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Items: 1 to 20 of 121

1.

Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs.

Majoros WH, Ohler U.

PLoS Comput Biol. 2010 Dec 16;6(12):e1001037. doi: 10.1371/journal.pcbi.1001037.

2.

MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules.

Sinha S, He X.

PLoS Comput Biol. 2007 Nov;3(11):e216. Epub 2007 Sep 24.

3.

Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

He X, Ling X, Sinha S.

PLoS Comput Biol. 2009 Mar;5(3):e1000299. doi: 10.1371/journal.pcbi.1000299. Epub 2009 Mar 13.

4.
5.

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.

6.

Simulations of enhancer evolution provide mechanistic insights into gene regulation.

Duque T, Samee MA, Kazemian M, Pham HN, Brodsky MH, Sinha S.

Mol Biol Evol. 2014 Jan;31(1):184-200. doi: 10.1093/molbev/mst170. Epub 2013 Oct 4.

7.

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.

8.

Incorporating evolution of transcription factor binding sites into annotated alignments.

Bais AS, Grossmann S, Vingron M.

J Biosci. 2007 Aug;32(5):841-50.

9.

Pair hidden Markov models on tree structures.

Sakakibara Y.

Bioinformatics. 2003;19 Suppl 1:i232-40.

PMID:
12855464
10.

Phylogeny based discovery of regulatory elements.

Gertz J, Fay JC, Cohen BA.

BMC Bioinformatics. 2006 May 22;7:266.

11.

Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models.

Wong WS, Nielsen R.

Bioinformatics. 2007 Aug 15;23(16):2031-7. Epub 2007 Jun 5.

PMID:
17550911
12.

Large-scale turnover of functional transcription factor binding sites in Drosophila.

Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB.

PLoS Comput Biol. 2006 Oct;2(10):e130. Epub 2006 Aug 21.

13.

Enhancing the quality of phylogenetic analysis using fuzzy hidden Markov model alignments.

Collyda C, Diplaris S, Mitkas P, Maglaveras N, Pappas C.

Stud Health Technol Inform. 2007;129(Pt 2):1245-9.

PMID:
17911914
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16.

Vestige: maximum likelihood phylogenetic footprinting.

Wakefield MJ, Maxwell P, Huttley GA.

BMC Bioinformatics. 2005 May 29;6:130.

17.

Parametric alignment of Drosophila genomes.

Dewey CN, Huggins PM, Woods K, Sturmfels B, Pachter L.

PLoS Comput Biol. 2006 Jun 23;2(6):e73. Epub 2006 Jun 23.

18.

Mulan: multiple-sequence local alignment and visualization for studying function and evolution.

Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W.

Genome Res. 2005 Jan;15(1):184-94. Epub 2004 Dec 8.

19.

SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model.

Alexandersson M, Cawley S, Pachter L.

Genome Res. 2003 Mar;13(3):496-502.

20.

Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish.

Hiller M, Agarwal S, Notwell JH, Parikh R, Guturu H, Wenger AM, Bejerano G.

Nucleic Acids Res. 2013 Aug;41(15):e151. doi: 10.1093/nar/gkt557. Epub 2013 Jun 27.

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