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Determining promoter location based on DNA structure first-principles calculations
J Ramon Goñi, Alberto Pérez, David Torrents, Modesto Orozco
Genome Biol. 2007; 8(12): R263. Published online 2007 December 11. doi: 10.1186/gb-2007-8-12-r263
PMCID:
PMC2246265
Abstract Full Text PDF–360K Supplementary Material

Is Cited by the Following 17 Articles in this Archive:

Impact of Methylation on the Physical Properties of DNA
Alberto Pérez, Chiara Lara Castellazzi, Federica Battistini, Kathryn Collinet, Oscar Flores, Ozgen Deniz, Maria Luz Ruiz, David Torrents, Ramon Eritja, Montserrat Soler-López, Modesto Orozco
Biophys J. 2012 May 2; 102(9): 2140–2148. doi: 10.1016/j.bpj.2012.03.056
PMCID:
PMC3341543
Free in PMC on 2013/05/02
ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites
Santi González, Bàrbara Montserrat-Sentís, Friman Sánchez, Montserrat Puiggròs, Enrique Blanco, Alex Ramirez, David Torrents
Bioinformatics. 2012 March 15; 28(6): 763–770. Published online 2012 January 16. doi: 10.1093/bioinformatics/bts024
PMCID:
PMC3307110
Abstract Full Text PDF–627K Supplementary Material
A comparison study on feature selection of DNA structural properties for promoter prediction
Yanglan Gan, Jihong Guan, Shuigeng Zhou
BMC Bioinformatics. 2012; 13: 4. Published online 2012 January 7. doi: 10.1186/1471-2105-13-4
PMCID:
PMC3280155
Abstract Full Text PDF–1.6M Supplementary Material
Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast
Özgen Deniz, Oscar Flores, Federica Battistini, Alberto Pérez, Montserrat Soler-López, Modesto Orozco
BMC Genomics. 2011; 12: 489. Published online 2011 October 7. doi: 10.1186/1471-2164-12-489
PMCID:
PMC3224377
Abstract Full Text PDF–937K Supplementary Material
Ensemble approach combining multiple methods improves human transcription start site prediction
David G Dineen, Markus Schröder, Desmond G Higgins, Pádraig Cunningham
BMC Genomics. 2010; 11: 677. Published online 2010 November 30. doi: 10.1186/1471-2164-11-677
PMCID:
PMC3053590
Abstract Full Text PDF–266K Supplementary Material
Toward a Consensus View of Duplex RNA Flexibility
Ignacio Faustino, Alberto Pérez, Modesto Orozco
Biophys J. 2010 September 22; 99(6): 1876–1885. doi: 10.1016/j.bpj.2010.06.061
PMCID:
PMC2941024
Abstract Full Text PDF–918K Supplementary Material
Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data
Ravi Gupta, Priyankara Wikramasinghe, Anirban Bhattacharyya, Francisco A Perez, Sharmistha Pal, Ramana V Davuluri
BMC Bioinformatics. 2010; 11(Suppl 1): S65. Published online 2010 January 18. doi: 10.1186/1471-2105-11-S1-S65
PMCID:
PMC3009539
Abstract Full Text PDF–904K
High DNA melting temperature predicts transcription start site location in human and mouse
David G. Dineen, Andreas Wilm, Pádraig Cunningham, Desmond G. Higgins
Nucleic Acids Res. 2009 December; 37(22): 7360–7367. Published online 2009 December. doi: 10.1093/nar/gkp821
PMCID:
PMC2794178
Abstract Full Text PDF–1.1M
Profile analysis and prediction of tissue-specific CpG island methylation classes
Christopher Previti, Oscar Harari, Igor Zwir, Coral del Val
BMC Bioinformatics. 2009; 10: 116. Published online 2009 April 21. doi: 10.1186/1471-2105-10-116
PMCID:
PMC2683815
Abstract Full Text PDF–861K Supplementary Material
A transcription factor affinity-based code for mammalian transcription initiation
Molly Megraw, Fernando Pereira, Shane T. Jensen, Uwe Ohler, Artemis G. Hatzigeorgiou
Genome Res. 2009 April; 19(4): 644–656. doi: 10.1101/gr.085449.108
PMCID:
PMC2665783
Abstract Full Text PDF–1.1M
RBF-TSS: Identification of Transcription Start Site in Human Using Radial Basis Functions Network and Oligonucleotide Positional Frequencies
Rami N. Mahdi, Eric C. Rouchka
PLoS ONE. 2009; 4(3): e4878. Published online 2009 March 16. doi: 10.1371/journal.pone.0004878
PMCID:
PMC2654504
Abstract Full Text PDF–229K
ContDist: a tool for the analysis of quantitative gene and promoter properties
Michael Hackenberg, Gorka Lasso, Rune Matthiesen
BMC Bioinformatics. 2009; 10: 7. Published online 2009 January 7. doi: 10.1186/1471-2105-10-7
PMCID:
PMC2631519
Abstract Full Text PDF–728K
DiProDB: a database for dinucleotide properties
Maik Friedel, Swetlana Nikolajewa, Jürgen Sühnel, Thomas Wilhelm
Nucleic Acids Res. 2009 January; 37(Database issue): D37–D40. Published online 2009 January. doi: 10.1093/nar/gkn597
PMCID:
PMC2686603
Abstract Full Text PDF–3.9M
Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum
Kevin Brick, Junichi Watanabe, Elisabetta Pizzi
Genome Biol. 2008; 9(12): R178. Published online 2008 December 18. doi: 10.1186/gb-2008-9-12-r178
PMCID:
PMC2646282
Abstract Full Text PDF–783K Supplementary Material
Genome and proteome annotation: organization, interpretation and integration
Gabrielle A. Reeves, David Talavera, Janet M. Thornton
J R Soc Interface. 2009 February 6; 6(31): 129–147. Published online 2008 November 11. doi: 10.1098/rsif.2008.0341
PMCID:
PMC2658791
Abstract Full Text PDF–570K
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles
Thomas Abeel, Yvan Saeys, Pierre Rouzé, Yves Van de Peer
Bioinformatics. 2008 July 1; 24(13): i24–i31. doi: 10.1093/bioinformatics/btn172
PMCID:
PMC2718650
Abstract Full Text PDF–259K
Towards a molecular dynamics consensus view of B-DNA flexibility
Alberto Pérez, Filip Lankas, F. Javier Luque, Modesto Orozco
Nucleic Acids Res. 2008 April; 36(7): 2379–2394. Published online 2008 April. doi: 10.1093/nar/gkn082
PMCID:
PMC2367714
Abstract Full Text PDF–1.8M
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