Integrated network reconstruction, visualization and analysis using YANAsquare

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Schwarz, Roland ^a   Liang, Chunguang ^a   Kaleta, Christoph ^b   Kühnel, Mark ^c   Hoffmann, Eik ^d   Kuznetsov, Sergei ^d   Hecker, Michael ^e   Griffiths, Gareth ^c   Schuster, Stefan ^b   Dandekar, Thomas ^a,c  

^a UNIVERSITY OF WÜRZBURG   (Germany)

^b FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^d UNIVERSITY OF ROSTOCK   (Germany)

^e UNIVERSITY OF GREIFSWALD   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION EXAMPLES; APPLICATION SOFTWARES; GENOME-SCALE METABOLIC NETWORK; INTEGRATED NETWORKS; METABOLITE NETWORKS; NETWORK PERFORMANCE ANALYSIS; SOFTWARE FRAMEWORKS; VISUALIZATION AND ANALYSIS;

COMPUTER PROGRAMMING; GENE EXPRESSION; METABOLISM; PHOSPHOLIPIDS; PROGRAM TRANSLATORS; SOFTWARE PACKAGES;

VISUALIZATION;

ARTICLE; BACTERIAL GENETICS; BACTERIAL METABOLISM; BIOINFORMATICS; CALCULATION; COMPUTER MODEL; COMPUTER NETWORK; COMPUTER PROGRAM; ENZYME DEFICIENCY; GENE EXPRESSION; GENE MAPPING; GENOME ANALYSIS; NONHUMAN; PHAGOSOME; STAPHYLOCOCCUS AUREUS; STAPHYLOCOCCUS EPIDERMIDIS; STAPHYLOCOCCUS SAPROPHYTICUS; ALGORITHM; BIOLOGY; COMPUTER SIMULATION; METABOLISM; STANDARD; STATISTICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; METABOLIC NETWORKS AND PATHWAYS; SOFTWARE; STATISTICS AS TOPIC;

EID: 35248849697     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-313     Document Type: Article

References (32)

1. Schilling CH Schuster S Palsson BO Heinrich R Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era Biotechnol Prog 1999, 15(3):296-303 10.1021/bp990048k 10356246
2. Schuster S Dandekar T Fell DA Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering Trends Biotechnol 1999, 17(2):53-60 10.1016/ S0167-7799(98)01290-6 10087604
3. Papin JA Stelling J Price ND Klamt S Schuster S Palsson BO Comparison of network-based pathway analysis methods Trends Biotechnol 2004, 22(8):400-405 10.1016/j.tibtech.2004.06.010 15283984
4. Kauffman KJ Prakash P Edwards JS Advances in flux balance analysis Curr Opin Biotechnol 2003, 14(5):491-496 10.1016/j.copbio.2003.08.001 14580578
5. Klamt S Gilles ED Minimal cut sets in biochemical reaction networks Bioinformatics 2004, 20(2):226-234 10.1093/bioinformatics/btg395 14734314
6. Becker D Selbach M Rollenhagen C Ballmaier M Meyer TF Mann M Bumann D Robust Salmonella metabolism limits possibilities for new antimicrobials Nature 2006, 440(7082):303-307 10.1038/nature04616 16541065
7. Trawick JD Schilling CH Use of constraint-based modeling for the prediction and validation of antimicrobial targets Biochem Pharmacol 2006, 71(7):1026-1035 10.1016/j.bcp.2005.10.049 16329998
8. Edwards JS Palsson BO Robustness analysis of the Escherichia coli metabolic network Biotechnol Prog 2000, 16(6):927-939 10.1021/bp0000712 11101318
9. Wilhelm T Behre J Schuster S Analysis of structural robustness of metabolic networks Systems Biology 2004, 1:114-120 10.1049/sb:20045004 17052121
10. Schuster S Fell DA Dandekar T A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks Nat Biotechnol 2000, 18(3):326-332 10.1038/73786 10700151
11. Pfeiffer T Snchez-Valdenebro I Nuo JC Montero F Schuster S METATOOL: For studying metabolic networks Bioinformatics 1999, 15(3):251-257 10.1093/ bioinformatics/15.3.251 10222413
12. von Kamp A Schuster S Metatool 5.0: Fast and flexible elementary modes analysis Bioinformatics 2006, 22(15):1930-1931 10.1093/bioinformatics/ btl267 16731697
13. Mendes P GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems Comput Appl Biosci 1993, 9(5):563-571 8293329
14. Urbanczik R SNA-a toolbox for the stoichiometric analysis of metabolic networks BMC Bioinformatics 2006, 7:129 1431567 16533403 10.1186/ 1471-2105-7-129
15. Schwarz R Musch P von Kamp A Engels B Schirmer H Schuster S Dandekar T YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities BMC Bioinformatics 2005, 6:135 1175843 15929789 10.1186/1471-2105-6-135
16. Poolman MG Venkatesh KV Pidcock MK Fell DA A method for the determination of flux in elementary modes, and its application to Lactobacillus rhamnosus Biotechnol Bioeng 2004, 88(5):601-612 10.1002/ bit.20273 15470705
17. Eisenreich W Slaghuis J Laupitz R Bussemer J Stritzker J Schwarz C Schwarz R Dandekar T Goebel W Bacher A 13C isotopologue perturbation studies of Listeria monocytogenes carbon metabolism and its modulation by the virulence regulator PrfA Proc Natl Acad Sci USA 2006, 103(7):2040-2045 1413697 16461909 10.1073/pnas.0507580103
18. Kanehisa M Goto S Kawashima S Okuno Y Hattori M The KEGG resource for deciphering the genome Nucleic Acids Res 2004, 32(Database):D277-D280 308797 14681412 10.1093/nar/gkh063
19. Gagneur J Klamt S Computation of elementary modes: A unifying framework and the new binary approach BMC Bioinformatics 2004, 5:175 544875 15527509 10.1186/1471-2105-5-175
20. Dittrich P di Fenizio PS Chemical Organization Theory Bulletin of Mathematical Biology 2007, 69(4):1199-1231 [In print] 10.1007/ s11538-006-9130-8 17415616
21. Barthelmes J Ebeling C Chang A Schomburg I Schomburg D BRENDA, AMENDA and FRENDA: The enzyme information system in 2007 Nucleic Acids Res 2007, 35(Database):D511-D514 1899097 17202167 10.1093/nar/gkl972
22. Bairoch A The ENZYME database in 2000 Nucleic Acids Res 2000, 28:304-305 102465 10592255 10.1093/nar/28.1.304
23. Anes E Khnel MP Bos E Moniz-Pereira J Habermann A Griffiths G Selected lipids activate phagosome actin assembly and maturation resulting in killing of pathogenic mycobacteria Nat Cell Biol 2003, 5(9):793-802 10.1038/ncb1036 12942085
24. Heinemann M Kmmel A Ruinatscha R Panke S In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network Biotechnol Bioeng 2005, 92(7):850-864 10.1002/bit.20663 16155945
25. Klamt S Stelling J Ginkel M Gilles ED FluxAnalyzer: Exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps Bioinformatics 2003, 19(2):261-269 10.1093/bioinformatics/ 19.2.261 12538248
26. Sauro HM Hucka M Finney A Wellock C Bolouri H Doyle J Kitano H Next generation simulation tools: The Systems Biology Workbench and BioSPICE integration OMICS 2003, 7(4):355-372 10.1089/153623103322637670 14683609
27. Mendes P Biochemistry by numbers: Simulation of biochemical pathways with Gepasi 3 Trends Biochem Sci 1997, 22(9):361-363 10.1016/ S0968-0004(97)01103-1 9301339
28. Hoops S Sahle S Gauges R Lee C Pahle J Simus N Singhal M Xu L Mendes P Kummer U COPASI-a COmplex PAthway SImulator Bioinformatics 2006, 22(24):3067-3074 10.1093/bioinformatics/btl485 17032683
29. Schuster S Pfeiffer T Moldenhauer F Koch I Dandekar T Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae Bioinformatics 2002, 18(2):351-361 10.1093/bioinformatics/18.2.351 11847093
30. Ren Q Kang KH Paulsen IT TransportDB: A relational database of cellular membrane transport systems Nucleic Acids Res 2004, 32(Database):D284-D288 308751 14681414 10.1093/nar/gkh016
31. Ren Q Chen K Paulsen IT TransportDB: A comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels Nucleic Acids Res 2007, 35(Database):D274-D279 1747178 17135193 10.1093/ nar/gkl925
32. Becker SA Palsson B Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: An initial draft to the two-dimensional annotation BMC Microbiol 2005, 5:8 1079855 15752426 10.1186/1471-2180-5-8