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A stitch in time: efficient computation of genomic DNA melting bubbles.

Tøstesen E.

Algorithms Mol Biol. 2008 Jul 17;3:10.PMID: 18637171 [PubMed]Related articlesFree article

Speed-up of DNA melting algorithm with complete nearest neighbor properties.

Tøstesen E, Liu F, Jenssen TK, Hovig E.

Biopolymers. 2003 Oct;70(3):364-76.PMID: 14579309 [PubMed - indexed for MEDLINE]Related articles

Partly melted DNA conformations obtained with a probability peak finding method.

Tøstesen E.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Jun;71(6 Pt 1):061922. Epub 2005 Jun 28.PMID: 16089780 [PubMed - indexed for MEDLINE]Related articles

Bubble nucleation and cooperativity in DNA melting.

Zeng Y, Montrichok A, Zocchi G.

J Mol Biol. 2004 May 21;339(1):67-75.PMID: 15123421 [PubMed - indexed for MEDLINE]Related articles

Melting of persistent double-stranded polymers.

Rahi SJ, Hertzberg MP, Kardar M.

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Faster exact Markovian probability functions for motif occurrences: a DFA-only approach.

Ribeca P, Raineri E.

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Length and statistical weight of bubbles in DNA melting.

Zeng Y, Montrichok A, Zocchi G.

Phys Rev Lett. 2003 Oct 3;91(14):148101. Epub 2003 Sep 30.PMID: 14611557 [PubMed - indexed for MEDLINE]Related articles

An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast.

Taneda A.

BMC Bioinformatics. 2008 Dec 5;9:521.PMID: 19061486 [PubMed - indexed for MEDLINE]Related articlesFree article

Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks.

Ispolatov I, Maslov S.

BMC Bioinformatics. 2008 Oct 8;9:424.PMID: 18842147 [PubMed - indexed for MEDLINE]Related articlesFree article

Time-dependent ARMA modeling of genomic sequences.

Zielinski JS, Bouaynaya N, Schonfeld D, O'Neill W.

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Computing paths and cycles in biological interaction graphs.

Klamt S, von Kamp A.

BMC Bioinformatics. 2009 Jun 15;10:181.PMID: 19527491 [PubMed - indexed for MEDLINE]Related articlesFree article

A transcription factor affinity-based code for mammalian transcription initiation.

Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG.

Genome Res. 2009 Apr;19(4):644-56. Epub 2009 Jan 13.PMID: 19141595 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolution of energy in flow driven by rising bubbles.

Mazzitelli IM, Lohse D.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Jun;79(6 Pt 2):066317. Epub 2009 Jun 30.PMID: 19658604 [PubMed]Related articles

Bubble velocity, diameter, and void fraction measurements in a multiphase flow using fiber optic reflectometer.

Lim HJ, Chang KA, Su CB, Chen CY.

Rev Sci Instrum. 2008 Dec;79(12):125105.PMID: 19123590 [PubMed]Related articles

Faster computation of exact RNA shape probabilities.

Janssen S, Giegerich R.

Bioinformatics. 2010 Mar 1;26(5):632-9. Epub 2010 Jan 14.PMID: 20080511 [PubMed - in process]Related articlesFree article

The efficient computation of the cumulative distribution and probability density functions in the diffusion model.

Tuerlinckx F.

Behav Res Methods Instrum Comput. 2004 Nov;36(4):702-16.PMID: 15641417 [PubMed - indexed for MEDLINE]Related articles

Variational upper and lower bounds for probabilistic graphical models.

Wexler Y, Geiger D.

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Efficient and accurate P-value computation for Position Weight Matrices.

Touzet H, Varré JS.

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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.

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A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery.

Xie L, Xie L, Bourne PE.

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