Published in Sci Rep on March 29, 2012
Critical slowing down as early warning for the onset and termination of depression. Proc Natl Acad Sci U S A (2013) 2.54
Modelling biological systems from molecules to dynamical networks. BMC Syst Biol (2012) 1.18
Identifying critical transitions and their leading biomolecular networks in complex diseases. Sci Rep (2012) 1.17
Perimenopause as a neurological transition state. Nat Rev Endocrinol (2015) 1.14
An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. J Am Med Inform Assoc (2012) 1.10
Identifying dysregulated pathways in cancers from pathway interaction networks. BMC Bioinformatics (2012) 1.09
Information dissipation as an early-warning signal for the Lehman Brothers collapse in financial time series. Sci Rep (2013) 0.99
The dynamics of DNA methylation covariation patterns in carcinogenesis. PLoS Comput Biol (2014) 0.96
Detecting early-warning signals of type 1 diabetes and its leading biomolecular networks by dynamical network biomarkers. BMC Med Genomics (2013) 0.96
ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions. Nucleic Acids Res (2012) 0.95
Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks. Nucleic Acids Res (2014) 0.95
Functionalized magnetic nanoparticles for the detection and quantitative analysis of cell surface antigen. Biomed Res Int (2012) 0.95
Spatio-temporal analysis of type 2 diabetes mellitus based on differential expression networks. Sci Rep (2013) 0.94
Discovery of a kernel for controlling biomolecular regulatory networks. Sci Rep (2013) 0.91
Transittability of complex networks and its applications to regulatory biomolecular networks. Sci Rep (2014) 0.89
Advanced Applications of RNA Sequencing and Challenges. Bioinform Biol Insights (2015) 0.88
Early warning signals of stochastic switching. Proc Biol Sci (2013) 0.87
Detecting causality from nonlinear dynamics with short-term time series. Sci Rep (2014) 0.86
Reconstructing dynamic gene regulatory networks from sample-based transcriptional data. Nucleic Acids Res (2012) 0.86
APG: an Active Protein-Gene network model to quantify regulatory signals in complex biological systems. Sci Rep (2013) 0.86
Identification of the molecular mechanisms for cell-fate selection in budding yeast through mathematical modeling. Biophys J (2013) 0.86
Network biomarkers, interaction networks and dynamical network biomarkers in respiratory diseases. Clin Transl Med (2014) 0.85
Progression from Excessive to Deficient Syndromes in Chronic Hepatitis B: A Dynamical Network Analysis of miRNA Array Data. Evid Based Complement Alternat Med (2013) 0.85
Identification of unstable network modules reveals disease modules associated with the progression of Alzheimer's disease. PLoS One (2013) 0.85
Cell Fate Decision as High-Dimensional Critical State Transition. PLoS Biol (2016) 0.83
Deciphering deterioration mechanisms of complex diseases based on the construction of dynamic networks and systems analysis. Sci Rep (2015) 0.83
Proteome-wide prediction of protein-protein interactions from high-throughput data. Protein Cell (2012) 0.83
Switch of sensitivity dynamics revealed with DyGloSA toolbox for dynamical global sensitivity analysis as an early warning for system's critical transition. PLoS One (2013) 0.81
Identifying early-warning signals of critical transitions with strong noise by dynamical network markers. Sci Rep (2015) 0.81
Pathway mapping and development of disease-specific biomarkers: protein-based network biomarkers. J Cell Mol Med (2015) 0.80
Evolution of network biomarkers from early to late stage bladder cancer samples. Biomed Res Int (2014) 0.80
Dynamic versus static biomarkers in cancer immune checkpoint blockade: unravelling complexity. Nat Rev Drug Discov (2017) 0.80
Major Depression as a Complex Dynamic System. PLoS One (2016) 0.79
Autophagy mediates phase transitions from cell death to life. Heliyon (2015) 0.79
Big biological data: challenges and opportunities. Genomics Proteomics Bioinformatics (2014) 0.79
Translational bioinformatics has now come of age: TBC 2012 collection. BMC Med Genomics (2013) 0.79
Inference of Gene Regulatory Network Based on Local Bayesian Networks. PLoS Comput Biol (2016) 0.78
Population dynamics of cancer cells with cell state conversions. Quant Biol (2013) 0.78
EEG and Neuronal Activity Topography analysis can predict effectiveness of shunt operation in idiopathic normal pressure hydrocephalus patients. Neuroimage Clin (2013) 0.78
Towards dynamical network biomarkers in neuromodulation of episodic migraine. Transl Neurosci (2013) 0.78
Identifying network biomarkers based on protein-protein interactions and expression data. BMC Med Genomics (2015) 0.78
Unravelling personalized dysfunctional gene network of complex diseases based on differential network model. J Transl Med (2015) 0.78
Dynamical Regulation Analysis Identifies Molecular Mechanisms of Fuzheng-Huayu Formula against Hepatitis B-Caused Liver Cirrhosis. Evid Based Complement Alternat Med (2015) 0.78
Predicting critical transitions in a model of systemic inflammation. J Theor Biol (2013) 0.78
Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia. BMC Bioinformatics (2015) 0.78
Identifying critical differentiation state of MCF-7 cells for breast cancer by dynamical network biomarkers. Front Genet (2015) 0.78
Differential network analysis reveals dysfunctional regulatory networks in gastric carcinogenesis. Am J Cancer Res (2015) 0.78
Integrative analysis of mutational and transcriptional profiles reveals driver mutations of metastatic breast cancers. Cell Discov (2016) 0.78
Identifying responsive modules by mathematical programming: an application to budding yeast cell cycle. PLoS One (2012) 0.77
Diagnostic prediction of complex diseases using phase-only correlation based on virtual sample template. BMC Bioinformatics (2013) 0.77
Rat hepatocytes weighted gene co-expression network analysis identifies specific modules and hub genes related to liver regeneration after partial hepatectomy. PLoS One (2014) 0.77
Tracing dynamic biological processes during phase transition. BMC Syst Biol (2012) 0.77
Applying computation biology and "big data" to develop multiplex diagnostics for complex chronic diseases such as osteoarthritis. Biomarkers (2016) 0.76
The effects of graded levels of calorie restriction: VII. Topological rearrangement of hypothalamic aging networks. Aging (Albany NY) (2016) 0.76
Metabolomic analysis reveals altered metabolic pathways in a rat model of gastric carcinogenesis. Oncotarget (2016) 0.75
Modeling the Attractor Landscape of Disease Progression: a Network-Based Approach. Front Genet (2017) 0.75
Increased firing irregularity as an emergent property of neural-state transition in monkey prefrontal cortex. PLoS One (2013) 0.75
Using Multi-objective Optimization to Identify Dynamical Network Biomarkers as Early-warning Signals of Complex Diseases. Sci Rep (2016) 0.75
Immuno-regulated common markers but different network signatures in two associated cancers: evidences from epigenetic treatment. Ann Transl Med (2016) 0.75
Transcriptional profiling and dynamical regulation analysis identify potential kernel target genes of SCYL1-BP1 in HEK293T cells. Mol Cells (2014) 0.75
Detecting early-warning signals for influenza A pandemic based on protein dynamical network biomarkers. Saudi J Biol Sci (2017) 0.75
Applying NGS Data to Find Evolutionary Network Biomarkers from the Early and Late Stages of Hepatocellular Carcinoma. Biomed Res Int (2015) 0.75
CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data. BMC Bioinformatics (2016) 0.75
The decrease of consistence probability: at the crossroad of catastrophic transition of a biological system. BMC Syst Biol (2016) 0.75
Clinical Study of Effects of Jian Ji Ning, a Chinese Herbal Medicine Compound Preparation, in Treating Patients with Myasthenia Gravis via the Regulation of Differential MicroRNAs Expression in Serum. Evid Based Complement Alternat Med (2014) 0.75
Cooperative genomic alteration network reveals molecular classification across 12 major cancer types. Nucleic Acids Res (2016) 0.75
Mechanical Control of Myotendinous Junction Formation and Tendon Differentiation during Development. Front Cell Dev Biol (2017) 0.75
Assessment of acculturation in minority health research. Soc Sci Med (2017) 0.75
Differential variability and correlation of gene expression identifies key genes involved in neuronal differentiation. BMC Syst Biol (2015) 0.75
Noise-induced regime shifts: A quantitative characterization. Eur Phys J E Soft Matter (2013) 0.75
Quantifying critical states of complex diseases using single-sample dynamic network biomarkers. PLoS Comput Biol (2017) 0.75
Forecasting influenza A pandemic outbreak using protein dynamical network biomarkers. BMC Syst Biol (2017) 0.75
Comorbidities in the diseasome are more apparent than real: What Bayesian filtering reveals about the comorbidities of depression. PLoS Comput Biol (2017) 0.75
Defining and characterizing the critical transition state prior to the type 2 diabetes disease. PLoS One (2017) 0.75
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Slowing down as an early warning signal for abrupt climate change. Proc Natl Acad Sci U S A (2008) 4.91
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Prediction of epileptic seizures: are nonlinear methods relevant? Nat Med (2003) 2.00
Differential gene expression between chronic hepatitis B and C hepatic lesion. Gastroenterology (2001) 1.46
Genomic analysis of murine pulmonary tissue following carbonyl chloride inhalation. Chem Res Toxicol (2005) 1.20
Hearing preservation after gamma knife stereotactic radiosurgery of vestibular schwannoma. Cancer (2005) 1.16
Transition models for change-point estimation in logistic regression. Stat Med (2003) 1.14
Microarray analysis identifies altered regulation of nuclear receptor family members in the pre-disease state of multiple sclerosis. Neurobiol Dis (2010) 1.09
Tumor-specific and proliferation-specific gene expression typifies murine transgenic B cell lymphomagenesis. J Biol Chem (2006) 1.08
PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res (2007) 19.07
Phenotypic characterization of human colorectal cancer stem cells. Proc Natl Acad Sci U S A (2007) 13.58
Dysregulated gene expression networks in human acute myelogenous leukemia stem cells. Proc Natl Acad Sci U S A (2009) 2.76
Modulation of cardiac growth and development by HOP, an unusual homeodomain protein. Cell (2002) 2.53
Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics (2006) 2.49
The Mg-chelatase H subunit of Arabidopsis antagonizes a group of WRKY transcription repressors to relieve ABA-responsive genes of inhibition. Plant Cell (2010) 2.13
Tet1 controls meiosis by regulating meiotic gene expression. Nature (2012) 2.01
Simultaneous time- and wavelength-resolved fluorescence spectroscopy for near real-time tissue diagnosis. Opt Lett (2008) 1.98
Spatial, sources and risk assessment of heavy metal contamination of urban soils in typical regions of Shenyang, China. J Hazard Mater (2009) 1.79
Maximal induction of a subset of interferon target genes requires the chromatin-remodeling activity of the BAF complex. Mol Cell Biol (2002) 1.73
GABA exerts protective and regenerative effects on islet beta cells and reverses diabetes. Proc Natl Acad Sci U S A (2011) 1.69
Optimization meets systems biology. BMC Syst Biol (2010) 1.66
Bayesian inference explains perception of unity and ventriloquism aftereffect: identification of common sources of audiovisual stimuli. Neural Comput (2007) 1.65
Left ventricular systolic dysfunction and the risk of ischemic stroke in a multiethnic population. Stroke (2006) 1.65
Alignment of molecular networks by integer quadratic programming. Bioinformatics (2007) 1.61
NOA: a novel Network Ontology Analysis method. Nucleic Acids Res (2011) 1.60
Older adults' perceived physical activity enablers and barriers: a multicultural perspective. J Aging Phys Act (2010) 1.57
Re-evaluating the roles of proposed modulators of mammalian target of rapamycin complex 1 (mTORC1) signaling. J Biol Chem (2008) 1.57
Prediction of protein-RNA binding sites by a random forest method with combined features. Bioinformatics (2010) 1.52
Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. Bioinformatics (2011) 1.45
The magnesium-chelatase H subunit binds abscisic acid and functions in abscisic acid signaling: new evidence in Arabidopsis. Plant Physiol (2009) 1.44
Coexpression network analysis in chronic hepatitis B and C hepatic lesions reveals distinct patterns of disease progression to hepatocellular carcinoma. J Mol Cell Biol (2012) 1.43
Quantifying collective attention from tweet stream. PLoS One (2013) 1.42
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Molecular communication through stochastic synchronization induced by extracellular fluctuations. Phys Rev Lett (2005) 1.40
Quercetin induces protective autophagy in gastric cancer cells: involvement of Akt-mTOR- and hypoxia-induced factor 1α-mediated signaling. Autophagy (2011) 1.40
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Mesenchymal stem cells induce mature dendritic cells into a novel Jagged-2-dependent regulatory dendritic cell population. Blood (2008) 1.39
Early diagnosis of complex diseases by molecular biomarkers, network biomarkers, and dynamical network biomarkers. Med Res Rev (2013) 1.34
Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. PLoS Comput Biol (2009) 1.32
Global and local synchrony of coupled neurons in small-world networks. Biol Cybern (2004) 1.31
Dynamics of 5-methylcytosine and 5-hydroxymethylcytosine during germ cell reprogramming. Cell Res (2013) 1.30
Organic cation and chiral anion templated 3D homochiral open-framework materials with unusual square-planar {M(4)(OH)} units. Angew Chem Int Ed Engl (2007) 1.29
Discovering functions and revealing mechanisms at molecular level from biological networks. Proteomics (2007) 1.29
RAGE modulates myocardial injury consequent to LAD infarction via impact on JNK and STAT signaling in a murine model. Am J Physiol Heart Circ Physiol (2008) 1.29
Detecting disease associated modules and prioritizing active genes based on high throughput data. BMC Bioinformatics (2010) 1.27
The knowledge-integrated network biomarkers discovery for major adverse cardiac events. J Proteome Res (2008) 1.27
Computational systems biology: integration of sequence, structure, network, and dynamics. BMC Syst Biol (2011) 1.26
Anti-high mobility group box-1 monoclonal antibody protects the blood-brain barrier from ischemia-induced disruption in rats. Stroke (2011) 1.26
H2O2 mediates the regulation of ABA catabolism and GA biosynthesis in Arabidopsis seed dormancy and germination. J Exp Bot (2010) 1.26
Quantitative proteomics identification of phosphoglycerate mutase 1 as a novel therapeutic target in hepatocellular carcinoma. Mol Cancer (2010) 1.24
Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains. BMC Syst Biol (2010) 1.24
miR-101 is down-regulated by the hepatitis B virus x protein and induces aberrant DNA methylation by targeting DNA methyltransferase 3A. Cell Signal (2012) 1.23
FoxO4 regulates tumor necrosis factor alpha-directed smooth muscle cell migration by activating matrix metalloproteinase 9 gene transcription. Mol Cell Biol (2007) 1.21
Gene function prediction using labeled and unlabeled data. BMC Bioinformatics (2008) 1.19
Global gene expression analysis of very small embryonic-like stem cells reveals that the Ezh2-dependent bivalent domain mechanism contributes to their pluripotent state. Stem Cells Dev (2012) 1.18
Snake cathelicidin from Bungarus fasciatus is a potent peptide antibiotics. PLoS One (2008) 1.18
Modelling biological systems from molecules to dynamical networks. BMC Syst Biol (2012) 1.18
Epiblast/germ line hypothesis of cancer development revisited: lesson from the presence of Oct-4+ cells in adult tissues. Stem Cell Rev (2010) 1.17
miR-143 and miR-145 synergistically regulate ERBB3 to suppress cell proliferation and invasion in breast cancer. Mol Cancer (2014) 1.17
A regulatory effect of IL-21 on T follicular helper-like cell and B cell in rheumatoid arthritis. Arthritis Res Ther (2012) 1.17
Identifying critical transitions and their leading biomolecular networks in complex diseases. Sci Rep (2012) 1.17
Development of a mathematical model that predicts the outcome of hormone therapy for prostate cancer. J Theor Biol (2010) 1.16
Dynamical Cell Assembly Hypothesis - Theoretical Possibility of Spatio-temporal Coding in the Cortex. Neural Netw (1996) 1.16
Inferring transcriptional regulatory networks from high-throughput data. Bioinformatics (2007) 1.15
Recurrent synaptic input and the timing of gamma-frequency-modulated firing of pyramidal cells during neocortical "UP" states. J Neurosci (2008) 1.15
Getting the message out about cognitive health: a cross-cultural comparison of older adults' media awareness and communication needs on how to maintain a healthy brain. Gerontologist (2009) 1.14
The histone trimethyllysine demethylase JMJD2A promotes cardiac hypertrophy in response to hypertrophic stimuli in mice. J Clin Invest (2011) 1.13
PKCbeta modulates ischemia-reperfusion injury in the heart. Am J Physiol Heart Circ Physiol (2008) 1.12
Macrophage migration inhibitory factor is secreted by rhabdomyosarcoma cells, modulates tumor metastasis by binding to CXCR4 and CXCR7 receptors and inhibits recruitment of cancer-associated fibroblasts. Mol Cancer Res (2010) 1.12
Proteomics identification of ITGB3 as a key regulator in reactive oxygen species-induced migration and invasion of colorectal cancer cells. Mol Cell Proteomics (2011) 1.12
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A systems biology approach to identify effective cocktail drugs. BMC Syst Biol (2010) 1.11
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Identifying dysregulated pathways in cancers from pathway interaction networks. BMC Bioinformatics (2012) 1.09
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Identifying disease genes and module biomarkers by differential interactions. J Am Med Inform Assoc (2011) 1.07
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Dynamical robustness in complex networks: the crucial role of low-degree nodes. Sci Rep (2012) 1.05
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miRNA27a is a biomarker for predicting chemosensitivity and prognosis in metastatic or recurrent gastric cancer. J Cell Biochem (2014) 1.05
Characterizing global evolutions of complex systems via intermediate network representations. Sci Rep (2012) 1.05