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Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment
Vladimir B Bajic, Michael R Brent, Randall H Brown, Adam Frankish, Jennifer Harrow, Uwe Ohler, Victor V Solovyev, Sin Lam Tan
Genome Biol. 2006; 7(Suppl 1): S3. Published online 2006 August 7. doi: 10.1186/gb-2006-7-s1-s3
PMCID:
PMC1810552
Abstract Full Text PDF–918K Supplementary Material
 Is Cited by the Following 16 Articles in this Archive:
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
High Sensitivity TSS Prediction: Estimates of Locations Where TSS Cannot Occur
Ulf Schaefer, Rimantas Kodzius, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Vladimir B. Bajic
PLoS One. 2010; 5(11): e13934. Published online 2010 November 15. doi: 10.1371/journal.pone.0013934
PMCID:
PMC2981523
Abstract Full Text PDF–381K Supplementary Material
Polymorphism in the flanking regions of the PbGP43 gene from the human pathogen Paracoccidioides brasiliensis: search for protein binding sequences and poly(A) cleavage sites
Antonio A Rocha, Flávia V Morais, Rosana Puccia
BMC Microbiol. 2009; 9: 277. Published online 2009 December 30. doi: 10.1186/1471-2180-9-277
PMCID:
PMC2809070
Abstract Full Text PDF–480K
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
Identifying regulatory elements in eukaryotic genomes
Leelavati Narlikar, Ivan Ovcharenko
Brief Funct Genomic Proteomic. 2009 July; 8(4): 215–230. Published online 2009 June 4. doi: 10.1093/bfgp/elp014
PMCID:
PMC2764519
Abstract Full Text PDF–177K
Toward a gold standard for promoter prediction evaluation
Thomas Abeel, Yves Van de Peer, Yvan Saeys
Bioinformatics. 2009 June 15; 25(12): i313–i320. Published online 2009 May 27. doi: 10.1093/bioinformatics/btp191
PMCID:
PMC2687945
Abstract Full Text PDF–315K
Integrating sequence, evolution and functional genomics in regulatory genomics
Martin Vingron, Alvis Brazma, Richard Coulson, Jacques van Helden, Thomas Manke, Kimmo Palin, Olivier Sand, Esko Ukkonen
Genome Biol. 2009; 10(1): 202. Published online 2009 January 30. doi: 10.1186/gb-2009-10-1-202
PMCID:
PMC2687781
Abstract Full Text PDF–822K
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
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
Profiling the Thermodynamic Softness of Adenoviral Promoters
Chu H. Choi, Zoi Rapti, Vladimir Gelev, Michele R. Hacker, Boian Alexandrov, Evelyn J. Park, Jae Suk Park, Nobuo Horikoshi, Augusto Smerzi, Kim Ø. Rasmussen, Alan R. Bishop, Anny Usheva
Biophys J. 2008 July 15; 95(2): 597–608. Published online 2008 April 4. doi: 10.1529/biophysj.107.123471
PMCID:
PMC2440440
Abstract Full Text PDF–172K
Accurate splice site prediction using support vector machines
Sören Sonnenburg, Gabriele Schweikert, Petra Philips, Jonas Behr, Gunnar Rätsch
BMC Bioinformatics. 2007; 8(Suppl 10): S7. Published online 2007 December 21. doi: 10.1186/1471-2105-8-S10-S7
PMCID:
PMC2230508
Abstract Full Text PDF–4.2M
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
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
The ENCODE Project Consortium
Nature. Author manuscript; available in PMC 2008 January 24.
Published in final edited form as: Nature. 2007 June 14; 447(7146): 799–816.
PMCID:
PMC2212820
Abstract Full Text PDF–2.0M Supplementary Material
The Human Genomic Melting Map
Fang Liu, Eivind Tøstesen, Jostein K Sundet, Tor-Kristian Jenssen, Christoph Bock, Geir Ivar Jerstad, William G Thilly, Eivind Hovig
PLoS Comput Biol. 2007 May; 3(5): e93. Prepublished online 2007 April 11. Published online 2007 May 18. doi: 10.1371/journal.pcbi.0030093
PMCID:
PMC1868775
Abstract Full Text PDF–532K
Boosting with stumps for predicting transcription start sites
Xiaoyue Zhao, Zhenyu Xuan, Michael Q Zhang
Genome Biol. 2007; 8(2): R17. Published online 2007 February 2. doi: 10.1186/gb-2007-8-2-r17
PMCID:
PMC1852414
Abstract Full Text PDF–380K Supplementary Material
EGASP: the human ENCODE Genome Annotation Assessment Project
Roderic Guigó, Paul Flicek, Josep F Abril, Alexandre Reymond, Julien Lagarde, France Denoeud, Stylianos Antonarakis, Michael Ashburner, Vladimir B Bajic, Ewan Birney, Robert Castelo, Eduardo Eyras, Catherine Ucla, Thomas R Gingeras, Jennifer Harrow, Tim Hubbard, Suzanna E Lewis, Martin G Reese
Genome Biol. 2006; 7(Suppl 1): S2. Published online 2006 August 7. doi: 10.1186/gb-2006-7-s1-s2
PMCID:
PMC1810551
Abstract Full Text PDF–2.1M
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