TY - JOUR AU - Babu, M. M. AU - Teichmann, S. A. PY - 2003 DA - 2003// TI - Evolution of Transcription Factors and the Gene Regulatory Network in Escherichia coli JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg210 DO - 10.1093/nar/gkg210 ID - Babu2003 ER - TY - JOUR AU - Balazsi, G. AU - Barabasi, A. -. L. AU - Oltvai, Z. N. PY - 2005 DA - 2005// TI - Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0500365102 DO - 10.1073/pnas.0500365102 ID - Balazsi2005 ER - TY - JOUR AU - Shen-Orr, S. AU - Milo, R. AU - Mangan, S. AU - Alon, U. PY - 2002 DA - 2002// TI - Network motifs in the transcriptional regulation network of Escherichia coli JO - Nature Genetics VL - 31 UR - https://doi.org/10.1038/ng881 DO - 10.1038/ng881 ID - Shen-Orr2002 ER - TY - JOUR AU - Holter, N. S. AU - Maritan, A. M. AU - Cieplak, N. V. AU - Banavar, J. R. PY - 2000 DA - 2000// TI - Dynamic modeling of gene expression data JO - Proc Natl Acad Sci USA VL - 98 UR - https://doi.org/10.1073/pnas.98.4.1693 DO - 10.1073/pnas.98.4.1693 ID - Holter2000 ER - TY - JOUR AU - Liebermeister, W. PY - 2002 DA - 2002// TI - Linear modes of gene expression determined by independent component analysis JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.1.51 DO - 10.1093/bioinformatics/18.1.51 ID - Liebermeister2002 ER - TY - JOUR AU - Liao, J. C. AU - Boscolo, R. AU - Tran, L. M. AU - Sabatti, C. AU - Roychowdhury, V. PY - 2003 DA - 2003// TI - Network component analysis: reconstruction of regulatory signals in biological systems JO - Proc Natl Acad Sci USA VL - 100 UR - https://doi.org/10.1073/pnas.2136632100 DO - 10.1073/pnas.2136632100 ID - Liao2003 ER - TY - JOUR AU - Gardner, T. S. AU - di Bernardo, D. AU - Lorenz, D. AU - Collins, J. J. PY - 2003 DA - 2003// TI - Inferring genetic networks and identifying compound mode of action via expression profiling JO - Science VL - 301 UR - https://doi.org/10.1126/science.1081900 DO - 10.1126/science.1081900 ID - Gardner2003 ER - TY - JOUR AU - Kyoda, K. M. AU - Morohashi, M. AU - Onami, S. AU - Kitano, H. PY - 2000 DA - 2000// TI - A gene network inference method from continuous-value gene expression data of wild-type and mutants JO - Genome Inform Ser Workshop Genome Inform VL - 11 ID - Kyoda2000 ER - TY - CHAP AU - Liang, S. AU - Fuhrman, S. AU - Somogyi, R. PY - 1998 DA - 1998// TI - Reveal, a general reverse engineering algorithm for inference of genetic network architectures BT - Pac Symp Biocomput ID - Liang1998 ER - TY - JOUR AU - Huang, S. PY - 1999 DA - 1999// TI - Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery JO - J Mol Med VL - 77 UR - https://doi.org/10.1007/s001099900023 DO - 10.1007/s001099900023 ID - Huang1999 ER - TY - JOUR AU - Azuaje, F. PY - 2002 DA - 2002// TI - A cluster validity framework for genome expression data JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.2.319 DO - 10.1093/bioinformatics/18.2.319 ID - Azuaje2002 ER - TY - JOUR AU - Bolshakova, N. AU - Azuaje, F. PY - 2003 DA - 2003// TI - cluster validation for gene expression data JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg356 DO - 10.1093/bioinformatics/btg356 ID - Bolshakova2003 ER - TY - JOUR AU - D'haeseleer, P. AU - Liang, S. AU - Somogyi, R. PY - 2000 DA - 2000// TI - Genetic network inference: from co-expression clustering to reverse engineering JO - Bioinformatics VL - 16 UR - https://doi.org/10.1093/bioinformatics/16.8.707 DO - 10.1093/bioinformatics/16.8.707 ID - D'haeseleer2000 ER - TY - STD TI - Encyclopedia of Escherichia coli K-12 Genes and Metabolism. http://www.ecocyc.com UR - http://www.ecocyc.com ID - ref14 ER - TY - JOUR AU - Basso, K. AU - Margolin, A. A. AU - Klein, U. AU - Dalla-Favera, R. AU - Califano, A. PY - 2005 DA - 2005// TI - Reverse engineering of regulatory networks in human B cells JO - Nat Genet VL - 37 UR - https://doi.org/10.1038/ng1532 DO - 10.1038/ng1532 ID - Basso2005 ER - TY - CHAP AU - Segal, E. AU - Wang, H. AU - Koller, D. PY - 2003 DA - 2003// TI - Discovering molecular pathways from protein interaction and gene expression data BT - Bioinformatics UR - https://doi.org/10.1093/bioinformatics/btg1037 DO - 10.1093/bioinformatics/btg1037 ID - Segal2003 ER - TY - JOUR AU - Brazma, A. AU - Jonassen, L. AU - Eidhammer, I. AU - Gilbert, D. PY - 1998 DA - 1998// TI - Approaches to the automatic discovery of patterns in biosequences JO - J Comput Biol VL - 5 UR - https://doi.org/10.1089/cmb.1998.5.279 DO - 10.1089/cmb.1998.5.279 ID - Brazma1998 ER - TY - CHAP AU - Haverty, P. M. AU - Weng, Z. AU - Hansen, U. PY - 2004 DA - 2004// TI - CARRIE web service: automated transcriptional regulatory network inference and interactive analysis BT - Nucleic Acids Res ID - Haverty2004 ER - TY - JOUR AU - Lee, I. AU - Date, S. V. AU - Adai, A. T. AU - Marcotte, E. M. PY - 2004 DA - 2004// TI - A probabilistic functional network of yeast genes JO - Science VL - 306 UR - https://doi.org/10.1126/science.1099511 DO - 10.1126/science.1099511 ID - Lee2004 ER - TY - JOUR AU - Wu, H. AU - Mao, F. AU - Su, Z. AU - Olman, V. AU - Xu, Y. PY - 2005 DA - 2005// TI - Prediction of functional modules based on comparative genome analysis and Gene Ontology application JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki573 DO - 10.1093/nar/gki573 ID - Wu2005 ER - TY - STD TI - Gene ontology. http://www.geneontology.org UR - http://www.geneontology.org ID - ref21 ER - TY - JOUR AU - Camon, E. AU - Magrane, M. AU - Barrell, D. AU - Lee, V. AU - Dimmer, E. AU - Maslen, J. AU - Binns, D. AU - Harte, N. AU - Lopez, R. AU - Apweiler, R. PY - 2003 DA - 2003// TI - The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.461403 DO - 10.1101/gr.461403 ID - Camon2003 ER - TY - STD TI - European Bioinformatics Institute. http://www.ebi.ac.uk UR - http://www.ebi.ac.uk ID - ref23 ER - TY - STD TI - NIH ftp site. ftp://ftp.ncbi.nih.gov/genomes/Bacteria UR - ftp://ftp.ncbi.nih.gov/genomes/Bacteria ID - ref24 ER - TY - JOUR AU - McCue, L. A. AU - Thompson, W. AU - Carmack, C. S. AU - Ryan, M. P. AU - Liu, J. S. AU - Derbyshire, V. AU - Lawrence, C. E. PY - 2001 DA - 2001// TI - Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes JO - Nucleic Acids Research VL - 29 UR - https://doi.org/10.1093/nar/29.3.774 DO - 10.1093/nar/29.3.774 ID - McCue2001 ER - TY - STD TI - Pathema Bioinformatics Resource Center. http://pathema.tigr.org UR - http://pathema.tigr.org ID - ref26 ER - TY - STD TI - HAMAP Project. http://us.expasy.org/sprot/hamap/bacteria.html UR - http://us.expasy.org/sprot/hamap/bacteria.html ID - ref27 ER - TY - CHAP AU - Rashevsky, N. PY - 1960 DA - 1960// BT - Mathematical Biophysics Physico-Mathematical Foundations of Biology PB - Dover Publications CY - New York ID - Rashevsky1960 ER - TY - JOUR AU - Slepchenko, B. AU - Schaff, J. PY - 2003 DA - 2003// TI - Quantitative cell biology with the virtual cell JO - Trends in Cell Biology VL - 13 UR - https://doi.org/10.1016/j.tcb.2003.09.002 DO - 10.1016/j.tcb.2003.09.002 ID - Slepchenko2003 ER - TY - JOUR AU - Weitzke, E. L. AU - Ortoleva, P. J. PY - 2003 DA - 2003// TI - Simulating cellular dynamics through a coupled transcription, translation, metabolic model JO - Computational Biology and Chemistry VL - 27 UR - https://doi.org/10.1016/j.compbiolchem.2003.08.002 DO - 10.1016/j.compbiolchem.2003.08.002 ID - Weitzke2003 ER - TY - JOUR AU - Navid, A. AU - Ortoleva, P. J. PY - 2004 DA - 2004// TI - Simulated Complex Dynamics of Glycolysis in the Protozoan Parasite Trypanosoma brucei JO - Journal of Theoretical Biology VL - 228 UR - https://doi.org/10.1016/j.jtbi.2004.02.007 DO - 10.1016/j.jtbi.2004.02.007 ID - Navid2004 ER - TY - JOUR AU - Ortoleva, P. AU - Berry, E. AU - Fan, J. AU - Fontus, M. AU - Navid, A. AU - Sayyed-Ahmad, A. AU - Sharif, Z. AU - Stanley, F. AU - Tuncay, K. AU - Weitzke, E. AU - Wu, L. PY - 2003 DA - 2003// TI - The Karyote Physico-Chemical Genomic, Proteomic, Metabolic Cell Modeling System JO - OMICS: A Journal of Integrative Biology VL - 7 UR - https://doi.org/10.1089/153623103322452396 DO - 10.1089/153623103322452396 ID - Ortoleva2003 ER - TY - JOUR AU - Mendes, P. AU - Kell, D. PY - 1998 DA - 1998// TI - Nonlinear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation JO - Bioinformatics VL - 14 UR - https://doi.org/10.1093/bioinformatics/14.10.869 DO - 10.1093/bioinformatics/14.10.869 ID - Mendes1998 ER - TY - JOUR AU - Sayyed-Ahmad, A. AU - Tuncay, K. AU - Ortoleva, P. PY - 2003 DA - 2003// TI - Automated cell model development through information theory JO - Journal of Physical Chemistry VL - 107 UR - https://doi.org/10.1021/jp0302921 DO - 10.1021/jp0302921 ID - Sayyed-Ahmad2003 ER - TY - STD TI - Systems biology portal, Center for Cell and Virus Theory at Indiana University. http://systemsbiology.indiana.edu UR - http://systemsbiology.indiana.edu ID - ref35 ER - TY - CHAP AU - Salgado, H. AU - Gama-Castro, S. AU - Martinez-Antonio, A. AU - Diaz-Peredo, E. AU - Sanchez-Solano, F. AU - Peralta-Gil, M. AU - Garcia-Alonso, D. AU - Jimenez-Jacinto, V. AU - Santos-Zavaleta, A. AU - Bonavides-Martinez, C. AU - Collado-Vides, J. PY - 2004 DA - 2004// TI - RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12 BT - Nucleic Acids Res ID - Salgado2004 ER - TY - STD TI - TRND Results portal. http://systemsbiology.indiana.edu/trndresults UR - http://systemsbiology.indiana.edu/trndresults ID - ref37 ER -