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Volumn 985, Issue , 2013, Pages 61-83

Linking genome-scale metabolic modeling and genome annotation

Author keywords

Flux balance analysis; Gap filling; Metabolic network; Orphan reactions

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; BIOMASS PRODUCTION; CELL GROWTH; ENZYME ACTIVITY; EUKARYOTE; FLUX BALANCE ANALYSIS; GENE; GENETIC MODEL; GENOME; HIGH THROUGHPUT SCREENING; METABOLISM; MITOCHONDRIAL MEMBRANE; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROKARYOTE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; DNA SEQUENCE; GENETIC DATABASE; GENETICS; HUMAN; METHODOLOGY; MOLECULAR GENETICS;

EID: 84880804276     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-299-5_4     Document Type: Article
Times cited : (6)

References (61)
  • 1
    • 79952705856 scopus 로고    scopus 로고
    • Mining high-throughput experimental data to link gene and function
    • doi:10.1016/j.tibtech.2011.01.001
    • Blaby-Haas CE, de Crecy-Lagard V (2011) Mining high-throughput experimental data to link gene and function. Trends Biotechnol 29 (4):174-182. doi:10.1016/j.tibtech.2011.01.001
    • (2011) Trends Biotechnol , vol.29 , Issue.4 , pp. 174-182
    • Blaby-Haas, C.E.1    De Crecy-Lagard, V.2
  • 2
    • 72449145463 scopus 로고    scopus 로고
    • Unknown' proteins and 'orphan' enzymes: The missing half of the engineering parts list-and how to find it
    • doi:10.1042/BJ20091328
    • Hanson AD, Pribat A, Waller JC, de Crecy-Lagard V (2010) 'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list-and how to find it. Biochem J 425(1):1-11. doi:10.1042/BJ20091328
    • (2010) Biochem J , vol.425 , Issue.1 , pp. 1-11
    • Hanson, A.D.1    Pribat, A.2    Waller, J.C.3    De Crecy-Lagard, V.4
  • 3
    • 34547852439 scopus 로고    scopus 로고
    • A survey of orphan enzyme activities
    • doi:10.1186/1471-2105-8-244
    • Pouliot Y, Karp PD (2007) A survey of orphan enzyme activities. BMC Bioinformatics 8:244. doi:10.1186/1471-2105-8-244
    • (2007) BMC Bioinformatics , vol.8 , pp. 244
    • Pouliot, Y.1    Karp, P.D.2
  • 4
    • 0037045398 scopus 로고    scopus 로고
    • ORF-FINDER: A vector for highthroughput gene identification
    • Rombel IT, Sykes KF, Rayner S, Johnston SA (2002) ORF-FINDER: a vector for highthroughput gene identification. Gene 282 (1-2):33-41
    • (2002) Gene , vol.282 , Issue.1-2 , pp. 33-41
    • Rombel, I.T.1    Sykes, K.F.2    Rayner, S.3    Johnston, S.A.4
  • 6
    • 34548246519 scopus 로고    scopus 로고
    • Protein annotation at genomic scale: The current status
    • doi:10.1021/cr068303k
    • Frishman D (2007) Protein annotation at genomic scale: the current status. Chem Rev 107(8):3448-3466. doi:10.1021/cr068303k
    • (2007) Chem Rev , vol.107 , Issue.8 , pp. 3448-3466
    • Frishman, D.1
  • 7
    • 79953077647 scopus 로고    scopus 로고
    • Protein function prediction: Towards integration of similarity metrics
    • doi:10.1016/j.sbi.2011.02.001
    • Erdin S, Lisewski AM, Lichtarge O (2011) Protein function prediction: towards integration of similarity metrics. Curr Opin Struct Biol 21(2):180-188. doi:10.1016/j.sbi.2011.02.001
    • (2011) Curr Opin Struct Biol , vol.21 , Issue.2 , pp. 180-188
    • Erdin, S.1    Lisewski, A.M.2    Lichtarge, O.3
  • 8
    • 84934439678 scopus 로고    scopus 로고
    • Inferring function from homology
    • doi:10.1007/978-1-60327-429-6-6
    • Emes RD (2008) Inferring function from homology. Methods Mol Biol 453:149-168. doi:10.1007/978-1-60327-429-6-6
    • (2008) Methods Mol Biol , vol.453 , pp. 149-168
    • Emes, R.D.1
  • 9
    • 34250790725 scopus 로고    scopus 로고
    • Estimating the annotation error rate of curated GO database sequence annotations
    • doi:10.1186/1471-2105-8-170
    • Jones CE, Brown AL, Baumann U (2007) Estimating the annotation error rate of curated GO database sequence annotations. BMC Bioinformatics 8:170. doi:10.1186/1471-2105-8-170
    • (2007) BMC Bioinformatics , vol.8 , pp. 170
    • Jones, C.E.1    Brown, A.L.2    Baumann, U.3
  • 10
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • doi:10.1038/nprot.2009.203
    • Thiele I, Palsson BO (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5(1):93-121. doi:10.1038/nprot.2009.203
    • (2010) Nat Protoc , vol.5 , Issue.1 , pp. 93-121
    • Thiele, I.1    Palsson, B.O.2
  • 12
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • doi:10.1016/S0022-2836(05)80360-2
    • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403-410. doi:10.1016/S0022-2836(05) 80360-2
    • (1990) J Mol Biol , vol.215 , Issue.3 , pp. 403-410
    • Altschul, S.F.1    Gish, W.2    Miller, W.3    Myers, E.W.4    Lipman, D.J.5
  • 14
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27-30
    • (2000) Nucleic Acids Res , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 15
    • 0345863935 scopus 로고    scopus 로고
    • The KEGG resource for deciphering the genome
    • doi:10.1093/nar/gkh063
    • Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32(Database issue):D277-D280. doi:10.1093/nar/gkh063
    • (2004) Nucleic Acids Res , vol.32 , Issue.DATABASE ISSUE
    • Kanehisa, M.1    Goto, S.2    Kawashima, S.3    Okuno, Y.4    Hattori, M.5
  • 18
    • 13444306342 scopus 로고    scopus 로고
    • The Swiss-Prot protein knowledgebase and ExPASy: Providing the plant community with high quality proteomic data and tools
    • doi:10.1016/j.plaphy.2004.10.009
    • Schneider M, Tognolli M, Bairoch A (2004) The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools. Plant Physiol Biochem 42(12):1013-1021. doi:10.1016/j.plaphy.2004.10.009
    • (2004) Plant Physiol Biochem , vol.42 , Issue.12 , pp. 1013-1021
    • Schneider, M.1    Tognolli, M.2    Bairoch, A.3
  • 19
    • 77956696072 scopus 로고    scopus 로고
    • Highthroughput generation, optimization and analysis of genome-scale metabolic models
    • doi:10.1038/nbt.1672
    • Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL (2010) Highthroughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol 28(9):977-982. doi:10.1038/nbt.1672
    • (2010) Nat Biotechnol , vol.28 , Issue.9 , pp. 977-982
    • Henry, C.S.1    Dejongh, M.2    Best, A.A.3    Frybarger, P.M.4    Linsay, B.5    Stevens, R.L.6
  • 21
    • 80052719812 scopus 로고    scopus 로고
    • A survey of metabolic databases emphasizing the MetaCyc family
    • doi:10.1007/s00204-011-0705-2
    • Karp PD, Caspi R (2011) A survey of metabolic databases emphasizing the MetaCyc family. Arch Toxicol 85(9):1015-1033. doi:10.1007/s00204-011-0705-2
    • (2011) Arch Toxicol , vol.85 , Issue.9 , pp. 1015-1033
    • Karp, P.D.1    Caspi, R.2
  • 23
    • 84855499408 scopus 로고    scopus 로고
    • MetRxn: A knowledgebase of metabolites and reactions spanning metabolic models and databases
    • doi:10.1186/1471-2105-13-6
    • Kumar A, Suthers PF, Maranas CD (2012) MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinformatics 13(1):6. doi:10.1186/1471-2105-13-6
    • (2012) BMC Bioinformatics , vol.13 , Issue.1 , pp. 6
    • Kumar, A.1    Suthers, P.F.2    Maranas, C.D.3
  • 28
    • 0346494858 scopus 로고    scopus 로고
    • DEG: A database of essential genes
    • doi:10.1093/nar/gkh024
    • Zhang R, Ou HY, Zhang CT (2004) DEG: a database of essential genes. Nucleic Acids Res 32(Database issue):D271-D272. doi:10.1093/nar/gkh024
    • (2004) Nucleic Acids Res , vol.32 , Issue.DATABASE ISSUE
    • Zhang, R.1    Ou, H.Y.2    Zhang, C.T.3
  • 29
    • 58149197597 scopus 로고    scopus 로고
    • DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes
    • doi:10.1093/nar/gkn858
    • Zhang R, Lin Y (2009) DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res 37(Database issue): D455-D458. doi:10.1093/nar/gkn858
    • (2009) Nucleic Acids Res , vol.37 , Issue.DATABASE ISSUE
    • Zhang, R.1    Lin, Y.2
  • 30
    • 84862165032 scopus 로고    scopus 로고
    • OGEE: An online gene essentiality database
    • doi:10.1093/nar/gkr986
    • Chen WH, Minguez P, Lercher MJ, Bork P (2012) OGEE: an online gene essentiality database. Nucleic Acids Res 40(Database issue):D901-D906. doi:10.1093/nar/gkr986
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE
    • Chen, W.H.1    Minguez, P.2    Lercher, M.J.3    Bork, P.4
  • 32
    • 77951612556 scopus 로고    scopus 로고
    • BiGG: A Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
    • doi:10.1186/1471-2105-11-213
    • Schellenberger J, Park JO, Conrad TM, Palsson BO (2010) BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11:213. doi:10.1186/1471-2105-11-213
    • (2010) BMC Bioinformatics , vol.11 , pp. 213
    • Schellenberger, J.1    Park, J.O.2    Conrad, T.M.3    Palsson, B.O.4
  • 33
    • 79251546728 scopus 로고    scopus 로고
    • MEMOSys: Bioinformatics platform for genome-scale metabolic models
    • doi:10.1186/1752-0509-5-20
    • Pabinger S, Rader R, Agren R, Nielsen J, Trajanoski Z (2011) MEMOSys: bioinformatics platform for genome-scale metabolic models. BMC Syst Biol 5:20. doi:10.1186/1752-0509-5-20
    • (2011) BMC Syst Biol , vol.5 , pp. 20
    • Pabinger, S.1    Rader, R.2    Agren, R.3    Nielsen, J.4    Trajanoski, Z.5
  • 35
    • 33646884848 scopus 로고    scopus 로고
    • SBMLToolbox: An SBML toolbox for MATLAB users
    • doi:10.1093/bioinformatics/btl111
    • Keating SM, Bornstein BJ, Finney A, HuckaM (2006) SBMLToolbox: an SBML toolbox for MATLAB users. Bioinformatics 22 (10):1275-1277. doi:10.1093/ bioinformatics/btl111
    • (2006) Bioinformatics , vol.22 , Issue.10 , pp. 1275-1277
    • Keating, S.M.1    Bornstein, B.J.2    Finney, A.3    Hucka, M.4
  • 36
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraintbased genome-scale metabolic models
    • Mahadevan R, Schilling CH (2003) The effects of alternate optimal solutions in constraintbased genome-scale metabolic models. Metab Eng 5(4):264-276
    • (2003) Metab Eng , vol.5 , Issue.4 , pp. 264-276
    • Mahadevan, R.1    Schilling, C.H.2
  • 37
    • 84857999389 scopus 로고    scopus 로고
    • A metabolic network approach for the identification and prioritization of antimicrobial drug targets
    • doi:10.1016/j.tim.2011.12.004
    • Chavali AK, D'Auria KM, Hewlett EL, Pearson RD, Papin JA (2012) A metabolic network approach for the identification and prioritization of antimicrobial drug targets. Trends Microbiol 20(3):113-123. doi:10.1016/j.tim. 2011.12.004
    • (2012) Trends Microbiol , vol.20 , Issue.3 , pp. 113-123
    • Chavali, A.K.1    D'Auria, K.M.2    Hewlett, E.L.3    Pearson, R.D.4    Papin, J.A.5
  • 38
    • 34547676311 scopus 로고    scopus 로고
    • Optimization based automated curation of metabolic reconstructions
    • doi:10.1186/1471-2105-8-212
    • Satish Kumar V, Dasika MS, Maranas CD (2007) Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 8:212. doi:10.1186/1471-2105-8-212
    • (2007) BMC Bioinformatics , vol.8 , pp. 212
    • Satish Kumar, V.1    Dasika, M.S.2    Maranas, C.D.3
  • 40
  • 42
    • 84856568013 scopus 로고    scopus 로고
    • Construction and completion of flux balance models from pathway databases
    • doi:10.1093/bioinformatics/btr681
    • Latendresse M, Krummenacker M, Trupp M, Karp PD (2012) Construction and completion of flux balance models from pathway databases. Bioinformatics 28(3):388-396. doi:10.1093/bioinformatics/btr681
    • (2012) Bioinformatics , vol.28 , Issue.3 , pp. 388-396
    • Latendresse, M.1    Krummenacker, M.2    Trupp, M.3    Karp, P.D.4
  • 43
    • 13244268322 scopus 로고    scopus 로고
    • A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
    • doi:10.1186/1471-2105-5-76
    • Green ML, Karp PD (2004) A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 5:76. doi:10.1186/1471-2105-5-76
    • (2004) BMC Bioinformatics , vol.5 , pp. 76
    • Green, M.L.1    Karp, P.D.2
  • 44
    • 34547840249 scopus 로고    scopus 로고
    • Using genomecontext data to identify specific types of functional associations in pathway/genome databases
    • doi:10.1093/bioinformatics/btm213
    • Green ML, Karp PD (2007) Using genomecontext data to identify specific types of functional associations in pathway/genome databases. Bioinformatics 23(13):i205-i211. doi:10.1093/bioinformatics/btm213
    • (2007) Bioinformatics , vol.23 , Issue.13
    • Green, M.L.1    Karp, P.D.2
  • 45
    • 63549108441 scopus 로고    scopus 로고
    • GrowMatch: An automated method for reconciling in silico/ in vivo growth predictions
    • doi:10.1371/journal.pcbi.1000308
    • Kumar VS, Maranas CD (2009)GrowMatch: an automated method for reconciling in silico/ in vivo growth predictions. PLoS Comput Biol 5(3):e1000308. doi:10.1371/journal.pcbi.1000308
    • (2009) PLoS Comput Biol , vol.5 , Issue.3
    • Kumar, V.S.1    Maranas, C.D.2
  • 46
    • 33746660425 scopus 로고    scopus 로고
    • Identification of genome-scale metabolic network models using experimentally measured flux profiles
    • doi:10.1371/journal.pcbi.0020072
    • Herrgard MJ, Fong SS, Palsson BO (2006) Identification of genome-scale metabolic network models using experimentally measured flux profiles. PLoS Comput Biol 2(7):e72. doi:10.1371/journal.pcbi.0020072
    • (2006) PLoS Comput Biol , vol.2 , Issue.7
    • Herrgard, M.J.1    Fong, S.S.2    Palsson, B.O.3
  • 48
    • 79958821230 scopus 로고    scopus 로고
    • Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii
    • doi:10.1186/1471-2164-12-S1-S4
    • Ghamsari L, Balaji S, Shen Y, Yang X, Balcha D, Fan C, Hao T, Yu H, Papin JA, Salehi-Ashtiani K (2011) Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii. BMC Genomics 12(Suppl 1):S4. doi: 10.1186/1471-2164-12-S1-S4
    • (2011) BMC Genomics , vol.12 , Issue.SUPPL. 1
    • Ghamsari, L.1    Balaji, S.2    Shen, Y.3    Yang, X.4    Balcha, D.5    Fan, C.6    Hao, T.7    Yu, H.8    Papin, J.A.9    Salehi-Ashtiani, K.10
  • 51
    • 78651335279 scopus 로고    scopus 로고
    • Systematizing the generation of missing metabolic knowledge
    • doi:10.1002/bit.22844
    • Orth JD, Palsson BO (2010) Systematizing the generation of missing metabolic knowledge. Biotechnol Bioeng 107(3):403-412. doi:10.1002/bit.22844
    • (2010) Biotechnol Bioeng , vol.107 , Issue.3 , pp. 403-412
    • Orth, J.D.1    Palsson, B.O.2
  • 52
    • 80053375237 scopus 로고    scopus 로고
    • The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions
    • doi:10.1186/1752-0509-5-155
    • Rolfsson O, Palsson BO, Thiele I (2011) The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. BMC Syst Biol 5:155. doi:10.1186/1752-0509-5-155
    • (2011) BMC Syst Biol , vol.5 , pp. 155
    • Rolfsson, O.1    Palsson, B.O.2    Thiele, I.3
  • 53
    • 65649126411 scopus 로고    scopus 로고
    • Flux balance analysis: Interrogating genomescale metabolic networks
    • doi:10.1007/978-1-59745-525-1-3
    • Oberhardt MA, Chavali AK, Papin JA (2009) Flux balance analysis: interrogating genomescale metabolic networks. Methods Mol Biol 500:61-80. doi:10.1007/978-1-59745-525-1-3
    • (2009) Methods Mol Biol , vol.500 , pp. 61-80
    • Oberhardt, M.A.1    Chavali, A.K.2    Papin, J.A.3
  • 55
    • 77952886804 scopus 로고    scopus 로고
    • The biomass objective function
    • doi:10.1016/j.mib.2010.03.003
    • Feist AM, Palsson BO (2010) The biomass objective function. Curr Opin Microbiol 13 (3):344-349. doi:10.1016/j.mib.2010.03.003
    • (2010) Curr Opin Microbiol , vol.13 , Issue.3 , pp. 344-349
    • Feist, A.M.1    Palsson, B.O.2
  • 56
    • 41149169317 scopus 로고    scopus 로고
    • Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major
    • doi:10.1038/msb.2008.15
    • Chavali AK, Whittemore JD, Eddy JA, Williams KT, Papin JA (2008) Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major. Mol Syst Biol 4:177. doi:10.1038/msb.2008.15
    • (2008) Mol Syst Biol , vol.4 , pp. 177
    • Chavali, A.K.1    Whittemore, J.D.2    Eddy, J.A.3    Williams, K.T.4    Papin, J.A.5
  • 57
    • 84862159261 scopus 로고    scopus 로고
    • Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
    • doi:10.1186/1752-0509-6-30
    • Orth JD, Palsson BO (2012) Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. BMC Syst Biol 6(1):30. doi:10.1186/1752-0509-6-30
    • (2012) BMC Syst Biol , vol.6 , Issue.1 , pp. 30
    • Orth, J.D.1    Palsson, B.O.2
  • 59
    • 79952601486 scopus 로고    scopus 로고
    • Rapid amplification of cDNA ends (RACE)
    • doi:10.1007/978-1-59745-248-9-8
    • Yeku O, Frohman MA (2011) Rapid amplification of cDNA ends (RACE). Methods Mol Biol 703:107-122. doi:10.1007/978-1-59745-248-9-8
    • (2011) Methods Mol Biol , vol.703 , pp. 107-122
    • Yeku, O.1    Frohman, M.A.2
  • 60
    • 0024212067 scopus 로고
    • Rapid production of full-length cDNAs from rare transcripts: Amplification using a single gene-specific oligonucleotide primer
    • Frohman MA, Dush MK, Martin GR (1988) Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci U S A 85(23):8998-9002
    • (1988) Proc Natl Acad Sci U S A , vol.85 , Issue.23 , pp. 8998-9002
    • Frohman, M.A.1    Dush, M.K.2    Martin, G.R.3
  • 61
    • 33750298722 scopus 로고    scopus 로고
    • Prediction of genomic functional elements
    • doi:10.1146/annurev.genom.7.080505.115745
    • Jones SJ (2006) Prediction of genomic functional elements. Annu Rev Genomics Hum Genet 7:315-338. doi:10.1146/annurev.genom.7.080505.115745
    • (2006) Annu Rev Genomics Hum Genet , vol.7 , pp. 315-338
    • Jones, S.J.1


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