TY - JOUR AU - Brown, P. O. AU - Botstein, D. PY - 1999 DA - 1999// TI - Exploring the new world of the genome with DNA microarrays JO - Nat Genet VL - 21 UR - https://doi.org/10.1038/4462 DO - 10.1038/4462 ID - Brown1999 ER - TY - JOUR AU - Tyers, M. AU - Mann, M. PY - 2003 DA - 2003// TI - From genomics to proteomics JO - Nature VL - 422 UR - https://doi.org/10.1038/nature01510 DO - 10.1038/nature01510 ID - Tyers2003 ER - TY - JOUR AU - Kitano, H. PY - 2002 DA - 2002// TI - Systems biology: a brief overview JO - Science VL - 295 UR - https://doi.org/10.1126/science.1069492 DO - 10.1126/science.1069492 ID - Kitano2002 ER - TY - JOUR AU - Hornberg, J. J. AU - Bruggeman, F. J. AU - Westerhoff, H. V. AU - Lankelma, J. PY - 2006 DA - 2006// TI - Cancer: a Systems Biology disease JO - Biosystems VL - 83 UR - https://doi.org/10.1016/j.biosystems.2005.05.014 DO - 10.1016/j.biosystems.2005.05.014 ID - Hornberg2006 ER - TY - JOUR AU - Perco, P. AU - Rapberger, R. AU - Siehs, C. AU - Lukas, A. AU - Oberbauer, R. AU - Mayer, G. AU - Mayer, B. PY - 2006 DA - 2006// TI - Transforming omics data into context: bioinformatics on genomics and proteomics raw data JO - Electrophoresis VL - 27 UR - https://doi.org/10.1002/elps.200600064 DO - 10.1002/elps.200600064 ID - Perco2006 ER - TY - JOUR AU - Hwang, D. AU - Rust, A. G. AU - Ramsey, S. AU - Smith, J. J. AU - Leslie, D. M. AU - Weston, A. D. AU - de Atauri, P. AU - Aitchison, J. D. AU - Hood, L. AU - Siegel, A. F. AU - Bolouri, H. PY - 2005 DA - 2005// TI - A data integration methodology for systems biology JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0508647102 DO - 10.1073/pnas.0508647102 ID - Hwang2005 ER - TY - JOUR AU - Hwang, D. AU - Smith, J. J. AU - Leslie, D. M. AU - Weston, A. D. AU - Rust, A. G. AU - Ramsey, S. AU - de Atauri, P. AU - Siegel, A. F. AU - Bolouri, H. AU - Aitchison, J. D. AU - Hood, L. PY - 2005 DA - 2005// TI - A data integration methodology for systems biology: Experimental verification JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0508649102 DO - 10.1073/pnas.0508649102 ID - Hwang2005 ER - TY - JOUR AU - Fields, S. AU - Song, O. PY - 1989 DA - 1989// TI - A novel genetic system to detect protein-protein interactions JO - Nature VL - 340 UR - https://doi.org/10.1038/340245a0 DO - 10.1038/340245a0 ID - Fields1989 ER - TY - JOUR AU - Smith, E. A. AU - Corn, R. M. PY - 2003 DA - 2003// TI - Surface plasmon resonance imaging as a tool to monitor biomolecular interactions in an array based format JO - Appl Spectrosc VL - 57 UR - https://doi.org/10.1366/000370203322554446 DO - 10.1366/000370203322554446 ID - Smith2003 ER - TY - JOUR AU - Kersten, B. AU - Wanker, E. E. AU - Hoheisel, J. D. AU - Angenendt, P. PY - 2005 DA - 2005// TI - Multiplex approaches in protein microarray technology JO - Expert Rev Proteomics VL - 2 UR - https://doi.org/10.1586/14789450.2.4.499 DO - 10.1586/14789450.2.4.499 ID - Kersten2005 ER - TY - JOUR AU - Stelzl, U. AU - Wanker, E. E. PY - 2006 DA - 2006// TI - The value of high quality protein-protein interaction networks for systems biology JO - Curr Opin Chem Biol VL - 10 UR - https://doi.org/10.1016/j.cbpa.2006.10.005 DO - 10.1016/j.cbpa.2006.10.005 ID - Stelzl2006 ER - TY - JOUR AU - Brown, K. R. AU - Jurisica, I. PY - 2005 DA - 2005// TI - Online predicted human interaction database JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti273 DO - 10.1093/bioinformatics/bti273 ID - Brown2005 ER - TY - JOUR AU - Shannon, P. AU - Markiel, A. AU - Ozier, O. AU - Baliga, N. S. AU - Wang, J. T. AU - Ramage, D. AU - Amin, N. AU - Schwikowski, B. AU - Ideker, T. PY - 2003 DA - 2003// TI - Cytoscape: a software environment for integrated models of biomolecular interaction networks JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1239303 DO - 10.1101/gr.1239303 ID - Shannon2003 ER - TY - JOUR AU - Breitkreutz, B. J. AU - Stark, C. AU - Tyers, M. PY - 2004 DA - 2004// TI - Osprey: a network visualization system JO - Genome Biol VL - 4 UR - https://doi.org/10.1186/gb-2003-4-3-r22 DO - 10.1186/gb-2003-4-3-r22 ID - Breitkreutz2004 ER - TY - CHAP AU - Chen, J. Y. AU - Shen, C. AU - Sivachenko, A. Y. PY - 2006 DA - 2006// TI - Mining alzheimer disease relevant proteins from integrated protein interactome data BT - Pac Symp Biocomput ID - Chen2006 ER - TY - JOUR AU - Jeong, H. AU - Tombor, B. AU - Albert, R. AU - Oltvai, Z. N. AU - Barabasi, A. L. PY - 2000 DA - 2000// TI - The large-scale organization of metabolic networks JO - Nature VL - 407 UR - https://doi.org/10.1038/35036627 DO - 10.1038/35036627 ID - Jeong2000 ER - TY - JOUR AU - Wagner, A. AU - Fell, D. A. PY - 2001 DA - 2001// TI - The small world inside large metabolic networks JO - Proc Biol Sci VL - 268 UR - https://doi.org/10.1098/rspb.2001.1711 DO - 10.1098/rspb.2001.1711 ID - Wagner2001 ER - TY - JOUR AU - Han, J. D. AU - Bertin, N. AU - Hao, T. AU - Goldberg, D. S. AU - Berriz, G. F. AU - Zhang, L. V. AU - Dupuy, D. AU - Walhout, A. J. AU - Cusick, M. E. AU - Roth, F. P. AU - Vidal, M. PY - 2004 DA - 2004// TI - Evidence for dynamically organized modularity in the yeast protein-protein interaction network JO - Nature VL - 430 UR - https://doi.org/10.1038/nature02555 DO - 10.1038/nature02555 ID - Han2004 ER - TY - JOUR AU - Lu, X. AU - Jain, V. V. AU - Finn, P. W. AU - Perkins, D. L. PY - 2007 DA - 2007// TI - Hubs in biological interaction networks exhibit low changes in expression in experimental asthma JO - Mol Syst Biol VL - 3 UR - https://doi.org/10.1038/msb4100138 DO - 10.1038/msb4100138 ID - Lu2007 ER - TY - JOUR AU - Milo, R. AU - Shen-Orr, S. AU - Itzkovitz, S. AU - Kashtan, N. AU - Chklovskii, D. AU - Alon, U. PY - 2002 DA - 2002// TI - Network motifs: simple building blocks of complex networks JO - Science VL - 298 UR - https://doi.org/10.1126/science.298.5594.824 DO - 10.1126/science.298.5594.824 ID - Milo2002 ER - TY - JOUR AU - Barabasi, A. L. AU - Oltvai, Z. N. PY - 2004 DA - 2004// TI - Network biology: understanding the cell's functional organization JO - Nat Rev Genet VL - 5 UR - https://doi.org/10.1038/nrg1272 DO - 10.1038/nrg1272 ID - Barabasi2004 ER - TY - JOUR AU - Jonsson, P. F. AU - Bates, P. A. PY - 2006 DA - 2006// TI - Global topological features of cancer proteins in the human interactome JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl390 DO - 10.1093/bioinformatics/btl390 ID - Jonsson2006 ER - TY - JOUR AU - Wachi, S. AU - Yoneda, K. AU - Wu, R. PY - 2005 DA - 2005// TI - Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti688 DO - 10.1093/bioinformatics/bti688 ID - Wachi2005 ER - TY - JOUR AU - Tuck, D. P. AU - Kluger, H. M. AU - Kluger, Y. PY - 2006 DA - 2006// TI - Characterizing disease states from topological properties of transcriptional regulatory networks JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-236 DO - 10.1186/1471-2105-7-236 ID - Tuck2006 ER - TY - JOUR AU - Hamosh, A. AU - Scott, A. F. AU - Amberger, J. AU - Bocchini, C. AU - Valle, D. AU - McKusick, V. A. PY - 2002 DA - 2002// TI - Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.1.52 DO - 10.1093/nar/30.1.52 ID - Hamosh2002 ER - TY - JOUR AU - Xu, J. AU - Li, Y. PY - 2006 DA - 2006// TI - Discovering disease-genes by topological features in human protein-protein interaction network JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl467 DO - 10.1093/bioinformatics/btl467 ID - Xu2006 ER - TY - JOUR AU - Segal, E. AU - Friedman, N. AU - Kaminski, N. AU - Regev, A. AU - Koller, D. PY - 2005 DA - 2005// TI - From signatures to models: understanding cancer using microarrays JO - Nat Genet VL - 37 UR - https://doi.org/10.1038/ng1561 DO - 10.1038/ng1561 ID - Segal2005 ER - TY - JOUR AU - Junker, B. H. AU - Koschutzki, D. AU - Schreiber, F. PY - 2006 DA - 2006// TI - Exploration of biological network centralities with CentiBiN JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-219 DO - 10.1186/1471-2105-7-219 ID - Junker2006 ER - TY - JOUR AU - Jonsson, P. F. AU - Cavanna, T. AU - Zicha, D. AU - Bates, P. A. PY - 2006 DA - 2006// TI - Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-2 DO - 10.1186/1471-2105-7-2 ID - Jonsson2006 ER - TY - JOUR AU - Jeong, H. AU - Mason, S. P. AU - Barabasi, A. L. AU - Oltvai, Z. N. PY - 2001 DA - 2001// TI - Lethality and centrality in protein networks JO - Nature VL - 411 UR - https://doi.org/10.1038/35075138 DO - 10.1038/35075138 ID - Jeong2001 ER - TY - JOUR AU - Rhodes, D. R. AU - Yu, J. AU - Shanker, K. AU - Deshpande, N. AU - Varambally, R. AU - Ghosh, D. AU - Barrette, T. AU - Pandey, A. AU - Chinnaiyan, A. M. PY - 2004 DA - 2004// TI - ONCOMINE: a cancer microarray database and integrated data-mining platform JO - Neoplasia VL - 6 UR - https://doi.org/10.1016/S1476-5586(04)80047-2 DO - 10.1016/S1476-5586(04)80047-2 ID - Rhodes2004 ER - TY - JOUR AU - Joy, M. P. AU - Brock, A. AU - Ingber, D. E. AU - Huang, S. PY - 2005 DA - 2005// TI - High-betweenness proteins in the yeast protein interaction network JO - J Biomed Biotechnol VL - 2005 UR - https://doi.org/10.1155/JBB.2005.96 DO - 10.1155/JBB.2005.96 ID - Joy2005 ER - TY - JOUR AU - Yu, H. AU - Zhu, X. AU - Greenbaum, D. AU - Karro, J. AU - Gerstein, M. PY - 2004 DA - 2004// TI - TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh164 DO - 10.1093/nar/gkh164 ID - Yu2004 ER - TY - JOUR AU - Ghim, C. M. AU - Goh, K. I. AU - Kahng, B. PY - 2005 DA - 2005// TI - Lethality and synthetic lethality in the genome-wide metabolic network of Escherichia coli JO - J Theor Biol VL - 237 UR - https://doi.org/10.1016/j.jtbi.2005.04.025 DO - 10.1016/j.jtbi.2005.04.025 ID - Ghim2005 ER - TY - JOUR AU - Ye, P. AU - Peyser, B. D. AU - Pan, X. AU - Boeke, J. D. AU - Spencer, F. A. AU - Bader, J. S. PY - 2005 DA - 2005// TI - Gene function prediction from congruent synthetic lethal interactions in yeast JO - Mol Syst Biol VL - 1 ID - Ye2005 ER - TY - JOUR AU - Peri, S. AU - Navarro, J. D. AU - Kristiansen, T. Z. AU - Amanchy, R. AU - Surendranath, V. AU - Muthusamy, B. AU - Gandhi, T. K. B. AU - Chandrika, K. N. AU - Deshpande, N. AU - Suresh, S. PY - 2004 DA - 2004// TI - Human protein reference database as a discovery resource for proteomics JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh070 DO - 10.1093/nar/gkh070 ID - Peri2004 ER - TY - JOUR AU - Zanzoni, A. AU - Montecchi-Palazzi, L. AU - Quondam, M. AU - Ausiello, G. AU - Helmer-Citterich, M. AU - Cesareni, G. PY - 2002 DA - 2002// TI - MINT: a Molecular INTeraction database JO - FEBS Lett VL - 513 UR - https://doi.org/10.1016/S0014-5793(01)03293-8 DO - 10.1016/S0014-5793(01)03293-8 ID - Zanzoni2002 ER - TY - JOUR AU - Suzuki, H. AU - Fukunishi, Y. AU - Kagawa, I. AU - Saito, R. AU - Oda, H. AU - Endo, T. AU - Kondo, S. AU - Bono, H. AU - Okazaki, Y. AU - Hayashizaki, Y. PY - 2001 DA - 2001// TI - Protein-protein interaction panel using mouse full-length cDNAs JO - Genome Res VL - 11 UR - https://doi.org/10.1101/gr.180101 DO - 10.1101/gr.180101 ID - Suzuki2001 ER - TY - JOUR AU - Bader, G. D. AU - Betel, D. AU - Hogue, C. W. V. PY - 2003 DA - 2003// TI - BIND: the Biomolecular Interaction Network Database JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg056 DO - 10.1093/nar/gkg056 ID - Bader2003 ER - TY - JOUR AU - Mewes, H. W. AU - Frishman, D. AU - Mayer, K. F. AU - Munsterkotter, M. AU - Noubibou, O. AU - Pagel, P. AU - Rattei, T. AU - Oesterheld, M. AU - Ruepp, A. AU - Stumpflen, V. PY - 2006 DA - 2006// TI - MIPS: analysis and annotation of proteins from whole genomes in 2005 JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj148 DO - 10.1093/nar/gkj148 ID - Mewes2006 ER - TY - JOUR AU - Dupuy, A. AU - Simon, R. M. PY - 2007 DA - 2007// TI - Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting JO - J Natl Cancer Inst VL - 99 UR - https://doi.org/10.1093/jnci/djk018 DO - 10.1093/jnci/djk018 ID - Dupuy2007 ER - TY - CHAP AU - da Fontoura Costa, L. AU - Rodrigues, F. A. AU - Travieso, G. AU - Boas, P. R. V. PY - 2005 DA - 2005// BT - Characterization of complex networks: A survey of measurements ID - da Fontoura Costa2005 ER - TY - JOUR AU - Bonchev, D. PY - 2004 DA - 2004// TI - Complexity Analysis of Yeast Proteome Network JO - Chem Biodivers VL - 1 UR - https://doi.org/10.1002/cbdv.200490028 DO - 10.1002/cbdv.200490028 ID - Bonchev2004 ER - TY - JOUR AU - Holme, P. PY - 2004 DA - 2004// TI - Efficient local strategies for vaccination and network attack JO - Europhys Lett VL - 68 UR - https://doi.org/10.1209/epl/i2004-10286-2 DO - 10.1209/epl/i2004-10286-2 ID - Holme2004 ER - TY - CHAP AU - Claussen, J. C. PY - 2004 DA - 2004// BT - Offdiagonal Complexity: A computationally quick complexity measure for graphs and networks ID - Claussen2004 ER - TY - JOUR AU - Bader, G. D. AU - Hogue, C. W. V. PY - 2003 DA - 2003// TI - An automated method for finding molecular complexes in large protein interaction networks JO - BMC Bioinformatics VL - 4 UR - https://doi.org/10.1186/1471-2105-4-2 DO - 10.1186/1471-2105-4-2 ID - Bader2003 ER - TY - JOUR AU - Radicchi, F. AU - Castellano, C. AU - Cecconi, F. AU - Loreto, V. AU - Parisi, D. PY - 2004 DA - 2004// TI - Defining and identifying communities in networks JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0400054101 DO - 10.1073/pnas.0400054101 ID - Radicchi2004 ER - TY - JOUR AU - Kieffer, J. AU - Yang, E. H. PY - 1997 DA - 1997// TI - Ergodic behavior of graph entropy JO - ERA Amer Math Soc VL - 3 ID - Kieffer1997 ER - TY - JOUR AU - Muff, S. AU - Rao, F. AU - Caflisch, A. PY - 2005 DA - 2005// TI - Local modularity measure for network clusterizations JO - Phys Rev E VL - 72 UR - https://doi.org/10.1103/PhysRevE.72.056107 DO - 10.1103/PhysRevE.72.056107 ID - Muff2005 ER - TY - JOUR AU - Chung, F. AU - Lu, L. AU - Vu, V. PY - 2003 DA - 2003// TI - Spectra of random graphs with given expected degrees JO - Proc Natl Acad Sci USA VL - 100 UR - https://doi.org/10.1073/pnas.0937490100 DO - 10.1073/pnas.0937490100 ID - Chung2003 ER -