Publications

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2010
J. Schneider, Vorhölter, F. - J., Trost, E., Blom, J., Musa, Y. R., Neuweger, H., Niehaus, K., Schatschneider, S., Tauch, A., and Goesmann, A., CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks, vol. 9, pp. 1660-1672, 2010.
Altenhoff AM and Dessimoz C (2009). Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS. Comput. Biol. 5: e1000262. http://dx.doi.org/10.1371/journal.pcbi.1000262 PMid:19148271 PMCid:2612752   Altermann E and Klaenhammer TR (2003). GAMOLA: a new local solution for sequence annotation and analyzing draft and finished prokaryotic genomes. OMICS 7: 161-169. http://dx.doi.org/10.1089/153623103322246557 PMid:14506845   Blom J, Albaum SP, Doppmeier D, Puhler A, et al. (2009). EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 10: 154. http://dx.doi.org/10.1186/1471-2105-10-154 PMid:19457249 PMCid:2696450   Bryson K, Loux V, Bossy R, Nicolas P, et al. (2006). AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res. 34: 3533-3545. http://dx.doi.org/10.1093/nar/gkl471 PMid:16855290 PMCid:1524909   Caspi R, Foerster H, Fulcher CA, Kaipa P, et al. (2008). The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 36: D623-D631. http://dx.doi.org/10.1093/nar/gkm900 PMid:17965431 PMCid:2238876   Collins MD, Falsen E, Akervall E, Sjoden B, et al. (1998). Corynebacterium kroppenstedtii sp. nov., a novel corynebacterium that does not contain mycolic acids. Int. J. Syst. Bacteriol. 48 (Pt 4): 1449-1454. http://dx.doi.org/10.1099/00207713-48-4-1449 PMid:9828448   Da Silva AC, Ferro JA, Reinach FC, Farah CS, et al. (2002). Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417: 459-463. http://dx.doi.org/10.1038/417459a PMid:12024217   Durot M, Bourguignon PY and Schachter V (2009). Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol. Rev. 33: 164-190. http://dx.doi.org/10.1111/j.1574-6976.2008.00146.x PMid:19067749 PMCid:2704943   Funahashi A, Tanimura N, Morohashi M and Kitano H (2003). CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. BIOSILICO 1: 159-162. http://dx.doi.org/10.1016/S1478-5382(03)02370-9   Funahashi A, Jouraku A and Kitano H (2004). Converting KEGG pathway database to SBML. Proceedings of the 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004), San Diego.   Hucka M, Finney A, Sauro HM, Bolouri H, et al. (2003). The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19: 524-531. http://dx.doi.org/10.1093/bioinformatics/btg015 PMid:12611808   Junker BH, Klukas C and Schreiber F (2006). VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 7: 109. http://dx.doi.org/10.1186/1471-2105-7-109 PMid:16519817 PMCid:1413562   Kitano H, Funahashi A, Matsuoka Y and Oda K (2005). Using process diagrams for the graphical representation of biological networks. Nat. Biotechnol. 23: 961-966. http://dx.doi.org/10.1038/nbt1111 PMid:16082367   Kjeldsen KR and Nielsen J (2009). In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network. Biotechnol. Bioeng. 102: 583-597. http://dx.doi.org/10.1002/bit.22067 PMid:18985611   Klamt S, Saez-Rodriguez J and Gilles ED (2007). Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol. 1: 2. http://dx.doi.org/10.1186/1752-0509-1-2 PMid:17408509 PMCid:1847467   Krieger CJ, Zhang P, Mueller LA, Wang A, et al. (2004). MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 32: D438-D442. http://dx.doi.org/10.1093/nar/gkh100 PMid:14681452 PMCid:308834   Krömer JO, Wittmann C, Schroder H and Heinzle E (2006). Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum. Metab. Eng. 8: 353-369. http://dx.doi.org/10.1016/j.ymben.2006.02.001 PMid:16621639   Lee DS, Burd H, Liu J, Almaas E, et al. (2009). Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets. J. Bacteriol. 191: 4015-4024. http://dx.doi.org/10.1128/JB.01743-08 PMid:19376871 PMCid:2698402   Meyer F, Goesmann A, McHardy AC, Bartels D, et al. (2003). GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 31: 2187-2195. http://dx.doi.org/10.1093/nar/gkg312 PMid:12682369 PMCid:153740   Moriya Y, Itoh M, Okuda S, Yoshizawa AC, et al. (2007). KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35: W182-W185. http://dx.doi.org/10.1093/nar/gkm321 PMid:17526522 PMCid:1933193   Neuweger H, Persicke M, Albaum SP, Bekel T, et al. (2009). Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. BMC Syst. Biol. 3: 82. http://dx.doi.org/10.1186/1752-0509-3-82 PMid:19698148 PMCid:2744654   Nogales J, Palsson BO and Thiele I (2008). A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst. Biol. 2: 79. http://dx.doi.org/10.1186/1752-0509-2-79 PMid:18793442 PMCid:2569920   Ogata H, Goto S, Sato K, Fujibuchi W, et al. (1999). KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27: 29-34.   Pielken P, Schimz KL, Eggeling L and Sahm H (1988). Glucose metabolism in Xanthomonas campestris and influence of methionine on the carbon flow. Can. J. Microbiol. 34: 1333-1337. http://dx.doi.org/10.1139/m88-234 PMid:3148363   Price ND, Reed JL and Palsson BO (2004). Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat. Rev. Microbiol. 2: 886-897. http://dx.doi.org/10.1038/nrmicro1023 PMid:15494745   Puchalka J, Oberhardt MA, Godinho M, Bielecka A, et al. (2008). Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS. Comput. Biol. 4: e1000210. http://dx.doi.org/10.1371/journal.pcbi.1000210 PMid:18974823 PMCid:2563689   Qian W, Jia Y, Ren SX, He YQ, et al. (2005). Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris. Genome Res. 15: 757-767. http://dx.doi.org/10.1101/gr.3378705 PMid:15899963 PMCid:1142466   Schilling CH and Palsson BO (2000). Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J. Theor. Biol. 203: 249-283. http://dx.doi.org/10.1006/jtbi.2000.1088 PMid:10716908   Seisun D (2006). The market of hydrocolloids and other uses of seaweeds, Aqua Sur. Proceedings of the 3rd International Conference on Aquaculture, Puerto Varas, Chile.   Shannon P, Markiel A, Ozier O, Baliga NS, et al. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13: 2498-2504. http://dx.doi.org/10.1101/gr.1239303 PMid:14597658 PMCid:403769   Sidhu VK, Vorholter FJ, Niehaus K and Watt SA (2008). Analysis of outer membrane vesicle associated proteins isolated from the plant pathogenic bacterium Xanthomonas campestris pv. campestris. BMC Microbiol. 8: 87. http://dx.doi.org/10.1186/1471-2180-8-87 PMid:18518965 PMCid:2438364   Stults JT and Arnott D (2005). Proteomics. Methods Enzymol. 402: 245-289. http://dx.doi.org/10.1016/S0076-6879(05)02008-2   Sun J and Zeng AP (2004). Identics-identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. BMC Bioinformatics 5: 112. http://dx.doi.org/10.1186/1471-2105-5-112 PMid:15312235 PMCid:514700   Sun J, Lu X, Rinas U and Zeng AP (2007). Metabolic peculiarities of Aspergillus niger disclosed by comparative metabolic genomics. Genome Biol. 8: R182. http://dx.doi.org/10.1186/gb-2007-8-9-r182 PMid:17784953 PMCid:2375020   Swings JG (1993). Xanthomonas. 1st edn. Chapman and Hall, London. http://dx.doi.org/10.1007/978-94-011-1526-1 PMid:8250550 PMCid:182442   Tauch A, Schneider J, Szczepanowski R, Tilker A, et al. (2008). Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic Corynebacterium that lacks mycolic acids. J. Biotechnol. 136: 22-30. http://dx.doi.org/10.1016/j.jbiotec.2008.03.004 PMid:18430482   Taylor GB, Paviour SD, Musaad S, Jones WO, et al. (2003). A clinicopathological review of 34 cases of inflammatory breast disease showing an association between corynebacteria infection and granulomatous mastitis. Pathology 35: 109-119. PMid:12745457   Trost E, Gotker S, Schneider J, Schneiker-Bekel S, et al. (2010). Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion. BMC Genomics 11: 91. http://dx.doi.org/10.1186/1471-2164-11-91 PMid:20137072 PMCid:2830990   Vorhölter FJ, Schneiker S, Goesmann A, Krause L, et al. (2008). The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis. J. 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