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Items: 1 to 20 of 97

1.

Quantifying the similarity of topological domains across normal and cancer human cell types.

Sauerwald N, Kingsford C.

Bioinformatics. 2018 Jul 1;34(13):i475-i483. doi: 10.1093/bioinformatics/bty265.

2.

Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes.

Zhan Y, Mariani L, Barozzi I, Schulz EG, Blüthgen N, Stadler M, Tiana G, Giorgetti L.

Genome Res. 2017 Mar;27(3):479-490. doi: 10.1101/gr.212803.116. Epub 2017 Jan 5.

3.

Modelling genome-wide topological associating domains in mouse embryonic stem cells.

Zhan Y, Giorgetti L, Tiana G.

Chromosome Res. 2017 Mar;25(1):5-14. doi: 10.1007/s10577-016-9544-6. Epub 2017 Jan 20.

4.

Identification of copy number variations and translocations in cancer cells from Hi-C data.

Chakraborty A, Ay F.

Bioinformatics. 2017 Oct 18. doi: 10.1093/bioinformatics/btx664. [Epub ahead of print]

PMID:
29048467
5.

Comparison of computational methods for the identification of topologically associating domains.

Zufferey M, Tavernari D, Oricchio E, Ciriello G.

Genome Biol. 2018 Dec 10;19(1):217. doi: 10.1186/s13059-018-1596-9.

6.

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.

Yan KK, Lou S, Gerstein M.

PLoS Comput Biol. 2017 Jul 24;13(7):e1005647. doi: 10.1371/journal.pcbi.1005647. eCollection 2017 Jul.

7.

ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data.

Oluwadare O, Cheng J.

BMC Bioinformatics. 2017 Nov 14;18(1):480. doi: 10.1186/s12859-017-1931-2.

8.

MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps.

Ye Y, Gao L, Zhang S.

Nucleic Acids Res. 2019 Apr 3. pii: gkz201. doi: 10.1093/nar/gkz201. [Epub ahead of print]

PMID:
30941409
9.

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus.

Smith EM, Lajoie BR, Jain G, Dekker J.

Am J Hum Genet. 2016 Jan 7;98(1):185-201. doi: 10.1016/j.ajhg.2015.12.002.

10.

Structural heterogeneity and functional diversity of topologically associating domains in mammalian genomes.

Wang XT, Dong PF, Zhang HY, Peng C.

Nucleic Acids Res. 2015 Sep 3;43(15):7237-46. doi: 10.1093/nar/gkv684. Epub 2015 Jul 6.

11.

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains.

Ulianov SV, Khrameeva EE, Gavrilov AA, Flyamer IM, Kos P, Mikhaleva EA, Penin AA, Logacheva MD, Imakaev MV, Chertovich A, Gelfand MS, Shevelyov YY, Razin SV.

Genome Res. 2016 Jan;26(1):70-84. doi: 10.1101/gr.196006.115. Epub 2015 Oct 30.

12.

Identification of hierarchical chromatin domains.

Weinreb C, Raphael BJ.

Bioinformatics. 2016 Jun 1;32(11):1601-9. doi: 10.1093/bioinformatics/btv485. Epub 2015 Aug 26.

13.

Evolutionary stability of topologically associating domains is associated with conserved gene regulation.

Krefting J, Andrade-Navarro MA, Ibn-Salem J.

BMC Biol. 2018 Aug 7;16(1):87. doi: 10.1186/s12915-018-0556-x.

14.

Reconstructing high-resolution chromosome three-dimensional structures by Hi-C complex networks.

Liu T, Wang Z.

BMC Bioinformatics. 2018 Dec 28;19(Suppl 17):496. doi: 10.1186/s12859-018-2464-z.

15.

4D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilities.

Seaman L, Rajapakse I.

Bioinformatics. 2018 Jan 1;34(1):104-106. doi: 10.1093/bioinformatics/btx484.

PMID:
28961756
16.

GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs.

Ursu O, Boley N, Taranova M, Wang YXR, Yardimci GG, Stafford Noble W, Kundaje A.

Bioinformatics. 2018 Aug 15;34(16):2701-2707. doi: 10.1093/bioinformatics/bty164.

PMID:
29554289
17.

Rich Chromatin Structure Prediction from Hi-C Data.

Malik L, Patro R.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Jun 28. doi: 10.1109/TCBB.2018.2851200. [Epub ahead of print]

PMID:
29994683
18.

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation.

Le Dily F, Baù D, Pohl A, Vicent GP, Serra F, Soronellas D, Castellano G, Wright RH, Ballare C, Filion G, Marti-Renom MA, Beato M.

Genes Dev. 2014 Oct 1;28(19):2151-62. doi: 10.1101/gad.241422.114.

19.

Topologically associating domains are stable units of replication-timing regulation.

Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM.

Nature. 2014 Nov 20;515(7527):402-5. doi: 10.1038/nature13986.

20.

HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.

Yan KK, Yardimci GG, Yan C, Noble WS, Gerstein M.

Bioinformatics. 2017 Jul 15;33(14):2199-2201. doi: 10.1093/bioinformatics/btx152.

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