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Results: 1 to 20 of 83

1.

ArchAlign: coordinate-free chromatin alignment reveals novel architectures.

Lai WK, Buck MJ.

Genome Biol. 2010;11(12):R126. doi: 10.1186/gb-2010-11-12-r126. Epub 2010 Dec 23.

PMID:
21182771
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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
3.

Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae.

Morris RT, O'Connor TR, Wyrick JJ.

Bioinformatics. 2010 Jan 15;26(2):168-74. doi: 10.1093/bioinformatics/btp657. Epub 2009 Dec 2.

PMID:
19959498
[PubMed - indexed for MEDLINE]
Free Article
4.

ChromatinDB: a database of genome-wide histone modification patterns for Saccharomyces cerevisiae.

O'Connor TR, Wyrick JJ.

Bioinformatics. 2007 Jul 15;23(14):1828-30. Epub 2007 May 7.

PMID:
17485428
[PubMed - indexed for MEDLINE]
Free Article
5.

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

Siddharthan R, Siggia ED, van Nimwegen E.

PLoS Comput Biol. 2005 Dec;1(7):e67. Epub 2005 Dec 9.

PMID:
16477324
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

High-resolution mapping and characterization of open chromatin across the genome.

Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE.

Cell. 2008 Jan 25;132(2):311-22. doi: 10.1016/j.cell.2007.12.014.

PMID:
18243105
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.

Liu XS, Brutlag DL, Liu JS.

Nat Biotechnol. 2002 Aug;20(8):835-9. Epub 2002 Jul 8.

PMID:
12101404
[PubMed - indexed for MEDLINE]
8.

CATCHprofiles: clustering and alignment tool for ChIP profiles.

Nielsen FG, Markus KG, Friborg RM, Favrholdt LM, Stunnenberg HG, Huynen M.

PLoS One. 2012;7(1):e28272. doi: 10.1371/journal.pone.0028272. Epub 2012 Jan 4.

PMID:
22238575
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

High-resolution, genome-wide mapping of chromatin modifications by GMAT.

Roh TY, Zhao K.

Methods Mol Biol. 2008;387:95-108.

PMID:
18287625
[PubMed - indexed for MEDLINE]
10.

Podbat: a novel genomic tool reveals Swr1-independent H2A.Z incorporation at gene coding sequences through epigenetic meta-analysis.

Sadeghi L, Bonilla C, Strålfors A, Ekwall K, Svensson JP.

PLoS Comput Biol. 2011 Aug;7(8):e1002163. doi: 10.1371/journal.pcbi.1002163. Epub 2011 Aug 25.

PMID:
21901086
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Regulatory motif finding by logic regression.

Keles S, van der Laan MJ, Vulpe C.

Bioinformatics. 2004 Nov 1;20(16):2799-811. Epub 2004 May 27.

PMID:
15166027
[PubMed - indexed for MEDLINE]
Free Article
12.

ChIPseqR: analysis of ChIP-seq experiments.

Humburg P, Helliwell CA, Bulger D, Stone G.

BMC Bioinformatics. 2011 Jan 31;12:39. doi: 10.1186/1471-2105-12-39.

PMID:
21281468
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.

Wang JP, Fondufe-Mittendorf Y, Xi L, Tsai GF, Segal E, Widom J.

PLoS Comput Biol. 2008 Sep 12;4(9):e1000175. doi: 10.1371/journal.pcbi.1000175.

PMID:
18787693
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq.

Zhang Y, Shin H, Song JS, Lei Y, Liu XS.

BMC Genomics. 2008 Nov 13;9:537. doi: 10.1186/1471-2164-9-537.

PMID:
19014516
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
16.

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains.

Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K.

Genome Res. 2009 Jan;19(1):24-32. doi: 10.1101/gr.082800.108. Epub 2008 Dec 3.

PMID:
19056695
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

Genome Inform. 2005;16(1):83-94.

PMID:
16362910
[PubMed - indexed for MEDLINE]
18.

ArchTEx: accurate extraction and visualization of next-generation sequence data.

Lai WK, Bard JE, Buck MJ.

Bioinformatics. 2012 Apr 1;28(7):1021-3. doi: 10.1093/bioinformatics/bts063. Epub 2012 Feb 2.

PMID:
22302569
[PubMed - indexed for MEDLINE]
Free Article
19.

Compound cis-regulatory elements with both boundary and enhancer sequences in the human genome.

Jjingo D, Wang J, Conley AB, Lunyak VV, Jordan IK.

Bioinformatics. 2013 Dec 15;29(24):3109-12. doi: 10.1093/bioinformatics/btt542. Epub 2013 Oct 1.

PMID:
24085569
[PubMed - indexed for MEDLINE]
20.

Toward almost closed genomes with GapFiller.

Boetzer M, Pirovano W.

Genome Biol. 2012 Jun 25;13(6):R56. doi: 10.1186/gb-2012-13-6-r56.

PMID:
22731987
[PubMed - indexed for MEDLINE]
Free PMC Article

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