012) Christine Queitsch et al.   PLoS Genetics

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

(2012) Ulrike Ober et al.   PLoS Genetics

Novel Loci for Metabolic Networks and Multi-Tissue Expression Studies Reveal Genes for Atherosclerosis

(2012) Michael Inouye et al.   PLoS Genetics

A Hierarchical Bayesian Approach to Multi-Trait Clinical Quantitative Trait Locus Modeling

(2012) Crispin M. Mutshinda 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

Naïve Bayesian Classifier and Genetic Risk Score for Genetic Risk Prediction of a Categorical Trait: Not so Different after all!

(2012) Paola Sebastiani et al.   Frontiers in Genetics

Gene-gene interaction filtering with ensemble of filters

(2011) Pengyi Yang et al.   BMC BIOINFORMATICS

Random forest Gini importance favours SNPs with large minor allele frequency: impact, sources and recommendations

(2011) A.-L. Boulesteix et al.   BRIEFINGS IN BIOINFORMATICS

Genetic Interactions in Cancer Progression and Treatment

(2011) Alan Ashworth et al.   CELL

Searching for synthetic lethality in cancer

(2011) Rachel Brough et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Mining gold dust under the genome wide significance level: a two-stage approach to analysis of GWAS

(2011) Gang Shi et al.   GENETIC EPIDEMIOLOGY

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

(2011) Ulrike Ober et al.   GENETICS

Genetic risk prediction in complex disease

(2011) Luke Jostins et al.   HUMAN MOLECULAR GENETICS

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

The Bayesian lasso for genome-wide association studies

(2010) Jiahan Li et al.   BIOINFORMATICS

Bioinformatics challenges for genome-wide association studies

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

Association screening of common and rare genetic variants by penalized regression

(2010) H. Zhou et al.   BIOINFORMATICS

A variable selection method for genome-wide association studies

(2010) Qianchuan He et al.   BIOINFORMATICS

An application of Random Forests to a genome-wide association dataset: Methodological considerations & new findings

(2010) Benjamin A Goldstein et al.   BMC GENETICS

Risk prediction using genome-wide association studies

(2010) Charles Kooperberg et al.   GENETIC EPIDEMIOLOGY

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

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

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

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

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

Genome-wide association analysis by lasso penalized logistic regression

(2009) Tong Tong Wu et al.   BIOINFORMATICS

Performance of random forest when SNPs are in linkage disequilibrium

(2009) Yan A Meng et al.   BMC BIOINFORMATICS

Machine learning in genome-wide association studies

(2009) Silke Szymczak et al.   GENETIC EPIDEMIOLOGY

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

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

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

Accommodating Linkage Disequilibrium in Genetic-Association Analyses via Ridge Regression

(2008) Nathalie Malo et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Personal genomes: The case of the missing heritability

(2008) Brendan Maher   NATURE

Spectral Algorithms for Supervised Learning

(2008) L. Lo Gerfo et al.   NEURAL COMPUTATION

Simultaneous Analysis of All SNPs in Genome-Wide and Re-Sequencing Association Studies

(2008) Clive J. Hoggart et al.   PLoS Genetics