Published in Bioinformatics on March 22, 2003
Recent developments in parameter estimation and structure identification of biochemical and genomic systems. Math Biosci (2009) 2.58
Parameter estimation in biochemical systems models with alternating regression. Theor Biol Med Model (2006) 1.69
Identification of metabolic system parameters using global optimization methods. Theor Biol Med Model (2006) 1.59
System estimation from metabolic time-series data. Bioinformatics (2008) 1.43
Automated smoother for the numerical decoupling of dynamics models. BMC Bioinformatics (2007) 1.27
Priming nonlinear searches for pathway identification. Theor Biol Med Model (2004) 1.22
Parameter estimation in systems biology models using spline approximation. BMC Syst Biol (2011) 1.14
Parameter optimization in S-system models. BMC Syst Biol (2008) 1.12
Identification of neutral biochemical network models from time series data. BMC Syst Biol (2009) 1.10
A new pheromone trail-based genetic algorithm for comparative genome assembly. Nucleic Acids Res (2008) 1.09
Reverse engineering gene regulatory network from microarray data using linear time-variant model. BMC Bioinformatics (2010) 1.06
On the attenuation and amplification of molecular noise in genetic regulatory networks. BMC Bioinformatics (2006) 1.04
Comparison of evolutionary algorithms in gene regulatory network model inference. BMC Bioinformatics (2010) 1.01
Estimation of dynamic flux profiles from metabolic time series data. BMC Syst Biol (2012) 1.00
Inferring cluster-based networks from differently stimulated multiple time-course gene expression data. Bioinformatics (2010) 0.99
Function approximation approach to the inference of reduced NGnet models of genetic networks. BMC Bioinformatics (2008) 0.94
A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data. BMC Bioinformatics (2007) 0.93
Evolving cell models for systems and synthetic biology. Syst Synth Biol (2010) 0.93
A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles. Theor Biol Med Model (2006) 0.92
Parameter estimation for stiff equations of biosystems using radial basis function networks. BMC Bioinformatics (2006) 0.90
Inferring robust gene networks from expression data by a sensitivity-based incremental evolution method. BMC Bioinformatics (2012) 0.90
Calibration of dynamic models of biological systems with KInfer. Eur Biophys J (2009) 0.90
The TAO-Gen algorithm for identifying gene interaction networks with application to SOS repair in E. coli. Environ Health Perspect (2004) 0.90
Parameter estimate of signal transduction pathways. BMC Neurosci (2006) 0.89
Set-base dynamical parameter estimation and model invalidation for biochemical reaction networks. BMC Syst Biol (2010) 0.89
Stochastic S-system modeling of gene regulatory network. Cogn Neurodyn (2015) 0.88
Benchmarks for identification of ordinary differential equations from time series data. Bioinformatics (2009) 0.87
Identification of temporal association rules from time-series microarray data sets. BMC Bioinformatics (2009) 0.85
Identification of parameter correlations for parameter estimation in dynamic biological models. BMC Syst Biol (2013) 0.84
Using evolutionary computations to understand the design and evolution of gene and cell regulatory networks. Methods (2013) 0.83
Biological systems modeling and analysis: a biomolecular technique of the twenty-first century. J Biomol Tech (2006) 0.82
Inferring genetic interactions via a nonlinear model and an optimization algorithm. BMC Syst Biol (2010) 0.82
Regulatory network reconstruction using an integral additive model with flexible kernel functions. BMC Syst Biol (2008) 0.81
Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment. BMC Syst Biol (2014) 0.81
An S-System Parameter Estimation Method (SPEM) for biological networks. J Comput Biol (2012) 0.81
Incorporating time-delays in S-System model for reverse engineering genetic networks. BMC Bioinformatics (2013) 0.79
Dynamical pathway analysis. BMC Syst Biol (2008) 0.79
Bayesian experts in exploring reaction kinetics of transcription circuits. Bioinformatics (2010) 0.78
BioCAD: an information fusion platform for bio-network inference and analysis. BMC Bioinformatics (2007) 0.78
Approximate Bayesian computation schemes for parameter inference of discrete stochastic models using simulated likelihood density. BMC Bioinformatics (2014) 0.78
A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-off on Phenotype Robustness in Biological Networks Part I: Gene Regulatory Networks in Systems and Evolutionary Biology. Evol Bioinform Online (2013) 0.78
Identification of growth phases and influencing factors in cultivations with AGE1.HN cells using set-based methods. PLoS One (2013) 0.78
Analysis of Network Topologies Underlying Ethylene Growth Response Kinetics. Front Plant Sci (2016) 0.77
Reverse-engineering gene-regulatory networks using evolutionary algorithms and grid computing. J Clin Monit Comput (2005) 0.77
Estimating parameters for generalized mass action models with connectivity information. BMC Bioinformatics (2009) 0.77
Estimate hidden dynamic profiles of siRNA effect on apoptosis. BMC Bioinformatics (2013) 0.77
An integer optimization algorithm for robust identification of non-linear gene regulatory networks. BMC Syst Biol (2012) 0.77
A survey on evolutionary algorithm based hybrid intelligence in bioinformatics. Biomed Res Int (2014) 0.76
Applying intelligent computing techniques to modeling biological networks from expression data. Genomics Proteomics Bioinformatics (2008) 0.75
Parameter estimation from experimental laboratory data of HSV-1 by using alternative regression method. Syst Synth Biol (2013) 0.75
Construction of Gene Regulatory Networks Using Recurrent Neural Networks and Swarm Intelligence. Scientifica (Cairo) (2016) 0.75
Interactive network analysis of the plasma amino acids profile in a mouse model of hyperglycemia. Springerplus (2013) 0.75
Biochemical systems identification by a random drift particle swarm optimization approach. BMC Bioinformatics (2014) 0.75
Inference of Vohradský's models of genetic networks by solving two-dimensional function optimization problems. PLoS One (2013) 0.75
Grammatical Immune System Evolution for reverse engineering nonlinear dynamic Bayesian models. Cancer Inform (2008) 0.75
Reverse engineering gene regulatory networks: coupling an optimization algorithm with a parameter identification technique. BMC Bioinformatics (2014) 0.75
Genetic Network Inference Using Hierarchical Structure. Front Physiol (2016) 0.75
Evaluating influence of microRNA in reconstructing gene regulatory networks. Cogn Neurodyn (2013) 0.75
Estimation of the Mechanism of Adrenal Action of Endocrine-Disrupting Compounds Using a Computational Model of Adrenal Steroidogenesis in NCI-H295R Cells. J Toxicol (2016) 0.75
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol (2006) 40.15
MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom (2010) 6.16
Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science (2007) 5.87
Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. J Proteome Res (2003) 4.36
Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res (2006) 4.25
Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs. Proc Natl Acad Sci U S A (2009) 3.64
Quantitative metabolome profiling of colon and stomach cancer microenvironment by capillary electrophoresis time-of-flight mass spectrometry. Cancer Res (2009) 3.50
Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2004) 3.41
Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumption. J Biol Chem (2006) 3.23
Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res (2003) 2.63
Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Mol Syst Biol (2008) 2.49
Six classes of nuclear localization signals specific to different binding grooves of importin alpha. J Biol Chem (2008) 2.26
Analysis of pre- and post-operative symptoms of patients with mild trigonocephaly using several developmental and psychological tests. Childs Nerv Syst (2014) 2.15
Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol Syst Biol (2009) 2.11
Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics (2009) 2.03
Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry. Anal Chem (2002) 2.00
Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae. Science (2007) 1.98
Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications. Mol Cell Proteomics (2007) 1.95
Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants. Plant Physiol (2010) 1.93
Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico. FEBS Lett (2005) 1.87
Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics (2009) 1.73
MathDAMP: a package for differential analysis of metabolite profiles. BMC Bioinformatics (2006) 1.68
Guidelines for the diagnosis and treatment of primary aldosteronism--the Japan Endocrine Society 2009. Endocr J (2011) 1.67
Visualization of three-way comparisons of omics data. BMC Bioinformatics (2007) 1.66
On dynamics of overlapping genes in bacterial genomes. Gene (2003) 1.65
Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis. J Proteome Res (2008) 1.64
KEGG-based pathway visualization tool for complex omics data. In Silico Biol (2005) 1.64
Simultaneous determination of the main metabolites in rice leaves using capillary electrophoresis mass spectrometry and capillary electrophoresis diode array detection. Plant J (2004) 1.63
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. PLoS One (2009) 1.57
Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism. Mol Syst Biol (2009) 1.52
A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics (2004) 1.48
Complete mutation analysis panel of the 39 human HOX genes. Teratology (2002) 1.47
Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes. Gene (2005) 1.46
MEGU: pathway mapping web-service based on KEGG and SVG. In Silico Biol (2006) 1.44
Effect of switching from amlodipine to combination therapy with telmisartan and low-dose hydrochlorothiazide. Hypertens Res (2009) 1.43
emPAI Calc--for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. Bioinformatics (2009) 1.43
A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. FEBS Lett (2003) 1.42
Depiction of metabolome changes in histidine-starved Escherichia coli by CE-TOFMS. Mol Biosyst (2007) 1.41
Metabolomic profiling of anionic metabolites by capillary electrophoresis mass spectrometry. Anal Chem (2009) 1.40
Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure. Physiol Genomics (2003) 1.39
Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila. Genes Cells (2005) 1.36
Nuclear export signal consensus sequences defined using a localization-based yeast selection system. Traffic (2008) 1.36
Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales. Mol Biol Evol (2008) 1.36
SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level. In Silico Biol (2006) 1.33
Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes. RNA (2004) 1.33
Computational methods for microRNA target prediction. Methods Enzymol (2007) 1.32
Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis. Curr Bioinform (2012) 1.31
Serum metabolomics reveals γ-glutamyl dipeptides as biomarkers for discrimination among different forms of liver disease. J Hepatol (2011) 1.30
Design of peptide inhibitors for the importin alpha/beta nuclear import pathway by activity-based profiling. Chem Biol (2008) 1.30
Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants. Mol Cell Proteomics (2009) 1.30
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. BMC Bioinformatics (2010) 1.30
A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation. Syst Synth Biol (2009) 1.26
GC-compositional strand bias around transcription start sites in plants and fungi. BMC Genomics (2005) 1.25
Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana. BMC Syst Biol (2007) 1.25
Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data. Anal Chem (2009) 1.25
Metabolomic anatomy of an animal model revealing homeostatic imbalances in dyslipidaemia. Mol Biosyst (2011) 1.24
Roles of hemoglobin Allostery in hypoxia-induced metabolic alterations in erythrocytes: simulation and its verification by metabolome analysis. J Biol Chem (2007) 1.24
Quantitative assay for TALEN activity at endogenous genomic loci. Biol Open (2013) 1.22
An extreme thermophile, Thermus thermophilus, is a polyploid bacterium. J Bacteriol (2010) 1.22
Comparative expression analysis uncovers novel features of endogenous antisense transcription. Hum Mol Genet (2008) 1.18
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. BMC Bioinformatics (2006) 1.18
Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns. Bioinformatics (2006) 1.18
One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale. Anal Chem (2010) 1.18
Metabolomic profiling of lung and prostate tumor tissues by capillary electrophoresis time-of-flight mass spectrometry. Metabolomics (2012) 1.17
A comprehensive resource of interacting protein regions for refining human transcription factor networks. PLoS One (2010) 1.17
In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs. RNA (2007) 1.17
Integrated omics approaches in plant systems biology. Curr Opin Chem Biol (2009) 1.17
Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach. BMC Syst Biol (2011) 1.17
Metabolomics approach for enzyme discovery. J Proteome Res (2006) 1.16
A new role for expressed pseudogenes as ncRNA: regulation of mRNA stability of its homologous coding gene. J Mol Med (Berl) (2004) 1.16
Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. BMC Genomics (2011) 1.16
GC/MS based metabolomics: development of a data mining system for metabolite identification by using soft independent modeling of class analogy (SIMCA). BMC Bioinformatics (2011) 1.15
Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non-pathogenic Pseudomonas species. Proteomics (2009) 1.15
Bioinformatic analysis of post-transcriptional regulation by uORF in human and mouse. FEBS Lett (2007) 1.14
Reverse engineering of biochemical equations from time-course data by means of genetic programming. Biosystems (2004) 1.13
Signaling flux redistribution at toll-like receptor pathway junctions. PLoS One (2008) 1.12
A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in cyanobacteria. J Biol Rhythms (2007) 1.12
Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7. Nucleic Acids Res (2004) 1.12
Analysis of nucleotides by pressure-assisted capillary electrophoresis-mass spectrometry using silanol mask technique. J Chromatogr A (2007) 1.12
Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data. Genome Res (2002) 1.11
Pressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anions. Anal Chem (2002) 1.09
Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column. Anal Sci (2008) 1.08
Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea. Proc Natl Acad Sci U S A (2009) 1.07
Indeterminacy of reverse engineering of Gene Regulatory Networks: the curse of gene elasticity. PLoS One (2007) 1.07
13C-metabolic flux analysis for batch culture of Escherichia coli and its Pyk and Pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites. Biotechnol Prog (2010) 1.06
A strategy for identification of oligosaccharide structures using observational multistage mass spectral library. Anal Chem (2005) 1.06
Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model. Gene (2006) 1.05
A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic Acids Res (2011) 1.04
Emergent genome-wide control in wildtype and genetically mutated lipopolysaccarides-stimulated macrophages. PLoS One (2009) 1.04
Prediction of liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome using artificial neural networks. J Proteome Res (2006) 1.03
Informatics for peptide retention properties in proteomic LC-MS. Proteomics (2008) 1.03
Characteristics and clustering of human ribosomal protein genes. BMC Genomics (2006) 1.03
Position-specific expression of Hox genes along the gastrointestinal tract. Congenit Anom (Kyoto) (2004) 1.02
Databases on food phytochemicals and their health-promoting effects. J Agric Food Chem (2011) 1.02
The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection. Evol Bioinform Online (2007) 1.02
Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes. BMC Evol Biol (2007) 1.01
Computational analysis of microRNA-mediated antiviral defense in humans. FEBS Lett (2007) 1.01
Alignment-based approach for durable data storage into living organisms. Biotechnol Prog (2007) 1.00
Metabolite profiling reveals YihU as a novel hydroxybutyrate dehydrogenase for alternative succinic semialdehyde metabolism in Escherichia coli. J Biol Chem (2009) 1.00
Computational analysis of microRNA targets in Caenorhabditis elegans. Gene (2005) 1.00