Published in J Bioinform Comput Biol on July 01, 2003
Inferring cellular networks--a review. BMC Bioinformatics (2007) 3.49
Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. Signal Processing (2006) 1.61
Reconstructing generalized logical networks of transcriptional regulation in mouse brain from temporal gene expression data. EURASIP J Bioinform Syst Biol (2009) 1.41
Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. BMC Syst Biol (2012) 1.16
High Dimensional ODEs Coupled with Mixed-Effects Modeling Techniques for Dynamic Gene Regulatory Network Identification. J Am Stat Assoc (2012) 1.01
Incremental parameter estimation of kinetic metabolic network models. BMC Syst Biol (2012) 1.01
Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast. IET Syst Biol (2009) 0.90
Understanding endothelial cell apoptosis: what can the transcriptome, glycome and proteome reveal? Philos Trans R Soc Lond B Biol Sci (2007) 0.89
Bayesian network prior: network analysis of biological data using external knowledge. Bioinformatics (2013) 0.87
Network completion using dynamic programming and least-squares fitting. ScientificWorldJournal (2012) 0.87
Sparse Additive Ordinary Differential Equations for Dynamic Gene Regulatory Network Modeling. J Am Stat Assoc (2014) 0.86
A bayesian framework that integrates heterogeneous data for inferring gene regulatory networks. Front Bioeng Biotechnol (2014) 0.83
A multi-layer inference approach to reconstruct condition-specific genes and their regulation. Bioinformatics (2013) 0.81
Estimation of Directed Acyclic Graphs Through Two-stage Adaptive Lasso for Gene Network Inference. J Am Stat Assoc (2016) 0.80
Exact and heuristic methods for network completion for time-varying genetic networks. Biomed Res Int (2014) 0.78
Bayesian pathway analysis of cancer microarray data. PLoS One (2014) 0.78
Integrative random forest for gene regulatory network inference. Bioinformatics (2015) 0.78
Bayesian inference based modelling for gene transcriptional dynamics by integrating multiple source of knowledge. BMC Syst Biol (2012) 0.78
Network Medicine: New Paradigm in the -Omics Era. Anat Physiol (2011) 0.76
Network completion for static gene expression data. Adv Bioinformatics (2014) 0.76
Modelling nonstationary gene regulatory processes. Adv Bioinformatics (2010) 0.75
Modeling regulatory cascades using Artificial Neural Networks: the case of transcriptional regulatory networks shaped during the yeast stress response. Front Genet (2013) 0.75
Using multi-step proposal distribution for improved MCMC convergence in Bayesian network structure learning. EURASIP J Bioinform Syst Biol (2015) 0.75
International network of cancer genome projects. Nature (2010) 20.35
Frequent pathway mutations of splicing machinery in myelodysplasia. Nature (2011) 11.44
Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res (2011) 6.02
Genome sequencing and analysis of Aspergillus oryzae. Nature (2005) 5.47
Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc Natl Acad Sci U S A (2002) 5.40
Extensive feature detection of N-terminal protein sorting signals. Bioinformatics (2002) 5.16
Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat Genet (2012) 4.84
Integrated molecular analysis of clear-cell renal cell carcinoma. Nat Genet (2013) 4.61
Somatic Mutations and Clonal Hematopoiesis in Aplastic Anemia. N Engl J Med (2015) 3.42
Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas. Cancer Res (2011) 2.81
Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis. DNA Res (2008) 2.72
Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection. Proc Natl Acad Sci U S A (2005) 2.64
Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput Biol (2005) 2.54
Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation. Proc Natl Acad Sci U S A (2004) 2.38
Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression. Pac Symp Biocomput (2002) 2.30
Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms. Nat Genet (2013) 2.14
Somatic SETBP1 mutations in myeloid malignancies. Nat Genet (2013) 2.12
Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat Genet (2010) 2.08
Inferring gene networks from time series microarray data using dynamic Bayesian networks. Brief Bioinform (2003) 2.08
Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics (2003) 1.95
Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. Proc IEEE Comput Soc Bioinform Conf (2003) 1.89
Variant ALDH2 is associated with accelerated progression of bone marrow failure in Japanese Fanconi anemia patients. Blood (2013) 1.79
Exome sequencing identifies secondary mutations of SETBP1 and JAK3 in juvenile myelomonocytic leukemia. Nat Genet (2013) 1.71
Modeling gene expression regulatory networks with the sparse vector autoregressive model. BMC Syst Biol (2007) 1.69
The tumor-suppressive miR-497-195 cluster targets multiple cell-cycle regulators in hepatocellular carcinoma. PLoS One (2013) 1.69
Functional gene screening system identified TRPV4 as a regulator of chondrogenic differentiation. J Biol Chem (2007) 1.66
ppGpp with DksA controls gene expression in the locus of enterocyte effacement (LEE) pathogenicity island of enterohaemorrhagic Escherichia coli through activation of two virulence regulatory genes. Mol Microbiol (2006) 1.53
Genome sequence of the cat pathogen, Chlamydophila felis. DNA Res (2006) 1.50
ACTN1 mutations cause congenital macrothrombocytopenia. Am J Hum Genet (2013) 1.49
Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data. Biosystems (2004) 1.47
Whole-genome sequencing of sake yeast Saccharomyces cerevisiae Kyokai no. 7. DNA Res (2011) 1.45
A neural network method for identification of RNA-interacting residues in protein. Genome Inform (2004) 1.42
Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus. Nucleic Acids Res (2009) 1.41
Identification of novel adrenomedullin in mammals: a potent cardiovascular and renal regulator. FEBS Lett (2004) 1.40
Inferring the global structure of chromosomes from structural variations. BMC Genomics (2015) 1.37
Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic Escherichia coli strains of O157 and non-O157 serotypes. Genome Biol (2007) 1.37
Biopathways representation and simulation on hybrid functional Petri net. In Silico Biol (2003) 1.37
Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations. Pac Symp Biocomput (2003) 1.34
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinformatics (2008) 1.33
Identification of BMP and activin membrane-bound inhibitor (BAMBI), an inhibitor of transforming growth factor-beta signaling, as a target of the beta-catenin pathway in colorectal tumor cells. J Biol Chem (2003) 1.31
The landscape of somatic mutations in Down syndrome-related myeloid disorders. Nat Genet (2013) 1.31
Plastin3 is a novel marker for circulating tumor cells undergoing the epithelial-mesenchymal transition and is associated with colorectal cancer prognosis. Cancer Res (2013) 1.29
Global regulation by horizontally transferred regulators establishes the pathogenicity of Escherichia coli. DNA Res (2008) 1.27
Genomic Object Net: I. A platform for modelling and simulating biopathways. Appl Bioinformatics (2003) 1.26
Comparative genomic analysis using microarray demonstrates a strong correlation between the presence of the 80-kilobase pathogenicity island and pathogenicity in Kanagawa phenomenon-positive Vibrio parahaemolyticus strains. Infect Immun (2008) 1.26
A top-r feature selection algorithm for microarray gene expression data. IEEE/ACM Trans Comput Biol Bioinform (2012) 1.25
An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data. Nucleic Acids Res (2013) 1.24
Pre-treatment neutrophil to lymphocyte ratio as a prognostic marker to predict chemotherapeutic response and survival outcomes in metastatic advanced gastric cancer. Gastric Cancer (2014) 1.23
Identification of a two-component VirR/VirS regulon in Clostridium perfringens. Anaerobe (2009) 1.22
Cell system ontology: representation for modeling, visualizing, and simulating biological pathways. In Silico Biol (2007) 1.20
BCOR and BCORL1 mutations in myelodysplastic syndromes and related disorders. Blood (2013) 1.16
Combining microarrays and biological knowledge for estimating gene networks via bayesian networks. J Bioinform Comput Biol (2004) 1.16
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. BMC Bioinformatics (2011) 1.15
Nucleotide substitutions in Staphylococcus aureus strains, Mu50, Mu3, and N315. DNA Res (2004) 1.15
Periodic gene expression patterns during the highly synchronized cell nucleus and organelle division cycles in the unicellular red alga Cyanidioschyzon merolae. DNA Res (2009) 1.14
A new Zn(II)(2)Cys(6)-type transcription factor BglR regulates β-glucosidase expression in Trichoderma reesei. Fungal Genet Biol (2012) 1.09
Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species. DNA Res (2013) 1.09
Deep sequencing reveals stepwise mutation acquisition in paroxysmal nocturnal hemoglobinuria. J Clin Invest (2014) 1.09
Regulation of virulence by butyrate sensing in enterohaemorrhagic Escherichia coli. Microbiology (2009) 1.08
Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. Nucleic Acids Res (2011) 1.08
Dual regulatory pathways integrating the RcsC-RcsD-RcsB signalling system control enterohaemorrhagic Escherichia coli pathogenicity. Mol Microbiol (2005) 1.07
Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Syst Biol (2009) 1.06
Genome sequence of the white koji mold Aspergillus kawachii IFO 4308, used for brewing the Japanese distilled spirit shochu. Eukaryot Cell (2011) 1.04
Cell fate simulation model of gustatory neurons with MicroRNAs double-negative feedback loop by hybrid functional Petri net with extension. Genome Inform (2006) 1.04
Complete genome sequence of Finegoldia magna, an anaerobic opportunistic pathogen. DNA Res (2008) 1.03
The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis). PLoS One (2013) 1.03
Constructing biological pathway models with hybrid functional Petri nets. In Silico Biol (2004) 1.01
Response of genes associated with mitochondrial function to mild heat stress in yeast Saccharomyces cerevisiae. J Biochem (2003) 1.00
Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. BMC Syst Biol (2009) 1.00
Kernel mixture survival models for identifying cancer subtypes, predicting patient's cancer types and survival probabilities. Genome Inform (2004) 1.00
Inhibition of histone demethylase JMJD1A improves anti-angiogenic therapy and reduces tumor-associated macrophages. Cancer Res (2013) 0.99
An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinformatics (2007) 0.99
Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets. J Biosci (2007) 0.99
Association between single-nucleotide polymorphisms in selectin genes and immunoglobulin A nephropathy. Am J Hum Genet (2002) 0.98
Association of single-nucleotide polymorphisms in the polymeric immunoglobulin receptor gene with immunoglobulin A nephropathy (IgAN) in Japanese patients. J Hum Genet (2003) 0.98
Ontology-based instance data validation for high-quality curated biological pathways. BMC Bioinformatics (2011) 0.98
X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils. Proc Natl Acad Sci U S A (2010) 0.97
Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data. Bioinformatics (2005) 0.96
Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma. PLoS One (2012) 0.95
Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension. Mol Biosyst (2011) 0.95
Gene expression profiles in peripheral blood as a biomarker in cancer patients receiving peptide vaccination. Cancer (2011) 0.95
Ligand-based gene expression profiling reveals novel roles of glucocorticoid receptor in cardiac metabolism. Am J Physiol Endocrinol Metab (2009) 0.94
MIRACH: efficient model checker for quantitative biological pathway models. Bioinformatics (2011) 0.94
A versatile petri net based architecture for modeling and simulation of complex biological processes. Genome Inform (2004) 0.94