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Results: 1 to 20 of 99

1.

DNA motif elucidation using belief propagation.

Wong KC, Chan TM, Peng C, Li Y, Zhang Z.

Nucleic Acids Res. 2013 Sep;41(16):e153. doi: 10.1093/nar/gkt574. Epub 2013 Jun 29.

PMID:
23814189
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions.

Agius P, Arvey A, Chang W, Noble WS, Leslie C.

PLoS Comput Biol. 2010 Sep 9;6(9). pii: e1000916. doi: 10.1371/journal.pcbi.1000916.

PMID:
20838582
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors.

Chen X, Hughes TR, Morris Q.

Bioinformatics. 2007 Jul 1;23(13):i72-9.

PMID:
17646348
[PubMed - indexed for MEDLINE]
Free Article
4.

A fast weak motif-finding algorithm based on community detection in graphs.

Jia C, Carson MB, Yu J.

BMC Bioinformatics. 2013 Jul 17;14:227. doi: 10.1186/1471-2105-14-227.

PMID:
23865838
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions.

Newburger DE, Bulyk ML.

Nucleic Acids Res. 2009 Jan;37(Database issue):D77-82. doi: 10.1093/nar/gkn660. Epub 2008 Oct 8.

PMID:
18842628
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Inferring direct DNA binding from ChIP-seq.

Bailey TL, Machanick P.

Nucleic Acids Res. 2012 Sep 1;40(17):e128. Epub 2012 May 18.

PMID:
22610855
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Identification of context-dependent motifs by contrasting ChIP binding data.

Mason MJ, Plath K, Zhou Q.

Bioinformatics. 2010 Nov 15;26(22):2826-32. doi: 10.1093/bioinformatics/btq546. Epub 2010 Sep 23.

PMID:
20870645
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Assessment of algorithms for inferring positional weight matrix motifs of transcription factor binding sites using protein binding microarray data.

Orenstein Y, Linhart C, Shamir R.

PLoS One. 2012;7(9):e46145. doi: 10.1371/journal.pone.0046145. Epub 2012 Sep 28.

PMID:
23029415
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.

Zambelli F, Pesole G, Pavesi G.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W535-43. doi: 10.1093/nar/gkt448. Epub 2013 Jun 7.

PMID:
23748563
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif.

Drawid A, Gupta N, Nagaraj VH, Gélinas C, Sengupta AM.

BMC Bioinformatics. 2009 Jul 7;10:208. doi: 10.1186/1471-2105-10-208.

PMID:
19583839
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs.

Seitzer P, Wilbanks EG, Larsen DJ, Facciotti MT.

BMC Bioinformatics. 2012 Nov 27;13:317. doi: 10.1186/1471-2105-13-317.

PMID:
23181585
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

A general approach for discriminative de novo motif discovery from high-throughput data.

Grau J, Posch S, Grosse I, Keilwagen J.

Nucleic Acids Res. 2013 Nov;41(21):e197. doi: 10.1093/nar/gkt831. Epub 2013 Sep 20.

PMID:
24057214
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

Jothi R, Cuddapah S, Barski A, Cui K, Zhao K.

Nucleic Acids Res. 2008 Sep;36(16):5221-31. doi: 10.1093/nar/gkn488. Epub 2008 Aug 6.

PMID:
18684996
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Motif finding in DNA sequences based on skipping nonconserved positions in background Markov chains.

Zhao X, Sze SH.

J Comput Biol. 2011 May;18(5):759-70. doi: 10.1089/cmb.2010.0197.

PMID:
21554019
[PubMed - indexed for MEDLINE]
15.

A transdimensional Bayesian model for pattern recognition in DNA sequences.

Li SM, Wakefield J, Self S.

Biostatistics. 2008 Oct;9(4):668-85. doi: 10.1093/biostatistics/kxm058. Epub 2008 Mar 18.

PMID:
18349034
[PubMed - indexed for MEDLINE]
Free Article
16.

MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis.

Klepper K, Drabløs F.

BMC Bioinformatics. 2013 Jan 16;14:9. doi: 10.1186/1471-2105-14-9.

PMID:
23323883
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data.

Xing H, Mo Y, Liao W, Zhang MQ.

PLoS Comput Biol. 2012;8(7):e1002613. doi: 10.1371/journal.pcbi.1002613. Epub 2012 Jul 26.

PMID:
22844240
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences.

Li W, Meyer CA, Liu XS.

Bioinformatics. 2005 Jun;21 Suppl 1:i274-82.

PMID:
15961467
[PubMed - indexed for MEDLINE]
Free Article
19.

A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information.

Ma X, Kulkarni A, Zhang Z, Xuan Z, Serfling R, Zhang MQ.

Nucleic Acids Res. 2012 Apr;40(7):e50. doi: 10.1093/nar/gkr1135. Epub 2012 Jan 6.

PMID:
22228832
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites.

Naughton BT, Fratkin E, Batzoglou S, Brutlag DL.

Nucleic Acids Res. 2006;34(20):5730-9. Epub 2006 Oct 13.

PMID:
17041233
[PubMed - indexed for MEDLINE]
Free PMC Article

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