Published in Signal Processing on April 01, 2006
Inverse perturbation for optimal intervention in gene regulatory networks. Bioinformatics (2010) 1.79
Comparison of co-expression measures: mutual information, correlation, and model based indices. BMC Bioinformatics (2012) 1.47
Reconstructing generalized logical networks of transcriptional regulation in mouse brain from temporal gene expression data. EURASIP J Bioinform Syst Biol (2009) 1.41
Inference of a probabilistic Boolean network from a single observed temporal sequence. EURASIP J Bioinform Syst Biol (2007) 1.32
Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. Microbiol Mol Biol Rev (2009) 1.25
Inference of gene regulatory networks using time-series data: a survey. Curr Genomics (2009) 1.24
Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks. BMC Bioinformatics (2007) 1.15
Inference of gene regulatory networks based on a universal minimum description length. EURASIP J Bioinform Syst Biol (2008) 1.14
Stochastic Boolean networks: an efficient approach to modeling gene regulatory networks. BMC Syst Biol (2012) 1.09
Biochemical and statistical network models for systems biology. Curr Opin Biotechnol (2007) 1.07
Deterministic and stochastic models of genetic regulatory networks. Methods Enzymol (2009) 0.98
A Survey of Statistical Models for Reverse Engineering Gene Regulatory Networks. IEEE Signal Process Mag (2009) 0.97
Finding consistent disease subnetworks across microarray datasets. BMC Bioinformatics (2011) 0.95
Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast. IET Syst Biol (2009) 0.90
A tutorial on analysis and simulation of boolean gene regulatory network models. Curr Genomics (2009) 0.88
Recent development and biomedical applications of probabilistic Boolean networks. Cell Commun Signal (2013) 0.81
Dynamic modeling of gene expression in prokaryotes: application to glucose-lactose diauxie in Escherichia coli. Syst Synth Biol (2011) 0.80
Methods for Optimal Intervention in Gene Regulatory Networks. IEEE Signal Process Mag (2012) 0.78
Rule-based regulatory and metabolic model for Quorum sensing in P. aeruginosa. BMC Syst Biol (2013) 0.77
Biological Resource Centers and Systems Biology. Bioscience (2009) 0.76
Gene regulatory network inference and validation using relative change ratio analysis and time-delayed dynamic Bayesian network. EURASIP J Bioinform Syst Biol (2014) 0.75
Systems biology of cancer: a challenging expedition for clinical and quantitative biologists. Front Bioeng Biotechnol (2014) 0.75
Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size. BMC Syst Biol (2017) 0.75
A Probabilistic Boolean Network Approach for the Analysis of Cancer-Specific Signalling: A Case Study of Deregulated PDGF Signalling in GIST. PLoS One (2016) 0.75
Statistical Analysis of Discrete Dynamical System Models for Biological Networks. Proc Int Joint Conf Bioinforma Syst Biol Intell Comput (2009) 0.75
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
Genome-wide location and function of DNA binding proteins. Science (2000) 31.25
Using Bayesian networks to analyze expression data. J Comput Biol (2000) 15.98
Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol (1969) 13.14
Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol (2002) 9.97
Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet (2001) 7.74
Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics (2002) 6.90
Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pac Symp Biocomput (2001) 3.97
Inferring subnetworks from perturbed expression profiles. Bioinformatics (2001) 3.93
Combining location and expression data for principled discovery of genetic regulatory network models. Pac Symp Biocomput (2002) 3.05
Gene networks inference using dynamic Bayesian networks. Bioinformatics (2003) 2.74
Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression. Pac Symp Biocomput (2002) 2.30
Gene perturbation and intervention in probabilistic Boolean networks. Bioinformatics (2002) 1.98
Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. Proc IEEE Comput Soc Bioinform Conf (2003) 1.89
The role of certain Post classes in Boolean network models of genetic networks. Proc Natl Acad Sci U S A (2003) 1.89
Mining for putative regulatory elements in the yeast genome using gene expression data. Proc Int Conf Intell Syst Mol Biol (2000) 1.73
From topology to dynamics in biochemical networks. Chaos (2001) 1.62
A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks. Bioinformatics (2004) 1.57
General nonlinear framework for the analysis of gene interaction via multivariate expression arrays. J Biomed Opt (2000) 1.49
Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. J Bioinform Comput Biol (2003) 1.44
Discovery of causal relationships in a gene-regulation pathway from a mixture of experimental and observational DNA microarray data. Pac Symp Biocomput (2002) 1.35
Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations. Pac Symp Biocomput (2003) 1.34
The somatic genomic landscape of glioblastoma. Cell (2013) 11.73
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet (2013) 11.29
Association of BRCA1 and BRCA2 mutations with survival, chemotherapy sensitivity, and gene mutator phenotype in patients with ovarian cancer. JAMA (2011) 6.81
Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Res (2002) 5.99
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci U S A (2007) 4.80
Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals. Nat Immunol (2009) 3.60
High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nat Biotechnol (2010) 3.21
Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. Genome Biol (2008) 3.16
Are data from different gene expression microarray platforms comparable? Genomics (2004) 3.13
Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Comput Biol (2008) 3.02
Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Mol Syst Biol (2006) 3.01
Integrated network analysis platform for protein-protein interactions. Nat Methods (2008) 2.63
Dual role of FoxA1 in androgen receptor binding to chromatin, androgen signalling and prostate cancer. EMBO J (2011) 2.55
Nonsense-mediated decay microarray analysis identifies mutations of EPHB2 in human prostate cancer. Nat Genet (2004) 2.44
Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas. Proc Natl Acad Sci U S A (2007) 2.38
Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer. Cancer Cell (2013) 2.34
CGH-Plotter: MATLAB toolbox for CGH-data analysis. Bioinformatics (2003) 2.28
In silico microdissection of microarray data from heterogeneous cell populations. BMC Bioinformatics (2005) 2.26
PINA v2.0: mining interactome modules. Nucleic Acids Res (2011) 2.23
Robust detection of periodic time series measured from biological systems. BMC Bioinformatics (2005) 2.14
Gene expression dynamics in the macrophage exhibit criticality. Proc Natl Acad Sci U S A (2008) 1.95
Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme. Genome Med (2010) 1.94
Fewer permutations, more accurate P-values. Bioinformatics (2009) 1.91
The role of certain Post classes in Boolean network models of genetic networks. Proc Natl Acad Sci U S A (2003) 1.89
The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma. J Clin Invest (2013) 1.76
Software for quantification of labeled bacteria from digital microscope images by automated image analysis. Biotechniques (2005) 1.76
Optimized LOWESS normalization parameter selection for DNA microarray data. BMC Bioinformatics (2004) 1.73
FoxA1 specifies unique androgen and glucocorticoid receptor binding events in prostate cancer cells. Cancer Res (2012) 1.72
Computational framework for simulating fluorescence microscope images with cell populations. IEEE Trans Med Imaging (2007) 1.69
ProbCD: enrichment analysis accounting for categorization uncertainty. BMC Bioinformatics (2007) 1.68
High-resolution analysis of gene copy number alterations in human prostate cancer using CGH on cDNA microarrays: impact of copy number on gene expression. Neoplasia (2004) 1.66
Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX. Nature (2013) 1.65
Adaptable data management for systems biology investigations. BMC Bioinformatics (2009) 1.63
Allelic imbalance at rs6983267 suggests selection of the risk allele in somatic colorectal tumor evolution. Cancer Res (2008) 1.59
Probabilistic inference of transcription factor binding from multiple data sources. PLoS One (2008) 1.58
Gene-expression profiling predicts recurrence in Dukes' C colorectal cancer. Gastroenterology (2005) 1.56
RNAi microarray analysis in cultured mammalian cells. Genome Res (2003) 1.51
Gene-pair expression signatures reveal lineage control. Nat Methods (2013) 1.49
Growing genetic regulatory networks from seed genes. Bioinformatics (2004) 1.49
Global gene expression profile of human cord blood-derived CD133+ cells. Stem Cells (2005) 1.42
Use of IgE and IgG4 epitope binding to predict the outcome of oral immunotherapy in cow's milk allergy. Pediatr Allergy Immunol (2014) 1.41
Post-transcriptional regulatory network of epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions. J Hematol Oncol (2014) 1.39
Robust quantification of in vitro angiogenesis through image analysis. IEEE Trans Med Imaging (2005) 1.36
Critical dynamics in genetic regulatory networks: examples from four kingdoms. PLoS One (2008) 1.35
Identification of combination gene sets for glioma classification. Mol Cancer Ther (2002) 1.35
The gene expression signature of genomic instability in breast cancer is an independent predictor of clinical outcome. Int J Cancer (2009) 1.34
High-resolution genomic and expression profiling reveals 105 putative amplification target genes in pancreatic cancer. Neoplasia (2004) 1.33
Systems biology driven software design for the research enterprise. BMC Bioinformatics (2008) 1.32
MiR-506 suppresses proliferation and induces senescence by directly targeting the CDK4/6-FOXM1 axis in ovarian cancer. J Pathol (2014) 1.31
Probabilistic analysis of gene expression measurements from heterogeneous tissues. Bioinformatics (2010) 1.31
Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Immunity (2010) 1.28
Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics. Bioinformatics (2009) 1.28
NGAL decreases E-cadherin-mediated cell-cell adhesion and increases cell motility and invasion through Rac1 in colon carcinoma cells. Lab Invest (2009) 1.28
Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. Immunity (2013) 1.27
Novel proteomics strategy brings insight into the prevalence of SUMO-2 target sites. Mol Cell Proteomics (2009) 1.26
Jointly analyzing gene expression and copy number data in breast cancer using data reduction models. IEEE/ACM Trans Comput Biol Bioinform (2006) 1.24
Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinformatics (2007) 1.24
A novel strategy for microarray quality control using Bayesian networks. Bioinformatics (2003) 1.23
Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. Bioinformatics (2010) 1.22
Fast gene ontology based clustering for microarray experiments. BioData Min (2008) 1.21
ErbB2-driven breast cancer cell invasion depends on a complex signaling network activating myeloid zinc finger-1-dependent cathepsin B expression. Mol Cell (2012) 1.21
Early recovery from cow's milk allergy is associated with decreasing IgE and increasing IgG4 binding to cow's milk epitopes. J Allergy Clin Immunol (2010) 1.21
Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images. PLoS One (2009) 1.19
Deciphering downstream gene targets of PI3K/mTOR/p70S6K pathway in breast cancer. BMC Genomics (2008) 1.14
CNAmet: an R package for integrating copy number, methylation and expression data. Bioinformatics (2011) 1.14
Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data. Brief Bioinform (2014) 1.12
Effects of Herceptin treatment on global gene expression patterns in HER2-amplified and nonamplified breast cancer cell lines. Oncogene (2004) 1.12
Critical networks exhibit maximal information diversity in structure-dynamics relationships. Phys Rev Lett (2008) 1.12
Simulation of microarray data with realistic characteristics. BMC Bioinformatics (2006) 1.12
KSHV-initiated notch activation leads to membrane-type-1 matrix metalloproteinase-dependent lymphatic endothelial-to-mesenchymal transition. Cell Host Microbe (2011) 1.11
The Innate Immune Database (IIDB). BMC Immunol (2008) 1.11
Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. BMC Bioinformatics (2010) 1.10
Candidate driver genes in microsatellite-unstable colorectal cancer. Int J Cancer (2011) 1.08
Insulin-like growth factor binding protein 2 promotes ovarian cancer cell invasion. Mol Cancer (2005) 1.08
Biochemical and statistical network models for systems biology. Curr Opin Biotechnol (2007) 1.07
Microarray reveals differences in both tumors and vascular specific gene expression in de novo CD5+ and CD5- diffuse large B-cell lymphomas. Cancer Res (2003) 1.07
Effects of transcriptional pausing on gene expression dynamics. PLoS Comput Biol (2010) 1.06
Pathway alterations during glioma progression revealed by reverse phase protein lysate arrays. Proteomics (2006) 1.06
Differential gene expression in adipose stem cells cultured in allogeneic human serum versus fetal bovine serum. Tissue Eng Part A (2010) 1.05
Analysis of signaling pathways in 90 cancer cell lines by protein lysate array. J Proteome Res (2007) 1.04
Stochastic differential equation model for cerebellar granule cell excitability. PLoS Comput Biol (2008) 1.04
Decision tree modeling predicts effects of inhibiting contractility signaling on cell motility. BMC Syst Biol (2007) 1.03
Large-scale molecular characterization and analysis of gastric cancer. Chin J Cancer (2014) 1.03
Basin entropy in Boolean network ensembles. Phys Rev Lett (2007) 1.02
Integrated mechanistic and data-driven modelling for multivariate analysis of signalling pathways. J R Soc Interface (2006) 1.02
Simulating fluorescent microscope images of cell populations. Conf Proc IEEE Eng Med Biol Soc (2005) 1.01
RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Stem Cells (2012) 1.01
Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations. BMC Bioinformatics (2009) 1.01