Current Research Trends in Systems Biology
|
|
Kim, Do-Han
(Department of Life Science, GIST)
Shreenivasaiah, Pradeep Kumar (Department of Life Science, GIST) Hong, Seong-Eui (Department of Life Science, GIST) Kim, Tae-Yong (Department of Life Science, GIST) Song, Hong-Ki (Department of Life Science, GIST) |
| 1 | Albert R, Jeong H, and Barabasi AL (2000) Error and attack tolerance of complex networks. Nature 406: 378-382 DOI ScienceOn |
| 2 | Aldridge BB, Burke JM, Lauffenburger DA, and Sorger PK (2006) Physicochemical modelling of cell signalling pathways. Nat cell biol 8: 1195-1203 DOI ScienceOn |
| 3 | Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2: 2366-2382 DOI ScienceOn |
| 4 | Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, et al. (2008) Ensembl 2008. Nucleic Acids Res 36: D707-714 DOI ScienceOn |
| 5 | Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, et al. (2005) Reactome: a knowledgebase of biological pathways. Nucleic acids res 33: D428-432 DOI |
| 6 | Joyce AR and Palsson BO (2006) The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol 7: 198-210 DOI ScienceOn |
| 7 | Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, et al. (2006) The RNA Ontology Consortium: an open invitation to the RNA community. RNA 12: 533-541 DOI ScienceOn |
| 8 | Liu Y and Zhao H (2004) A computational approach for ordering signal transduction pathway components from genomics and proteomics Data. BMC Bioinformatics 5: 158 DOI |
| 9 | Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, et al. (2008) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res |
| 10 | Van Dien S and Schilling CH (2006) Bringing metabolomics data into the forefront of systems biology. Mol Syst Biol 2: 2006 0035 |
| 11 | Xia T and Dickerson JA (2008) OmicsViz: Cytoscape plug-in for visualizing omics data across species. Bioinformatics 24: 2557-2558 DOI ScienceOn |
| 12 | Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322: 104-110 DOI |
| 13 | Jaqaman K and Danuser G (2006) Linking data to models: data regression. Nat Rev Mol Cell Biol 7: 813-819 DOI ScienceOn |
| 14 | Andersen MR, Nielsen ML, and Nielsen J (2008) Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol syst biol 4: 178 |
| 15 | Chee M, Yang R, Hubbell E, Berno A, Huang XC, Stern D, Winkler J, Lockhart DJ, Morris MS, and Fodor SP (1996) Accessing genetic information with high-density DNA arrays. Science 274: 610-614 DOI |
| 16 | Lin R, Dai S, Irwin RD, Heinloth AN, Boorman GA, and Li L (2008) Gene set enrichment analysis for non-monotone association and multiple experimental categories. BMC Bioinformatics 9: 481 DOI |
| 17 | Wang E (Edwin Wang) MicroRNA systems biology. RNA Technologies in Cardiovascular Medicine and Research, Springer-Verlag: 69-80 |
| 18 | Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, and Alon U (2002) Network motifs: simple building blocks of complex networks. Science 298: 824-827 DOI |
| 19 | Murray DB, Beckmann M, and Kitano H (2007) Regulation of yeast oscillatory dynamics. Proc Natl Acad Sci USA 104: 2241-2246 |
| 20 | Bray D (2001) Reasoning for results. Nature 412: 863 DOI |
| 21 | 't Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, van Ommen GJ, and den Dunnen JT (2008) Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 36: e141 DOI |
| 22 | Guerrero C, Milenkovic T, Przulj N, Kaiser P, and Huang L (2008) Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis. Proc Natl Acad Sci USA. 105: 13333-13338 |
| 23 | Nickell S, Kofler C, Leis AP, and Baumeister W (2006) A visual approach to proteomics. Nat Rev Mol Cell Biol 7: 225-230 DOI ScienceOn |
| 24 | Yang K, Bai H, Ouyang Q, Lai L, and Tang C (2008) Finding multiple target optimal intervention in disease-related molecular network. Mol Syst Biol 4: 228 |
| 25 | Bansal M, Belcastro V, Ambesi-Impiombato A, and di Bernardo D (2007) How to infer gene networks from expression profiles. Mol syst biol 3: 78 |
| 26 | Kahlem P and Birney E (2007) ENFIN a network to enhance integrative systems biology. Ann N Y Acad Sci 1115: 23-31 DOI |
| 27 | Kwon YK and Cho KH (2008) Coherent coupling of feedback loops: a design principle of cell signaling networks. Bioinformatics 24: 1926-1932 DOI ScienceOn |
| 28 | Ma H, Sorokin A, Mazein A, Selkov A, Selkov E, Demin O, and Goryanin I (2007) The Edinburgh human metabolic network reconstruction and its functional analysis. Mol Syst Biol 3: 135 |
| 29 | Sprinzak E and Margalit H (2001) Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol 311: 681-692 DOI ScienceOn |
| 30 | Toyoda T, Mochizuki Y, Player K, Heida N, Kobayashi N, and Sakaki Y (2007) OmicBrowse: a browser of multidimensional omics annotations. Bioinformatics 23: 524-526 DOI ScienceOn |
| 31 | Boxem M, Maliga Z, Klitgord N, Li N, Lemmens I, Mana M, de Lichtervelde L, Mul JD, van de Peut D, Devos M, et al. (2008) A protein domain-based interactome network for C. elegans early embryogenesis. Cell 134: 534-545 DOI ScienceOn |
| 32 | Bard JB and Rhee SY (2004) Ontologies in biology: design, applications and future challenges. Nat Rev Genet 5: 213-222 DOI ScienceOn |
| 33 | Lenhard B, Wahlestedt C, and Wasserman WW (2003) GeneLynx mouse: integrated portal to the mouse genome. Genome Res 13: 1501-1504 DOI ScienceOn |
| 34 | Stemke-Hale K, Gonzalez-Angulo AM, Lluch A, Neve RM, Kuo WL, Davies M, Carey M, Hu Z, Guan Y, Sahin A, et al. (2008) An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer. Cancer Res 68: 6084-6091 DOI ScienceOn |
| 35 | Choi C, R Munch et al. (2007) SYSTOMONAS-an integrated database for systems biology analysis of Pseudomonas Nucleic Acids Res 35: D533-7 DOI ScienceOn |
| 36 | Cox B, Kislinger T, and Emili A (2005) Integrating gene and protein expression data: pattern analysis and profile mining. Methods 35: 303-314 DOI ScienceOn |
| 37 | Wright J and Wagner A (2008) The Systems Biology Research Tool: evolvable open-source software. BMC Syst Biol 2: 55 DOI ScienceOn |
| 38 | Aloy P and Russell RB (2006) Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 7: 188-197 DOI ScienceOn |
| 39 | Guerrero C, Tagwerker C, Kaiser P, and Huang L (2006) An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo crosslinked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Mol Cell Proteomics 5: 366-378 DOI |
| 40 | Rousseau F and Schymkowitz J (2005) A systems biology perspective on protein structural dynamics and signal transduction. Curr Opin Struct Biol 15: 23-30 DOI ScienceOn |
| 41 | Hall DA, Ptacek J, and Snyder M (2007) Protein microarray technology. Mech Ageing Dev 128: 161-167 DOI ScienceOn |
| 42 | Kitano H (2002) Systems biology: a brief overview. Science 295: 1662-1664 DOI ScienceOn |
| 43 | De Keersmaecker SC, Thijs IM, Vanderleyden J, and Marchal K (2006) Integration of omics data: how well does it work for bacteria? Mol Microbiol 62: 1239-1250 DOI ScienceOn |
| 44 | Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, et al. (2007) Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 316: 593-597 DOI |
| 45 | Jeong H, Tombor B, Albert R, Oltvai ZN, and Barabasi AL (2000) The large-scale organization of metabolic networks. Nature 407: 651-654 DOI ScienceOn |
| 46 | Schena M, Shalon D, Davis RW, and Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470 DOI |
| 47 | Aloy P, Bottcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin AC, Bork P, Superti-Furga G, Serrano L, and Russell RB (2004) Structure-based assembly of protein complexes in yeast. Science 303: 2026-2029 |
| 48 | Cerami EG, Bader GD, Gross BE, and Sander C (2006) cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics 7: 497 DOI |
| 49 | Holden M, Deng S, Wojnowski L, and Kulle B (2008) GSEASNP: applying gene set enrichment analysis to SNP data from genome-wide association studies. Bioinformatics 24: 2784-2785 DOI ScienceOn |
| 50 | Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, and Gifford DK (2003) Computational discovery of gene modules and regulatory networks. Nat biotechnol 21: 1337-1342 DOI ScienceOn |
| 51 | Hartwell LH, Hopfield JJ, Leibler S, and Murray AW (1999) From molecular to modular cell biology. Nature 402: C47-52 DOI ScienceOn |
| 52 | Rubin DL, Shah NH, and Noy NF (2008) Biomedical ontologies: a functional perspective. Brief Bioinform 9: 75-90 |
| 53 | Safran M, Solomon I, Shmueli O, Lapidot M, Shen-Orr S, Adato A, Ben-Dor U, Esterman N, Rosen N, Peter I, et al. (2002) GeneCards 2002: towards a complete, object-oriented, human gene compendium. Bioinformatics 18: 1542-1543 DOI |
| 54 | Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25: 1251-1255 DOI ScienceOn |
| 55 | Alves R, Antunes F, and Salvador A (2006) Tools for kinetic modeling of biochemical networks. Nat biotechnol 24: 667-672 DOI ScienceOn |
| 56 | Hardiman G (2004) Microarray platforms--comparisons and contrasts. Pharmacogenomics 5: 487-502 DOI ScienceOn |
| 57 | Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, and Barkai N (2002) Revealing modular organization in the yeast transcriptional network. Nat Genet. 31: 370-377 DOI |
| 58 | Hwang D, Rust AG, Ramsey S, Smith JJ, Leslie DM, Weston AD, de Atauri P, Aitchison JD, Hood L, Siegel AF, and Bolouri H (2005a) A data integration methodology for systems biology. Proc Natl Acad Sci U S A 102: 17296-17301 |
| 59 | Lu L, Arakaki AK, Lu H, Skolnick J (2003) Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome. Genome Res. 13:1146-1154 DOI ScienceOn |
| 60 | Shah AR, Singhal M, Klicker KR, Stephan EG, Wiley HS, and Waters KM (2007) Enabling high-throughput data management for systems biology: the Bioinformatics Resource Manager. Bioinformatics 23: 906-909 DOI ScienceOn |
| 61 | Kell DB (2004) Metabolomics and systems biology: making sense of the soup. Curr Opin Microbiol. 7: 296-307 DOI ScienceOn |
| 62 | Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, et al. (2004) MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic acids res 32: D217-222 DOI |
| 63 | Ravasz E, Somera AL, Mongru DA, Oltvai ZN, and Barabasi AL (2002) Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555 DOI ScienceOn |
| 64 | Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, et al. (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24: 1151-1161 DOI ScienceOn |
| 65 | Medalia O, Weber I, Frangakis AS, Nicastro D, Gerisch G, and Baumeister W (2002) Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science 298: 1209-1213 DOI |
| 66 | Sali A, Glaeser R, Earnest T, and Baumeister W (2003) From words to literature in structural proteomics. Nature 422: 216-225 DOI ScienceOn |
| 67 | Aloy P and Russell RB (2002) Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci U S A. 99: 5896-5901 |
| 68 | Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, and Palsson BO (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A 104: 1777-1782 |
| 69 | Hwang D, Smith JJ, Leslie DM, Weston AD, Rust AG, Ramsey S, de Atauri P, Siegel AF, Bolouri H, Aitchison JD, and Hood L (2005b) A data integration methodology for systems biology: experimental verification. Proc Natl Acad Sci U S A 102: 17302-17307 |
| 70 | Lynn DJ, Winsor GL, Chan C, Richard N, Laird MR, Barsky A, Gardy JL, Roche FM, Chan THW, Shah N, et al. (2008) InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol 4 |
| 71 | Neduva V, Linding R, Su-Angrand I, Stark A, de Masi F, Gibson TJ, Lewis J, Serrano L, and Russell RB (2005) Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS biology 3: e405 DOI |
| 72 | Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627 DOI ScienceOn |
| 73 | Blake JA and Bult CJ (2006) Beyond the data deluge: data integration and bio-ontologies. J Biomed Inform 39: 314-320 DOI ScienceOn |
| 74 | Legewie S, Herzel H, Westerhoff HV, and Bluthgen N (2008) Recurrent design patterns in the feedback regulation of the mammalian signalling network. Mol syst biol 4: 190 |
| 75 | Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, and Eisenberg D (1999) A combined algorithm for genome-wide prediction of protein function. Nature 402: 83-86 DOI ScienceOn |
| 76 | Wu X, Jiang R, Zhang MQ, and Li S (2008) Network-based global inference of human disease genes. Mol Syst Biol 4: 189 |
| 77 | Busch H, Camacho-Trullio D, Rogon Z, Breuhahn K, Angel P, Eils R, and Szabowski A (2008) Gene network dynamics controlling keratinocyte migration. Mol syst biol 4: 199 |
| 78 | Melo RC, Dvorak AM, and Weller PF (2008) Electron tomography and immunonanogold electron microscopy for investigating intracellular trafficking and secretion in human eosinophils. J Cell Mol Med 12: 1416-1419 DOI ScienceOn |
| 79 | Muller SA, Aebi U, and Engel A (2008) What transmission electron microscopes can visualize now and in the future. J Struct Biol 163: 235-245 DOI ScienceOn |
| 80 | Stein LD (2003) Integrating biological databases. Nat Rev Genet 4: 337-345 |
| 81 | Sauer U, Heinemann M, and Zamboni N (2007) Genetics. Getting closer to the whole picture. Science 316: 550-551 DOI |
| 82 | Shreenivasaiah PK, Rho SH, Kim T, and Kim DH (2008) An overview of cardiac systems biology. J Mol Cell Cardiol 44: 460-469 DOI ScienceOn |
| 83 | Zhang W, Zhang Y, Zheng H, Zhang C, Xiong W, Olyarchuk JG, Walker M, Xu W, Zhao M, Zhao S, et al. (2007) SynDB: a Synapse protein DataBase based on synapse ontology. Nucleic Acids Res 35: D737-741 DOI ScienceOn |
| 84 | Gray JJ (2006) High-resolution protein-protein docking. Curr Opin Struct Biol. 16: 183-193 DOI ScienceOn |
| 85 | Sugawara H, Ogasawara O, Okubo K, Gojobori T, and Tateno Y (2008) DDBJ with new system and face. Nucleic Acids Res 36: D22-24 DOI |
| 86 | Templin MF, Stoll D, Schwenk JM, Potz O, Kramer S, and Joos TO (2003) Protein microarrays: promising tools for proteomic research. Proteomics 3: 2155-2166 DOI ScienceOn |
| 87 | Brosh R, Shalgi R, Liran A, Landan G, Korotayev K, Nguyen GH, Enerly E, Johnsen H, Buganim Y, Solomon H, et al. (2008) p53-repressed miRNAs are involved with E2F in a feed-forward loop promoting proliferation. Mol syst biol 4: 229 |
| 88 | Chechik G, Oh E, Rando O, Weissman J, Regev A, and Koller D (2008) Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network. Nat biotechnol 26: 1251-1259 DOI ScienceOn |
| 89 | Funahashi A, Jouraku A, Matsuoka Y, and Kitano H (2007) Integration of CellDesigner and SABIO-RK. In silico biol 7: S81-90 |
| 90 | Ideker T and D Lauffenburger (2003) Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends Biotechnol 21(6): 255-62 DOI ScienceOn |
| 91 | Waters KM, Pounds JG, and Thrall BD (2006) Data merging for integrated microarray and proteomic analysis. Brief Funct Genomic Proteomic 5: 261-272 DOI ScienceOn |
| 92 | Albeck JG, MacBeath G, White FM, Sorger PK, Lauffenburger DA, and Gaudet S (2006) Collecting and organizing systematic sets of protein data. Nat Rev Mol Cell Biol 7: 803-812 DOI ScienceOn |
| 93 | Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804 DOI |
 |
Korea Institute of Science and Technology Information
Gwahangno, Yuseong-gu, Daejeon, 305-806, Korea TEL : +82-42-869-1752
Copyright (c) 2009 KISTI. All Rights Reserved. For more information mail to
webmaster
