SPNE: sample-perturbed network entropy for revealing critical states of complex biological systems

Hallmarks of Cancer: New Dimensions

(2022) Douglas Hanahan   Cancer Discovery

Detecting the critical states during disease development based on temporal network flow entropy

(2022) Rong Gao et al.   BRIEFINGS IN BIOINFORMATICS

Identifying the critical states and dynamic network biomarkers of cancers based on network entropy

(2022) Juntan Liu et al.   Journal of Translational Medicine

Identifying the critical state of complex biological systems by the directed-network rank score method

(2022) Jiayuan Zhong et al.   BIOINFORMATICS

The single-sample network module biomarkers (sNMB) method reveals the pre-deterioration stage of disease progression

(2022) Jiayuan Zhong et al.   Journal of Molecular Cell Biology

Predicting local COVID-19 outbreaks and infectious disease epidemics based on landscape network entropy

(2021) Rui Liu et al.   Science Bulletin

Identifying Critical States of Complex Diseases by Single-Sample Jensen-Shannon Divergence

(2021) Jinling Yan et al.   Frontiers in Oncology

Identifying critical state of complex diseases by single-sample Kullback–Leibler divergence

(2020) Jiayuan Zhong et al.   BMC GENOMICS

Identifying critical states of hepatocellular carcinoma based on landscape dynamic network biomarkers

(2020) Yichen Sun et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Targeting the JAK/STAT Signaling Pathway Using Phytocompounds for Cancer Prevention and Therapy

(2020) Sankhadip Bose et al.   Cells

Autoreservoir computing for multistep ahead prediction based on the spatiotemporal information transformation

(2020) Pei Chen et al.   Nature Communications

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

(2019) Yuxing Liao et al.   NUCLEIC ACIDS RESEARCH

Single-sample landscape entropy reveals the imminent phase transition during disease progression

(2019) Rui Liu et al.   BIOINFORMATICS

Direct pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program

(2018) Marisa Karow et al.   NATURE NEUROSCIENCE

Single-cell RNA sequencing reveals metallothionein heterogeneity during hESC differentiation to definitive endoderm

(2018) Junjie Lu et al.   Stem Cell Research

Detection for disease tipping points by landscape dynamic network biomarkers

(2018) Xiaoping Liu et al.   National Science Review

Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells

(2017) Rhishikesh Bargaje et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting critical state before phase transition of complex biological systems by hidden Markov model

(2016) Pei Chen et al.   BIOINFORMATICS

A novel prognostic factor TRIM44 promotes cell proliferation and migration, and inhibits apoptosis in testicular germ cell tumor

(2016) Yuta Yamada et al.   CANCER SCIENCE

Personalized characterization of diseases using sample-specific networks

(2016) Xiaoping Liu et al.   NUCLEIC ACIDS RESEARCH

Cell Fate Decision as High-Dimensional Critical State Transition

(2016) Mitra Mojtahedi et al.   PLOS BIOLOGY

PI3K/AKT signaling pathway and cancer: an updated review

(2014) Miriam Martini et al.   ANNALS OF MEDICINE

Deciphering early development of complex diseases by progressive module network

(2014) Tao Zeng et al.   METHODS

SOX2 regulates apoptosis through MAP4K4-Survivin signaling pathway in human lung cancer cells

(2013) Si Chen et al.   CARCINOGENESIS

Validation of the 7th Edition TNM Staging System for Hepatocellular Carcinoma: An Analysis of 8,828 Patients in a Single Medical Center

(2013) Kwong-Ming Kee et al.   DIGESTIVE DISEASES AND SCIENCES

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

(2013) Rui Liu et al.   MEDICINAL RESEARCH REVIEWS

Cdc25A promotes cell survival by stimulating NF-κB activity through IκB-α phosphorylation and destabilization

(2012) Hey-Young Hong et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Chemokine C-C motif receptor 5 and C-C motif ligand 5 promote cancer cell migration under hypoxia

(2012) Sensen Lin et al.   CANCER SCIENCE

A Review of Integrated Staging Systems for Renal Cell Carcinoma

(2012) Malek Meskawi et al.   EUROPEAN UROLOGY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

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

(2012) Luonan Chen et al.   Scientific Reports

A closer look at the effect of preliminary goodness-of-fit testing for normality for the one-sample t-test

(2010) Justine Rochon et al.   BRITISH JOURNAL OF MATHEMATICAL & STATISTICAL PSYCHOLOGY

EZH2 is a mediator of EWS/FLI1 driven tumor growth and metastasis blocking endothelial and neuro-ectodermal differentiation

(2009) G. H. S. Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

C-Fos expression is a molecular predictor of progression and survival in epithelial ovarian carcinoma

(2008) S Mahner et al.   BRITISH JOURNAL OF CANCER

Wogonin suppresses tumor growth in vivo and VEGF-induced angiogenesis through inhibiting tyrosine phosphorylation of VEGFR2

(2008) Na Lu et al.   LIFE SCIENCES

Molecular Basis of Metastasis

(2008) Anne C. Chiang et al.   NEW ENGLAND JOURNAL OF MEDICINE