Module cover - A new approach to genotype-phenotype studies

Pacific Symposium on Biocomputing

Volumn , Issue , 2013, Pages 135-146

  Kim, Yoo Ah ^a   Salari, Raheleh ^a,b   Wuchty, Stefan ^a   Przytycka, Teresa M ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CANDIDATE SETS; COVER PROBLEM; GENOMIC ALTERATIONS; HETEROGENEOUS DATASETS; INTEGRATED METHOD; NETWORK-CENTRIC APPROACH; NEW APPROACHES; TWO STEP METHOD;

INTEGRATED CONTROL;

ALGORITHM; BIOLOGICAL MODEL; BIOLOGY; CASE CONTROL STUDY; FEMALE; GENE REGULATORY NETWORK; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC EPIGENESIS; GENETICS; GLIOBLASTOMA; HUMAN; NEOPLASM; OVARY TUMOR; QUANTITATIVE TRAIT LOCUS; STATISTICAL ANALYSIS; STATISTICS AND NUMERICAL DATA; ARTICLE; STATISTICS;

ALGORITHMS; CASE-CONTROL STUDIES; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; DATABASES, GENETIC; EPIGENESIS, GENETIC; FEMALE; GENE REGULATORY NETWORKS; GENETIC ASSOCIATION STUDIES; GLIOBLASTOMA; HUMANS; MODELS, GENETIC; NEOPLASMS; OVARIAN NEOPLASMS; QUANTITATIVE TRAIT LOCI;

EID: 84886022540     PISSN: 23356928     EISSN: 23356936     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (34)

1. I. Ulitsky, R. Karp, R. Shamir, in Research in Computational Molecular Biology. (2008), pp. 347-359.
2. S. A. Chowdhury, M. Koyuturk, Pac Symp Biocomput, 133 (2010).
3. H. Y. Chuang, E. Lee, Y. T. Liu, D. Lee, T. Ideker, Mol Syst Biol 3, 140 (2007).
4. E. Lee, H. Y. Chuang, J. W. Kim, T. Ideker, D. Lee, PLoS Comput Biol 4, e1000217 (Nov, 2008).
5. I. Ulitsky, A. Krishnamurthy, R. M. Karp, R. Shamir, PLoS One 5, e13367 (2010).
6. T. Ideker, O. Ozier, B. Schwikowski, A. F. Siegel, Bioinformatics 18 Suppl 1, S233 (2002).
7. F. Vandin, E. Upfal, B. J. Raphael, J Comput Biol 18, 507 (Mar, 2011).
8. Vandin F., P. Clay, E. Upfal, R. B.J., in Pacific Symposium on Biocomputing. (2012).
9. I. Lee, U. M. Blom, P. I. Wang, J. E. Shim, E. M. Marcotte, Genome Res 21, 1109 (Jul, 2011).
10. Y. A. Kim, J. H. Przytycki, S. Wuchty, T. M. Przytycka, Phys Biol 8, 035012 (Jun, 2011).
11. Y. A. Kim, S. Wuchty, T. M. Przytycka, PLoS Comput Biol 7, e1001095 (Mar, 2011).
12. S. Kim, K. A. Sohn, E. P. Xing, Bioinformatics 25, i204 (Jun 15, 2009).
13. W. Zhang, J. Zhu, E. E. Schadt, J. S. Liu, PLoS Comput Biol 6, e1000642 (Jan, 2010).
14. A. J. Enright, S. Van Dongen, C. A. Ouzounis, Nucleic Acids Res 30, 1575 (Apr 1, 2002).
15. S. Maere, K. Heymans, M. Kuiper, Bioinformatics 21, 3448 (Aug 15, 2005).
16. A. Li et al., Cancer Res 69, 2091 (Mar 1, 2009).
17. R. Shen et al., PLoS One 7, e35236 (2012).
18. Nature 474, 609 (Jun 30, 2011).
19. C. Li, W. H. Wong, Proc Natl Acad Sci U S A 98, 31 (Jan 2, 2001).
20. Y. Kotliarov et al., Cancer Res 66, 9428 (Oct 1, 2006).
21. R. C. Gentleman et al, Genome Biol 5, R80 (2004).
22. J. Fridlyand, A. M. Snijders, D. Pinkel, G. Albertson, A. N. Jain, Journal of Multivariate Analysis 90, 132 (2004).
23. R. M. Ewing et al, Mol Syst Biol 3, 89 (2007).
24. J. F. Rual et al, Nature 437, 1173 (Oct 20, 2005).
25. U. Stelzl et al., Cell 122, 957 (Sep 23, 2005).
26. A. Chatr-aryamontri et al., Nucleic Acids Res 35, D572 (Jan, 2007).
27. S. Kerrien et al., Nucleic Acids Res 35, D561 (Jan, 2007).
28. L. Matthews et al., Nucleic Acids Res, (Nov 3, 2008).
29. S. Peri et al., Nucleic Acids Res 32, D497 (Jan 1, 2004).
30. C. Jiang, Z. Xuan, F. Zhao, M. Q. Zhang, Nucleic Acids Res 35, D137 (Jan, 2007).
31. R. Linding et al., Cell 129, 1415 (Jun 29, 2007).
32. R. Linding et al., Nucleic Acids Res 36, D695 (Jan, 2008).
33. F. Diella, C. M. Gould, C. Chica, A. Via, T. J. Gibson, Nucleic Acids Res 36, D240 (Jan, 2008).
34. R. Beroukhim et al., Proc Natl Acad Sci U S A 104, 20007 (Dec 11, 2007). Online appendix: http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/Modue-Cover/Appendix