MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning

(2020) Janine Arloth et al.   PLoS Computational Biology

A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data

(2020) David Lamparter et al.   PLoS Computational Biology

Abnormal Hypermethylation of CpG Dinucleotides in Promoter Regions of Matrix Metalloproteinases Genes in Breast Cancer and its Relation to Epigenomic Subtypes and HER2 Overexpression

(2020) Olga A. Simonova et al.   Biomedicines

Bayesian Genome-wide TWAS Method to Leverage both cis- and trans-eQTL Information through Summary Statistics

(2020) Justin M. Luningham et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk

(2019) Iris E. Jansen et al.   NATURE GENETICS

Probabilistic fine-mapping of transcriptome-wide association studies

(2019) Nicholas Mancuso et al.   NATURE GENETICS

Trans Effects on Gene Expression Can Drive Omnigenic Inheritance

(2019) Xuanyao Liu et al.   CELL

Imputed gene associations identify replicable trans ‐acting genes enriched in transcription pathways and complex traits

(2019) Heather E. Wheeler et al.   GENETIC EPIDEMIOLOGY

KCTD : A new gene family involved in neurodevelopmental and neuropsychiatric disorders

(2019) Xinchen Teng et al.   CNS Neuroscience & Therapeutics

TIGAR: An Improved Bayesian Tool for Transcriptomic Data Imputation Enhances Gene Mapping of Complex Traits

(2019) Sini Nagpal et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Integrative transcriptome imputation reveals tissue-specific and shared biological mechanisms mediating susceptibility to complex traits

(2019) Wen Zhang et al.   Nature Communications

A Comprehensive cis -eQTL Analysis Revealed Target Genes in Breast Cancer Susceptibility Loci Identified in Genome-wide Association Studies

(2018) Xingyi Guo et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr

(2018) Florian Privé et al.   BIOINFORMATICS

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression

(2018) Naomi R. Wray et al.   NATURE GENETICS

Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights

(2018) Alexander Gusev et al.   NATURE GENETICS

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

(2018) Jian Zhou et al.   NATURE GENETICS

Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms

(2018) Brandon L. Pierce et al.   Nature Communications

Inferring Novel Tumor Suppressor Genes with a Protein-Protein Interaction Network and Network Diffusion Algorithms

(2018) Lei Chen et al.   Molecular Therapy-Methods & Clinical Development

ROCK inhibitor enhances the growth and migration of BRAF-mutant skin melanoma cells

(2018) Fei Chang et al.   CANCER SCIENCE

Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility

(2018) Towfique Raj et al.   NATURE GENETICS

Common and rare GCH1 variants are associated with Parkinson disease

(2018) Uladzislau Rudakou et al.   NEUROBIOLOGY OF AGING

A multi-omic atlas of the human frontal cortex for aging and Alzheimer’s disease research

(2018) Philip L. De Jager et al.   Scientific Data

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

(2018) Michael J. Gandal et al.   SCIENCE

Identifyingcis-mediators fortrans-eQTLs across many human tissues using genomic mediation analysis

(2017) Fan Yang et al.   GENOME RESEARCH

TP73-AS1 promotes breast cancer cell proliferation through miR-200a-mediated TFAM inhibition

(2017) Jia Yao et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Case–control association mapping by proxy using family history of disease

(2017) Jimmy Z Liu et al.   NATURE GENETICS

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

(2017) Rebecca Sims et al.   NATURE GENETICS

Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue

(2017) Alejandro Quiroz-Zárate et al.   PLoS One

Improved regulatory element prediction based on tissue-specific local epigenomic signatures

(2017) Yupeng He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Meta-analysis of three genome-wide association studies identifies two loci that predict survival and treatment outcome in breast cancer

(2017) Sofia Khan et al.   Oncotarget

An Efficient Elastic Net with Regression Coefficients Method for Variable Selection of Spectrum Data

(2017) Wenya Liu et al.   PLoS One

Clinicopathological and prognostic significance of mitogen-activated protein kinases (MAPK) in breast cancers

(2016) Dena A. J. Ahmad et al.   BREAST CANCER RESEARCH AND TREATMENT

Integrative approaches for large-scale transcriptome-wide association studies

(2016) Alexander Gusev et al.   NATURE GENETICS

Inhibitors of Rho kinase (ROCK) signaling revert the malignant phenotype of breast cancer cells in 3D context

(2016) Masahiro Matsubara et al.   Oncotarget

Systematic drug perturbations on cancer cells reveal diverse exit paths from proliferative state

(2016) Joseph X. Zhou et al.   Oncotarget

Matrix metalloproteinases as drivers and therapeutic targets in breast cancer

(2015) Evette S. Radisky   Frontiers in Bioscience-Landmark

BatchJobsandBatchExperiments: Abstraction Mechanisms for UsingRin Batch Environments

(2015) Bernd Bischl et al.   Journal of Statistical Software

Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer

(2015) Kyriaki Michailidou et al.   NATURE GENETICS

Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index

(2015) Jian Yang et al.   NATURE GENETICS

A gene-based association method for mapping traits using reference transcriptome data

(2015) Eric R Gamazon et al.   NATURE GENETICS

Spatiotemporal 16p11.2 Protein Network Implicates Cortical Late Mid-Fetal Brain Development and KCTD13-Cul3-RhoA Pathway in Psychiatric Diseases

(2015) Guan Ning Lin et al.   NEURON

Tissue-Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing

(2015) Maria Gutierrez-Arcelus et al.   PLoS Genetics

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Fast and accurate imputation of summary statistics enhances evidence of functional enrichment

(2014) Bogdan Pasaniuc et al.   BIOINFORMATICS

A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness

(2014) Jared O'Connell et al.   PLoS Genetics

Mediation Analysis Demonstrates That Trans-eQTLs Are Often Explained by Cis-Mediation: A Genome-Wide Analysis among 1,800 South Asians

(2014) Brandon L. Pierce et al.   PLoS Genetics

Sherlock: Detecting Gene-Disease Associations by Matching Patterns of Expression QTL and GWAS

(2013) Xin He et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Overview and Findings from the Rush Memory and Aging Project

(2013) David A. Bennett et al.   Current Alzheimer Research

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

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

(2013) Kyriaki Michailidou et al.   NATURE GENETICS

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease

(2013) Jean-Charles Lambert et al.   NATURE GENETICS

Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge

(2013) Sara Mostafavi et al.   PLoS One

Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs

(2013) Christopher D. Brown et al.   PLoS Genetics

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

(2013) Patrik Waldmann et al.   Frontiers in Genetics

A General Framework for Two-Stage Analysis of Genome-wide Association Studies and Its Application to Case-Control Studies

(2012) James M.S. Wason et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

An atlas of tissue-specific conserved coexpression for functional annotation and disease gene prediction

(2011) Rosario Michael Piro et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

A linear complexity phasing method for thousands of genomes

(2011) Olivier Delaneau et al.   NATURE METHODS

A genome-wide scan for common variants affecting the rate of age-related cognitive decline

(2011) Philip L. De Jager et al.   NEUROBIOLOGY OF AGING

Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP

(2011) Jeffrey B. Endelman   Plant Genome

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE