Resources for Systems Biology Research
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Kim Jin-Sik
(Metabolic and Biomolecular Engineering National Research Laboratory)
Yun Hong-Seok (Metabolic and Biomolecular Engineering National Research Laboratory) Kim Hyun-Uk (Metabolic and Biomolecular Engineering National Research Laboratory) Choi Hyung-Seok (Metabolic and Biomolecular Engineering National Research Laboratory) Kim Tae-Yong (Metabolic and Biomolecular Engineering National Research Laboratory) Woo Han-Min (Metabolic and Biomolecular Engineering National Research Laboratory) Lee Sang-Yup (Metabolic and Biomolecular Engineering National Research Laboratory) |
1 | Joshi-Tope, G., M. Gillespie, I. Vastrik, P. D'Eustachio, E. Schmidt, B. de Bono, B. Jassal, G. R. Gopinath, G. R. Wu, L. Matthews, S. Lewis, E. Birney, and L. Stein. 2005. Reactome: A knowledge base of biological pathways. Nucleic Acids Res. 33: D428-D432 DOI |
2 | Keseler, I. M., J. Collado-Vides, S. Gama-Castro, J. Ingraham, S. Paley, I. T. Paulsen, M. Peralta-Gil, and P. D. Karp. 2005. EcoCyc: A comprehensive database resource for Escherichia coli. Nucleic Acids Res. 33: D334-D337 DOI ScienceOn |
3 | Klamt, S., J. Stelling, M. Ginkel, and E. D. Gilles. 2003. FluxAnalyzer: Exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19: 261-269 DOI ScienceOn |
4 | Lee, Y., J. Tsai, S. Sunkara, S. Karamycheva, G. Pertea, R. Sultana, V. Antonescu, A. Chan, F. Cheung, and J. Quackenbush. 2005. The TIGR gene indices: Clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res. 33: D71-D74 DOI ScienceOn |
5 | Lemer, C., E. Antezana, F. Couche, F. Fays, X. Santolaria, R. Janky, Y. Deville, J. Richelle, and S. J. Wodak. 2004. The aMAZE LightBench: A Web interface to a relational database of cellular processes. Nucleic Acids Res. 32: D443-D448 DOI |
6 | Maglott, D., J. Ostell, K. D. Pruitt, and T. Tatusova. 2005. Entrez gene: Gene-centered information at NCBI. Nucleic Acids Res. 33: D54-D58 DOI ScienceOn |
7 | McGinnis, S. and T. L. Madden. 2004. BLAST: At the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32: W20-W25 DOI ScienceOn |
8 | Sauro, H. M., M. Hucka, A. Finney, C. Wellock, H. Bolouri, J. Doyle, and H. Kitano. 2003. Next generation simulation tools: The systems biology workbench and BioSPICE integration. OMICS 7: 355-372 DOI ScienceOn |
9 | Steinhauser, D., B. Usadel, A. Luedemann, O. Thimm, and J. Kopka. 2004. CSB.DB: A comprehensive systemsbiology database. Bioinformatics 20: 3647-3651 DOI ScienceOn |
10 | Ball, C. A., I. A. Awad, J. Demeter, J. Gollub, J. M. Hebert, T. Hernandez-Boussard, H. Jin, J. C. Matese, M. Nitzberg, F. Wymore, Z. K. Zachariah, P. O. Brown, and G. Sherlock. 2005. The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res. 33: D580-D582 DOI |
11 | Birney, E., D. Andrews, M. Caccamo, Y. Chen, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, P. Flicek, S. Graf, M. Hammond, J. Herrero, K. Howe, V. Iyer, K. Jekosch, A. Kahari, A. Kasprzyk, D. Keefe, F. Kokocinski, E. Kulesha, D. London, I. Longden, C. Melsopp, P. Meidl, B. Overduin, A. Parker, G. Proctor, A. Prlic, M. Rae, D. Rios, S. Redmond, M. Schuster, I. Sealy, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, A. Stabenau, J. Stalker, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark, and T. J. Hubbard. 2006. Ensembl 2006. Nucleic Acids Res. 34: D556-D561 DOI ScienceOn |
12 | Garvey, T. D., P. Lincoln, C. J. Pedersen, D. Martin, and M. Johnson. 2003. BioSPICE: Access to the most current computational tools for biologists. OMICS 7: 411-420 DOI ScienceOn |
13 | Caspi, R., H. Foerster, C. A. Fulcher, R. Hopkinson, J. Ingraham, P. Kaipa, M. Krummenacker, S. Paley, J. Pick, S. Y. Rhee, C. Tissier, P. Zhang, and P. D. Karp. 2006. MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 34: D511-D516 DOI ScienceOn |
14 | Dhar, P., T. C. Meng, S. Somani, L. Ye, A. Sairam, M. Chitre, Z. Hao, and K. Sakharkar. 2004. Cellware -- A multi-algorithmic software for computational systems biology. Bioinformatics 20: 1319-1321 DOI ScienceOn |
15 | Edgar, R., M. Domrachev, and A. E. Lash. 2002. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30: 207-210 DOI ScienceOn |
16 | Hou, B. K., J. S. Kim, J. H. Jun, D. Y. Lee, Y. W. Kim, S. Chae, M. Roh, Y. H. In, and S. Y. Lee. 2004. BioSilico: An integrated metabolic database system. Bioinformatics 20: 3270-3272 DOI ScienceOn |
17 | Hucka, M., A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle, H. Kitano, A. P. Arkin, B. J. Bornstein, D. Bray, A. Cornish- Bowden, A. A. Cuellar, S. Dronov, E. D. Gilles, M. Ginkel, V. Gor, I. I. Goryanin, W. J. Hedley, T. C. Hodgman, J. H. Hofmeyr, P. J. Hunter, N. S. Juty, J. L. Kasberger, A. Kremling, U. Kummer, N. Le Novere, L. M. Loew, D. Lucio, P. Mendes, E. Minch, E. D. Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, J. C. Schaff, B. E. Shapiro, T. S. Shimizu, H. D. Spence, J. Stelling, K. Takahashi, M. Tomita, J. Wagner, J. Wang, and SBML Forum. 2003. The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19: 524-531 DOI ScienceOn |
18 | Jaiswal, P., J. Ni, I. Yap, D. Ware, W. Spooner, K. Youens- Clark, L. Ren, C. Liang, W. Zhao, K. Ratnapu, B. Faga, P. Canaran, M. Fogleman, C. Hebbard, S. Avraham, S. Schmidt, T. M. Casstevens, E. S. Buckler, L. Stein, and S. McCouch. 2006. Gramene: A bird's eye view of cereal genomes. Nucleic Acids Res. 34: D717-D723 DOI ScienceOn |
19 | Olivier, B. G. and J. L. Snoep. 2004. Web-based kinetic modelling using JWS online. Bioinformatics 20: 2143-2144 DOI ScienceOn |
20 | Mendes, P. 1997. Biochemistry by numbers: Simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 22: 361-363 DOI ScienceOn |
21 | Salgado, H., S. Gama-Castro, M. Peralta-Gil, E. Diaz-Peredo, F. Sanchez-Solano, A. Santos-Zavaleta, I. Martinez-Flores, V. Jimenez-Jacinto, C. Bonavides-Martinez, J. Segura-Salazar, A. Martinez-Antonio, and J. Collado-Vides. 2006. RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res. 34: D394-D397 DOI ScienceOn |
22 | Blinov, M. L., J. R. Faeder, B. Goldstein, and W. S. Hlavacek. 2004. BioNetGen: Software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics 20: 3289-3291 DOI ScienceOn |
23 | Shapiro, B. E., A. Levchenko, E. M. Meyerowitz, B. J. Wold, and E. D. Mjolsness. 2003. Cellerator: Extending a computer algebra system to include biochemical arrows for signal transduction simulations. Bioinformatics 19: 677-678 DOI ScienceOn |
24 | Krummenacker, M., S. Paley, L. Mueller, T. Yan, and P. D. Karp. 2005. Querying and computing with BioCyc databases. Bioinformatics 21: 3454-3455 DOI ScienceOn |
25 | Parkinson, H., U. Sarkans, M. Shojatalab, N. Abeygunawardena, S. Contrino, R. Coulson, A. Farne, G. G. Lara, E. Holloway, M. Kapushesky, P. Lilja, G. Mukherjee, A. Oezcimen, T. Rayner, P. Rocca-Serra, A. Sharma, S. Sansone, and A. Brazma. 2005. ArrayExpress -- A public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 33: D553-D555 DOI ScienceOn |
26 | Kanehisa, M., S. Goto, M. Hattori, K. F. Aoki-Kinoshita, M. Itoh, S. Kawashima, T. Katayama, M. Araki, and M. Hirakawa. 2006. From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Res. 34: D354-D357 DOI ScienceOn |
27 | Blake, J. A., J. T. Eppig, C. J. Bult, J. A. Kadin, J. E. Richardson, and Mouse Genome Database Group. 2006. The Mouse Genome Database (MGD): Updates and enhancements. Nucleic Acids Res. 34: D562-D567 DOI ScienceOn |
28 | Hattne, J., D. Fange, and J. Elf. 2005. Stochastic reactiondiffusion simulation with MesoRD. Bioinformatics 21: 2923-2924 DOI ScienceOn |
29 | Hirschman, J. E., R. Balakrishnan, K. R. Christie, M. C. Costanzo, S. S. Dwight, S. R. Engel, D. G. Fisk, E. L. Hong, M. S. Livstone, R. Nash, J. Park, R. Oughtred, M. Skrzypek, B. Starr, C. L. Theesfeld, J. Williams, R. Andrada, G. Binkley, Q. Dong, C. Lane, S. Miyasato, A. Sethuraman, M. Schroeder, M. K. Thanawala, S. Weng, K. Dolinski, D. Botstein, and J. M. Cherry. 2006. Genome Snapshot: A new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res. 34: D442-D445 DOI ScienceOn |
30 | Kierzek, A. M. 2002. STOCKS: STOChastic kinetic simulations of biochemical systems with Gillespie algorithm. Bioinformatics 18: 470-481 DOI ScienceOn |
31 | Whetzel, P. L., H. Parkinson, H. C. Causton, L. Fan, J. Fostel, G. Fragoso, L. Game, M. Heiskanen, N. Morrison, P. Rocca-Serra, S. A. Sansone, C. Taylor, J. White, and C. J. Stoeckert Jr. 2006. The MGED Ontology; A resource for semantics-based description of microarray experiments. Bioinformatics [in press] |
32 | Ramsey, S., D. Orrell, and H. Bolouri. 2005. Dizzy: Stochastic simulation of large-scale genetic regulatory networks. J. Bioinform. Comput. Biol. 3: 415-436 DOI ScienceOn |
33 | Fleischmann, R. D., M. D. Adams, O. White, R. A. Clayton, E. F. Kirkness, A. R. Kerlavage, C. J. Bult, J. F. Tomb, B. A. Dougherty, J. M. Merrick, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512 DOI |
34 | Lloyd, C. M., M. D. Halstead, and P. F. Nielsen. 2004. CellML: Its future, present and past. Prog. Biophys. Mol. Biol. 85: 433-450 DOI ScienceOn |
35 | Lee, D. Y., H. Yun, S. Park, and S. Y. Lee. 2003. MetaFluxNet: The management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics 19: 2144-2146 DOI ScienceOn |
36 | Kahraman, A., A. Avramov, L. G. Nashev, D. Popov, R. Ternes, H. D. Pohlenz, and B. Weiss. PhenomicDB: A multi-species genotype/phenotype database for comparative phenomics. Bioinformatics 21: 418-420 DOI ScienceOn |
37 | Le Novere, N. and T. S. Shimizu. 2001. STOCHSIM: Modelling of stochastic biomolecular processes. Bioinformatics 17: 575-576 DOI ScienceOn |
38 | Schomburg, I., A. Chang, C. Ebeling, M. Gremse, C. Heldt, G. Huhn, and D. Schomburg. 2004. BRENDA, the enzyme database: Updates and major new developments. Nucleic Acids Res. 32: D431-D433 DOI ScienceOn |
39 | Bairoch, A. 2000. The ENZYME database in 2000. Nucleic Acids Res. 28: 304-305 DOI |
40 | Ludemann, A., D. Weicht, J. Selbig, and J. Kopka. 2004. PaVESy: Pathway visualization and editing system. Bioinformatics 20: 2841-2844 DOI ScienceOn |
41 | Shannon, P., A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker. 2003. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13: 2498-2504 DOI ScienceOn |
42 | Slepchenko, B. M., J. C. Schaff, I. Macara, and L. M. Loew. 2003. Quantitative cell biology with the virtual cell. Trends Cell Biol. 13: 570-576 DOI ScienceOn |
43 | Gene Ontology Consortium. 2006. The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 34: D322-D326 DOI ScienceOn |
44 | Finn, R. D., J. Mistry, B. Schuster-Bockler, S. Griffiths- Jones, V. Hollich, T. Lassmann, S. Moxon, M. Marshall, A. Khanna, R. Durbin, S. R. Eddy, E. L. Sonnhammer, and A. Bateman. 2006. Pfam: Clans, Web tools and services. Nucleic Acids Res. 34: D247-D251 DOI ScienceOn |
45 | Kurata, H., K. Masaki, Y. Sumida, and R. Iwasaki. 2005. CADLIVE dynamic simulator: Direct link of biochemical networks to dynamic models. Genome Res. 15: 590-600 DOI ScienceOn |
46 | Goto, S., Y. Okuno, M. Hattori, T. Nishioka, and M. Kanehisa. 2002. LIGAND: Database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. 30: 402-404 DOI ScienceOn |
47 | Rhee, S. Y., W. Beavis, T. Z. Berardini, G. Chen, D. Dixon, A. Doyle, M. Garcia-Hernandez, E. Huala, G. Lander, M. Montoya, N. Miller, L. A. Mueller, S. Mundodi, L. Reiser, J. Tacklind, D. C. Weems, Y. Wu, I. Xu, D. Yoo, J. Yoon, and P. Zhang. 2003. The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res. 31: 224-228 DOI ScienceOn |
48 | Lee, S. Y., D. Y. Lee, and T. Y. Kim. 2005. Systems biotechnology for strain improvement. Trends Biotechnol. 23: 349-358 DOI ScienceOn |
49 | Kanehisa, M., S. Goto, S. Kawashima, Y. Okuno, and M. Hattori. 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32: D277-D280 DOI ScienceOn |
50 | McCarthy, A. A. 2005. Broad Institute: Bringing genomics to real-world medicine. Chem. Biol. 12: 717-718 DOI ScienceOn |
51 | Takahashi, K., N. Ishikawa, Y. Sadamoto, H. Sasamoto, S. Ohta, A. Shiozawa, F. Miyoshi, Y. Naito, Y. Nakayama, and M. Tomita. 2003. E-Cell 2: Multi-platform E-Cell simulation system. Bioinformatics 19: 1727-1729 DOI ScienceOn |
52 | Cheung, K. H., K. White, J. Hager, M. Gerstein, V. Reinke, K. Nelson, P. Masiar, R. Srivastava, Y. Li, J. Li, H. Zhao, J. Li, D. B. Allison, M. Snyder, P. Miller, and K. Williams. 2002. YMD: A microarray database for large-scale gene expression analysis. Proc. AMIA Symp. 140-144 |
53 | Tatusov, R. L., D. A. Natale, I. V. Garkavtsev, T. A. Tatusova, U. T. Shankavaram, B. S. Rao, B. Kiryutin, M. Y. Galperin, N. D. Fedorova, and E. V. Koonin. 2001. The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29: 22-28 DOI ScienceOn |
54 | Wu, C. H., L. S. Yeh, H. Huang, L. Arminski, J. Castro- Alvear, Y. Chen, Z. Hu, P. Kourtesis, R. S. Ledley, B. E. Suzek, C. R. Vinayaka, J. Zhang, and W. C. Barker. 2003. The Protein Information Resource. Nucleic Acids Res. 31: 345-347 DOI ScienceOn |
55 | Lok, L. and R. Brent. 2005. Automatic generation of cellular reaction networks with Moleculizer 1.0. Nat. Biotechnol. 23: 131-136 DOI ScienceOn |
56 | Chalkley, R. J., P. R. Baker, L. Huang, K. C. Hansen, N. P. Allen, M. Rexach, and A. L. Burlingame. 2005. Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-offlight mass spectrometer: II. New developments in Protein Prospector allow for reliable and comprehensive automatic analysis of large datasets. Mol. Cell Proteomics 4: 1194-1204 DOI ScienceOn |
57 | Gasteiger, E., A. Gattiker, C. Hoogland, I. Ivanyi, R. D. Appel, and A. Bairoch. 2003. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 31: 3784-3788 DOI ScienceOn |
58 | Mi, H., B. Lazareva-Ulitsky, R. Loo, A. Kejariwal, J. Vandergriff, S. Rabkin, N. Guo, A. Muruganujan, O. Doremieux, M. J. Campbell, H. Kitano, and P. D. Thomas. 2005. The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 33: D284-D288 DOI ScienceOn |
59 | Lee, D. Y., C. Yun, A. Cho, B. K. Hou, S. Park, and S. Y. Lee. 2006. WebCell: A Web-based environment for kinetic modeling and dynamic simulation of cellular networks. Bioinformatics [in press] |
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