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Items: 1 to 20 of 94

1.

A motif-based framework for recognizing sequence families.

Sharan R, Myers EW.

Bioinformatics. 2005 Jun;21 Suppl 1:i387-93.

2.

RASE: recognition of alternatively spliced exons in C.elegans.

Rätsch G, Sonnenburg S, Schölkopf B.

Bioinformatics. 2005 Jun;21 Suppl 1:i369-77.

3.

MUSA: a parameter free algorithm for the identification of biologically significant motifs.

Mendes ND, Casimiro AC, Santos PM, Sá-Correia I, Oliveira AL, Freitas AT.

Bioinformatics. 2006 Dec 15;22(24):2996-3002. Epub 2006 Oct 26.

4.

Fast model-based protein homology detection without alignment.

Hochreiter S, Heusel M, Obermayer K.

Bioinformatics. 2007 Jul 15;23(14):1728-36. Epub 2007 May 8.

5.

Detection of generic spaced motifs using submotif pattern mining.

Wijaya E, Rajaraman K, Yiu SM, Sung WK.

Bioinformatics. 2007 Jun 15;23(12):1476-85. Epub 2007 May 5.

7.

Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure.

Lewis DP, Jebara T, Noble WS.

Bioinformatics. 2006 Nov 15;22(22):2753-60. Epub 2006 Sep 11.

8.

Finding motifs from all sequences with and without binding sites.

Leung HC, Chin FY.

Bioinformatics. 2006 Sep 15;22(18):2217-23. Epub 2006 Jul 26.

9.

RSIR: regularized sliced inverse regression for motif discovery.

Zhong W, Zeng P, Ma P, Liu JS, Zhu Y.

Bioinformatics. 2005 Nov 15;21(22):4169-75. Epub 2005 Sep 15.

10.

Prediction of cis-regulatory elements: from high-information content analysis to motif identification.

Li G, Lu J, Olman V, Xu Y.

J Bioinform Comput Biol. 2007 Aug;5(4):817-38.

PMID:
17787058
11.

Combining sequence and time series expression data to learn transcriptional modules.

Kundaje A, Middendorf M, Gao F, Wiggins C, Leslie C.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Jul-Sep;2(3):194-202.

PMID:
17044183
12.

Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes.

Brahmachary M, Schönbach C, Yang L, Huang E, Tan SL, Chowdhary R, Krishnan SP, Lin CY, Hume DA, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bajic VB.

BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S8.

13.

A generic motif discovery algorithm for sequential data.

Jensen KL, Styczynski MP, Rigoutsos I, Stephanopoulos GN.

Bioinformatics. 2006 Jan 1;22(1):21-8. Epub 2005 Oct 27.

14.

Adaptive multi-agent architecture for functional sequence motifs recognition.

Zeng J, Alhajj R, Demetrick D.

Bioinformatics. 2009 Dec 1;25(23):3084-92. doi: 10.1093/bioinformatics/btp567. Epub 2009 Oct 6.

15.

Promoter classifier: software package for promoter database analysis.

Gershenzon NI, Ioshikhes IP.

Appl Bioinformatics. 2005;4(3):205-9.

PMID:
16231962
16.

Establishing glucose- and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a Relevance Vector Machine.

Li Y, Lee KK, Walsh S, Smith C, Hadingham S, Sorefan K, Cawley G, Bevan MW.

Genome Res. 2006 Mar;16(3):414-27. Epub 2006 Jan 19.

17.

Transcription factor binding site identification using the self-organizing map.

Mahony S, Hendrix D, Golden A, Smith TJ, Rokhsar DS.

Bioinformatics. 2005 May 1;21(9):1807-14. Epub 2005 Jan 12.

18.
19.

Identifying promoter features of co-regulated genes with similar network motifs.

Harari O, del Val C, Romero-Zaliz R, Shin D, Huang H, Groisman EA, Zwir I.

BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S1. doi: 10.1186/1471-2105-10-S4-S1.

20.

Fast and practical algorithms for planted (l, d) motif search.

Davila J, Balla S, Rajasekaran S.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec;4(4):544-52.

PMID:
17975266
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