메뉴 건너뛰기




Volumn 11, Issue 8, 2013, Pages

The COMBREX Project: Design, Methodology, and Initial Results

(74)  Anton, Brian P a   Chang, Yi Chien b   Brown, Peter c   Choi, Han Pil c   Faller, Lina L b   Guleria, Jyotsna c   Hu, Zhenjun b   Klitgord, Niels b   Levy Moonshine, Ami c   Maksad, Almaz c   Mazumdar, Varun b   McGettrick, Mark d   Osmani, Lais c   Pokrzywa, Revonda c   Rachlin, John d   Swaminathan, Rajeswari c   Allen, Benjamin e,f   Housman, Genevieve c   Monahan, Caitlin c   Rochussen, Krista c   more..


Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMBREX DATABASE; DATA BASE; DNA SEQUENCE; ESCHERICHIA COLI; EXPERIMENTAL TEST; FUNDING; HELICOBACTER PYLORI; HUMAN; MATHEMATICAL ANALYSIS; METHODOLOGY; NONBIOLOGICAL MODEL; NONHUMAN; ONLINE SYSTEM; PREDICTION; PROTEIN FUNCTION; SEARCH ENGINE; SEQUENCE ANALYSIS;

EID: 84883152491     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.1001638     Document Type: Article
Times cited : (47)

References (31)
  • 1
    • 19344377263 scopus 로고    scopus 로고
    • Identifying protein function-a call for community action
    • doi:10.1371/journal.pbio.0020042
    • Roberts RJ, (2004) Identifying protein function-a call for community action. PLoS Biol 2: e42 doi:10.1371/journal.pbio.0020042.
    • (2004) PLoS Biol , vol.2
    • Roberts, R.J.1
  • 2
    • 78651305142 scopus 로고    scopus 로고
    • COMBREX: a project to accelerate the functional annotation of prokaryotic genomes
    • Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, et al. (2011) COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Res 39: D11-14.
    • (2011) Nucleic Acids Res , vol.39
    • Roberts, R.J.1    Chang, Y.C.2    Hu, Z.3    Rachlin, J.N.4    Anton, B.P.5
  • 3
    • 0028424239 scopus 로고
    • Improving generalization with active learning
    • Cohn D, Atlas L, Ladner R, (1994) Improving generalization with active learning. Machine Learning 15: 201-221.
    • (1994) Machine Learning , vol.15 , pp. 201-221
    • Cohn, D.1    Atlas, L.2    Ladner, R.3
  • 4
    • 84862940317 scopus 로고    scopus 로고
    • Characterization of type II and III restriction-modification systems from Bacillus cereus strains ATCC 10987 and ATCC 14579
    • Xu SY, Nugent RL, Kasamkattil J, Fomenkov A, Gupta Y, et al. (2012) Characterization of type II and III restriction-modification systems from Bacillus cereus strains ATCC 10987 and ATCC 14579. J Bacteriol 194: 49-60.
    • (2012) J Bacteriol , vol.194 , pp. 49-60
    • Xu, S.Y.1    Nugent, R.L.2    Kasamkattil, J.3    Fomenkov, A.4    Gupta, Y.5
  • 5
    • 84857877933 scopus 로고    scopus 로고
    • Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing
    • Clark TA, Murray IA, Morgan RD, Kislyuk AO, Spittle KE, et al. (2012) Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res 40: e29.
    • (2012) Nucleic Acids Res , vol.40
    • Clark, T.A.1    Murray, I.A.2    Morgan, R.D.3    Kislyuk, A.O.4    Spittle, K.E.5
  • 6
    • 84857387516 scopus 로고    scopus 로고
    • The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA
    • Chatterjee K, Blaby IK, Thiaville PC, Majumder M, Grosjean H, et al. (2012) The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA. RNA 18: 421-433.
    • (2012) RNA , vol.18 , pp. 421-433
    • Chatterjee, K.1    Blaby, I.K.2    Thiaville, P.C.3    Majumder, M.4    Grosjean, H.5
  • 8
    • 84858705258 scopus 로고    scopus 로고
    • Selenomodification of tRNA in archaea requires a bipartite rhodanese enzyme
    • Su D, Ojo TT, Soll D, Hohn MJ, (2012) Selenomodification of tRNA in archaea requires a bipartite rhodanese enzyme. FEBS Lett 586: 717-721.
    • (2012) FEBS Lett , vol.586 , pp. 717-721
    • Su, D.1    Ojo, T.T.2    Soll, D.3    Hohn, M.J.4
  • 9
    • 79951926801 scopus 로고    scopus 로고
    • A guide to UniProt for protein scientists
    • O'Donovan C, Apweiler R, (2011) A guide to UniProt for protein scientists. Methods Mol Biol 694: 25-35.
    • (2011) Methods Mol Biol , vol.694 , pp. 25-35
    • O'Donovan, C.1    Apweiler, R.2
  • 11
    • 84859436530 scopus 로고    scopus 로고
    • NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
    • Pruitt KD, Tatusova T, Brown GR, Maglott DR, (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 40: D130-135.
    • (2012) Nucleic Acids Res , vol.40
    • Pruitt, K.D.1    Tatusova, T.2    Brown, G.R.3    Maglott, D.R.4
  • 12
    • 1542271409 scopus 로고    scopus 로고
    • Predicting protein function from protein/protein interaction data: a probabilistic approach
    • Letovsky S, Kasif S, (2003) Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics 19 Suppl 1: i197-204.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL.
    • Letovsky, S.1    Kasif, S.2
  • 13
    • 33845701686 scopus 로고    scopus 로고
    • The art of gene function prediction
    • author reply 1475-1476
    • Murali TM, Wu CJ, Kasif S, (2006) The art of gene function prediction. Nat Biotechnol 24: 1474-1475; author reply 1475-1476.
    • (2006) Nat Biotechnol , vol.24 , pp. 1474-1475
    • Murali, T.M.1    Wu, C.J.2    Kasif, S.3
  • 14
    • 1542327694 scopus 로고    scopus 로고
    • Whole-genome annotation by using evidence integration in functional-linkage networks
    • Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, et al. (2004) Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A 101: 2888-2893.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 2888-2893
    • Karaoz, U.1    Murali, T.M.2    Letovsky, S.3    Zheng, Y.4    Ding, C.5
  • 15
    • 6044244615 scopus 로고    scopus 로고
    • Conserved hypothetical' proteins: prioritization of targets for experimental study
    • Galperin MY, Koonin EV, (2004) 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res 32: 5452-5463.
    • (2004) Nucleic Acids Res , vol.32 , pp. 5452-5463
    • Galperin, M.Y.1    Koonin, E.V.2
  • 18
    • 0000710299 scopus 로고
    • Queries and concept learning
    • Angluin D, (1988) Queries and concept learning. Machine Learning 2: 319-342.
    • (1988) Machine Learning , vol.2 , pp. 319-342
    • Angluin, D.1
  • 19
    • 1642336155 scopus 로고    scopus 로고
    • Functional genomic hypothesis generation and experimentation by a robot scientist
    • King RD, Whelan KE, Jones FM, Reiser PG, Bryant CH, et al. (2004) Functional genomic hypothesis generation and experimentation by a robot scientist. Nature 427: 247-252.
    • (2004) Nature , vol.427 , pp. 247-252
    • King, R.D.1    Whelan, K.E.2    Jones, F.M.3    Reiser, P.G.4    Bryant, C.H.5
  • 20
    • 0031797096 scopus 로고    scopus 로고
    • What we do not know about sequence analysis and sequence databases
    • Karp PD, (1998) What we do not know about sequence analysis and sequence databases. Bioinformatics 14: 753-754.
    • (1998) Bioinformatics , vol.14 , pp. 753-754
    • Karp, P.D.1
  • 21
    • 0033119399 scopus 로고    scopus 로고
    • Errors in genome annotation
    • Brenner SE, (1999) Errors in genome annotation. Trends Genet: TIG 15: 132-133.
    • (1999) Trends Genet: TIG , vol.15 , pp. 132-133
    • Brenner, S.E.1
  • 22
    • 74549221383 scopus 로고    scopus 로고
    • Annotation error in public databases: misannotation of molecular function in enzyme superfamilies
    • doi:10.1371/journal.pcbi.1000605
    • Schnoes AM, Brown SD, Dodevski I, Babbitt PC, (2009) Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 5: e1000605 doi:10.1371/journal.pcbi.1000605.
    • (2009) PLoS Comput Biol , vol.5
    • Schnoes, A.M.1    Brown, S.D.2    Dodevski, I.3    Babbitt, P.C.4
  • 23
    • 38549101119 scopus 로고    scopus 로고
    • The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions
    • Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, et al. (2008) The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res 36: D528-533.
    • (2008) Nucleic Acids Res , vol.36
    • Markowitz, V.M.1    Szeto, E.2    Palaniappan, K.3    Grechkin, Y.4    Chu, K.5
  • 24
    • 25644458211 scopus 로고    scopus 로고
    • The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    • Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33: 5691-5702.
    • (2005) Nucleic Acids Res , vol.33 , pp. 5691-5702
    • Overbeek, R.1    Begley, T.2    Butler, R.M.3    Choudhuri, J.V.4    Chuang, H.Y.5
  • 25
    • 84859165788 scopus 로고    scopus 로고
    • The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
    • Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, et al. (2012) The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 40: D571-579.
    • (2012) Nucleic Acids Res , vol.40
    • Pagani, I.1    Liolios, K.2    Jansson, J.3    Chen, I.M.4    Smirnova, T.5
  • 26
    • 84860490976 scopus 로고    scopus 로고
    • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    • Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, et al. (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 40: D742-753.
    • (2012) Nucleic Acids Res , vol.40
    • Caspi, R.1    Altman, T.2    Dreher, K.3    Fulcher, C.A.4    Subhraveti, P.5
  • 27
    • 84868000088 scopus 로고    scopus 로고
    • Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima
    • Rodionova IA, Scott DA, Grishin NV, Osterman AL, Rodionov DA, (2012) Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima. Environ Microbiol 14: 2920-2934.
    • (2012) Environ Microbiol , vol.14 , pp. 2920-2934
    • Rodionova, I.A.1    Scott, D.A.2    Grishin, N.V.3    Osterman, A.L.4    Rodionov, D.A.5
  • 28
    • 84874801003 scopus 로고    scopus 로고
    • A broad specificity nucleoside kinase from Thermoplasma acidophilum
    • Elkin SR, Kumar A, Price CW, Columbus L, (2013) A broad specificity nucleoside kinase from Thermoplasma acidophilum. Proteins 81: 568-582.
    • (2013) Proteins , vol.81 , pp. 568-582
    • Elkin, S.R.1    Kumar, A.2    Price, C.W.3    Columbus, L.4
  • 29
    • 0032871834 scopus 로고    scopus 로고
    • Finding families for genomic ORFans
    • Fischer D, Eisenberg D, (1999) Finding families for genomic ORFans. Bioinformatics 15: 759-762.
    • (1999) Bioinformatics , vol.15 , pp. 759-762
    • Fischer, D.1    Eisenberg, D.2
  • 30
    • 0037228878 scopus 로고    scopus 로고
    • Twenty thousand ORFan microbial protein families for the biologist?
    • Siew N, Fischer D, (2003) Twenty thousand ORFan microbial protein families for the biologist? Structure 11: 7-9.
    • (2003) Structure , vol.11 , pp. 7-9
    • Siew, N.1    Fischer, D.2
  • 31
    • 61349194462 scopus 로고    scopus 로고
    • Estimating the size of the bacterial pan-genome
    • Lapierre P, Gogarten JP, (2009) Estimating the size of the bacterial pan-genome. Trends Genet 25: 107-110.
    • (2009) Trends Genet , vol.25 , pp. 107-110
    • Lapierre, P.1    Gogarten, J.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.