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

Identifying critical transitions of complex diseases based on a single sample

(2014) Rui Liu et al.   BIOINFORMATICS

Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks

(2014) James C. Chen et al.   CELL

Network-based biomarkers for complex diseases

(2014) Xing-Ming Zhao et al.   JOURNAL OF THEORETICAL BIOLOGY

A survey on computational approaches to identifying disease biomarkers based on molecular networks

(2014) Guimin Qin et al.   JOURNAL OF THEORETICAL BIOLOGY

Equitability, mutual information, and the maximal information coefficient

(2014) Justin B. Kinney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regression Analysis of Combined Gene Expression Regulation in Acute Myeloid Leukemia

(2014) Yue Li et al.   PLoS Computational Biology

Quantifying causal influences

(2013) Dominik Janzing et al.   ANNALS OF STATISTICS

Early Diagnosis of Complex Diseases by Molecular Biomarkers, Network Biomarkers, and Dynamical Network Biomarkers

(2013) Rui Liu et al.   MEDICINAL RESEARCH REVIEWS

Network cleanup

(2013) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Network link prediction by global silencing of indirect correlations

(2013) Baruch Barzel et al.   NATURE BIOTECHNOLOGY

Network deconvolution as a general method to distinguish direct dependencies in networks

(2013) Soheil Feizi et al.   NATURE BIOTECHNOLOGY

High-resolution network biology: connecting sequence with function

(2013) Colm J. Ryan et al.   NATURE REVIEWS GENETICS

Integrative approaches for finding modular structure in biological networks

(2013) Koyel Mitra et al.   NATURE REVIEWS GENETICS

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Canonical correlation analysis for RNA-seq co-expression networks

(2013) Shengjun Hong et al.   NUCLEIC ACIDS RESEARCH

Reconstructing regulatory networks from the dynamic plasticity of gene expression by mutual information

(2013) Jianxin Wang et al.   NUCLEIC ACIDS RESEARCH

Gene network reconstruction reveals cell cycle and antiviral genes as major drivers of cervical cancer

(2013) Karina L. Mine et al.   Nature Communications

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

(2012) Xiujun Zhang et al.   BIOINFORMATICS

Inferring gene regulatory networks by ANOVA

(2012) Robert Küffner et al.   BIOINFORMATICS

Identifying dysregulated pathways in cancers from pathway interaction networks

(2012) Ke-Qin Liu et al.   BMC BIOINFORMATICS

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Reconstructing dynamic gene regulatory networks from sample-based transcriptional data

(2012) Hailong Zhu et al.   NUCLEIC ACIDS RESEARCH

Quantifying causal coupling strength: A lag-specific measure for multivariate time series related to transfer entropy

(2012) Jakob Runge et al.   PHYSICAL REVIEW E

Escaping the Curse of Dimensionality in Estimating Multivariate Transfer Entropy

(2012) Jakob Runge et al.   PHYSICAL REVIEW LETTERS

Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers

(2012) Luonan Chen et al.   Scientific Reports

Identifying critical transitions and their leading biomolecular networks in complex diseases

(2012) Rui Liu et al.   Scientific Reports

Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data

(2012) Santiago Treviño et al.   PLoS Computational Biology

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods

(2011) Thomas Schaffter et al.   BIOINFORMATICS

Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis

(2011) Zheng Li et al.   BIOINFORMATICS

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

(2011) Xiujun Zhang et al.   BIOINFORMATICS

An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma

(2011) Pavel Sumazin et al.   CELL

Identifying disease genes and module biomarkers by differential interactions

(2011) Xiaoping Liu et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Gene network inference and visualization tools for biologists: application to new human transcriptome datasets

(2011) Daniel Hurley et al.   NUCLEIC ACIDS RESEARCH

Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function

(2011) Vincenzo Belcastro et al.   NUCLEIC ACIDS RESEARCH

Functional characterization of bacterial sRNAs using a network biology approach

(2011) S. R. Modi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Construction of regulatory networks using expression time-series data of a genotyped population

(2011) K. Y. Yeung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting Novel Associations in Large Data Sets

(2011) D. N. Reshef et al.   SCIENCE

MISS: a non-linear methodology based on mutual information for genetic association studies in both population and sib-pairs analysis

(2010) Helena Brunel et al.   BIOINFORMATICS

Revealing differences in gene network inference algorithms on the network level by ensemble methods

(2010) Gökmen Altay et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Discovery of Chemical Compound Groups with Common Structures by a Network Analysis Approach (Affinity Prediction Method)

(2010) Shigeru Saito et al.   Journal of Chemical Information and Modeling

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Model-based method for transcription factor target identification with limited data

(2010) Antti Honkela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches

(2009) Irene Cantone et al.   CELL

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells

(2009) Kai Wang et al.   NATURE BIOTECHNOLOGY

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Uncovering signal transduction networks from high-throughput data by integer linear programming

(2008) Xing-Ming Zhao et al.   NUCLEIC ACIDS RESEARCH