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BMCBI
2004

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Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks

13 years 11 months ago

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Background: Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true ...

David Adalsteinsson, David McMillen, Timothy C. El...

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Id	Views	Title	Status

1	323	Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks	claim
2	265	ASAView: Database and tool for solvent accessibility representation in proteins	claim
3	252	Applying Support Vector Machines for Gene ontology based gene function prediction	claim
4	229	Automatic annotation of protein motif function with Gene Ontology terms	claim
5	228	An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results	claim
6	211	GenomeViz: visualizing microbial genomes	claim
7	208	Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures	claim
8	208	Hybrid clustering for microarray image analysis combining intensity and shape features	claim
9	207	Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrep-resented upstream motifs	claim
10	206	Combining gene expression data from different generations of oligonucleotide arrays	claim
11	205	A combinational feature selection and ensemble neural network method for classification of gene expression data	claim
12	200	ABC: software for interactive browsing of genomic multiple sequence alignment data	claim
13	196	MUSCLE: a multiple sequence alignment method with reduced time and space complexity	claim
14	190	RAG: RNA-As-Graphs web resource	claim
15	189	B.E.A.R. GeneInfo: A tool for identifying gene-related biomedical publications through user modifiable queries	claim
16	185	Linear fuzzy gene network models obtained from microarray data by exhaustive search	claim
17	181	Iterative class discovery and feature selection using Minimal Spanning Trees	claim
18	180	Noise filtering and nonparametric analysis of microarray data underscores discriminating markers of oral, prostate, lung, ovarian and breast cancer	claim
19	177	Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model	claim
20	176	Boosting accuracy of automated classification of fluorescence microscope images for location proteomics	claim
21	174	Implications for domain fusion protein-protein interactions based on structural information	claim
22	174	SeeGH - A software tool for visualization of whole genome array comparative genomic hybridization data	claim
23	173	d-matrix - database exploration, visualization and analysis	claim
24	169	A power law global error model for the identification of differentially expressed genes in microarray data	claim
25	167	Feature selection for splice site prediction: A new method using EDA-based feature ranking	claim
26	166	Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models	claim
27	165	Analysis of oligonucleotide array experiments with repeated measures using mixed models	claim
28	162	Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations	claim
29	161	Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment	claim
30	159	Extractor for ESI quadrupole TOF tandem MS data enabled for high throughput batch processing	claim
31	158	Improvement of alignment accuracy utilizing sequentially conserved motifs	claim
32	158	Incremental genetic K-means algorithm and its application in gene expression data analysis	claim
33	158	A novel Mixture Model Method for identification of differentially expressed genes from DNA microarray data	claim
34	156	GeneXplorer: an interactive web application for microarray data visualization and analysis	claim
35	156	DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors	claim
36	154	Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments	claim
37	154	Computation of elementary modes: a unifying framework and the new binary approach	claim
38	154	Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells	claim
39	153	Computational protein biomarker prediction: a case study for prostate cancer	claim
40	151	A computational approach for ordering signal transduction pathway components from genomics and proteomics Data	claim
41	151	Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics	claim
42	150	Graph-based iterative Group Analysis enhances microarray interpretation	claim
43	150	Rank Difference Analysis of Microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data	claim
44	150	Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila	claim
45	150	SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters	claim
46	150	Inter-residue distances derived from fold contact propensities correlate with evolutionary substitution costs	claim
47	149	MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states	claim
48	148	Bioinformatics analysis of SARS coronavirus genome polymorphism	claim
49	146	Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data	claim
50	146	The InDeVal insertion/deletion evaluation tool: a program for finding target regions in DNA sequences and for aiding in sequence comparison	claim
51	146	Multivariate search for differentially expressed gene combinations	claim
52	144	GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes	claim
53	144	PASBio: predicate-argument structures for event extraction in molecular biology	claim
54	143	Comparing functional annotation analyses with Catmap	claim
55	142	GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies	claim
56	141	Estimates of statistical significance for comparison of individual positions in multiple sequence alignments	claim
57	140	What can we learn from noncoding regions of similarity between genomes?	claim
58	139	mlstdbNet - distributed multi-locus sequence typing (MLST) databases	claim
59	139	Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays	claim
60	138	Constraint Logic Programming approach to protein structure prediction	claim
61	136	A SNP-centric database for the investigation of the human genome	claim
62	135	Determination of the differentially expressed genes in microarray experiments using local FDR	claim
63	135	Information assessment on predicting protein-protein interactions	claim
64	134	Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE)	claim
65	133	Esub8: A novel tool to predict protein subcellular localizations in eukaryotic organisms	claim
66	133	Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction	claim
67	133	Artificial neural network approach for selection of susceptible single nucleotide polymorphisms and construction of prediction model on childhood allergic asthma	claim
68	132	Two-stage normalization using background intensities in cDNA microarray data	claim
69	131	Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma	claim
70	131	Alternative mapping of probes to genes for Affymetrix chips	claim
71	131	A web services choreography scenario for interoperating bioinformatics applications	claim
72	130	PATTERNFINDER: combined analysis of DNA regulatory sequences and double-helix stability	claim
73	129	Integrating partonomic hierarchies in anatomy ontologies	claim
74	128	Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics	claim
75	128	cuticleDB: a relational database of Arthropod cuticular proteins	claim
76	128	Comparing transformation methods for DNA microarray data	claim
77	127	Optimized LOWESS normalization parameter selection for DNA microarray data	claim
78	127	MolTalk - a programming library for protein structures and structure analysis	claim
79	126	Visualization and analysis of microarray and gene ontology data with treemaps	claim
80	126	A probabilistic model for the evolution of RNA structure	claim
81	126	Visualising very large phylogenetic trees in three dimensional hyperbolic space	claim
82	125	A fast algorithm for determining the best combination of local alignments to a query sequence	claim
83	125	A functional hierarchical organization of the protein sequence space	claim
84	124	XHM: A system for detection of potential cross hybridizations in DNA microarrays	claim
85	124	Tests for finding complex patterns of differential expression in cancers: towards individualized medicine	claim
86	124	The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet)	claim
87	123	Interaction profile-based protein classification of death domain	claim
88	123	galaxieEST: addressing EST identity through automated phylogenetic analysis	claim
89	123	A two-way interface between limited Systems Biology Markup Language and R	claim
90	122	A comprehensive comparison of comparative RNA structure prediction approaches	claim
91	121	DEDB: a database of Drosophila melanogaster exons in splicing graph form	claim
92	121	Asynchronous adaptive time step in quantitative cellular automata modeling	claim
93	120	Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information	claim
94	120	An approach to large scale identification of non-obvious structural similarities between proteins	claim
95	120	pdb-care (PDB CArbohydrate REsidue check): a program to support annotation of complex carbohydrate structures in PDB files	claim
96	120	Clustering under the line graph transformation: application to reaction network	claim
97	119	PASS2: an automated database of protein alignments organised as structural superfamilies	claim
98	119	Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains : a web-based resource	claim
99	119	Genome SEGE: A database for 'intronless' genes in eukaryotic genomes	claim
100	117	CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting	claim
101	117	Cancer characterization and feature set extraction by discriminative margin clustering	claim
102	116	Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction	claim
103	116	Array-A-Lizer: A serial DNA microarray quality analyzer	claim
104	115	Quantifying the relationship between co-expression, co-regulation and gene function	claim
105	115	An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage	claim
106	114	Profiled support vector machines for antisense oligonucleotide efficacy prediction	claim
107	114	Analysis of superfamily specific profile-profile recognition accuracy	claim
108	114	HMM Logos for visualization of protein families	claim
109	114	Extending the mutual information measure to rank inferred literature relationships	claim
110	113	Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering	claim
111	113	Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays	claim
112	113	Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites	claim
113	112	MuTrack: a genome analysis system for large-scale mutagenesis in the mouse	claim
114	112	SPOC: A widely distributed domain associated with cancer, apoptosis and transcription	claim
115	112	A double classification tree search algorithm for index SNP selection	claim
116	112	Predicting co-complexed protein pairs using genomic and proteomic data integration	claim
117	111	The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases	claim
118	111	Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network	claim
119	111	Multiclass discovery in array data	claim
120	110	Estimating mutual information using B-spline functions - an improved similarity measure for analysing gene expression data	claim
121	110	Tools for loading MEDLINE into a local relational database	claim
122	108	Improving the scaling normalization for high-density oligonucleotide GeneChip expression microarrays	claim
123	108	Enhanced protein domain discovery using taxonomy	claim
124	106	ESTIMA, a tool for EST management in a multi-project environment	claim
125	106	Spotting effect in microarray experiments	claim
126	105	eL-DASionator: an LDAS upload file generator	claim
127	104	Discriminative topological features reveal biological network mechanisms	claim
128	102	Detection of transposable elements by their compositional bias	claim
129	102	No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions	claim
130	102	FRAGS: estimation of coding sequence substitution rates from fragmentary data	claim
131	101	A database for G proteins and their interaction with GPCRs	claim
132	100	Functionally specified protein signatures distinctive for each of the different blue copper proteins	claim
133	100	Auto-validation of fluorescent primer extension genotyping assay using signal clustering and neural networks	claim
134	100	Handling multiple testing while interpreting microarrays with the Gene Ontology Database	claim
135	98	Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE)	claim
136	98	STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes	claim
137	97	Calibration and assessment of channel-specific biases in microarray data with extended dynamical range	claim
138	97	Performance of a genetic algorithm for mass spectrometry proteomics	claim
139	97	Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns	claim
140	96	GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes	claim
141	96	A hybrid clustering approach to recognition of protein families in 114 microbial genomes	claim
142	96	Gene finding in novel genomes	claim
143	96	Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome	claim
144	95	PCOGR: Phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms	claim
145	94	Caryoscope: An Open Source Java application for viewing microarray data in a genomic context	claim
146	94	The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource	claim
147	94	GASP: Gapped Ancestral Sequence Prediction for proteins	claim
148	94	The MB2 gene family of Plasmodium species has a unique combination of S1 and GTP-binding domains	claim
149	93	Predicting binding sites of hydrolase-inhibitor complexes by combining several methods	claim
150	92	BioBuilder as a database development and functional annotation platform for proteins	claim
151	91	SIGI: score-based identification of genomic islands	claim
152	91	Improved hit criteria for DNA local alignment	claim
153	90	Statistical monitoring of weak spots for improvement of normalization and ratio estimates in microarrays	claim
154	90	Haplotype frequency estimation error analysis in the presence of missing genotype data	claim
155	89	Network analysis of metabolic enzyme evolution in Escherichia coli	claim
156	88	Coronavirus 3CLpro proteinase cleavage sites: Possible relevance to SARS virus pathology	claim
157	88	PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences	claim
158	87	GECKO: a complete large-scale gene expression analysis platform	claim
159	87	Selection of informative clusters from hierarchical cluster tree with gene classes	claim
160	87	prot4EST: Translating Expressed Sequence Tags from neglected genomes	claim
161	86	Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA	claim
162	86	A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in estimating genetic relationships: an application to papillomavirus DNA sequence	claim
163	85	Frequent occurrence of recognition Site-like sequences in the restriction endonucleases	claim
164	85	Benchmarking tools for the alignment of functional noncoding DNA	claim
165	84	Comparison of computational methods for identifying translation initiation sites in EST data	claim
166	83	VKCDB: Voltage-gated potassium channel database	claim
167	83	SUPFAM: A database of sequence superfamilies of protein domains	claim
168	81	Few amino acid positions in rpoB are associated with most of the rifampin resistance in Mycobacterium tuberculosis	claim
169	79	A new mixture model approach to analyzing allelic-loss data using Bayes factors	claim
170	79	Modeling of cell signaling pathways in macrophages by semantic networks	claim
171	77	Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals	claim
172	77	A structural study for the optimisation of functional motifs encoded in protein sequences	claim
173	77	Target SNP selection in complex disease association studies	claim
174	76	An imaging system for standardized quantitative analysis of C. elegans behavior	claim
175	76	VisANT: an online visualization and analysis tool for biological interaction data	claim
176	75	Structural characterization of genomes by large scale sequence-structure threading	claim
177	75	Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes	claim
178	75	Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries	claim
179	73	Use of a structural alphabet for analysis of short loops connecting repetitive structures	claim
180	70	M-CGH: Analysing microarray-based CGH experiments	claim
181	69	ArrayD: A general purpose software for Microarray design	claim
182	64	Reuse of imputed data in microarray analysis increases imputation efficiency	claim
183	62	Protein family comparison using statistical models and predicted structural information	claim
184	62	Pegasys: software for executing and integrating analyses of biological sequences	claim
185	61	PyEvolve: a toolkit for statistical modelling of molecular evolution	claim
186	59	Content-rich biological network constructed by mining PubMed abstracts	claim
187	56	Integrated web service for improving alignment quality based on segments comparison	claim
188	43	A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions	claim

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