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Results: 1 to 20 of 77

1.

Discover regulatory DNA elements using chromatin signatures and artificial neural network.

Firpi HA, Ucar D, Tan K.

Bioinformatics. 2010 Jul 1;26(13):1579-86. doi: 10.1093/bioinformatics/btq248. Epub 2010 May 7.

PMID:
20453004
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Prediction of regulatory elements in mammalian genomes using chromatin signatures.

Won KJ, Chepelev I, Ren B, Wang W.

BMC Bioinformatics. 2008 Dec 18;9:547. doi: 10.1186/1471-2105-9-547.

PMID:
19094206
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Finding combinatorial histone code by semi-supervised biclustering.

Teng L, Tan K.

BMC Genomics. 2012 Jul 3;13:301. doi: 10.1186/1471-2164-13-301.

PMID:
22759587
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Chromatin signature discovery via histone modification profile alignments.

Wang J, Lunyak VV, Jordan IK.

Nucleic Acids Res. 2012 Nov;40(21):10642-56. doi: 10.1093/nar/gks848. Epub 2012 Sep 18.

PMID:
22989711
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.

Hon G, Ren B, Wang W.

PLoS Comput Biol. 2008 Oct;4(10):e1000201. doi: 10.1371/journal.pcbi.1000201. Epub 2008 Oct 17.

PMID:
18927605
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B.

Nat Genet. 2007 Mar;39(3):311-8. Epub 2007 Feb 4.

PMID:
17277777
[PubMed - indexed for MEDLINE]
7.

Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering.

Ucar D, Hu Q, Tan K.

Nucleic Acids Res. 2011 May;39(10):4063-75. doi: 10.1093/nar/gkr016. Epub 2011 Jan 25.

PMID:
21266477
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Discovery and annotation of functional chromatin signatures in the human genome.

Hon G, Wang W, Ren B.

PLoS Comput Biol. 2009 Nov;5(11):e1000566. doi: 10.1371/journal.pcbi.1000566. Epub 2009 Nov 13.

PMID:
19918365
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes.

Zhang Z, Zhang MQ.

BMC Bioinformatics. 2011 May 14;12:155. doi: 10.1186/1471-2105-12-155.

PMID:
21569556
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

An integrative approach to understanding the combinatorial histone code at functional elements.

Lai WK, Buck MJ.

Bioinformatics. 2013 Sep 15;29(18):2231-7. doi: 10.1093/bioinformatics/btt382. Epub 2013 Jul 2.

PMID:
23821650
[PubMed - indexed for MEDLINE]
Free Article
11.

Signal analysis for genome-wide maps of histone modifications measured by ChIP-seq.

Beck D, Brandl MB, Boelen L, Unnikrishnan A, Pimanda JE, Wong JW.

Bioinformatics. 2012 Apr 15;28(8):1062-9. doi: 10.1093/bioinformatics/bts085. Epub 2012 Feb 17.

PMID:
22345622
[PubMed - indexed for MEDLINE]
Free Article
12.

Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network.

Brusic V, Rudy G, Honeyman G, Hammer J, Harrison L.

Bioinformatics. 1998;14(2):121-30.

PMID:
9545443
[PubMed - indexed for MEDLINE]
Free Article
13.

Predicting functional regulatory polymorphisms.

Torkamani A, Schork NJ.

Bioinformatics. 2008 Aug 15;24(16):1787-92. doi: 10.1093/bioinformatics/btn311. Epub 2008 Jun 18.

PMID:
18562267
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Computational tools for the modern andrologist.

Niederberger C.

J Androl. 1996 Sep-Oct;17(5):462-6. Review.

PMID:
8957688
[PubMed - indexed for MEDLINE]
15.

Biological network mapping and source signal deduction.

Brynildsen MP, Wu TY, Jang SS, Liao JC.

Bioinformatics. 2007 Jul 15;23(14):1783-91. Epub 2007 May 11.

PMID:
17495996
[PubMed - indexed for MEDLINE]
Free Article
16.

GlobalMIT: learning globally optimal dynamic bayesian network with the mutual information test criterion.

Vinh NX, Chetty M, Coppel R, Wangikar PP.

Bioinformatics. 2011 Oct 1;27(19):2765-6. doi: 10.1093/bioinformatics/btr457. Epub 2011 Aug 3.

PMID:
21813478
[PubMed - indexed for MEDLINE]
Free Article
17.

Identifying novel constrained elements by exploiting biased substitution patterns.

Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X.

Bioinformatics. 2009 Jun 15;25(12):i54-62. doi: 10.1093/bioinformatics/btp190.

PMID:
19478016
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation.

Hu Z, Fu Y, Halees AS, Kielbasa SM, Weng Z.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W235-41.

PMID:
15215387
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities.

Sanguinetti G, Lawrence ND, Rattray M.

Bioinformatics. 2006 Nov 15;22(22):2775-81. Epub 2006 Sep 11.

PMID:
16966362
[PubMed - indexed for MEDLINE]
Free Article
20.

A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences.

Sreeskandarajan S, Flowers MM, Karro JE, Liang C.

Bioinformatics. 2014 Mar 15;30(6):887-8. doi: 10.1093/bioinformatics/btt651. Epub 2013 Nov 8.

PMID:
24215021
[PubMed - indexed for MEDLINE]

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