Network biomarkers reveal dysfunctional gene regulations during disease progression

Tracing dynamic biological processes during phase transition

(2013) Tao Zeng et al.   BMC Systems Biology

Detecting tissue-specific early warning signals for complex diseases based on dynamical network biomarkers: study of type 2 diabetes by cross-tissue analysis

(2013) M. Li et al.   BRIEFINGS IN BIOINFORMATICS

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

(2013) Rui Liu et al.   MEDICINAL RESEARCH REVIEWS

Clinical Relevance of Plasma Prostaglandin F2α Metabolite Concentrations in Patients with Idiopathic Pulmonary Fibrosis

(2013) Kensaku Aihara et al.   PLoS One

APG: an Active Protein-Gene Network Model to Quantify Regulatory Signals in Complex Biological Systems

(2013) Jiguang Wang et al.   Scientific Reports

Spatio-temporal analysis of type 2 diabetes mellitus based on differential expression networks

(2013) Shao-Yan Sun et al.   Scientific Reports

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

(2012) Xiujun Zhang et al.   BIOINFORMATICS

Comparative evaluation of set-level techniques in predictive classification of gene expression samples

(2012) Matej Holec et al.   BMC BIOINFORMATICS

Identifying dysregulated pathways in cancers from pathway interaction networks

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

IL28B polymorphisms predict interferon-related hepatitis B surface antigen seroclearance in genotype D hepatitis B e antigen-negative patients with chronic hepatitis B

(2012) Pietro Lampertico et al.   HEPATOLOGY

An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer

(2012) Zhenshu Wen et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

Novel biomarkers for pre-diabetes identified by metabolomics

(2012) Rui Wang-Sattler et al.   Molecular Systems Biology

Family history versus SNPs for disease predictions

(2012) Hannah Stower   NATURE REVIEWS GENETICS

ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions

(2012) Xianwen Ren et al.   NUCLEIC ACIDS RESEARCH

Reconstructing dynamic gene regulatory networks from sample-based transcriptional data

(2012) Hailong Zhu et al.   NUCLEIC ACIDS RESEARCH

Anti-IL-7 receptor-  reverses established type 1 diabetes in nonobese diabetic mice by modulating effector T-cell function

(2012) L.-F. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coexpression network analysis in chronic hepatitis B and C hepatic lesions reveals distinct patterns of disease progression to hepatocellular carcinoma

(2012) Danning He et al.   Journal of Molecular Cell Biology

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

Differential network entropy reveals cancer system hallmarks

(2012) James West et al.   Scientific Reports

Early Warning Signals for Critical Transitions: A Generalized Modeling Approach

(2012) Steven J. Lade et al.   PLoS Computational Biology

Caveolin-1 and Cancer Metabolism in the Tumor Microenvironment: Markers, Models, and Mechanisms

(2011) Federica Sotgia et al.   Annual Review of Pathology-Mechanisms of Disease

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

(2011) Xiujun Zhang et al.   BIOINFORMATICS

DART: Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference

(2011) Yan Jiao et al.   BMC BIOINFORMATICS

A comparative study on gene-set analysis methods for assessing differential expression associated with the survival phenotype

(2011) Seungyeoun Lee et al.   BMC BIOINFORMATICS

Association of IL28B gene polymorphism with development of hepatocellular carcinoma in Japanese patients with chronic hepatitis C virus infection

(2011) Satoru Joshita et al.   HUMAN IMMUNOLOGY

Identifying disease genes and module biomarkers by differential interactions

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

Algorithms in nature: the convergence of systems biology and computational thinking

(2011) S. Navlakha et al.   Molecular Systems Biology

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

BioNet: an R-Package for the functional analysis of biological networks

(2010) D. Beisser et al.   BIOINFORMATICS

Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context

(2010) Gad Abraham et al.   BMC BIOINFORMATICS

Increased entropy of signal transduction in the cancer metastasis phenotype

(2010) Andrew E Teschendorff et al.   BMC Systems Biology

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

Structure and Function of the Human Breast Cancer Resistance Protein (BCRP/ABCG2)

(2010) Zhanglin Ni et al.   CURRENT DRUG METABOLISM

Increased Expression of  -N-Acetylglucosaminidase in Erythrocytes From Individuals With Pre-diabetes and Diabetes

(2010) K. Park et al.   DIABETES

Development of a mathematical model that predicts the outcome of hormone therapy for prostate cancer

(2010) Yoshito Hirata et al.   JOURNAL OF THEORETICAL BIOLOGY

Signatures of mutation and selection in the cancer genome

(2010) Graham R. Bignell et al.   NATURE

Early warning signals of extinction in deteriorating environments

(2010) John M. Drake et al.   NATURE

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

DEGAS: De Novo Discovery of Dysregulated Pathways in Human Diseases

(2010) Igor Ulitsky et al.   PLoS One

Identification of high-quality cancer prognostic markers and metastasis network modules

(2010) Jie Li et al.   Nature Communications

Mixture classification model based on clinical markers for breast cancer prognosis

(2009) Tao Zeng et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

A Gene Signature Predictive for Outcome in Advanced Ovarian Cancer Identifies a Survival Factor: Microfibril-Associated Glycoprotein 2

(2009) Samuel C. Mok et al.   CANCER CELL

Cross-platform method for identifying candidate network biomarkers for prostate cancer

(2009) G. Jin et al.   IET Systems Biology

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Maximization of negative correlations in time-course gene expression data for enhancing understanding of molecular pathways

(2009) Tao Zeng et al.   NUCLEIC ACIDS RESEARCH

Prognostic gene signatures for non-small-cell lung cancer

(2009) Paul C. Boutros et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic brain networks in neurodegenerative disorders: a functional imaging approach

(2009) David Eidelberg   TRENDS IN NEUROSCIENCES

Identifying functional modules in protein-protein interaction networks: an integrated exact approach

(2008) M. T. Dittrich et al.   BIOINFORMATICS

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

Integrated Weighted Gene Co-expression Network Analysis with an Application to Chronic Fatigue Syndrome

(2008) Angela P Presson et al.   BMC Systems Biology

Tissue- and age-specific changes in gene expression during disease induction and progression in NOD mice

(2008) Keiichi Kodama et al.   CLINICAL IMMUNOLOGY

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology