3D chromosome modeling with semi-definite programming and Hi-C data

Journal of Computational Biology

Volumn 20, Issue 11, 2013, Pages 831-846

  Zhang, Zhizhuo ^a   Li, Guoliang ^b   Toh, Kim Chuan ^a   Sung, Wing Kin ^a,b  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b GENOME INSTITUTE OF SINGAPORE   (Singapore)

Author keywords

chromatin interaction; Hi C; semi definite programming; three dimensional genome

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; CHEMICAL STRUCTURE; CHROMOSOME; COMPUTER SIMULATION; CONFORMATION; GENETICS; GENOMICS; HUMAN;

ALGORITHMS; ANIMALS; CHROMOSOMES; COMPUTER SIMULATION; GENOMICS; HUMANS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION;

EID: 84887416171     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2013.0076     Document Type: Article

References (29)

1. Bau D. and Marti-Renom M.A. 2012. Genome structure determination via 3C-based data integration by the integrative modeling platform. Methods 58 300-306.
2. Biswas P. Liang T. Toh K., et al. 2006. Semidefinite programming approaches for sensor network localization with noisy distance measurements. IEEE Transactions on Automation Science and Engineering 3 360-371. (Pubitemid 44574330)
3. Dekker J. 2008. Gene regulation in the third dimension. Science Signalling 319 1793-1794. (Pubitemid 351451557)
4. Dekker J. Rippe K. Dekker M. and Kleckner N. 2002. Capturing chromosome conformation. Science 295 1306-1311. (Pubitemid 34157624)
5. Dixon J. Selvaraj S. Yue F., et al. 2012. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485(7398):376-380.
6. Dostie J. and Dekker J. 2007. Mapping networks of physical interactions between genomic elements using 5c technology. Nat. Protoc. 2 988-1002. (Pubitemid 46745595)
7. Duan Z. Andronescu M. Schutz K., et al. 2010. A three-dimensional model of the yeast genome. Nature 465 363-367.
8. Fraser P. and Bickmore W. 2007. Nuclear organization of the genome and the potential for gene regulation. Nature 447 413-417. (Pubitemid 46816747)
9. Fullwood M. and Ruan Y. 2009. Chip-based methods for the identification of long-range chromatin interactions. Journal of Cellular Biochemistry 107 30-39.
10. Hu M. Deng K. Qin Z., et al. 2013. Bayesian inference of spatial organizations of chromosomes. PLoS Computational Biology 9 e1002893.
11. Jiang K. Sun D. and Toh K. 2012. A partial proximal point algorithm for nuclear norm regularized matrix least squares problems. Mathematical Programming Computation [Epub ahead of print]
12. Kalhor R. Tjong H. Jayathilaka N., et al. 2012. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat. Biotechnol. 30 90-98.
13. Karolchik D. Hinrichs A. and Kent W. 2009. The UCSC genome browser. Current Protocols in Bioinformatics 40 1.4.1-1.4.33.
14. Leung N. and Toh K. 2009. An SDP-based divide-and-conquer algorithm for large-scale noisy anchor-free graph realization. SIAM Journal on Scientific Computing 31 4351-4372.
15. Li G. Ruan X. Auerbach R.K. 2012. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148 84-98.
16. Lieberman-Aiden E. van Berkum N.L. Williams L., et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326 289-293.
17. Liu Y. Sun D. and Toh K. 2012. An implementable proximal point algorithmic framework for nuclear norm minimization. Mathematical Programming 133 399-436.
18. Miele A. and Dekker J. 2008. Long-range chromosomal interactions and gene regulation. Mol. BioSyst. 4 1046-1057.
19. Misteli T. 2004. Spatial positioning: A new dimension in genome function. Cell 119 153-156. (Pubitemid 39360898)
20. Misteli T., et al. 2007. Beyond the sequence: cellular organization of genome function. Cell 128 787-800. (Pubitemid 46273571)
21. Neal R. 1993. Probabilistic inference using Markov chain Monte Carlo methods. Technical Report CRG-TR-93-1.University of Toronto.
22. Rousseau M. Fraser J. Ferraiuolo M., et al. 2011. Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. BMC Bioinformatics 12 414.
23. Russel D. Lasker K. Webb B. 2012. Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol. 10 e1001244.
24. So A. and Ye Y. 2007. Theory of semidefinite programming for sensor network localization. Mathematical Programming 109 367-384. (Pubitemid 46197861)
25. Toh K. Todd M. and Tütüncü R. 1999. Sdpt3-matlab software package for semidefinite programming version 1.3. Optimization Methods and Software 11 545-581.
26. Wächter A. and Biegler L. 2006. On the implementation of an interior-point filter line-search algorithm for large-scale nonlinear programming. Mathematical Programming 106 25-57. (Pubitemid 41813168)
27. Weinberger K. and Saul L. 2004. Unsupervised learning of image manifolds by semidefinite programming. IEEE 2 pages II-988-II-995.
28. Yaffe E. and Tanay A. 2011. Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nature Genetics 43 1059-65.
29. Zhao Z. Tavoosidana G. Sjolinder M., et al. 2006. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra-and interchromosomal interactions. Nat. Genet. 38 1341-1347. (Pubitemid 44646299)