Spectral identification of topological domains

Bioinformatics

Volumn 32, Issue 14, 2016, Pages 2151-2158

  Chen, Jie ^a,b,c   Hero, Alfred O ^b   Rajapakse, Indika ^b,c  

^a NORTHWESTERN POLYTECHNICAL UNIVERSITY   (China)

^b UNIVERSITY OF MICHIGAN   (United States)

^c UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CHROMOSOME; COMPUTER LANGUAGE; GENETIC TRANSCRIPTION; THEORETICAL MODEL; ULTRASTRUCTURE;

ALGORITHMS; CHROMOSOMES; MODELS, THEORETICAL; PROGRAMMING LANGUAGES; TRANSCRIPTION, GENETIC;

EID: 84992417447     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw221     Document Type: Article

References (29)

1. Anscombe, F.J. (1948) The transformation of Poisson, binomial and negativebinomial data. Biometrika, 35, 246-254.
2. Anscombe, F.J. (1953) Contribution of discussion paper by H. Hotelling. New light on the correlation coefficient and its transforms. J. R. Stat. Soc. B, 15, 229-230.
3. Botta, M. et al. (2010) Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide. Mol. Syst. Biol., 6, 1-6.
4. Boulos, R.E. et al. (2013) Revealing long-range interconnected hubs in human chromatin interaction data using graph theory. Phys. Rev. Lett., 111, 118102.
5. Cavalli, G. and Misteli, T. (2013) Functional implications of genome topology. Nat. Struct. Mol. Biol., 20, 290-299.
6. Chen, H. et al. (2015a) Chromosome conformation of human fibroblasts grown in 3-dimensional spheroids. Nucleus, 6, 55-65.
7. Chen, H. et al. (2015b) Functional organization of the human 4D nucleome. Proc. Natl. Acad. Sci. (PNAS), 112, 8002-8007.
8. Chung, F.R. (1997) Spectral Graph Theory, vol. 91. American Mathematical Society.
9. Dixon, J.R. et al. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376-380.
10. Filippova, D. et al. (2014) Identification of alternative topological domains in chromatin. Algorithms Mol. Biol., 9, 1-11.
11. Gorkin, D.U. et al. (2014) The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell, 14, 762-775.
12. Hu, M. et al. (2012) HiCNorm: removing biases in Hi-C data via Poisson regression. Bioinformatics, 28, 3131-3133.
13. Kang, U. et al. (2011) Spectral analysis for billion-scale graphs: discoveries and implementation. In: Advances in Knowledge Discovery and Data Mining. Springer-Verlag Berlin Heidelberg, pp. 13-25.
14. Le Dily, F. et al. (2014) Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation. Genes Development, 28, 2151-2161.
15. Levy-Leduc, C. et al. (2014) Two-dimensional segmentation for analyzing Hi- C data. Bioinformatics, 30, i386-i392.
16. Lieberman-Aiden, E. et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326, 289-293.
17. Liu, L. et al. (2012) GeSICA: Genome segmentation from intra-chromosomal association. BMC Genomics, 13, 1-10.
18. Mesbahi, M. and Egerstedt, M. (2010) Graph Theoretic Methods in Multiagent Networks. Princeton University Press, Princeton, NJ.
19. Nora, E.P. et al. (2012) Spatial partitioning of the regulatory landscape of the x-inactivation centre. Nature, 485, 381-385.
20. Pope, B.D. et al. (2014) Topologically-associating domains are stable units of replication-timing regulation. Nature, 515, 402-405.
21. Rao, S.S.P. et al. (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell, 159, 1665-1680.
22. Saad, Y. (1992) Numerical Methods for Large Eigenvalue Problems. Manchester University Press, Manchester.
23. Schuettengruber, B. and Cavalli, G. (2013) Polycomb domain formation depends on short and long distance regulatory cues. PLoS One, 8, e56531.
24. Schwartz, Y.B. et al. (2012) Nature and function of insulator protein binding sites in the drosophila genome. Genome Res., 22, 2188-2198.
25. Sexton, T. et al. (2012) Three-dimensional folding and functional organization principles of the drosophila genome. Cell, 148, 458-472.
26. Shi, J. and Malik, J. (2000) Normalized cuts and image segmentation. IEEE Trans. Pattern Anal. Machine Intell., 22, 888-905.
27. Van Bortle, K. et al. (2012) Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains. Genome Res., 22, 2176-2187.
28. Van Bortle, K. et al. (2014) Insulator function and topological domain border strength scale with architectural protein occupancy. Genome Biol., 15, R82.
29. Ziebarth, J.D. et al. (2013) CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization. Nucleic Acids Res., 41, D188-D194.