Improving functional module detection

OCCBIO'09: 2009 Ohio Collaborative Conference on Bioinformatics

Volumn , Issue , 2009, Pages 110-115

  Abraham, K J ^a   Sameith, Katrin ^b   Falciani, Francesco ^c  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^c UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL TECHNIQUE; FUNCTIONAL MODULES; GENE EXPRESSION DATA; GENETIC DATA; HAPLOTYPES; MONTE CARLO; PROTEIN INTERACTION;

BIOINFORMATICS; GENE EXPRESSION; MONTE CARLO METHODS;

SIMULATED ANNEALING;

EID: 70350413752     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/OCCBIO.2009.11     Document Type: Conference Paper

References (13)

1. E. Segal, M.I. Shapira, A. Regev, D. Pe'er, D. Botstein, D. Koller,and N. Friedman; Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data Nature Genetics (2003), 34, 166-176.
2. T. Ideker, O. Ozier, B. Schwikowski, and A.F. Siegel; Discovering regulatory networks and signalling circuits in molecular interaction networks Bioinformatics (2002), 18, 233-240.
3. K. Basso, A.A. Margolin, G. Stolovitzky, U. Klein, R. Dalla-Favera, and A. Califano; Reverse Engineering of regulatory networks in human B cells Nature Genetics, (2005) 37, 382-390.
4. K. Sameith, P. Antczak, E. Marston, N. Turan, D. Maier, T. Stankovic, and F. Falciani; Functional Modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage Bioinformatics (2008), 199, 133-154.
5. S. Kirkpatrick, C.D. Gelatt, and M.P. Vecchi; Optimization by simulated annealing Science 220 671-680 (1983)
6. W.R. Gilks, S.Richardson, and D.J. Spiegelhalter; Markov Chain Monte Carlo In Practise Chapman & Hall (1995)
7. Roger Guimera and Luis A. Nunes Amaral; Functional cartography of complex metabolic networks Nature 433(7028) 895-900 (2005).
8. Jing Yu, V. Anne Smith, Paul. P. Wang, Alexander J. Hartemink & Erich Javis Advances to Bayesian network inference for generating causal networks from observational biological data Bioinformatics 20 3594-3603 (2004)
9. K. Zhang, and L. Jin; HaploBlockFinder: haplotype block analyses Bioinformatics, 19, 1300-1301 (2003).
10. Jose B. Pereira-Leal, Anton J. Enright, and Christos A. Ouzounis; Detection of Functional Modules from Protein Interaction Networks PROTEINS: Structure, Function and Bioinformatics, 54: 49-57 (2004)
11. S. Geman and D. Geman; Stochastic relaxation, Gibbs Distributions and the Bayesian restoration of images IEEE Trans. Pattn Anal. Mach. Intell 6 721-724 (1984).
12. Marcello Blatt, Shai Wiseman, and Eytan Domany; Superparamagnetic Clustering of Data Physical Review Letters 76 18, 3215-3254 (1996)
13. Victor Spirin and Leonid A. Mirny; Protein complexes and functional modules in molecular networks Proceedings of the National Academy of Sciences of the United States of America Vol. 100 21, 12123-12128 (2003)