Linking genotype to phenotype in multi-omics data of small sample

HAPPI GWAS: Holistic Analysis with Pre and Post Integration GWAS

(2020) Marianne L Slaten et al.   BIOINFORMATICS

From Genotype to Phenotype: Through Chromatin

(2019) Julia Romanowska et al.   Genes

Identification of trans-eQTLs using mediation analysis with multiple mediators

(2019) Nayang Shan et al.   BMC BIOINFORMATICS

Integration of methylation QTL and enhancer–target gene maps with schizophrenia GWAS summary results identifies novel genes

(2019) Chong Wu et al.   BIOINFORMATICS

Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits

(2018) Yang Wu et al.   Nature Communications

The Pathway Coexpression Network: Revealing pathway relationships

(2018) Yered Pita-Juárez et al.   PLoS Computational Biology

Medullary Breast Carcinoma, a Triple-Negative Breast Cancer Associated with BCLG Overexpression

(2018) Pierre Romero et al.   AMERICAN JOURNAL OF PATHOLOGY

Tissue-specific Network Analysis of Genetic Variants Associated with Coronary Artery Disease

(2018) Xiao Miao et al.   Scientific Reports

simGWAS: a fast method for simulation of large scale case-control GWAS summary statistics

(2018) Mary Fortune et al.   BIOINFORMATICS

A powerful method to integrate genotype and gene expression data for dissecting the genetic architecture of a disease

(2018) Sarmistha Das et al.   GENOMICS

An integrative tissue-network approach to identify and test human disease genes

(2018) Victoria Yao et al.   NATURE BIOTECHNOLOGY

Backward genotype-transcript-phenotype association mapping

(2017) Seunghak Lee et al.   METHODS

Integrative analysis reveals disrupted pathways regulated by microRNAs in cancer

(2017) Gary Wilk et al.   NUCLEIC ACIDS RESEARCH

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology

(2017) Aris Gioutlakis et al.   PLoS One

A network-driven approach for genome-wide association mapping

(2016) Seunghak Lee et al.   BIOINFORMATICS

PhenoScanner: a database of human genotype–phenotype associations

(2016) James R. Staley et al.   BIOINFORMATICS

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

(2015) Eric R Gamazon et al.   NATURE GENETICS

Methods of integrating data to uncover genotype–phenotype interactions

(2015) Marylyn D. Ritchie et al.   NATURE REVIEWS GENETICS

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Group descent algorithms for nonconvex penalized linear and logistic regression models with grouped predictors

(2013) Patrick Breheny et al.   STATISTICS AND COMPUTING

Penalized methods for bi-level variable selection

(2013) Patrick Breheny et al.   Statistics and Its Interface

ATHENA: Identifying interactions between different levels of genomic data associated with cancer clinical outcomes using grammatical evolution neural network

(2013) Dokyoon Kim et al.   BioData Mining

A Bayesian Integrative Genomic Model for Pathway Analysis of Complex Traits

(2012) Brooke L. Fridley et al.   GENETIC EPIDEMIOLOGY

SPICi: a fast clustering algorithm for large biological networks

(2010) Peng Jiang et al.   BIOINFORMATICS

Enumeration of condition-dependent dense modules in protein interaction networks

(2009) Elisabeth Georgii et al.   BIOINFORMATICS

Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space

(2008) Y. Loewenstein et al.   BIOINFORMATICS