gene recognition papers (2003)

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2003

VB Bajic, SH Seah (2003), "Dragon Gene Start Finder: An advanced system for finding approximate locations of the start of gene transcriptional units", Genome Research, to appear.
VB Bajic, SH Seah (2003),
"Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes",
Nucleic Acids Research, 31(13):3560-3563.
[PDF] [supplement material from the authors: Dragon Gene Start Finder]
VB Bajic, SH Seah, A Chong, SPT Krishnan, JLY Koh, V Brusic (2003), "Computer model for recognition of functional transcription start sites in polymerase II promoters of vertebrates," Journal of Molecular Graphics & Modeling, 21(5):323-332.
[PDF]
Vladimir B Bajic, Sin Lam Tan, Allen Chong, Suisheng Tang, Anders Strom, Jan-Ake Gustafsson, Chin-Yo Lin, Edison T Liu (2003),
"Dragon ERE Finder ver.2: A tool for accurate detection and analysis of estrogen response elements in vertebrate genomes",
Nucleic Acids Research, 31(13):3605-3607.
[PDF] [supplement material from the authors: Dragon ERE Finder]
Y Barash, G Elidan, N Friedman, T Kaplan (2003), "Moldeing dependencies in protein-DNA binding sites", Proceedings of the Seventh International Conference on Research in Computational Molecular Biology , pp.28-37.
G Bejerano (2003), "A comparative analysis method for detecting binding sites in coding regions", Proceedings of the Seventh International Conference on Research in Computational Molecular Biology , pp.57-66.
Paul E Boardman, Stephen G Oliver, Simon J Hubbard (2003), "SiteSeer: visualisation and analysis of transcription factor binding sites in nucleotide sequences", Nucleic Acids Reseach, 31:3572-3575.
[supplement material from the authors: SiteSeer]
Joseph Bockhorst, Mark Craven, David Page, Jude Shavlik, Jeremy Glasner (2003), "A Bayesian network approach to operon prediction", Bioinformatics, 19:1227-1235.
Joseph Bockhorst, Yu Qiu, Jeremy Glasner, Mingzhu Liu, Frederick Blattner, Mark Craven (2003), "Predicting bacterial transcription units using sequence and expression data", Bioinformatics, 19:i34-i43.
Luca Cartegni, Jinhua Wang, Zhengwei Zhu, Michael Q Zhang, Adrian R Krainer (2003), "ESEfinder: a web resource to identify exonic splicing enhancers", Nucleic Acids Research, 31:3568-3571.
[supplement material from the authors: ESEfinder]
Simon Cawley, Lior Pachter, Marina Alexandersson (2003), "SLAM web server for comparative gene finding and alignment", Nucleic Acids Reseach, 31:3507-3509.
[supplement material from the authors: SLAM]
LL Chen, HY Ou, R Zhang, CT Zhang (2003), "ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes", Biochemical and Biophysical Research Communications, 307:382-388.
[ ZCURVE_CoV site ]
A Chong, G Zhang, VB Bajic (2003)
"FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes", Nucleic Acids Research, 31(13):3546-3553.
[PDF] [supplement material from the authors: FIE2]
Bert Coessens, Gert Thijs, Stein Aerts, Kathleen Marchal, Frank De Smet, Kristof Engelen, Patrick Glenisson, Yves Moreau, Janick Mathys, Bart De Moor (2003), "INCLUSive: a web portal and service registry for microarray and regulatory sequence analysis", Nucleic Acids Reseach, 31:3468-3470.
Yvonne JK Edwards, Tim J Carver, Tanya Vavouri, Martin Frith, Martin J Bishop, Greg Elgar (2003), "Theatre: a software tool for detailed comparative analysis and visualization of genomic sequence", Nucleic Acids Reseach, 31:3510-3517.
[supplement material from the authors: Theatre ]
Eli Eisenberg, Erez Y Levanon (2003), "Human housekeeping genes are compact", Trends in Genetics, 19:362-365.
F Enault, K Suhre, C Abergel, O Poirot, JM Claverie (2003), "Annotation of bacterial genomes using improved phylogenomic profiles", Bioinformatics, 19:i105-i107.
Domenec Farre, Roma Roset, Mario Huerta, Jose E Adsuara, Llorenc Rosello, M Mar Alba, Xavier Messeguer (2003), "Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN", Nucleic Acids Research, 31:3651-3653.
[supplement material from the authors: ALGGEN's homepage]
Sylvain Foissac, Philippe Bardou, Annick Moisan, Marie-Josee Cros, Thomas Schiex (2003), "EUGENE'HOM: a generic similarity-based gene finder using multiple homologous sequences", Nucleic Acids Research, 31:3742-3745.
FB Guo, HY Ou, CT Zhang (2003), "ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes", Nucleic Acids Research, 31:1780-1789.
[ webpage from the authors]
Anason S Halees, Dmitriy Leyfer, Zhiping Weng (2003), "PromoSer: a large-scale mammalian promoter and transcription start site identification service", Nucleic Acids Reseach, 31:3554-3559.
[supplement material from the authors: PromoSer]
AE Kel, E Gößling, I Reuter, E Cheremushkin, OV Kel-Margoulis, E Wingender (2003), "MATCHTM: a tool for searching transcription factor binding sites in DNA sequences", Nucleic Acids Research, 31:3576-3579.
[supplement material from the authors: MATCH]
B Krishnapuran, L Carin, AJ Hartemink (2003), "Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species", Proceedings of the Seventh International Conference on Research in Computational Molecular Biology , pp.157-166.
Thomas Schou Larsen1, Anders Krogh (2003), "EasyGene? a prokaryotic gene finder that ranks ORFs by statistical significance", BMC Bioinformatics, 4:21.
[html]
Bernett T K Lee, Tin Wee Tan, Shoba Ranganathan (2003), "MGAlignIt: a web service for the alignment of mRNA/EST and genomic sequences", Nucleic Acids Reseach, 31:3533-3536.
[supplement material from the authors: MGAlignIt]
Huiqing Liu, Limsoon Wong (2003), "Data mining tools for biological sequences", Journal of Bioinformatics and Computational Biology, 1(1):139-167.
PW Lord, RD Stevens, A Brass, CA Goble (2003), "Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation", Bioinformatics, 19:1275-1283.
William H Majoros, Mihaela Pertea, Corina Antonescu, Steven L Salzberg (2003), "GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders", Nucleic Acids Research, 31:3601-3604. [supplement material from the authors: gene finding programs at TIGR]
Anton Nekrutenko, Wen-Yu Chung, Wen-Hsiung Li (2003), "ETOPE: evolutionary test of predicted exons", Nucleic Acids Research, 31:3564-3567.
[supplement material from the authors: ETOPE]
Henrik Bjørn Nielsen, Rasmus Wernersson, Steen Knudsen (2003), "Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays", Nucleic Acids Reseach, 31:3491-3496.
Victor Olman, Dong Xu, Ying Xu (2003) "CUBIC: identification of regulatory binding sites through data clustering", Journal of Bioinformatics and Computational Biology, 1(1):21-40.
Crispin Roven, Harmen J Bussemaker (2003), "REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data", Nucleic Acids Research, 31:3487-3490.
[supplement material from the authors: REDUCE]
Thomas Schiex, Jerome Gouzy, Annick Moisan, Yannick de Oliveira (2003), "FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences", Nucleic Acids Research, 31:3738-3741.
Shannon D. Schlueter, Qunfeng Dong, Volker Brendel (2003), "GeneSeqer@PlantGDB: gene structure prediction in plant genomes", Nucleic Acids Research, 31:3597-3600. [supplement material from the authors: GeneSeqer@PlantGDB]
Sohrab P Shah, Graham P McVicker, Alan K Mackworth, Sanja Rogic, B F Francis Ouellette (2003), "GeneComber: combining outputs of gene prediction programs for improved results", Bioinformatics, 19:1296-1297.
Saurabh Sinha, Martin Tompa (2003), "YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation", Nucleic Acids Research, 31:3586-3588. [supplement material from the authors: YMF]
V Solovyev, I Shahmuradov (2003), "PromH: promoters identification using orthologous genomic sequences", Nucleic Acids Reseach, 31:3540-3545.
[supplement material from the authors: PromH]
Rotem Sorek, Gil Ast (2003), "Intronic sequences flanking alternatively spliced exons are conserved between human and mouse", Genome Research, 13:1631-1637.
Alona Sosinsky, Christopher P Bonin, Richard S Mann, Barry Honig (2003), "Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors", Nucleic Acids Research, 31:3589-3592. [supplement material from the authors: Target Explorer]
T A Thanaraj, Francis Clark, Juha Muilu (2003), "Conservation of human alternative splice events in mouse", Nucleic Acids Research, 31:2544-2552.
William Thompson, Eric C Rouchka, Charles E Lawrence (2003), "Gibbs Recursive Sampler: finding transcription factor binding sites", Nucleic Acids Research, 31:3580-3585.
Jacques van Helden (2003), "Regulatory Sequence Analysis Tools", Nucleic Acids Research, 31:3593-3596. [supplement material from the authors: regulatory sequence analysis tools (RSAT)]
Rasmus Wernersson, Anders Gorm Pedersen (2003), "RevTrans: multiple alignment of coding DNA from aligned amino acid sequences", Nucleic Acids Reseach, 31:3537-3539.
[supplement material from the authors: RevTrans]
G Yeo, CB Burge (2003), "Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals", Proceedings of the Seventh International Conference on Research in Computational Molecular Biology , pp. 322-331.
Edouard Yeramian, Louis Jones (2003), "GeneFizz: a web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives", Nucleic Acids Research, 31:3843-3849.
[supplement material from the authors: GeneFizz]