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Items: 10

1.

Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models.

Maaskola J, Rajewsky N.

Nucleic Acids Res. 2014 Dec 1;42(21):12995-3011. doi: 10.1093/nar/gku1083. Epub 2014 Nov 11.

2.

STEME: a robust, accurate motif finder for large data sets.

Reid JE, Wernisch L.

PLoS One. 2014 Mar 13;9(3):e90735. doi: 10.1371/journal.pone.0090735. eCollection 2014.

3.

The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option.

Wenger AM, Clarke SL, Notwell JH, Chung T, Tuteja G, Guturu H, Schaar BT, Bejerano G.

PLoS Genet. 2013 Aug;9(8):e1003728. doi: 10.1371/journal.pgen.1003728. Epub 2013 Aug 29.

4.

cWords - systematic microRNA regulatory motif discovery from mRNA expression data.

Rasmussen SH, Jacobsen A, Krogh A.

Silence. 2013 May 20;4(1):2. doi: 10.1186/1758-907X-4-2.

5.

TherMos: Estimating protein-DNA binding energies from in vivo binding profiles.

Sun W, Hu X, Lim MH, Ng CK, Choo SH, Castro DS, Drechsel D, Guillemot F, Kolatkar PR, Jauch R, Prabhakar S.

Nucleic Acids Res. 2013 Jun;41(11):5555-68. doi: 10.1093/nar/gkt250. Epub 2013 Apr 16.

6.

AMD, an automated motif discovery tool using stepwise refinement of gapped consensuses.

Shi J, Yang W, Chen M, Du Y, Zhang J, Wang K.

PLoS One. 2011;6(9):e24576. doi: 10.1371/journal.pone.0024576. Epub 2011 Sep 12.

7.

MotifClick: prediction of cis-regulatory binding sites via merging cliques.

Zhang S, Li S, Niu M, Pham PT, Su Z.

BMC Bioinformatics. 2011 Jun 16;12:238. doi: 10.1186/1471-2105-12-238.

8.

GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge.

Carvalho AM, Oliveira AL.

Algorithms Mol Biol. 2011 Apr 22;6:13. doi: 10.1186/1748-7188-6-13.

9.

NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes.

Salimullah M, Sakai M, Plessy C, Carninci P.

Cold Spring Harb Protoc. 2011 Jan 1;2011(1):pdb.prot5559. doi: 10.1101/pdb.prot5559. Erratum in: Cold Spring Harb Protoc. 2011 Feb;(2). doi: 10.1101/pdb.erratum2011_01. Mizuho, Sakai [corrected to Sakai, Mizuho].

10.

CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments.

Kuttippurathu L, Hsing M, Liu Y, Schmidt B, Maskell DL, Lee K, He A, Pu WT, Kong SW.

Bioinformatics. 2011 Mar 1;27(5):715-7. doi: 10.1093/bioinformatics/btq707. Epub 2010 Dec 23.

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