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Items: 1 to 20 of 87

1.

Finding Occurrences of Relevant Functional Elements in Genomic Signatures.

Jacox E, Elnitski L.

Int J Comput Sci. 2008 Oct 1;2(5):599-606.

2.

Word-based characterization of promoters involved in human DNA repair pathways.

Lichtenberg J, Jacox E, Welch JD, Kurz K, Liang X, Yang MQ, Drews F, Ecker K, Lee SS, Elnitski L, Welch LR.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S18. doi: 10.1186/1471-2164-10-S1-S18.

4.

A novel data mining method to identify assay-specific signatures in functional genomic studies.

Rollins DK, Zhai D, Joe AL, Guidarelli JW, Murarka A, Gonzalez R.

BMC Bioinformatics. 2006 Aug 14;7:377.

6.

Phylogeny based discovery of regulatory elements.

Gertz J, Fay JC, Cohen BA.

BMC Bioinformatics. 2006 May 22;7:266.

7.

MATLIGN: a motif clustering, comparison and matching tool.

Kankainen M, Löytynoja A.

BMC Bioinformatics. 2007 Jun 8;8:189.

8.

Using SCOPE to identify potential regulatory motifs in coregulated genes.

Martyanov V, Gross RH.

J Vis Exp. 2011 May 31;(51). pii: 2703. doi: 10.3791/2703.

9.

Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm.

Wolfertstetter F, Frech K, Herrmann G, Werner T.

Comput Appl Biosci. 1996 Feb;12(1):71-80.

PMID:
8670622
10.

Identification of Predictive Cis-Regulatory Elements Using a Discriminative Objective Function and a Dynamic Search Space.

Karnik R, Beer MA.

PLoS One. 2015 Oct 14;10(10):e0140557. doi: 10.1371/journal.pone.0140557. eCollection 2015.

11.

Bounded search for de novo identification of degenerate cis-regulatory elements.

Carlson JM, Chakravarty A, Khetani RS, Gross RH.

BMC Bioinformatics. 2006 May 15;7:254.

12.
13.

Prediction of nuclear proteins using nuclear translocation signals proposed by probabilistic latent semantic indexing.

Su EC, Chang JM, Cheng CW, Sung TY, Hsu WL.

BMC Bioinformatics. 2012;13 Suppl 17:S13. doi: 10.1186/1471-2105-13-S17-S13. Epub 2012 Dec 13.

14.

Binding matrix: a novel approach for binding site recognition.

Kim JT, Gewehr JE, Martinetz T.

J Bioinform Comput Biol. 2004 Jun;2(2):289-307.

PMID:
15297983
15.
17.

Context specific transcription factor prediction.

Yang E, Simcha D, Almon RR, Dubois DC, Jusko WJ, Androulakis IP.

Ann Biomed Eng. 2007 Jun;35(6):1053-67. Epub 2007 Mar 22.

18.

Flexible sequence similarity searching with the FASTA3 program package.

Pearson WR.

Methods Mol Biol. 2000;132:185-219.

PMID:
10547837
19.

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.

20.

Comprehensive DNA signature discovery and validation.

Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, Huq A, Colwell RR, Knight IT, Salzberg SL.

PLoS Comput Biol. 2007 May;3(5):e98. Epub 2007 Apr 20.

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