Quantifying Gene Regulatory Relationships with Association Measures: A Comparative Study

Part mutual information for quantifying direct associations in networks

(2016) Juan Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Causal inference and the data-fusion problem

(2016) Elias Bareinboim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data

(2015) Zhi-Ping Liu   CURRENT GENOMICS

Simple linear regression

(2015) Naomi Altman et al.   NATURE METHODS

Association, correlation and causation

(2015) Naomi Altman et al.   NATURE METHODS

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

(2015) Zhi-Ping Liu et al.   Database-The Journal of Biological Databases and Curation

Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection

(2014) Zhi-Ping Liu et al.   BMC BIOINFORMATICS

Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks

(2014) Xiujun Zhang et al.   NUCLEIC ACIDS RESEARCH

Modeling Genome-Wide Dynamic Regulatory Network in Mouse Lungs with Influenza Infection Using High-Dimensional Ordinary Differential Equations

(2014) Shuang Wu et al.   PLoS One

Gene coexpression measures in large heterogeneous samples using count statistics

(2014) Y. X. Rachel Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gaussian graphical model for identifying significantly responsive regulatory networks from time course high-throughput data

(2013) Zhi-Ping Liu et al.   IET Systems Biology

NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference

(2012) Xiujun Zhang et al.   BIOINFORMATICS

Network-based analysis of complex diseases

(2012) Z.-P. Liu et al.   IET Systems Biology

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information

(2011) Xiujun Zhang et al.   BIOINFORMATICS

Detecting Novel Associations in Large Data Sets

(2011) D. N. Reshef et al.   SCIENCE

Brownian distance covariance

(2010) Gábor J. Székely et al.   Annals of Applied Statistics

Gene Expression Profiling Indicates the Roles of Host Oxidative Stress, Apoptosis, Lipid Metabolism, and Intracellular Transport Genes in the Replication of Hepatitis C Virus

(2010) S. Blackham et al.   JOURNAL OF VIROLOGY

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS