Self-correcting maps of molecular pathways

PLoS ONE

Volumn 1, Issue 1, 2006, Pages

  Rzhetsky, Andrey ^a,b   Zheng, Tian ^a   Weinreb, Chani ^a  

^a Howard Hughes Medical Institute   (United States)

^b Department of Neurology and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALZHEIMER DISEASE; ARTICLE; AUTISM; AUTOMATION; BIOINFORMATICS; BIPOLAR DISORDER; DATA ANALYSIS; GENETIC ASSOCIATION; HYPOTHESIS; MOLECULAR BIOLOGY; MOLECULAR INTERACTION; MOLECULAR MODEL; SCHIZOPHRENIA; BAYES THEOREM; BIOLOGICAL MODEL; GENE REGULATORY NETWORK; GENETICS; HUMAN; METABOLISM; NEUROLOGIC DISEASE;

BAYES THEOREM; GENE REGULATORY NETWORKS; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; MODELS, GENETIC; NERVOUS SYSTEM DISEASES;

EID: 46849085966     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000061     Document Type: Article

References (29)

1. von Neumann J (1956) Probabilistic logics and the synthesis ofreliable organisms from unreliable components. In: Shannon CE, McCarthy J, editors. Automata Studies. Ptinceton NJ: Princeton University Press. pp. 13-98.
2. Pearl J (1988) Probabilistic reasoning in intelligent systems: networks of plausible inference. The Morgan Kaufmann series in representation and reasoning. San MateoCalif: Morgan Kaufmann Publishers.
3. Heckerman D, Geiger D, Chickering DM (1995) Learning Bayesian networks - the combination of knowledge and statistical-data. Machine Learning 20: 197-243.
4. Heckerman D, Wellman MP (t995) Bayesian, networks. Communications of the ACM 38: 27-30.
5. Szolovits P (1995) Uncertainty and decisions in medical informatics. Methods Inf Med 34: 111-121.
6. Kahn J C E, Roberts LM, Shaffer KA, Haddawy P (1997) Construction of a Bayesian network for mammographic diagnosis of breast cancer. Comput Biol Med 27: 19-29.
7. Pearl J (2000) Causality : models, reasoning, and inference. Cambridge, U.K. New York: Cambridge University Press.
8. Friedman N, Linial M, Nachman I, Pe'er D (2000) Using Bayesian networks to analyze expression data. J Comput Biol 7: 601-620.
9. Friedman N (2004) Inferring cellular networks using probabilistic graphical models. Science 303: 799-805.
10. Gilks WR, Richardson S, Spiegelhalter DJ, editors (1996) Markov chain Monte Carlo in practice. New York: Chapman & Hall/CRC.
11. Liu JS (2001) Monte Carlo Strategies in Scientific Computing. Springer Series in Statistics. New York: Springer.
12. Friedman G, Kra P, Yu H, Krauthammer M, Rzhetsky A (2001) GENIES: a naturallanguage processing system for the extraction of molecular pathways from journal articles. Bioinformatics 17 Suppl. 1: S74-S82.
13. Rhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, et al. (2004) GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform, 37: 43-53.
14. Gokol M, Iossirov I, Weinreb C, Rzhetsky A (2005) Emergent behavior of growing knowledge about molecular interactions. Nat Biotechnol 23: 1243-1247.
15. Sampson EM, Haque ZK, Ku MC, Tevosian SG, Albanese C, et al. (2001) Negative regulation of the Wnt-beta-catenin pathway by the transcriptional repressor HBP1. Embo J 20: 4500-4511.
16. Ligon KL, Echelard Y, Assimacopoulos S, Danielian PS, Kaing S, et al. (2003) Loss of Emx2 function leads to ectopic expression of Wnt1 in the developing telencephalon and cortical dysplasia. Development 130: 2275-2287.
17. McDonough PM, Hanford DS, Sprenkle AB, Mellon NR, Glembotski CC (1997) Collaborative roles for c-Jun N-terminal kinase, c-Jun, serum response factor, and Sp1 in calcium-regulated myocardial gene expression. J Biol Chem 272: 24046-24053.
18. Amson R, Lassalle JM, Halley H, Prieur S, Lethrosne F, et al. (2000) Behavioral alterations associated with apoptosis and down-regulation of presenilin 1 in the brains of p53-deficient mice. Proc Natl Acad Sci U S A 97: 5346-5350.
19. Alves da Costa C, Paitel E, Mattson MP, Amson R, Telerman A, et al. (2002) Wild-type and mutated presenilins 2 trigger p53-dependent apoptosis and down-regulate presenilin 1 expression in HEK293 human cells and in murine neurons. Proc Natl Acad Sci U S A 99: 4043-4048.
20. Alves da Costa C, Mattson MP, Ancolio K, Checler F (2003) The C-terminal fragment of presenilin 2 triggers p53-mediated staurosporine-induced apoptosis, a function independent of the presenilinase-derived N-terminal counterpart. J Biol Chem 278: 12064-12069.
21. Yeang CH, Ideker T, Jaakkola T (2004) Physical network models. J Comput Biol 11: 243-262.
22. Markowetz F, Bloch J, Spang R (2005) Non-transcriptional pathway features reconstructed from secondary effects of RNA interference. Bioinformatics 21: 4026-4032.
23. Hartemink AJ, Gifford DK, Jaakkola TS, Young RA (2001) Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pac Symp Biocomput: 422-433.
24. Frey BJ, Mohammad N, Morris QD, Zhang W, Robinson MD, et al. (2005) Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs. Nat Genet 37: 991-996.
25. Krauthammer M, Kaufmann CA, Gilliam TC, Rzhetsky A (2004) Molecular triangulation: Bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease. Proc Natl Acad Sci U S A 101: 15148-15153.
26. Bascompte J, Jordano P, Olesen JM (2006) Asymmetric coevolutionary networks facilitate biodiversity maintenance. Science 312: 431-433.
27. Barabasi AL (2005) Sociology, network theory - the emergence of the creative enterprise. Science 308: 639-641.
28. Hoff PD, Ward MD (2004) Modeling dependencies in international relations networks. Political Analysis 12: 160-175.
29. Rzhetsky A, Iossifov I, Loh JM, White KP (2006) Microparadigms: chains of collective reasoning in publications about molecular interactions. Proc Natl Acad Sci U S A.