TY - JOUR AU - Allison, D. B. AU - Cui, X. AU - Page, G. P. AU - Sabripour, M. PY - 2006 DA - 2006// TI - Microarray data analysis: from disarray to consolidation and consensus JO - Nat Rev Genet VL - 7 UR - https://doi.org/10.1038/nrg1749 DO - 10.1038/nrg1749 ID - Allison2006 ER - TY - JOUR AU - Gasch, A. P. AU - Spellman, P. T. AU - Kao, C. M. AU - Carmel-Harel, O. AU - Eisen, M. B. AU - Storz, G. AU - Botstein, D. AU - Brown, P. O. PY - 2000 DA - 2000// TI - Genomic expression programs in the response of yeast cells to environmental changes JO - Mol Biol Cell VL - 11 UR - https://doi.org/10.1091/mbc.11.12.4241 DO - 10.1091/mbc.11.12.4241 ID - Gasch2000 ER - TY - JOUR AU - Lin, X. AU - Floudas, C. A. AU - Wang, Y. AU - Broach, J. R. PY - 2003 DA - 2003// TI - Theoretical and computational studies of the glucose signaling pathways in yeast using global gene expression data JO - Biotechnol Bioeng VL - 84 UR - https://doi.org/10.1002/bit.10844 DO - 10.1002/bit.10844 ID - Lin2003 ER - TY - JOUR AU - Sokal, R. R. AU - Michener, C. D. PY - 1958 DA - 1958// TI - A statistical method for evaluating systematic relationships JO - Univ Kans Sci Bull VL - 38 ID - Sokal1958 ER - TY - JOUR AU - Hartigan, J. A. AU - Wong, M. A. PY - 1979 DA - 1979// TI - Algorithm AS 136: A K-means clustering algorithm JO - Appl Stat J Roy St C VL - 28 ID - Hartigan1979 ER - TY - CHAP AU - Zhang, B. AU - Hsu, M. AU - Dayal, U. PY - 1999 DA - 1999// TI - K-harmonic means – A data clustering algorithm BT - Hewlett Packard Research Laboratory Technical Report ID - Zhang1999 ER - TY - JOUR AU - Likas, A. AU - Vlassis, N. AU - Vebeek, J. L. PY - 2003 DA - 2003// TI - The global K-means clustering algorithm JO - Pattern Recogn VL - 36 UR - https://doi.org/10.1016/S0031-3203(02)00060-2 DO - 10.1016/S0031-3203(02)00060-2 ID - Likas2003 ER - TY - JOUR AU - Adams, W. P. AU - Sherali, H. D. PY - 1990 DA - 1990// TI - Linearization strategies for a class of zero-one mixed integer programming problems JO - Operations Research VL - 38 UR - https://doi.org/10.1287/opre.38.2.217 DO - 10.1287/opre.38.2.217 ID - Adams1990 ER - TY - JOUR AU - Sherali, H. D. PY - 2005 DA - 2005// TI - A global optimization RLT-based approach for solving the hard clustering problem JO - Journal of Global Optimization VL - 32 UR - https://doi.org/10.1007/s10898-004-2706-7 DO - 10.1007/s10898-004-2706-7 ID - Sherali2005 ER - TY - JOUR AU - Tan, M. P. AU - Broach, J. R. AU - Floudas, C. A. PY - 2007 DA - 2007// TI - A novel clustering approach and prediction of optimum number of clusters: Global optimum search with enhanced positioning JO - Journal of Global Optimization VL - 39 UR - https://doi.org/10.1007/s10898-007-9140-6 DO - 10.1007/s10898-007-9140-6 ID - Tan2007 ER - TY - JOUR AU - Ruspini, E. H. PY - 1969 DA - 1969// TI - A new approach to clustering JO - Inf Control VL - 15 UR - https://doi.org/10.1016/S0019-9958(69)90591-9 DO - 10.1016/S0019-9958(69)90591-9 ID - Ruspini1969 ER - TY - JOUR AU - Sherali, H. D. AU - Desai, J. PY - 2005 DA - 2005// TI - A global optimization RLT-based approach for solving the fuzzy clustering problem JO - Journal of Global Optimization VL - 33 UR - https://doi.org/10.1007/s10898-004-7390-0 DO - 10.1007/s10898-004-7390-0 ID - Sherali2005 ER - TY - JOUR AU - Heyer, L. J. AU - Kruglyak, S. AU - Yooseph, S. PY - 1999 DA - 1999// TI - Exploring expression data: identification and analysis of co-expressed genes JO - Genome Res VL - 9 UR - https://doi.org/10.1101/gr.9.11.1106 DO - 10.1101/gr.9.11.1106 ID - Heyer1999 ER - TY - BOOK AU - Kohonen, T. PY - 1997 DA - 1997// TI - Self-Organizing Maps PB - Springer Verlag CY - Berlin UR - https://doi.org/10.1007/978-3-642-97966-8 DO - 10.1007/978-3-642-97966-8 ID - Kohonen1997 ER - TY - JOUR AU - Herrero, J. AU - Valencia, A. AU - Dopazo, J. PY - 2001 DA - 2001// TI - A hierarchical unsupervised growing neural network for clustering gene expression patterns JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.2.126 DO - 10.1093/bioinformatics/17.2.126 ID - Herrero2001 ER - TY - CHAP AU - Tishby, N. AU - Pereira, F. AU - Bialek, W. PY - 1999 DA - 1999// TI - The information bottleneck method BT - Proceedings of the 37th Annual Allerton Conference on Communication, Control Comput ID - Tishby1999 ER - TY - JOUR AU - Slonim, N. AU - Atwal, G. S. AU - Tkacik, G. AU - Bialek, W. PY - 2005 DA - 2005// TI - Information-based clustering JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0507432102 DO - 10.1073/pnas.0507432102 ID - Slonim2005 ER - TY - JOUR AU - Kirkpatrick, S. AU - Gelatt, C. D. AU - Vecchi, M. P. PY - 1983 DA - 1983// TI - Optimization by simulated annealing JO - Science VL - 220 UR - https://doi.org/10.1126/science.220.4598.671 DO - 10.1126/science.220.4598.671 ID - Kirkpatrick1983 ER - TY - JOUR AU - Lukashin, A. V. AU - Fuchs, R. PY - 2001 DA - 2001// TI - Analysis of temporal gene expression profiles: clustering by simulated annealing and determining the optimal number of clusters JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.5.405 DO - 10.1093/bioinformatics/17.5.405 ID - Lukashin2001 ER - TY - JOUR AU - Jiang, D. AU - Tang, C. AU - Zhang, A. PY - 2004 DA - 2004// TI - Cluster analysis for gene expression data: A survey JO - IEEE Transactions on Knowledge and Data Engineering VL - 16 UR - https://doi.org/10.1109/TKDE.2004.68 DO - 10.1109/TKDE.2004.68 ID - Jiang2004 ER - TY - JOUR AU - Yeung, K. Y. AU - Haynor, D. R. AU - Ruzzo, W. L. PY - 2001 DA - 2001// TI - Validating clustering for gene expression data JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.4.309 DO - 10.1093/bioinformatics/17.4.309 ID - Yeung2001 ER - TY - JOUR AU - Davies, D. L. AU - Bouldin, D. W. PY - 1979 DA - 1979// TI - A cluster separation measure JO - IEEE Trans Pattern Anal Machine Intell VL - 1 UR - https://doi.org/10.1109/TPAMI.1979.4766909 DO - 10.1109/TPAMI.1979.4766909 ID - Davies1979 ER - TY - JOUR AU - Pavlidis, P. AU - Qin, J. AU - Arango, V. AU - Mann, J. J. AU - Sibille, E. PY - 2004 DA - 2004// TI - Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex JO - Neurochem Res VL - 29 UR - https://doi.org/10.1023/B:NERE.0000023608.29741.45 DO - 10.1023/B:NERE.0000023608.29741.45 ID - Pavlidis2004 ER - TY - JOUR AU - Guldener, U. AU - Munsterkotter, M. AU - Kastenmuller, G. AU - Strack, N. AU - van Helden, J. AU - Lemer, C. AU - Richelles, J. AU - Wodak, S. J. AU - Garcia-Martinez, J. AU - Perez-Ortin, J. E. PY - 2005 DA - 2005// TI - CYGD: the Comprehensive Yeast Genome Database JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki053 DO - 10.1093/nar/gki053 ID - Guldener2005 ER - TY - JOUR PY - 2000 DA - 2000// TI - Gene ontology: tool for unification of biology JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - ref25 ER - TY - JOUR AU - Cheng, J. AU - Cline, M. AU - Martin, J. AU - Finkelstein, D. AU - Awad, T. AU - Kulp, D. AU - Siani-Rose, M. A. PY - 2004 DA - 2004// TI - A knowledge-based clustering algorithm driven by gene ontology JO - J Biopharm Stat VL - 14 UR - https://doi.org/10.1081/BIP-200025659 DO - 10.1081/BIP-200025659 ID - Cheng2004 ER - TY - JOUR AU - Pan, W. PY - 2006 DA - 2006// TI - Incorporating gene functions as priors in model-based clustering of microarray gene expression data JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl011 DO - 10.1093/bioinformatics/btl011 ID - Pan2006 ER - TY - CHAP AU - Komura, D. AU - Nakamura, H. AU - Tsutsumi, S. AU - Aburatani, H. AU - Ihara, S. PY - 2004 DA - 2004// TI - Incorporating prior knowledge into clustering of gene expression profiles BT - 15th International Conference on Genome Informatics ID - Komura2004 ER - TY - JOUR AU - Dotan-Cohen, D. AU - Melkman, A. A. AU - Kasif, S. PY - 2007 DA - 2007// TI - Hierarchical tree snipping: clustering guided by prior knowledge JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm526 DO - 10.1093/bioinformatics/btm526 ID - Dotan-Cohen2007 ER - TY - JOUR AU - Huang, D. AU - Pan, W. PY - 2006 DA - 2006// TI - Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl065 DO - 10.1093/bioinformatics/btl065 ID - Huang2006 ER - TY - JOUR AU - Floudas, C. A. AU - Aggarwal, A. AU - Ciric, A. R. PY - 1989 DA - 1989// TI - Global optimum search for non convex NLP and MINLP problems JO - Comp Chem Eng VL - 13 UR - https://doi.org/10.1016/0098-1354(89)87016-4 DO - 10.1016/0098-1354(89)87016-4 ID - Floudas1989 ER - TY - JOUR AU - Paules, G. E. AU - Floudas, C. A. PY - 1989 DA - 1989// TI - APROS – Algorithmic development for discrete-continuous optimization problems JO - Operations Research VL - 37 UR - https://doi.org/10.1287/opre.37.6.902 DO - 10.1287/opre.37.6.902 ID - Paules1989 ER - TY - BOOK AU - Floudas, C. A. PY - 1995 DA - 1995// TI - Nonlinear and Mixed-Integer Optimization: Fundamentals and Applications PB - Oxford University Press CY - Oxford ID - Floudas1995 ER - TY - JOUR AU - Wang, Y. AU - Pierce, M. AU - Schneper, L. AU - Guldal, C. G. AU - Zhang, X. AU - Tavazoie, S. AU - Broach, J. R. PY - 2004 DA - 2004// TI - Ras and Gpa2 mediate one branch of a redundant glucose signaling pathway in yeast JO - PLoS Biol VL - 2 UR - https://doi.org/10.1371/journal.pbio.0020128 DO - 10.1371/journal.pbio.0020128 ID - Wang2004 ER - TY - JOUR AU - Broach, J. R. AU - Deschenes, R. J. PY - 1990 DA - 1990// TI - The function of ras genes in Saccharomyces cerevisiae JO - Adv Cancer Res VL - 54 UR - https://doi.org/10.1016/S0065-230X(08)60809-X DO - 10.1016/S0065-230X(08)60809-X ID - Broach1990 ER - TY - JOUR AU - Schneper, L. AU - Duvel, K. AU - Broach, J. R. PY - 2004 DA - 2004// TI - Sense and sensibility: nutritional response and signal integration in yeast JO - Curr Opin Microbiol VL - 7 UR - https://doi.org/10.1016/j.mib.2004.10.002 DO - 10.1016/j.mib.2004.10.002 ID - Schneper2004 ER - TY - JOUR AU - Santangelo, G. M. PY - 2006 DA - 2006// TI - Glucose signaling in Saccharomyces cerevisiae JO - Microbiol Mol Biol Rev VL - 70 UR - https://doi.org/10.1128/MMBR.70.1.253-282.2006 DO - 10.1128/MMBR.70.1.253-282.2006 ID - Santangelo2006 ER - TY - JOUR AU - Carlson, M. PY - 1999 DA - 1999// TI - Glucose repression in yeast JO - Curr Opin Microbiol VL - 2 UR - https://doi.org/10.1016/S1369-5274(99)80035-6 DO - 10.1016/S1369-5274(99)80035-6 ID - Carlson1999 ER - TY - JOUR AU - Johnston, M. AU - Kim, J. H. PY - 2005 DA - 2005// TI - Glucose as a hormone: receptor-mediated glucose sensing in the yeast Saccharomyces cerevisiae JO - Biochem Soc Trans VL - 33 UR - https://doi.org/10.1042/BST0330247 DO - 10.1042/BST0330247 ID - Johnston2005 ER - TY - JOUR AU - Crauwels, M. AU - Donaton, M. C. AU - Pernambuco, M. B. AU - Winderickx, J. AU - de Winde, J. H. AU - Thevelein, J. M. PY - 1997 DA - 1997// TI - The Sch9 protein kinase in the yeast Saccharomyces cerevisiae controls cAPK activity and is required for nitrogen activation of the fermentable-growth-medium-induced (FGM) pathway JO - Microbiology VL - 143 UR - https://doi.org/10.1099/00221287-143-8-2627 DO - 10.1099/00221287-143-8-2627 ID - Crauwels1997 ER - TY - STD TI - Elemento O, Slonim N, Tavazoie S: Uncovering regulatory elements from expression data using mutual information. Mol Cell, in press. ID - ref41 ER - TY - JOUR AU - Myers, C. L. AU - Barrett, D. R. AU - Hibbs, M. A. AU - Huttenhower, C. AU - Troyanskaya, O. G. PY - 2006 DA - 2006// TI - Finding function: evaluation methods for functional genomic data JO - BMC Genomics VL - 7 UR - https://doi.org/10.1186/1471-2164-7-187 DO - 10.1186/1471-2164-7-187 ID - Myers2006 ER - TY - JOUR AU - Brem, R. B. AU - Yvert, G. AU - Clinton, R. AU - Kruglyak, L. PY - 2002 DA - 2002// TI - Genetic dissection of transcriptional regulation in budding yeast JO - Science VL - 296 UR - https://doi.org/10.1126/science.1069516 DO - 10.1126/science.1069516 ID - Brem2002 ER - TY - JOUR AU - Yvert, G. AU - Brem, R. B. AU - Whittle, J. AU - Akey, J. M. AU - Foss, E. AU - Smith, E. N. AU - Mackelprang, R. AU - Kruglyak, L. PY - 2003 DA - 2003// TI - Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors JO - Nat Genet VL - 35 UR - https://doi.org/10.1038/ng1222 DO - 10.1038/ng1222 ID - Yvert2003 ER - TY - JOUR AU - Foat, B. C. AU - Houshmandi, S. S. AU - Olivas, W. M. AU - Bussemaker, H. J. PY - 2005 DA - 2005// TI - Profiling condition-specific, genome-wide regulation of mRNA stability in yeast JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0503803102 DO - 10.1073/pnas.0503803102 ID - Foat2005 ER - TY - STD TI - The Princeton University Microarray Database[http://puma.princeton.edu] UR - http://puma.princeton.edu ID - ref46 ER - TY - JOUR AU - Gollub, J. AU - Ball, C. a. AU - Binkley, G. AU - Demeter, J. AU - Finkelstein, D. B. AU - Hebert, J. M. AU - Hernandez-Boussard, T. AU - Jin, H. AU - Kaloper, M. AU - Matese, J. C. AU - Schroeder, M. AU - Brown, P. O. AU - Botstein, D. AU - Sherlock, G. PY - 2003 DA - 2003// TI - The Stanford microarray database: data access and quality assessment tools JO - Nuclei Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg078 DO - 10.1093/nar/gkg078 ID - Gollub2003 ER - TY - JOUR AU - Troyanskaya, O. AU - Cantor, M. AU - Sherlock, G. AU - Brown, P. AU - Hastie, T. AU - Tibshirani, R. AU - Botstein, S. AU - Altman, R. B. PY - 2001 DA - 2001// TI - Missing value estimation methods for DNA microarrays JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.6.520 DO - 10.1093/bioinformatics/17.6.520 ID - Troyanskaya2001 ER - TY - JOUR AU - Tan, M. P. AU - Broach, J. R. AU - Floudas, C. A. PY - 2007 DA - 2007// TI - Evaluation of normalization and pre-clustering issues in a novel clustering approach: global optimum search with enhanced positioning JO - J Bioinform Comput Biol VL - 5 UR - https://doi.org/10.1142/S0219720007002941 DO - 10.1142/S0219720007002941 ID - Tan2007 ER - TY - STD TI - The Saccharomyces Genome Database[http://www.yeastgenome.org] UR - http://www.yeastgenome.org ID - ref50 ER - TY - JOUR AU - Broman, K. W. AU - Wu, H. AU - Sen, S. AU - Churchill, G. A. PY - 2003 DA - 2003// TI - R/qtl: QTL mapping in experimental crosses JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg112 DO - 10.1093/bioinformatics/btg112 ID - Broman2003 ER - TY - JOUR AU - Churchill, G. A. AU - Doerge, R. W. PY - 1994 DA - 1994// TI - Empirical threshold values for quantitative trait mapping JO - Genetics VL - 138 ID - Churchill1994 ER - TY - STD TI - [http://function.princeton.edu/GRIFn] UR - http://function.princeton.edu/GRIFn ID - ref53 ER - TY - BOOK AU - Brooke, A. AU - Kendrick, D. AU - Meeraus, A. PY - 1988 DA - 1988// TI - GAMS: A User's Guide PB - The Scientific Press CY - San Francisco ID - Brooke1988 ER -