TY - JOUR AU - Hood, L. E. AU - Hunkapiller, M. W. AU - Smith, L. M. PY - 1987 DA - 1987// TI - Automated DNA sequencing and analysis of the human genome. JO - Genomics VL - 1 UR - https://doi.org/10.1016/0888-7543(87)90046-2 DO - 10.1016/0888-7543(87)90046-2 ID - Hood1987 ER - TY - JOUR AU - Lockhart, D. AU - Winzeler, E. PY - 2000 DA - 2000// TI - Genomics, gene expression and DNA arrays. JO - Nature VL - 405 UR - https://doi.org/10.1038/35015701 DO - 10.1038/35015701 ID - Lockhart2000 ER - TY - JOUR AU - Lee, T. I. AU - Rinaldi, N. J. AU - Robert, F. AU - Odom, D. T. AU - Bar-Joseph, Z. AU - Gerber, G. K. AU - Hannett, N. M. AU - Harbison, C. T. AU - Thompson, C. M. AU - Simon, I. PY - 2002 DA - 2002// TI - Transcriptional regulatory networks in Saccharomyces cerevisiae. JO - Science VL - 298 UR - https://doi.org/10.1126/science.1075090 DO - 10.1126/science.1075090 ID - Lee2002 ER - TY - JOUR AU - Uetz, P. AU - Giot, L. AU - Cagney, G. AU - Mansfield, T. A. AU - Judson, R. S. AU - Knight, J. R. AU - Lockshon, D. AU - Narayan, V. AU - Srinivasan, M. AU - Pochart, P. PY - 2000 DA - 2000// TI - A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. JO - Nature VL - 403 UR - https://doi.org/10.1038/35001009 DO - 10.1038/35001009 ID - Uetz2000 ER - TY - JOUR AU - de Jong, H. PY - 2002 DA - 2002// TI - Modeling and simulation of genetic regulatory systems: a literature review. JO - J Comput Biol VL - 9 UR - https://doi.org/10.1089/10665270252833208 DO - 10.1089/10665270252833208 ID - de Jong2002 ER - TY - JOUR AU - Eisen, M. B. AU - Spellman, P. T. AU - Brown, P. O. AU - Botstein, D. PY - 1998 DA - 1998// TI - Cluster analysis and display of genome-wide expression patterns. JO - Proc Natl Acad Sci USA VL - 95 UR - https://doi.org/10.1073/pnas.95.25.14863 DO - 10.1073/pnas.95.25.14863 ID - Eisen1998 ER - TY - JOUR AU - Segal, E. AU - Shapira, M. AU - Regev, A. AU - Pe'er, D. AU - Botstein, D. AU - Koller, D. AU - Friedman, N. PY - 2003 DA - 2003// TI - Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. JO - Nat Genet VL - 34 UR - https://doi.org/10.1038/ng1165 DO - 10.1038/ng1165 ID - Segal2003 ER - TY - JOUR AU - Akutsu, T. AU - Kuhara, S. AU - Maruyama, O. AU - Miyano, S. PY - 1998 DA - 1998// TI - A system for identifying genetic networks in gene expression patterns produced by gene disruptions and overexpressions. JO - Genome Inform Ser Workshop VL - 9 ID - Akutsu1998 ER - TY - JOUR AU - Wagner, A. PY - 2001 DA - 2001// TI - How to reconstruct a large genetic network from n gene perturbations in fewer than n(2) easy steps. JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.12.1183 DO - 10.1093/bioinformatics/17.12.1183 ID - Wagner2001 ER - TY - CHAP AU - Ideker, T. AU - Thorsson, V. AU - Karp, R. M. PY - 2000 DA - 2000// TI - Discovery of regulatory interactions through perturbation: inference and experimental design. BT - Pac Symp Biocomput ID - Ideker2000 ER - TY - JOUR AU - Ideker, T. AU - Thorsson, V. AU - Ranish, J. A. AU - Christmas, R. AU - Buhler, J. AU - Eng, J. K. AU - Bumgarner, R. AU - Goodlett, D. R. AU - Aebersold, R. AU - Hood, L. PY - 2001 DA - 2001// TI - Integrated genomic and proteomic analysis of a systematically perturbed metabolic network. JO - Science VL - 292 UR - https://doi.org/10.1126/science.292.5518.929 DO - 10.1126/science.292.5518.929 ID - Ideker2001 ER - TY - BOOK AU - Raiffa, H. AU - Shlaifer, R. PY - 1962 DA - 1962// TI - Applied Statistical Decision Theory PB - MIT Press CY - Cambridge, MA ID - Raiffa1962 ER - TY - BOOK AU - Fedorov, F. F. PY - 1972 DA - 1972// TI - Theory of Optimal Experimental Design PB - Academic Press CY - New York ID - Fedorov1972 ER - TY - CHAP AU - Tong, S. AU - Koller, D. PY - 2000 DA - 2000// TI - Active learning for parameter estimation in Bayesian networks. BT - Proc 13th Conf Neural Information Processing PB - Neural Information Processing Systems CY - Tübingen ID - Tong2000 ER - TY - JOUR AU - Abadir, M. S. AU - Ferguson, J. AU - Kirkland, T. E. PY - 1988 DA - 1988// TI - Logic design verification via test generation. JO - IEEE Trans Computer-Aided Design VL - 7 UR - https://doi.org/10.1109/43.3141 DO - 10.1109/43.3141 ID - Abadir1988 ER - TY - JOUR AU - Rea, C. AU - Settle, M. A. PY - 1996 DA - 1996// TI - An automated test approach for US Air Force fighter engines. JO - IEEE Aerospace Electron Syst Mag VL - 11 UR - https://doi.org/10.1109/62.486733 DO - 10.1109/62.486733 ID - Rea1996 ER - TY - JOUR AU - King, R. D. AU - Whelan, K. E. AU - Jones, F. M. AU - Reiser, P. G. AU - Bryant, C. H. AU - Muggleton, S. H. AU - Kell, D. B. AU - Oliver, S. G. PY - 2004 DA - 2004// TI - Functional genomic hypothesis generation and experimentation by a robot scientist. JO - Nature VL - 427 UR - https://doi.org/10.1038/nature02236 DO - 10.1038/nature02236 ID - King2004 ER - TY - JOUR AU - Yeang, C. H. AU - Ideker, T. AU - Jaakkola, T. PY - 2004 DA - 2004// TI - Physical network models. JO - J Comput Biol VL - 11 UR - https://doi.org/10.1089/1066527041410382 DO - 10.1089/1066527041410382 ID - Yeang2004 ER - TY - JOUR AU - Deane, C. M. AU - Salwinski, L. AU - Xenarios, I. AU - Eisenberg, D. PY - 2002 DA - 2002// TI - Protein interactions: two methods for assessment of the reliability of high throughput observations. JO - Mol Cell Proteomics VL - 1 UR - https://doi.org/10.1074/mcp.M100037-MCP200 DO - 10.1074/mcp.M100037-MCP200 ID - Deane2002 ER - TY - JOUR AU - Hughes, T. R. AU - Marton, M. J. AU - Jones, A. R. AU - Roberts, C. J. AU - Stoughton, R. AU - Armour, C. D. AU - Bennett, H. A. AU - Coffey, E. AU - Dai, H. AU - He, Y. D. PY - 2000 DA - 2000// TI - Functional discovery via a compendium of expression profiles. JO - Cell VL - 102 UR - https://doi.org/10.1016/S0092-8674(00)00015-5 DO - 10.1016/S0092-8674(00)00015-5 ID - Hughes2000 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 - STD TI - Cytoscape. [http://www.cytoscape.org] UR - http://www.cytoscape.org ID - ref22 ER - TY - STD TI - Cell Circuits Pathway Database. [http://www.cellcircuits.org/Yeang2005] UR - http://www.cellcircuits.org/Yeang2005 ID - ref23 ER - TY - JOUR AU - Natarajan, K. AU - Meyer, M. R. AU - Jackson, B. M. AU - Slade, D. AU - Roberts, C. AU - Hinnebusch, A. G. AU - Marton, M. J. PY - 2001 DA - 2001// TI - Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. JO - Mol Cell Biol VL - 21 UR - https://doi.org/10.1128/MCB.21.13.4347-4368.2001 DO - 10.1128/MCB.21.13.4347-4368.2001 ID - Natarajan2001 ER - TY - STD TI - Munich Information Center for Protein Sequences. [http://mips.gsf.de] UR - http://mips.gsf.de ID - ref25 ER - TY - STD TI - Proteome BioKnowledge Library. [http://www.proteome.com] UR - http://www.proteome.com ID - ref26 ER - TY - JOUR AU - Blom, J. AU - De Mattos, M. J. AU - Grivell, L. A. PY - 2000 DA - 2000// TI - Redirection of the respiro-fermentative flux distribution in Saccharomyces cerevisiaeby overexpression of the transcription factor Hap4p. JO - Appl Environ Microbiol VL - 66 UR - https://doi.org/10.1128/AEM.66.5.1970-1973.2000 DO - 10.1128/AEM.66.5.1970-1973.2000 ID - Blom2000 ER - TY - JOUR AU - Smith, A. AU - Ward, M. P. AU - Garrett, S. PY - 1998 DA - 1998// TI - Yeast PKA represses Msn2p/Msn4p-dependent gene expression to regulate growth, stress response and glycogen accumulation. JO - EMBO J VL - 17 UR - https://doi.org/10.1093/emboj/17.13.3556 DO - 10.1093/emboj/17.13.3556 ID - Smith1998 ER - TY - JOUR AU - Ward, M. P. AU - Gimeno, C. J. AU - Fink, G. R. AU - Garrett, S. PY - 1995 DA - 1995// TI - SOK2 may regulate cyclic AMP-dependent protein kinase-stimulated growth and pseudohyphal development by repressing transcription. JO - Mol Cell Biol VL - 15 UR - https://doi.org/10.1128/MCB.15.12.6854 DO - 10.1128/MCB.15.12.6854 ID - Ward1995 ER - TY - JOUR AU - Tong, A. H. AU - Lesage, G. AU - Bader, G. D. AU - Ding, H. AU - Xu, H. AU - Xin, X. AU - Young, J. AU - Berriz, G. F. AU - Brost, R. L. AU - Chang, M. PY - 2004 DA - 2004// TI - Global mapping of the yeast genetic interaction network. JO - Science VL - 303 UR - https://doi.org/10.1126/science.1091317 DO - 10.1126/science.1091317 ID - Tong2004 ER - TY - BOOK AU - Popper, K. PY - 1959 DA - 1959// TI - The Logic of Scientific Discovery PB - Basic Books CY - New York ID - Popper1959 ER - TY - JOUR AU - Kschischang, F. AU - Frey, B. AU - Loeliger, H. PY - 2001 DA - 2001// TI - Factor graphs and the sum-product algorithm. JO - IEEE Trans Inform Theory VL - 47 UR - https://doi.org/10.1109/18.910572 DO - 10.1109/18.910572 ID - Kschischang2001 ER - TY - JOUR AU - Winzeler, E. A. AU - Shoemaker, D. D. AU - Astromoff, A. AU - Liang, H. AU - Anderson, K. AU - Andre, B. AU - Bangham, R. AU - Benito, R. AU - Boeke, J. D. AU - Bussey, H. PY - 1999 DA - 1999// TI - Functional characterization of the S. cerevisiaegenome by gene deletion and parallel analysis. JO - Science VL - 285 UR - https://doi.org/10.1126/science.285.5429.901 DO - 10.1126/science.285.5429.901 ID - Winzeler1999 ER - TY - JOUR AU - Workman, C. AU - Jensen, L. J. AU - Jarmer, H. AU - Berka, R. AU - Gautier, L. AU - Nielser, H. B. AU - Saxild, H. H. AU - Nielsen, C. AU - Brunak, S. AU - Knudsen, S. PY - 2002 DA - 2002// TI - A new non-linear normalization method for reducing variability in DNA microarray experiments. JO - Genome Biol VL - 3 UR - https://doi.org/10.1186/gb-2002-3-9-research0048 DO - 10.1186/gb-2002-3-9-research0048 ID - Workman2002 ER - TY - STD TI - ArrayExpress Gene Expression Database. [http://www.ebi.ac.uk/arrayexpress] UR - http://www.ebi.ac.uk/arrayexpress ID - ref35 ER - TY - JOUR AU - Ideker, T. AU - Thorsson, V. AU - Siegel, A. AU - Hood, L. PY - 2000 DA - 2000// TI - Testing for differentially-expressed genes by maximum likelihood analysis of microarray data. JO - J Comput Biol VL - 7 UR - https://doi.org/10.1089/10665270050514945 DO - 10.1089/10665270050514945 ID - Ideker2000 ER - TY - JOUR AU - Ideker, T. AU - Ozier, O. AU - Schwikowski, B. AU - Siegel, A. F. PY - 2002 DA - 2002// TI - Discovering regulatory and signalling circuits in molecular interaction networks. JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.suppl_1.S233 DO - 10.1093/bioinformatics/18.suppl_1.S233 ID - Ideker2002 ER -