gene recognition papers (2003)

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2003

promoter/TF

Stein Aerts, Peter Van Loo, Gert Thijs, Yves Moreau, Bart De Moor (2003), "Computational detection of cis -regulatory modules", Bioinformatics, 19:ii5-ii14.
Gautam Aggarwal, EA Worthey, Paul D McDonagh, Peter J Myler (2003), "Importing statistical measures into Artemis enhances gene identification in the Leishmania genome project", BMC Bioinformatics, 4:23.
[html]
similarity

Marina Alexandersson, Simon Cawley, Lior Pachter (2003), "SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model", Genome Research, 13(3):496-502.
[ abstract]
annotation

JL Ashurst, JE Collins (2003), "Gene annotation: prediction and testing", Annual Review of Genomics and Human Genetics, 4:69-88.
[ abstract]
promoter/TF

Timothy L Baile, William Stafford Noble (2003), "Searching for statistically significant regulatory modules", Bioinformatics, 19:ii16-ii25.
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, 13:1923-1929.
[PDF]
promoter/TF

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: http://sdmc.lit.org.sg/promoter/dragonGSF1_0/genestart.htm (Dragon Gene Start Finder)]
promoter/TF

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: http://sdmc.lit.org.sg/ERE-V2/index (Dragon ERE Finder)]
promoter/TF

N Banerjee, MQ Zhang (2003), "Identification of cooperativity among transcription factors controlling cell cycle in yeast", Nucleic Acids Research, 31:7024-7031.
promoter/TF

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.
promoter/TF

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.
promoter/TF

M Blanchette, M Tompa (2003), "FootPrinter: A program designed for phylogenetic footprinting", Nucleic Acids Research, 31(13):3840-3842.
Philippe Blayo, Pierre Rouze, Marie-France Sagot (2003), "Orphan gene finding: an exon asembly approach", Theoretical Computer Science, 290(3):1407-1431.
Robert J Blick, Andrew T Revel, Eric J Hansen (2003), "FindGDPs: identification of primers for labeling microbial transcriptomes for DNA microarray analysis", Bioinformatics, 19:1718-1719.
promoter/TF

Paul E Boardman, Stephen G Oliver, Simon J Hubbard (2003), "SiteSeer: visualisation and analysis of transcription factor binding sites in nucleotide sequences", Nucleic Acids Research, 31:3572-3575.
[supplement material: http://rocky.bms.umist.ac.uk/SiteSeer/ (SiteSeer)]
Joseph Bockhorst, Mark Craven, David Page, Jude Shavlik, Jeremy Glasner (2003), "A Bayesian network approach to operon prediction", Bioinformatics, 19:1227-1235.
expression

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.
S Bocs, S Cruveiller, D Vallenet, G Nuel, C Medigue (2003), "AMIGene: Annotation of MIcrobial Genes", Nucleic Acids Research, 31(13):3723-3736.
alternative-splicing

Paola Bonizzoni, Graziano Pesole, Raffaella Rizzi (2003), "A method to detect gene structure and alternative splice sites by agreeing ESTs to a genomic sequence", in G Benson, R Page, ed. Algorithms and Bioinformatics: 3rd International Workshop (WABI), Lecture Notes in Bioinformatics, volume 2812. pp. 63-77 (Springer).
[ abstract ]
Brona Brejova, Daniel G. Brown, Tomas Vinar (2003), "Optimal DNA signal recognition models with a fixed amount of intrasignal dependency", In G Benson, R Page, ed., Algorithms and Bioinformatics: 3rd International Workshop (WABI), Lecture Notes in Bioinformatics, volume 2812. pp. 78-94 (Springer).
[ abstract]
translation

Chris M Brown, Grant Jacobs, Peter Stockwell, Mark Schreiber (2003), "Detection of signals in mRNAs that influence translation", Applied Bioinformatics, 2(3 suppl):S47-S51.
[abstract]
annotation

Vladimir Brusic, Rekha S. Pillai, Diego G. Silva, Nikolai Petrovsky, RIKEN GER Group, GSL Members, Christian Schönbach (2003), "Cytokine-related genes identified From the RIKEN full-length mouse cDNA data set", Genome Research, 13(6b):1307-1317.
[ abstract]
A Carbone, A Zinovyev, F Kepes (2003), "Codon adaptation index as a measure of dominating codon bias", Bioinformatics, 19(16):2005-2015.
annotation

Piero Carninci, Kazunori Waki, Toshiyuki Shiraki, Hideaki Konno, Kazuhiro Shibata, Masayoshi Itoh, Katsunori Aizawa, Takahiro Arakawa, Yoshiyuki Ishii, Daisuke Sasaki, Hidemasa Bono, Shinji Kondo, Yuichi Sugahara, Rintaro Saito, Naoki Osato, Shiro Fukuda, Kenjiro Sato, Akira Watahiki, Tomoko Hirozane-Kishikawa, Mari Nakamura, Yuko Shibata, Ayako Yasunishi, Noriko Kikuchi, Atsushi Yoshiki, Moriaki Kusakabe, Stefano Gustincich, Kirk Beisel, William Pavan, Vassilis Aidinis, Akira Nakagawara, William A. Held, Hiroo Iwata, Tomohiro Kono, Hiromitsu Nakauchi, Paul Lyons, Christine Wells, David A. Hume, Michela Fagiolini, Takao K. Hensch, Michelle Brinkmeier, Sally Camper, Junji Hirota, Peter Mombaerts, Masami Muramatsu, Yasushi Okazaki, Jun Kawai, Yoshihide Hayashizaki (2003), "Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia", Genome Research, 13(6b):1273-1289.
[ abstract]
splicing

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: http://exon.cshl.edu/ESE/ (ESEfinder)]
promoter/TF

M Caselle, F Di Cunto, P Provero (2003), "A computational approach to regulatory element discovery in eukaryotes", arXiv preprint, cond-mat/0305279.
[abstract]
similarity

Simon Cawley, Lior Pachter, Marina Alexandersson (2003), "SLAM web server for comparative gene finding and alignment", Nucleic Acids Research, 31:3507-3509.
[supplement material: http://baboon.math.berkeley.edu/~syntenic/slam.html (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.
[ http://tubic.tju.edu.cn/sars/ (ZCURVE_CoV) ]
expression

Derek Y Chiang, Alan M Moses, Manolis Kellis, Eric S Lander, Michael B Eisen (2003), "Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeast", Genome Biology, 4:R43.
[html]
translation

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: http://sdmc.lit.org.sg/FIE2.0/ (FIE2)
annotation

Trees-Juen Chuang, Wen-Chang Lin, Hurng-Chun Lee, Chi-Wei Wang, Keh-Lin Hsiao, Zi-Hao Wang, Danny Shieh, Simon C. Lin, Lan-Yang Ch'ang (2003), "A complexity reduction algorithm for analysis and annotation of large genomic sequences", Genome Research, 13(2):313-322.
[ abstract]
A Clare, RD King (2003), "Predicting gene function in Saccharomyces cerevisiae", Bioinformatics, 19:ii42-ii49.
annotation

Melody S. Clark, Yvonne J.K. Edwards, Dan Peterson, Sandra W. Clifton, Amanda J. Thompson, Masahide Sasaki, Yutaka Suzuki, Kiyoshi Kikuchi, Shugo Watabe, Koichi Kawakami, Sumio Sugano, Greg Elgar, Stephen L. Johnson (003), "Fugu ESTs: new resources for transcription analysis and genome annotation", Genome Research, 13:2747-2753.
[abstract]
JM Claverie, Cedric Notredame (2003), Bioinformatics for Dummies (John Wiley & Sons).
expression

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 Research, 31:3468-3470.
annotation

John E. Collins, Melanie E. Goward, Charlotte G. Cole, Luc J. Smink, Elizabeth J. Huckle, Sarah Knowles, Jacqueline M. Bye, David M. Beare, Ian Dunham (2003), "Reevaluating human gene annotation: a second-generation analysis of chromosome 22", Genome Research, 13(1):27-36.
[ abstract] [PDF]
similarity

Lesley J Collins, Anthony M Poole, David Penny (2003), "Using ancestral sequences to uncover potential gene homologues", Applied Bioinformatics, 2(3 suppl):S85-S95.
[ abstract]
expression

Erin M Conlon, X Shirley Liu, Jason D Lieb, Jun S Liu (2003), "Integrating regulatory motif discovery and genome-wide expression analysis", Proceedings of National Academy of Sciences, 100(6):3339-3344.
S Cruveiller, K Jabbari, O Clay, G Bernardi (2003), "Compositional features of eukaryotic genomes for checking predicted genes", Briefing in Bioinformatics, 4(1):31-42.
promoter/TF

LV Danilova, VA Lyubetsky, MS Gelfand (2003), "An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation", In Silico Biology, 3:0004.
promoter/TF

Ramana V Davuluri, Hao Sun, Saranyan K Palaniswamy, Nicole Matthews, Carlos Molina, Mike Kurtz, Erich Grotewold (2003), "AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors", BMC Bioinformatics, 4:25.
[html]
RV Davuluri, MQ Zhang (2003), "Computer software to find genes in plant genomic DNA", in Plant Functional Genomics: Methods and Protocols (Humana Press), pp.87-108.
Anabelle Decottignies, Isabel Sanchez-Perez, Paul Nurse (2003), "Schizosaccharomyces pombe essential genes: a pilot study", Genome Research, 13(3):399-406.
[ abstract]
annotation

Glynn Dennis Jr., Brad T Sherman, Douglas A Hosack, Jun Yang, Wei Gao, H Clifford Lane, Richard A Lempicki (2003), "DAVID: database for annotation, visualization, and integrated discovery", Genome Biology, 4:3.
promoter/TF

C Dieterich, R Herwig, M Vingron (2003), "Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites", Bioinformatics, 19:ii50-ii56.
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 Research, 31:3510-3517.
[supplement material: http://www.hgmp.mrc.ac.uk/Registered/Webapp/theatre/ (Theatre)]
Eli Eisenberg, Erez Y Levanon (2003), "Human housekeeping genes are compact", Trends in Genetics, 19:362-365.
promoter/TF

Laura Elnitski, Ross C. Hardison, Jia Li, Shan Yang, Diana Kolbe, Pallavi Eswara, Michael J. O'Connor, Scott Schwartz, Webb Miller, Francesca Chiaromonte (2003), "Distinguishing regulatory DNA from neutral sites", Genome Research, 13(1):64-72.
[ abstract]
annotation

F Enault, K Suhre, C Abergel, O Poirot, JM Claverie (2003), "Annotation of bacterial genomes using improved phylogenomic profiles", Bioinformatics, 19:i105-i107.
promoter/TF

E Eskin, U Keich, MS Gelfand, PA Pevzner (2003), "Genome-wide analysis of bacterial promoter regions", Pacific Symposium on Biocomputing, 8:29-40.
promoter/TF

Laurence M Ettwiller, Johan Rung, Ewan Birne (2003), "Discovering novel cis-regulatory motifs using functional networks", Genome Research, 13(5):883-895.
[ abstract]
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: http://www.lsi.upc.es/~alggen ]
similarity

Paul Flicek, Evan Keibler, Ping Hu, Ian Korf, Michael R. Brent (2003), "Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map", Genome Research, 13(1):46-54.
[ abstract]
similarity

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.
[abstract]
annotation

Masaaki Furuno, Takeya Kasukawa, Rintaro Saito, Jun Adachi, Harukazu Suzuki, Richard Baldarelli, Yoshihide Hayashizaki, Yasushi Okazaki (2003), "CDS annotation in full-length cDNA sequence", Genome Research, 13(6b):1478-1487.
[ abstract]
promoter/TF

Sashidhar Gadiraju, Carrie A Vyhlidal, J Steven Leeder, Peter K Rogan (2003), "Genome-wide prediction, display and refinement of binding sites with information theory-based models", BMC Bioinformatics, 4:38.
[html]
S Ghosh, A Roy, S Adhya, A Nandy (2003), "Identification of new genes in human chromosome 3 contig 7 by graphical representation technique", Current Science, 84(12):1534-1543.
AN Gorban, AY Zinovyev, TG Popova (2003), "Seven clusters in genomic triplet distributions", In Silico Biology, 3(4):471-82.
[supplement material: http://www.ihes.fr/~zinovyev/7clusters]
promoter/TF

Leo Gordon, Alexey Ya Chervonenkis, Alex J Gammerman, Ilham A Shahmuradov, Victor V Solovyev (2003), "Sequence alignment kernel for recognition of promoter regions", Bioinformatics, 19:1964-1971.
similarity

R Guigo, ET Dermitzakis, P Agarwal, CP Ponting, G Parra, A Reymond, JF Abril, E Keibler, R Lyle, C Ucla, SE Antonarakis, MR Brent (2003), "Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes." Proceedings of National Academy of Sciences, 100(3):1140-1145.
R Guigo, T Wiehe (2003), "Gene prediction accuracy in large DNA sequences" in Frontiers in Computational Genomics , eds. MY Galperin, EV Koonin (Caister Academic Press), pp. ?-?.
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.
[supplement material: http://tubic.tju.edu.cn/Zcurve_B/]
promoter/TF

Anason S Halees, Dmitriy Leyfer, Zhiping Weng (2003), "PromoSer: a large-scale mammalian promoter and transcription start site identification service", Nucleic Acids Research, 31:3554-3559.
[supplement material: http://biowulf.bu.edu/zlab/PromoSer/ (PromoSer)]
splicing

Loi Sy Ho, Jagath C. Rajapakse (2003), "Splice site detection with a higher-order markov model implemented on a neural network", Genome Informatics, 14:64-72.
Yair Horesh, Amihood Amir, Shulamit Michaeli, Ron Unger (2003), "A rapid method for detection of putative RNAi target genes in genomic data", Bioinformatics, 19:ii73-ii80.
annotation

Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas V, Liakopoulos T, Palaios G, Pasquier C, Hamodrakas S, Tamames J, Yagnik AT, Tramontano A, Devos D, Blaschke C, Valencia A, Brett D, Martin D, Leroy C, Rigoutsos I, Sander C, Ouzounis CA (2003), "Evaluation of annotation strategies using an entire genome sequence", Bioinformatics, 19(6):717-726.
alternative-splicing

JM Johnson, J Castle, P Garrett-Engele, Z Kan, PM Loerch, CD Armour, R Santos, EE Schadt, R Stoughton, DD Shoemaker (2003), "Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays", Science, 302(5653):2141-2144.
promoter/TF

AE Kel, E Gossling, I Reuter, E Cheremushkin, OV Kel-Margoulis, E Wingender (2003), "MATCH: a tool for searching transcription factor binding sites in DNA sequences", Nucleic Acids Research, 31:3576-3579.
[supplement material: http://www.gene-regulation.com/pub/programs.html (MATCH)]
promoter/TF

Olga V Kel-Margoulis, Dmitri Tchekmenev, Alexander E Kel, Ellen Goessling, Klaus Hornischer, Birgit Lewicki-Potapov, Edgar Wingender (2003), "Composition-sensitive analysis of the human genome for regulatory signals", In Silico Biology, 3:0013.
Marco M. Kessler, Qiandong Zeng, Sarah Hogan, Robin Cook, Arturo J. Morales, Guillaume Cottarel (2003), "Systematic discovery of new genes in the Saccharomyces cerevisiae genome", Genome Research, 13(2):264-271.
[ abstract]
Oliver D. King, Rebecca E. Foulger, Selina S. Dwight, James V. White, Frederick P. Roth (2003), "Predicting gene function from patterns of annotation", Genome Research, 13(5):896-904.
[ abstract]
Daniel Kotlar, Yizhar Lavner (2003), "Gene prediction by spectral rotation measure: a new method for identifying protein-coding regions", Genome Research, 13:1930-1937.
[abstract]
promoter/TF

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.
alternative-splicing

EV Kriventseva, I Koch, R Apweiler, M Vingron, P Bork, MS Gelfand, S Sunyaev (2003), "Increase of functional diversity by alternative splicing", Trends in Genetics, 19(3):124-128.
Eric C Lai, Pavel Tomancak, Robert W Williams, Gerald M Rubin (2003), "Computational identification of Drosophila microRNA genes", Genome Biology, 4:R42.
[html]
Thomas Schou Larsen1, Anders Krogh (2003), "EasyGene? a prokaryotic gene finder that ranks ORFs by statistical significance", BMC Bioinformatics, 4:21.
[html]
Rob Lavigne, Wei Dong Sun, Guido Volckaert (2003), "STORM towards protein function: systematic tailored ORF-data retrieval and management", Applied Bioinformatics, 2(3):177-179.
[abstract]
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 Research, 31:3533-3536.
[supplement material: http://origin.bic.nus.edu.sg/mgalign/mgalignit.html (MGAlignIt)]
alternative-splicing

C Lee, L Atanelov, B Modrek, Y Xing (2003), "ASAP: the alternative splicing annotation project", Nucleic Acids Research, 31:101-105.
alternative-splicing

C Lee, K Irizarry (2003), "Alternative splicing in the nervous system: an emerging source of diversity and regulation", Biological Psychiatry, 54(8):771-776.
[ abstract]
Martin J. Lercher, Thomas Blumenthal, Laurence D Hurst (2003), "Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes", Genome Research, 13(2):238-243.
[ abstract]
promoter/TF

Victor G Levitsky, Alexey V Katokhin (2003), "Recognition of eukaryotic promoters using a genetic algorithm based on iterative discriminant analysis", In Silico Biology, 3:0008.
C Li, PA He, J Wang (2003), "Artificial neural network method for predicting protein coding genes in the yeast genome", Internet Electronic Journal of Molecular Design, 2:527-538.
[abstract]
promoter/TF

Alexander P. Lifanov, Vsevolod J. Makeev, Anna G. Nazina, Dmitri A Papatsenko (2003), "Homotypic regulatory clusters in Drosophila", Genome Research, 13(4):579-588.
[ abstract]
M Linial (2003), "How incorrect annotations evolve - the case of short ORFs", Trends in Biotechnology, 21(7):298-300.
[ abstract]
LP Lim, NC Lau, EG Weinstein, A Abdelhakim, S Yekta, MW Rhoades, CB Burge, DP Bartel (2003), "The microRNAs of Caenorhabditis elegans", Genes & Development, 17(8):991-1008.
[ abstract]
similarity

Angelica Lindlöf (2003), "Gene identification through large-scale EST sequence processing", Applied Bioinformatics, 2(3):123-129.
[abstract]
annotation

Huiqing Liu, Limsoon Wong (2003), "Data mining tools for biological sequences", Journal of Bioinformatics and Computational Biology, 1(1):139-167.
[ abstract]
Rongxiang Liu, Richard C McEachin, David J States (2003), "Computationally identifying novel NF-B-regulated immune genes in the human genome ", Genome Research, 13(4):654-661.
[ abstract]
expression

Christopher R Lockwood, Timothy M Frayling (2003), "Combining genome and mouse knockout expression data to highlight binding sites for the transcription factor HNF1alpha", In Silico Biology, 3:0006.
alternative-splicing

Ann E. Loraine, Gregg A. Helt, Melissa S. Cline and Michael A. Siani-Rose (2003), "Exploring alternative transcript structure in the human genome using BLOCKS and InterPro", Journal of Bioinformatics and Computational Biology, 1(2):289-306.
[ abstract]
annotation

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.
LF Luo, H Li, LR Zhang (2003), "ORF organization and gene recognition in the yeast genome", Comparative and Functional Genomics, 4(3):318-328.
expression

Andreas Magusin (2003), "Complementary techniques of clustering and composite pattern analysis to Saccharomyces cerevisiae gene expression", Applied Bioinformatics, 2(3 suppl):S37-S46.
[abstract]
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.
[abstract] [supplement material: http://www.tigr.org/software/#gfa ]
promoter/TF

VJ Makeev, AP Lifanov, AG Nazina, DA Papatsenko (2003), "Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information", Nucleic Acids Research, 31:6016-6026.
promoter/TF

Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E (2003), "TRANSFAC: transcriptional regulation, from patterns to profiles", Nucleic Acids Research, 31(1):374-378.
alternative-splicing

Barmak Modrek, Christopher Lee (2003), "Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss", Nature Genetics, 34:177-180.
Michael M Mwangi, Eric D Siggia (2003), "Genome wide identification of regulatory motifs in Bacillus subtilis", BMC Bioinformatics, 4:18.
[html]
promoter/TF

Chandrasegaran Narasimhan, Philip LoCascio, Edward Uberbacher (2003), "Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection", Bioinformatics, 19:1952-1963.
promoter/TF

A Nazina, D Papatsenko (2003), "Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency", BMC Bioinformatics, 4:65-78.
Anton Nekrutenko, Wen-Yu Chung, Wen-Hsiung Li (2003), "ETOPE: evolutionary test of predicted exons", Nucleic Acids Research, 31:3564-3567.
[supplement material: http://nekrut.uchicago.edu/etope/ (ETOPE)]
MA Nobrega, I Ovcharenko, V Afzal, EM Rubin (2003), "Scanning human gene deserts for long-range enhancers", Science, 302(5644):413.
Koji Numata, Akio Kanai, Rintaro Saito, Shinji Kondo, Jun Adachi, Laurens G. Wilming, David A. Hume, RIKEN GER Group, GSL Members, Yoshihide Hayashizaki, and Masaru Tomita (2003), "Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection", Genome Research, 13(6b):1301-1306.
[ abstract]
alternative-splicing

RN Nurtdinov, II Artamonova, AA Mironov, MS Gelfand (2003), "Low conservation of alternative splicing patterns in the human and mouse genomes", Human Molecular Genetics, 12(11):1313-1320.
[supplement material: http://www.ig-msk.ru:8005/HMG_paper/ ]
annotation

Yasushi Okazaki, David A. Hume (2003), "A guide to the mammalian genome" (commentary), Genome Research, 13(6b):1267-1272.
[ abstract]
promoter/TF

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.
[ abstract]
promoter/TF

Ivan Ovcharenko, Gabriela G Loots (2003), "Finding the needle in the haystack: computational strategies for discovering regulatory sequences in genomes", Current Genomics, 4(7):557-568.
splicing

RA Padgett, CB Burge (2003), "Splice Sites", In Nature Encyclopedia of the Human Genome (Nature Press), ed. David N Cooper, pp.?-?.
similarity

G Parra, P Agarwal, JF Abril, T Wiehe, JW Fickett, R Guigo (2003), "Comparative gene prediction in human and mouse", Genome Research, 13(1):108-117.
[ abstract]
expression

Erin D Pleasance, Marco A Marra, Steven JM Jones (2003), "Assessment of SAGE in transcript identification", Genome Research, 13(6a):1203-1215.
[ abstract]
alternative-splicing

Heike Pospisil, Alexander Herrmann, Harald Pankow, Jens G Reich (2003), "A database on alternative splice forms on the Integrated Genetic Map Service (IGMS)", In Silico Biology, 3:0020.
[supplement material: http://www.bioinf.mdc-berlin.de/igms/ (integrated genetic map service)]
expression

Jiang Qian, Jimmy Lin, Nicholas M Luscombe, Haiyuan Yu, Mark Gerstein (2003), "Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data", Bioinformatics, 19:1917-1926.
Zhaohui S Qin, Lee Ann McCue, William Thompson, Linda Mayerhofer, Charles E Lawrence, Jun S Liu (2003), "Identification of co-regulated genes through Baysian clustering of predicted regulatory binding sites", Nature Biotechnology, 21:435-439.
promoter/TF

Sven Rahmann (2003), "Dynamic programming algorithms for two statistical problems in computational biology", In G Benson, R Page, ed., Algorithms and Bioinformatics: 3rd International Workshop (WABI), Lecture Notes in Bioinformatics, volume 2812. pp. 151-164 (Springer).
[ abstract]
annotation

Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M (2003), "The transcriptional activity of human Chromosome 22", Genes & Development, 17(4):529-540.
promoter/TF

S Rombauts, K Florquin, M Lescot, K Marchal, P Rouze, Y Van de Peer (2003), "Computational approaches to identify promoters and cis-regulatory elements in plant genomes", Plant Physiology, 132(3):1162-1176.
[abstract]
expression

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: http://lognormal.bio.columbia.edu/reduce/ (REDUCE)]
Yvan Saeys, Sven Degroeve, Dirk Aeyels, Yves Van de Peer, Pierre Rouze (2003), "Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction", Bioinformatics, 19:ii179-ii188.
Ryuichi Sakate, Naoki Osada, Munetomo Hida, Sumio Sugano, Ikuo Hayasaka, Naoko Shimohira, Shinsuke Yanagi, Yumiko Suto, Katsuyuki Hashimoto, and Momoki Hirai (2003), "Analysis of 5'-End sequences of chimpanzee cDNAs", Genome Research, 13(5):1022-1026.
[ abstract]
promoter/TF

Simona Santini, Jeffrey L. Boore, and Axel Meyer (2003), "Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters", Genome Research, 13(6a):1111-1122.
[ abstract]
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: http://www.plantgdb.org/cgi-bin/PlantGDB/GeneSeqer/PlantGDBgs.cgi (GeneSeqer@PlantGDB)]
expression

NH Shah, DC King, PN Shah, NV Fedoroff (2003), "A tool-kit for cDNA microarray and promoter analysis", Bioinformatics, 19:1846-1848.
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: http://bio.cs.washington.edu/software.html (YMF)]
promoter/TF

V Solovyev, I Shahmuradov (2003), "PromH: promoters identification using orthologous genomic sequences", Nucleic Acids Research, 31:3540-3545.
[supplement material: http://www.softberry.com/berry.phtml?topic=promh (PromH)]
alternative-splicing

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: http://trantor.bioc.columbia.edu/Target_Explorer/ (Target Explorer)]
Mario Stanke, Stephan Waack (2003), "Gene prediction with a hidden Markov model and a new intron submodel", Bioinformatics, 19:ii215-ii225.
promoter/TF

Elena D Stavrovskaya, Andrey A Mironov (2003), "Two genetic algorithms for identification of regulatory signals", In Silico Biology, 3:0005.
similarity

Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, Michael Brudno, Serafim Batzoglou, Burkhard Morgenstern (2003), "AGenDA: homology-based gene prediction", Bioinformatics, 19:1575-1577.
T Tatarinova, V Brover, M Troukhan, N Alexandrov (2003), "Skew in CG content near the transcription start site in Arabidopsis thaliana", Bioinformatics, 19(Suppl 1):i313-i314.
Maike Tech, Rainer Merkl (2003), "YACOP: Enhanced gene prediction obtained by a combination of existing methods", In Silico Biology, 3:37.
alternative-splicing

T A Thanaraj, Francis Clark, Juha Muilu (2003), "Conservation of human alternative splice events in mouse", Nucleic Acids Research, 31:2544-2552.
promoter/TF

William Thompson, Eric C Rouchka, Charles E Lawrence (2003), "Gibbs Recursive Sampler: finding transcription factor binding sites", Nucleic Acids Research, 31:3580-3585.
promoter/TF

Nathan D. Trinklein, Shelley J. Force Aldred, Alok J. Saldanha, Richard M. Myers (2003), "Identification and functional analysis of human transcriptional promoters", Genome Research, 13(2):308-312.
[ abstract]
Jacques van Helden (2003), "Regulatory sequence analysis tools", Nucleic Acids Research, 31:3593-3596.
[supplement material: http://rsat.ulb.ac.be/rsat/ (RSAT)]
promoter/TF

Jacques van Helden (2003), "Prediction of transcriptional regulation by analysis of the non-coding genome", Current Genomics, 4(3):217-224.
Erik van Nimwegen (2003), "Scaling Laws in the functional content of genomes", Trends in Genetics, 19:479-484.
Rogier Versteeg, Barbera DC van Schaik, Marinus F van Batenburg, Marco Roos, Ramin Monajemi, Huib Caron, Harmen J Bussemaker, Antoine HC van Kampen (2003), "The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes", Genome Research, 13:1998-2004.
[supplement material: http://bioinfo.amc.uva.nl/HTMseq]
J Vogel, I Axmann, H Herzel, W Hess (2003), "Experimental and computational analysis of transcriptional start sites in the cyanabacterium", Nucleic Acids Research, 31:2890-2899.
N Volfovsky, BJ Haas, SL Salzberg (2003), "Computational discovery of internal micro-exons", Genome Research, 13(6a):1216-1221.
[ abstract]
Jian Wang, Eileen Kraemer (2003), "GFPE: gene-finding program evaluation", Bioinformatics, 19:1712-1713.
Jun Wang, ShengTing Li, Yong Zhang, HongKun Zheng, Zhao Xu, Jia Ye, Jun Yu, Gane Ka-Shu Wong (2003), "Vertebrate gene predictions and the problem of large genes", Nature Reviews Genetics, 4(9):741-749.
[abstract]
Ting Wang, Gary D Stormo (2003), "Combining phylogenetic data with co-regulated genes to identify regulatory motifs", Bioinformatics, 19:2369-2380.
translation

Yonghong Wang, Jinwei Liu, Tongju Zhao, Qing Ji (2003), "Recognizing translation initiation sites of eukaryotic genes based on the cooperatively scanning model", Bioinformatics, 19:1972-1977.
translation

YH Wang, HY Ou, FB Guo (2003), "Recognition of translation initiation sites of eukaryotic genes based on EM algorithm", Journal of Computational Biology, 10:699-708.
annotation

Christian Weinel, Maria D Ermolaeva, Christos Ouzounis (2003), "PseuRECA: genome annotation and gene context analysis for Pseudomonas aeruginosa PAO1", Bioinformatics, 19:1457-1460.
promoter/TF

T Werner (2003), "The state of the art of mammalian promoter recognition", Briefings in Bioinformatics, 4(1):22-30.
Rasmus Wernersson, Anders Gorm Pedersen (2003), "RevTrans: multiple alignment of coding DNA from aligned amino acid sequences", Nucleic Acids Research, 31:3537-3539.
[supplement material: http://www.cbs.dtu.dk/services/RevTrans/ (RevTrans)]
EA Worthey, S Martinez-Calvillo, A Schnaufer, G Aggarwal, J Cawthra, G Fazelinia, C Fong, G Fu, M Hassebrock, G Hixson, AC Ivens, P Kiser, F Marsolini, E Rickell, R Salavati, E Sisk, SM Sunkin, KD Stuart, PJ Myler (2003), "Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene", Nucleic Acids Research, 31(14):4201-4210.
YH Wu, AWC Liew, H Yan, MS Yang (2003), "Classification of short human exons and introns based on statistical features", Physical Review E, 67(6):061916.
annotation

Kayoko Yamada, Jun Lim, Joseph M. Dale, Huaming Chen, Paul Shinn, Curtis J. Palm, Audrey M. Southwick, Hank C. Wu, Christopher Kim, Michelle Nguyen, Paul Pham, Rosa Cheuk, George Karlin-Newmann, Shirley X. Liu, Bao Lam, Hitomi Sakano, Troy Wu, Guixia Yu, Molly Miranda, Hong L. Quach, Matthew Tripp, Charlie H. Chang, Jeong M. Lee, Mitsue Toriumi, Marie M. H. Chan, Carolyn C. Tang, Courtney S. Onodera, Justine M. Deng, Kenji Akiyama, Yasser Ansari, Takahiro Arakawa, Jenny Banh, Fumika Banno, Leah Bowser, Shelise Brooks, Piero Carninci, Qimin Chao, Nathan Choy, Akiko Enju, Andrew D. Goldsmith, Mani Gurjal, Nancy F. Hansen, Yoshihide Hayashizaki, Chanda Johnson-Hopson, Vickie W. Hsuan, Kei Iida, Meagan Karnes, Shehnaz Khan, Eric Koesema, Junko Ishida, Paul X. Jiang, Ted Jones, Jun Kawai, Asako Kamiya, Cristina Meyers, Maiko Nakajima, Mari Narusaka, Motoaki Seki, Tetsuya Sakurai, Masakazu Satou, Racquel Tamse, Maria Vaysberg, Erika K. Wallender, Cecilia Wong, Yuki Yamamura, Shiaulou Yuan, Kazuo Shinozaki, Ronald W. Davis, Athanasios Theologis, Joseph R. Ecker (2003), "Empirical analysis of transcriptional activity in the Arabidopsis genome", Science, 302:842-846.
[ abstract]
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: http://pbga.pasteur.fr/GeneFizz/ (GeneFizz)]
Paola Zacchi, Daniele Sblattero, Fiorella Florian, Roberto Marzari, Andrew R.M. Bradbury (2003), "Selecting open reading frames from DNA", Genome Research, 13(5):980-990.
[ abstract]
alternative-splicing

M Zavolan, S Kondo, C Schonbach, J Adachi, DA Hume, Y Hayashizaki, T Gaasterland; RIKENGER Group; GSL Members (2003), "Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome", Genome Research, 13(6b):1290-1300.
[ abstract]
similarity

Lingang Zhang, Vladimir Pavlovic, Charles R Cantor, Simon Kasif (2003), "Human-Mouse gene identification by comparative evidence integration and evolutionary analysis", Genome Research, 13(6a):1190-1202.
[ abstract]
splicing

LR Zhang, LF Luo (2003), "Splice site prediction with quadratic discriminant analysis using diversity measure", Nucleic Acids Research, 31(21):6214-6220.
[abstract]
promoter/TF

Michael Q Zhang (2003), "Prediction, annotation and analysis of human promoters", in Cold Spring Harbor Laboratory Symposium on Quantitative Biology 68, pp.217-225.
splicing

Christina L. Zheng, Virginia R. de Sa, Michael Gribskov, T. Murlidharan Nair (2003), "On selecting features from splice junctions: an analysis using information theoretic and machine learning approaches", Genome Informatics, 14:73-83.
promoter/TF

Jiashun Zheng, Jiajin Wu and Zhirong Sun (2003), "An approach to identify over-represented cis-elements in related sequences", Nucleic Acids Research, 31(7):1995-2005.
[supplement material: http://www.bioinfo.tsinghua.edu.cn/%7Ezhengjsh/OTFBS/index.html (OTFBS) ]
promoter/TF

Weimou Zheng (2003), "Finding signals for plant promoters", Genomics, Proteomics & Bioinformatics, 1(1):?-?.
annotation

W Zhu, SD Schlueter, V Brendel (2003), "Refined annotation of the Arabidopsis thaliana genome by complete EST mapping", Plant Physiology, 132:469-484.
[abstract]
A Zinovyev, AN Gorban, T Popova (2003), "Self-organizing approach for automated gene identification", Open Systems and Information Dynamics, 10(4):321-333.