Published in Pac Symp Biocomput on January 01, 2003
Automated reverse engineering of nonlinear dynamical systems. Proc Natl Acad Sci U S A (2007) 1.76
Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. Signal Processing (2006) 1.61
ODB: a database of operons accumulating known operons across multiple genomes. Nucleic Acids Res (2006) 1.58
Inference of gene regulatory networks using time-series data: a survey. Curr Genomics (2009) 1.24
Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC Genomics (2007) 1.05
Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells. BMC Syst Biol (2010) 1.02
Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach. BMC Syst Biol (2012) 0.96
Evolving cell models for systems and synthetic biology. Syst Synth Biol (2010) 0.93
Functional data analysis for identifying nonlinear models of gene regulatory networks. BMC Genomics (2010) 0.93
Understanding endothelial cell apoptosis: what can the transcriptome, glycome and proteome reveal? Philos Trans R Soc Lond B Biol Sci (2007) 0.89
Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model. BMC Genomics (2009) 0.85
Rank-based edge reconstruction for scale-free genetic regulatory networks. BMC Bioinformatics (2008) 0.85
Modeling genome-wide dynamic regulatory network in mouse lungs with influenza infection using high-dimensional ordinary differential equations. PLoS One (2014) 0.81
Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network. Nucleic Acids Res (2014) 0.80
Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data. Front Microbiol (2016) 0.78
Inference of gene regulatory subnetworks from time course gene expression data. BMC Bioinformatics (2012) 0.77
Untangling statistical and biological models to understand network inference: the need for a genomics network ontology. Front Genet (2014) 0.76
A review of modeling techniques for genetic regulatory networks. J Med Signals Sens (2012) 0.75
Computational inference and analysis of genetic regulatory networks via a supervised combinatorial-optimization pattern. BMC Syst Biol (2010) 0.75
Kalman Filtering for Genetic Regulatory Networks with Missing Values. Comput Math Methods Med (2017) 0.75
International network of cancer genome projects. Nature (2010) 20.35
Frequent pathway mutations of splicing machinery in myelodysplasia. Nature (2011) 11.44
Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res (2011) 6.88
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
Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature (2004) 5.08
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
Macrophages in inflammation. Curr Drug Targets Inflamm Allergy (2005) 2.85
Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas. Cancer Res (2011) 2.81
DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res (2004) 2.61
Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput Biol (2005) 2.54
A widespread family of bacterial cell wall assembly proteins. EMBO J (2011) 2.33
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
Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res (2006) 2.11
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
Discovery of two novel families of proteins that are proposed to interact with prokaryotic SMC proteins, and characterization of the Bacillus subtilis family members ScpA and ScpB. Mol Microbiol (2002) 2.06
A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO. Science (2003) 2.03
Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK. J Bacteriol (2002) 2.01
Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics (2003) 1.95
An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol Cell (2003) 1.90
Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. Proc IEEE Comput Soc Bioinform Conf (2003) 1.89
Deletion of kasB in Mycobacterium tuberculosis causes loss of acid-fastness and subclinical latent tuberculosis in immunocompetent mice. Proc Natl Acad Sci U S A (2007) 1.86
Variant ALDH2 is associated with accelerated progression of bone marrow failure in Japanese Fanconi anemia patients. Blood (2013) 1.79
Highly frequent mutations in negative regulators of multiple virulence genes in group A streptococcal toxic shock syndrome isolates. PLoS Pathog (2010) 1.77
Six GTP-binding proteins of the Era/Obg family are essential for cell growth in Bacillus subtilis. Microbiology (2002) 1.76
Serodiagnosis of Mycobacterium avium-complex pulmonary disease using an enzyme immunoassay kit. Am J Respir Crit Care Med (2007) 1.75
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
Zinc is a key factor in controlling alternation of two types of L31 protein in the Bacillus subtilis ribosome. Mol Microbiol (2004) 1.65
Proteomics characterization of novel spore proteins of Bacillus subtilis. Microbiology (2002) 1.61
The BceRS two-component regulatory system induces expression of the bacitracin transporter, BceAB, in Bacillus subtilis. Mol Microbiol (2003) 1.58
Noc protein binds to specific DNA sequences to coordinate cell division with chromosome segregation. EMBO J (2009) 1.56
Syncope upon swallowing caused by an esophageal hiatal hernia compressing the left atrium: a case report. Echocardiography (2004) 1.55
Rothia aeria sp. nov., Rhodococcus baikonurensis sp. nov. and Arthrobacter russicus sp. nov., isolated from air in the Russian space laboratory Mir. Int J Syst Evol Microbiol (2004) 1.54
A new FtsZ-interacting protein, YlmF, complements the activity of FtsA during progression of cell division in Bacillus subtilis. Mol Microbiol (2006) 1.49
ACTN1 mutations cause congenital macrothrombocytopenia. Am J Hum Genet (2013) 1.49
Binding of response regulator DegU to the aprE promoter is inhibited by RapG, which is counteracted by extracellular PhrG in Bacillus subtilis. Mol Microbiol (2003) 1.47
Identification of a protein, YneA, responsible for cell division suppression during the SOS response in Bacillus subtilis. Mol Microbiol (2003) 1.47
Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data. Biosystems (2004) 1.47
Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA. Proc Natl Acad Sci U S A (2008) 1.45
Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. J Bioinform Comput Biol (2003) 1.44
A neural network method for identification of RNA-interacting residues in protein. Genome Inform (2004) 1.42
Dual-probe assay for rapid detection of drug-resistant Mycobacterium tuberculosis by real-time PCR. J Clin Microbiol (2004) 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
Biopathways representation and simulation on hybrid functional Petri net. In Silico Biol (2003) 1.37
Distribution of stable DnaA-binding sites on the Bacillus subtilis genome detected using a modified ChIP-chip method. DNA Res (2007) 1.37
The nitric oxide-responsive regulator NsrR controls ResDE-dependent gene expression. J Bacteriol (2006) 1.35
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinformatics (2008) 1.33
Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis. DNA Res (2008) 1.32
Chryseobacterium miricola sp. nov., a novel species isolated from condensation water of space station Mir. Syst Appl Microbiol (2003) 1.32
The GTP-binding protein YlqF participates in the late step of 50 S ribosomal subunit assembly in Bacillus subtilis. J Biol Chem (2006) 1.32
The landscape of somatic mutations in Down syndrome-related myeloid disorders. Nat Genet (2013) 1.31
Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation. Nucleic Acids Res (2010) 1.30
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
The role of G-protein-coupled receptor kinase 5 in pathogenesis of sporadic Parkinson's disease. J Neurosci (2006) 1.28
Global regulation by horizontally transferred regulators establishes the pathogenicity of Escherichia coli. DNA Res (2008) 1.27
Synergistic regulation of competence development in Bacillus subtilis by two Rap-Phr systems. J Bacteriol (2005) 1.27
Genomic Object Net: I. A platform for modelling and simulating biopathways. Appl Bioinformatics (2003) 1.26
A complete set of Escherichia coli open reading frames in mobile plasmids facilitating genetic studies. DNA Res (2005) 1.26
A top-r feature selection algorithm for microarray gene expression data. IEEE/ACM Trans Comput Biol Bioinform (2012) 1.25
Bacillus minimum genome factory: effective utilization of microbial genome information. Biotechnol Appl Biochem (2007) 1.25
An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data. Nucleic Acids Res (2013) 1.24
Systematic analysis of SigD-regulated genes in Bacillus subtilis by DNA microarray and Northern blotting analyses. Gene (2004) 1.22
Memory B cells in the lung participate in protective humoral immune responses to pulmonary influenza virus reinfection. Proc Natl Acad Sci U S A (2012) 1.20
Cell system ontology: representation for modeling, visualizing, and simulating biological pathways. In Silico Biol (2007) 1.20
Macrophage scavenger receptor down-regulates mycobacterial cord factor-induced proinflammatory cytokine production by alveolar and hepatic macrophages. Microb Pathog (2006) 1.20
BCOR and BCORL1 mutations in myelodysplastic syndromes and related disorders. Blood (2013) 1.16
Escherichia coli with a linear genome. EMBO Rep (2007) 1.16
Combining microarrays and biological knowledge for estimating gene networks via bayesian networks. J Bioinform Comput Biol (2004) 1.16
Serodiagnosis of pulmonary disease due to Mycobacterium avium complex with an enzyme immunoassay that uses a mixture of glycopeptidolipid antigens. Clin Infect Dis (2002) 1.15
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. BMC Bioinformatics (2011) 1.15
Selective transmission of R5 HIV-1 over X4 HIV-1 at the dendritic cell-T cell infectious synapse is determined by the T cell activation state. PLoS Pathog (2009) 1.11
Evaluation of variable numbers of tandem repeat as molecular epidemiological markers of Mycobacterium tuberculosis in Japan. J Med Microbiol (2007) 1.11
Dominant incidence of multidrug and extensively drug-resistant specific Mycobacterium tuberculosis clones in Osaka Prefecture, Japan. PLoS One (2012) 1.11
Extracellular mycobacterial DNA-binding protein 1 participates in mycobacterium-lung epithelial cell interaction through hyaluronic acid. J Biol Chem (2004) 1.10