A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

scientific article

A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases is …
instance of (P31):
scholarly articleQ13442814
review articleQ7318358

External links are
P8978DBLP publication IDjournals/bmcbi/GreenK04
P6179Dimensions Publication ID1024613569
P356DOI10.1186/1471-2105-5-76
P3181OpenCitations bibliographic resource ID3920334
P932PMC publication ID446185
P698PubMed publication ID15189570
P5875ResearchGate publication ID8516910

P50authorPeter D. KarpQ23823647
P2093author name stringMichelle L Green
P2860cites workMicrobial genomes and "missing" enzymes: redefining biochemical pathways.Q33767979
The Protein Information ResourceQ33963623
L-Aspartate oxidase, a newly discovered enzyme of Escherichia coli, is the B protein of quinolinate synthetaseQ34276571
Missing genes in metabolic pathways: a comparative genomics approachQ35114448
Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationshipsQ37379451
Statistics of large-scale sequence searchingQ38551663
Shotgun: getting more from sequence similarity searchesQ41692257
Molecular biology of pyridine nucleotide biosynthesis in Escherichia coli. Cloning and characterization of quinolinate synthesis genes nadA and nadB.Q42649141
GenBankQ78768024
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)Q21194867
Complete genome sequence of Caulobacter crescentusQ22066320
DNA sequence of both chromosomes of the cholera pathogen Vibrio choleraeQ22122394
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequenceQ22122411
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceQ24286950
Gapped BLAST and PSI-BLAST: a new generation of protein database search programsQ24545170
The EcoCyc DatabaseQ24548415
The COG database: new developments in phylogenetic classification of proteins from complete genomesQ24605347
Enzyme-specific profiles for genome annotation: PRIAMQ24642072
The TIGRFAMs database of protein familiesQ24681677
Basic local alignment search toolQ25938991
Fitting a mixture model by expectation maximization to discover motifs in biopolymersQ27860556
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003Q27860747
The Pathway Tools softwareQ28217270
Combining evidence using p-values: application to sequence homology searchesQ28265811
Hidden Markov models for sequence analysis: extension and analysis of the basic methodQ28286314
The MTCY428.08 gene of Mycobacterium tuberculosis codes for NAD+ synthetase.Q28486617
Assigning protein functions by comparative genome analysis: Protein phylogenetic profilesQ29039336
Hidden Markov models for detecting remote protein homologiesQ29614396
Hidden Markov models in computational biology. Applications to protein modelingQ29614397
Hidden Markov modelsQ29622874
P433issue1
P407language of work or nameEnglishQ1860
P921main subjectdatabaseQ8513
P304page(s)76
P577publication date2004-06-09
P1433published inBMC BioinformaticsQ4835939
P1476titleA Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
P478volume5

Reverse relations

cites work (P2860)
Q31120471'Conserved hypothetical' proteins: prioritization of targets for experimental study
Q372327036-pyruvoyltetrahydropterin synthase paralogs replace the folate synthesis enzyme dihydroneopterin aldolase in diverse bacteria
Q40664325A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism
Q33239310A case study in pathway knowledgebase verification
Q43519914A fast and accurate algorithm for comparative analysis of metabolic pathways.
Q33552496A geographically-diverse collection of 418 human gut microbiome pathway genome databases
Q24548560A metabolic network in the evolutionary context: multiscale structure and modularity
Q30562290A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus
Q33742075An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models
Q37341560An overview of bioinformatics methods for modeling biological pathways in yeast
Q33327740Analysis of Aspergillus nidulans metabolism at the genome-scale
Q33922321Analysis of complex metabolic behavior through pathway decomposition
Q33775602Analysis of ultra low genome conservation in Clostridium difficile
Q51564420AtIPD: a curated database of Arabidopsis isoprenoid pathway models and genes for isoprenoid network analysis.
Q24817211Automation of gene assignments to metabolic pathways using high-throughput expression data
Q31114178BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data
Q33237374BioWarehouse: a bioinformatics database warehouse toolkit
Q96816513Birth of a pathway for sulfur metabolism in early amniote evolution
Q34539646Chapter 12: Human microbiome analysis
Q21563379Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development
Q28654886Computational approaches for microalgal biofuel optimization: a review
Q21092879Computational prediction of human metabolic pathways from the complete human genome
Q28551270Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach
Q30499238Core and panmetabolism in Escherichia coli
Q35005439Dead end metabolites--defining the known unknowns of the E. coli metabolic network
Q24796847EcoCyc: a comprehensive database resource for Escherichia coli
Q36060603Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses
Q31039784Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical tests
Q24535096Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
Q30493380FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology.
Q35662809Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS.
Q59796897Functional analysis of Salmonella Typhi adaptation to survival in water
Q34252817Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
Q97420648Genome-Scale Metabolic Model Driven Design of a Defined Medium for Campylobacter jejuni M1cam
Q34475663Genome-derived insights into the biology of the hepatotoxic bloom-forming cyanobacterium Anabaena sp. strain 90
Q42658345Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism
Q39825053Genome-scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis.
Q46308193Genome-scale modeling of yeast: chronology, applications and critical perspectives.
Q33391538Genome-scale models of bacterial metabolism: reconstruction and applications
Q57282824Genome-wide analysis of fitness data and its application to improve metabolic models
Q33826880Genome-wide discovery of missing genes in biological pathways of prokaryotes
Q33412986Global networks of functional coupling in eukaryotes from comprehensive data integration
Q37742784Graph methods for the investigation of metabolic networks in parasitology
Q33417622GrowMatch: an automated method for reconciling in silico/in vivo growth predictions
Q29616791IMG ER: a system for microbial genome annotation expert review and curation
Q46843737Identification of fungal sphingolipid C9-methyltransferases by phylogenetic profiling
Q33237950Identifying metabolic enzymes with multiple types of association evidence
Q39801154In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments.
Q33577072Integration of bioinformatics to biodegradation.
Q57919415Link and Node Prediction in Metabolic Networks with Probabilistic Logic
Q30412056Linking genome-scale metabolic modeling and genome annotation
Q40586801MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks
Q35179413MP-Align: alignment of metabolic pathways
Q25257010MaGe: a microbial genome annotation system supported by synteny results
Q33523149Machine learning methods for metabolic pathway prediction
Q41773574MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks
Q38474125MetaCyc and AraCyc. Metabolic pathway databases for plant research
Q24538678MetaCyc: a multiorganism database of metabolic pathways and enzymes
Q34271370MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity
Q51339839Metabolic genomics.
Q34247874Metabolic network alignment in large scale by network compression
Q37033446Metabolic network model of a human oral pathogen.
Q28074539Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis
Q37749058Metabolic pathways in the apicoplast of apicomplexa.
Q33689651Metabolic reconstruction identifies strain-specific regulation of virulence in Toxoplasma gondii.
Q37273478Mining bacterial genomes for novel arylesterase activity
Q37198741Missing gene identification using functional coherence scores
Q42599526ModEnzA: Accurate Identification of Metabolic Enzymes Using Function Specific Profile HMMs with Optimised Discrimination Threshold and Modified Emission Probabilities
Q30030541Model-enabled gene search (MEGS) allows fast and direct discovery of enzymatic and transport gene functions in the marine bacterium Vibrio fischeri.
Q36360689Multidimensional annotation of the Escherichia coli K-12 genome
Q34538652Multireplicon genome architecture of Lactobacillus salivarius
Q28763948New metrics for comparative genomics
Q37008197New surveyor tools for charting microbial metabolic maps.
Q33600871New tools at the Candida Genome Database: biochemical pathways and full-text literature search
Q42431633Optimization based automated curation of metabolic reconstructions
Q36479565PatchSurfers: Two methods for local molecular property-based binding ligand prediction
Q24642068Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
Q36069213Pathway information for systems biology
Q43227038Predicting genes for orphan metabolic activities using phylogenetic profiles
Q28974902Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours
Q28492567Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa
Q55455574ProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies.
Q29616018Reconstruction of biochemical networks in microorganisms
Q35398119Reconstruction of metabolic pathways by combining probabilistic graphical model-based and knowledge-based methods
Q34987962Semi-automated curation of metabolic models via flux balance analysis: a case study with Mycoplasma gallisepticum
Q59793048Shortest path counting in probabilistic biological networks
Q35070376SubMAP: aligning metabolic pathways with subnetwork mappings
Q33978848Synergistic use of plant-prokaryote comparative genomics for functional annotations
Q51132952Synthetic Biology for Cell-Free Biosynthesis: Fundamentals of Designing Novel In Vitro Multi-Enzyme Reaction Networks.
Q33264473Systematic assignment of thermodynamic constraints in metabolic network models
Q35058632Systematizing the generation of missing metabolic knowledge
Q28484023The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes
Q29615370The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
Q22122045The complete genome sequence of Francisella tularensis, the causative agent of tularemia
Q42641021The conservation and evolutionary modularity of metabolism
Q34785166The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
Q34977461The outcomes of pathway database computations depend on pathway ontology
Q35855112Thematic review series: The pathogenesis of atherosclerosis. Toward a biological network for atherosclerosis
Q33282913Toward the automated generation of genome-scale metabolic networks in the SEED.
Q37696969Towards genome-scale signalling network reconstructions
Q36371202Towards multidimensional genome annotation
Q40807932Understanding the host-adapted state of Citrobacter rodentium by transcriptomic analysis
Q45113322Using the MetaCyc pathway database and the BioCyc database collection
Q26830669Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway

Search more.