Reaching the End-Game for GWAS: Machine Learning Approaches for the Prioritization of Complex Disease Loci

Making Sense of the Epigenome Using Data Integration Approaches

(2019) Emma Cazaly et al.   Frontiers in Pharmacology

A network approach to prioritizing susceptibility genes for genome-wide association studies

(2019) Somayeh Kafaie et al.   GENETIC EPIDEMIOLOGY

Prioritizing Crohn’s disease genes by integrating association signals with gene expression implicates monocyte subsets

(2019) Kyle Gettler et al.   GENES AND IMMUNITY

Identification of disease-associated loci using machine learning for genotype and network data integration

(2019) Luis G Leal et al.   BIOINFORMATICS

A Convergent Study of Genetic Variants Associated With Crohn’s Disease: Evidence From GWAS, Gene Expression, Methylation, eQTL and TWAS

(2019) Yulin Dai et al.   Frontiers in Genetics

Genome-wide association study identifies loci for arterial stiffness index in 127,121 UK Biobank participants

(2019) Kenneth Fung et al.   Scientific Reports

Genome-Wide Analysis of Left Ventricular Image-Derived Phenotypes Identifies Fourteen Loci Associated with Cardiac Morphogenesis and Heart Failure Development

(2019) Nay Aung et al.   CIRCULATION

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

(2019) Mike A Nalls et al.   LANCET NEUROLOGY

Targeting transcriptional control of soluble guanylyl cyclase via NOTCH for prevention of cardiovascular disease

(2018) C. Rippe et al.   Acta Physiologica

The revival of the Gini importance?

(2018) Stefano Nembrini et al.   BIOINFORMATICS

Prediction of enhancer-promoter interactions via natural language processing

(2018) Wanwen Zeng et al.   BMC GENOMICS

GWAS-based machine learning approach to predict duloxetine response in major depressive disorder

(2018) Malgorzata Maciukiewicz et al.   JOURNAL OF PSYCHIATRIC RESEARCH

Leveraging multiple gene networks to prioritize GWAS candidate genes via network representation learning

(2018) Mengmeng Wu et al.   METHODS

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk

(2018) Jian Zhou et al.   NATURE GENETICS

Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits

(2018) Evangelos Evangelou et al.   NATURE GENETICS

Uncovering association networks through an eQTL analysis involving human miRNAs and lincRNAs

(2018) Paulo R. Branco et al.   Scientific Reports

Leveraging Polygenic Functional Enrichment to Improve GWAS Power

(2018) Gleb Kichaev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

iMEGES: integrated mental-disorder GEnome score by deep neural network for prioritizing the susceptibility genes for mental disorders in personal genomes

(2018) Atlas Khan et al.   BMC BIOINFORMATICS

Trans-ethnic association study of blood pressure determinants in over 750,000 individuals

(2018) Ayush Giri et al.   NATURE GENETICS

Interethnic analyses of blood pressure loci in populations of East Asian and European descent

(2018) Fumihiko Takeuchi et al.   Nature Communications

The biological impact of blood pressure-associated genetic variants in the natriuretic peptide receptor C gene on human vascular smooth muscle

(2017) Meixia Ren et al.   HUMAN MOLECULAR GENETICS

Machine Learning–Based Gene Prioritization Identifies Novel Candidate Risk Genes for Inflammatory Bowel Disease

(2017) Ofer Isakov et al.   INFLAMMATORY BOWEL DISEASES

Imbalance-Aware Machine Learning for Predicting Rare and Common Disease-Associated Non-Coding Variants

(2017) Max Schubach et al.   Scientific Reports

Computational methods using genome-wide association studies to predict radiotherapy complications and to identify correlative molecular processes

(2017) Jung Hun Oh et al.   Scientific Reports

Hypertension reduces soluble guanylyl cyclase expression in the mouse aorta via the Notch signaling pathway

(2017) Catarina Rippe et al.   Scientific Reports

A machine-learning heuristic to improve gene score prediction of polygenic traits

(2017) Guillaume Paré et al.   Scientific Reports

Best (but oft-forgotten) practices: the design, analysis, and interpretation of Mendelian randomization studies

(2016) Philip C Haycock et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Impact of genetically supported target selection on R&D productivity

(2016) Mark R. Hurle et al.   NATURE REVIEWS DRUG DISCOVERY

Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies

(2016) Qiongshi Lu et al.   PLoS Genetics

r2VIM: A new variable selection method for random forests in genome-wide association studies

(2016) Silke Szymczak et al.   BioData Mining

Combining Multiple Hypothesis Testing with Machine Learning Increases the Statistical Power of Genome-wide Association Studies

(2016) Bettina Mieth et al.   Scientific Reports

GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation

(2015) Qiongshi Lu et al.   BIOINFORMATICS

Improved integrative framework combining association data with gene expression features to prioritize Crohn's disease genes

(2015) Kaida Ning et al.   HUMAN MOLECULAR GENETICS

Smoking Gun or Circumstantial Evidence? Comparison of Statistical Learning Methods using Functional Annotations for Prioritizing Risk Variants

(2015) Sarah A. Gagliano et al.   Scientific Reports

The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets

(2015) Takaya Saito et al.   PLoS One

Fast detection of high-order epistatic interactions in genome-wide association studies using information theoretic measure

(2014) Sangseob Leem et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Mutations in filamin C cause a new form of familial hypertrophic cardiomyopathy

(2014) Rafael Valdés-Mas et al.   Nature Communications

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

Random forests on Hadoop for genome-wide association studies of multivariate neuroimaging phenotypes

(2013) Yue Wang et al.   BMC BIOINFORMATICS

Comparative efficacy and tolerability of 15 antipsychotic drugs in schizophrenia: a multiple-treatments meta-analysis

(2013) Stefan Leucht et al.   LANCET

Gradient boosting machines, a tutorial

(2013) Alexey Natekin et al.   Frontiers in Neurorobotics

Convergent functional genomics of schizophrenia: from comprehensive understanding to genetic risk prediction

(2012) M Ayalew et al.   MOLECULAR PSYCHIATRY

Use of genome-wide association studies for drug repositioning

(2012) Philippe Sanseau et al.   NATURE BIOTECHNOLOGY

Prediction using step-wise L1, L2 regularization and feature selection for small data sets with large number of features

(2011) Ozgur Demir-Kavuk et al.   BMC BIOINFORMATICS

ProDiGe: Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples

(2011) Fantine Mordelet et al.   BMC BIOINFORMATICS

Achievement of treatment goals for primary prevention of cardiovascular disease in clinical practice across Europe: the EURIKA study

(2011) J. R. Banegas et al.   EUROPEAN HEART JOURNAL

New therapies for inflammatory bowel disease: from the bench to the bedside

(2011) Silvio Danese   GUT

Ranking causal variants and associated regions in genome-wide association studies by the support vector machine and random forest

(2011) Usman Roshan et al.   NUCLEIC ACIDS RESEARCH

A Latent Model for Prioritization of SNPs for Functional Studies

(2011) Brooke L. Fridley et al.   PLoS One