Accelerated search for biomolecular network models to interpret high-throughput experimental data

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Datta, Suman ^a   Sokhansanj, Bahrad A ^a  

^a DREXEL UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONSISTENT PERFORMANCE; EVOLUTIONARY SEARCH; EVOLUTIONARY SEARCH ALGORITHMS; GENE EXPRESSION MICROARRAY; HIGH-THROUGHPUT MEASUREMENTS; PROTEIN EXPRESSIONS; QUANTITATIVE PREDICTION; TRAINING DATA SETS;

COMPLEX NETWORKS; EVOLUTIONARY ALGORITHMS; MEASUREMENTS; MICROARRAYS; PROTEINS;

GENE EXPRESSION;

ALGORITHM; ARTICLE; BIOINFORMATICS; BIOLOGICAL MODEL; CELL CYCLE; CORRELATION ANALYSIS; FUZZY SYSTEM; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC CONSERVATION; HUMAN; HUMAN CELL; INFORMATION PROCESSING; MICROARRAY ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR MODEL; PROBABILITY; PROTEIN EXPRESSION; QUALITATIVE ANALYSIS; QUANTITATIVE GENETICS; COMPUTER PROGRAM; DNA MICROARRAY; FUZZY LOGIC; GENE REGULATORY NETWORK; GENETICS; HELA CELL; METHODOLOGY;

ALGORITHMS; CELL CYCLE; FUZZY LOGIC; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HELA CELLS; HUMANS; MODELS, BIOLOGICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROBABILITY; SOFTWARE;

EID: 34547757974     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-258     Document Type: Article

References (23)

1. Csete ME Doyle JC Reverse engineering of biological complexity Science 2002 295 1664-1669 10.1126/science.1069981 11872830
2. Gianchandani EP Brautigan DL Papin JA System analyses characterize integrated functions of biochemical networks Trends in Biochemical Sciences 2006 31 5 284-291 10.1016/j.tibs.2006.03.007 16616498
3. Arita M Robert M Tomita M All systems go: Launching cell simulation fueled by integrated experimental biology data Current Opinion in Biotechnology 2005 16 3 344-349 10.1016/j.copbio.2005.04.004 15961035
4. Friedman N Inferring cellular networks using probabilistic graphical models Science 2004 303 5659 799-805 10.1126/science.1094068 14764868
5. Liang S Fuhrman S Somogyi R REVEAL, a general reverse engineering algorithm for inference of genetic network archictectures. Pacific Symposium on Biocomputing 2000 3 18-29
6. Glass L Kauffman SA The logical analysis of continuous, nonlinear biochemical control networks Journal of Theoretical Biology 1973 39 103-129 10.1016/0022-5193(73)90208-7 4741704
7. Chen KC Csikasz-Nagy A Gyorffy B Val J Novak B Tyson J Kinetic analysis of a molecular model of the budding yeast cell cycle Molecular Biology Cell 2000 13 52-70
8. Tegner J Yeung MKS Hasty J Collins JJ Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling Proceedings of the National Academy of Sciences USA 2000 99 6163-6168
9. Yeung MKS Tegner J Collins JJ Reverse engineering gene networks using signular value decomposition and robust recognition. Proceedings of the National Academy of Sciences USA 2002 100 5944-5949
10. Sokhansanj BA Garnham JB Fitch JP Interpreting data from microarray experiments to build models of microbial genetic regulation networks Proceedings of the SPIE Functional Monitoring and Drug-Tissue Interaction 2002 4623 27-37
11. Sokhansanj BA Fitch JP Quong JN Quong AA Linear fuzzy gene networks obtained from microarray data by exhaustive search BMC Bioinformatics 2004 5 108 514698 15304201 10.1186/1471-2105-5-108
12. Woolf PJ Wang Y A fuzzy logic approach to analyzing gene expression data Physiological Genomics 2000 3 1 9-15 11015595
13. Gagneur J Casari G From molecular networks to qualitative cell behavior FEBS Letters 2005 579 1867-1871 10.1016/j.febslet.2005.02.007 15763565
14. Combs WE Andrews JE Combinatorial rule explosion eliminated by a fuzzy rule configuration IEEE Transactions in Fuzzy Systems 1998 6 1-11 10.1109/91.660804
15. Husmeier D Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks Bioinformatics 2003 19 17 2271-2282 10.1093/bioinformatics/btg313 14630656
16. Soinov LA Krestyaninova M Brazma A Towards reconstruction of gene networks from expression data by supervised learning Genome Biology 2003 4 R6 151290 12540298 10.1186/gb-2003-4-1-r6
17. Repsilber D Liljenstrom H Andersson SGE Reverse engineering of regulatory networks: Simulation studies on a genetic algorithm approach for ranking hypotheses Biosystems 2002 66 31-41 10.1016/ S0303-2647(02)00019-9 12204440
18. Whitfield ML Sherlock G Saldanha AJ Murray JI Ball CA Alexander KE Matese JC Perou CM Hurt MM Brown PO Bostein D Identification of genes periodically expressed in the human cell cycle and their expression in tumors Molecular Biology of the Cell 2002 13 1977-2000 117619 12058064 10.1091/mbc.02-02-0030.
19. Zhu XM Yin L Hood L Ao P Robustness, stability and efficiency of phage lambda genetic switch: Dynamical structure analysis J Bioinform Comput Biol 2004 2 4 785-817 10.1142/S0219720004000946 15617166
20. Kohn KW Riss J Aprelikova O Weinstein JN Pommier Y Barrett JC Properties of switch-like bioregulatory networks studied by simulation of the hypoxia response control system Mol Biol Cell 2004 15 7 3042-3052 452562 15107465 10.1091/mbc.E03-12-0897
21. Stelling J Gilles ED Mathematical modeling of complex regulatory networks IEEE Trans Nanobioscience 2004 3 3 172-179 10.1109/ TNB.2004.833688 15473069
22. Hu X Sokhansanj B Wu D Gang Y A novel approach for mining and fuzzy simulation of sub-networks from large biomolecular networks IEEE Trans Fuzzy Syst 2007
23. Holland JH Adaptation in natural and artificial systems Ann Arbor, MI, University of Michigan Press 1975