Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data

Shared regulatory sites are abundant in the human genome and shed light on genome evolution and disease pleiotropy

(2017) Pin Tong et al.   PLoS Genetics

cit: hypothesis testing software for mediation analysis in genomic applications

(2016) Joshua Millstein et al.   BIOINFORMATICS

Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets

(2016) Zhihong Zhu et al.   NATURE GENETICS

Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease

(2016) Husain A. Talukdar et al.   Cell Systems

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

kruX: matrix-based non-parametric eQTL discovery

(2014) Jianlong Qi et al.   BMC BIOINFORMATICS

The Functional Consequences of Variation in Transcription Factor Binding

(2014) Darren A. Cusanovich et al.   PLoS Genetics

Modeling Causality for Pairs of Phenotypes in System Genetics

(2013) E. C. Neto et al.   GENETICS

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Systems genetics approaches to understand complex traits

(2013) Mete Civelek et al.   NATURE REVIEWS GENETICS

miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions

(2013) Sheng-Da Hsu et al.   NUCLEIC ACIDS RESEARCH

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Simulating systems genetics data with SysGenSIM

(2011) A. Pinna et al.   BIOINFORMATICS

miRWalk – Database: Prediction of possible miRNA binding sites by “walking” the genes of three genomes

(2011) Harsh Dweep et al.   JOURNAL OF BIOMEDICAL INFORMATICS

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

(2011) T. Vergoulis et al.   NUCLEIC ACIDS RESEARCH

Critical reasoning on causal inference in genome-wide linkage and association studies

(2010) Yang Li et al.   TRENDS IN GENETICS

Lessons from the DREAM2 Challenges

(2009) Gustavo Stolovitzky et al.   Annals of the New York Academy of Sciences

Disentangling molecular relationships with a causal inference test

(2009) Joshua Millstein et al.   BMC GENETICS

Illustrating bias due to conditioning on a collider

(2009) Stephen R Cole et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Molecular networks as sensors and drivers of common human diseases

(2009) Eric E. Schadt   NATURE

Using genetic markers to orient the edges in quantitative trait networks: The NEO software

(2008) Jason E Aten et al.   BMC Systems Biology

Reverse engineering the genotype–phenotype map with natural genetic variation

(2008) Matthew V. Rockman   NATURE

miRecords: an integrated resource for microRNA-target interactions

(2008) F. Xiao et al.   NUCLEIC ACIDS RESEARCH