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Items: 1 to 20 of 78

1.

Similarity-Based Segmentation of Multi-Dimensional Signals.

Machné R, Murray DB, Stadler PF.

Sci Rep. 2017 Sep 27;7(1):12355. doi: 10.1038/s41598-017-12401-8.

2.

Emerging roles of chromatin in the maintenance of genome organization and function in plants.

Vergara Z, Gutierrez C.

Genome Biol. 2017 May 23;18(1):96. doi: 10.1186/s13059-017-1236-9. Review.

3.

A computational approach for the functional classification of the epigenome.

Gandolfi F, Tramontano A.

Epigenetics Chromatin. 2017 May 15;10:26. doi: 10.1186/s13072-017-0131-7. eCollection 2017.

4.
5.

Identification of recurrent combinatorial patterns of chromatin modifications at promoters across various tissue types.

Meng N, Machiraju R, Huang K.

BMC Bioinformatics. 2016 Dec 23;17(Suppl 17):534. doi: 10.1186/s12859-016-1346-5.

6.

Dynamic epigenetic mode analysis using spatial temporal clustering.

Gan Y, Tao H, Zou G, Yan C, Guan J.

BMC Bioinformatics. 2016 Dec 23;17(Suppl 17):537. doi: 10.1186/s12859-016-1331-z.

7.

ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining.

Park SH, Lee SM, Kim YJ, Kim S.

BMC Bioinformatics. 2016 Dec 13;17(Suppl 16):452. doi: 10.1186/s12859-016-1307-z.

8.

Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer.

Bernhart SH, Kretzmer H, Holdt LM, Jühling F, Ammerpohl O, Bergmann AK, Northoff BH, Doose G, Siebert R, Stadler PF, Hoffmann S.

Sci Rep. 2016 Nov 23;6:37393. doi: 10.1038/srep37393.

9.

Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity.

Ooi WF, Xing M, Xu C, Yao X, Ramlee MK, Lim MC, Cao F, Lim K, Babu D, Poon LF, Lin Suling J, Qamra A, Irwanto A, Qu Zhengzhong J, Nandi T, Lee-Lim AP, Chan YS, Tay ST, Lee MH, Davies JO, Wong WK, Soo KC, Chan WH, Ong HS, Chow P, Wong CY, Rha SY, Liu J, Hillmer AM, Hughes JR, Rozen S, Teh BT, Fullwood MJ, Li S, Tan P.

Nat Commun. 2016 Sep 28;7:12983. doi: 10.1038/ncomms12983.

10.

ChAsE: chromatin analysis and exploration tool.

Younesy H, Nielsen CB, Lorincz MC, Jones SJ, Karimi MM, Möller T.

Bioinformatics. 2016 Nov 1;32(21):3324-3326. Epub 2016 Jul 4.

PMID:
27378294
11.

CHANGE POINT ANALYSIS OF HISTONE MODIFICATIONS REVEALS EPIGENETIC BLOCKS LINKING TO PHYSICAL DOMAINS.

Chen M, Lin H, Zhao H.

Ann Appl Stat. 2016 Mar;10(1):506-526. Epub 2016 Mar 25.

12.

Constructing 3D interaction maps from 1D epigenomes.

Zhu Y, Chen Z, Zhang K, Wang M, Medovoy D, Whitaker JW, Ding B, Li N, Zheng L, Wang W.

Nat Commun. 2016 Mar 10;7:10812. doi: 10.1038/ncomms10812.

13.

Progress and challenges in bioinformatics approaches for enhancer identification.

Kleftogiannis D, Kalnis P, Bajic VB.

Brief Bioinform. 2016 Nov;17(6):967-979. Epub 2015 Dec 3.

14.
15.

Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome.

Mammana A, Chung HR.

Genome Biol. 2015 Jul 24;16:151. doi: 10.1186/s13059-015-0708-z.

16.

Uncovering correlated variability in epigenomic datasets using the Karhunen-Loeve transform.

Madrigal P, Krajewski P.

BioData Min. 2015 Jul 1;8:20. doi: 10.1186/s13040-015-0051-7. eCollection 2015.

17.

DELTA: A Distal Enhancer Locating Tool Based on AdaBoost Algorithm and Shape Features of Chromatin Modifications.

Lu Y, Qu W, Shan G, Zhang C.

PLoS One. 2015 Jun 19;10(6):e0130622. doi: 10.1371/journal.pone.0130622. eCollection 2015.

18.

ClusTrack: feature extraction and similarity measures for clustering of genome-wide data sets.

Rydbeck H, Sandve GK, Ferkingstad E, Simovski B, Rye M, Hovig E.

PLoS One. 2015 Apr 16;10(4):e0123261. doi: 10.1371/journal.pone.0123261. eCollection 2015.

19.

hiHMM: Bayesian non-parametric joint inference of chromatin state maps.

Sohn KA, Ho JW, Djordjevic D, Jeong HH, Park PJ, Kim JH.

Bioinformatics. 2015 Jul 1;31(13):2066-74. doi: 10.1093/bioinformatics/btv117. Epub 2015 Feb 27.

20.

Computational schemes for the prediction and annotation of enhancers from epigenomic assays.

Whitaker JW, Nguyen TT, Zhu Y, Wildberg A, Wang W.

Methods. 2015 Jan 15;72:86-94. doi: 10.1016/j.ymeth.2014.10.008. Epub 2014 Oct 15. Review.

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