gene recognition papers (1998)

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1998

K Asai, K Itou, Y Ueno, T Yada (1998), "Recognition of human genes by stochastic parsing", Pacific Symposium on Biocomputing, 3:228-239.
[ Medline entry]
Stephane Audic, Jean-Michel Claverie (1998), "Self-identification of protein-coding regions in microbial genomes", Proceedings of the National Academy of Sciences, 95:10026-10031.
[ PDF ]
[supplement material: http://igs-server.cnrs-mrs.fr/~audic/selfid.html (SELFID)]
annotation

LC Bailey, DB Searls, GC Overton (1998) "Analysis of EST-driven gene annotation in human genomic sequence", Genome Research, 8:362-376.
[abstract]
TL Bailey, M Gribskov (1998), "Methods and statistics for combining motif match scores", Journal of Computational Biology, 5:211-221.
promoter/TF

Alvis Brazma, Inge Jonassen, Jaak Vilo, and Esko Ukkonen (1998), "Predicting gene regulatory elements in silico on a genomic scale", Genome Research, 8:1202-1215.
promoter/TF

Stephane Audic, Jean-Michel Claverie (1998), "Visualizing the competitive recognition of TATA-boxes in vertebrate promoters" Trends in Genetics, 14:10-11.
Peer Bork, Thomas Dandekar, Yolande Diaz-Lazcoz, Frank Eisenhaber, Martijn Huynen, Yanping Yuan (1998), "Predicting function: from genes to genomes and back", Journal of Molecular Biology, 283:707-725.
[ PDF ]
splicing

Volker Brendel, Jurgen Kleffe (1998), "Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genome DNA" Nucleic Acids Research, 26(20):4748-4757.
[supplement material: http://gremlin1.zool.iastate.edu/~volker/SplicePredictor.html (SPLICEPREDICTOR)]
splicing

Christopher Burge (1998) "Modeling dependencies in Pre-mRNA splicing signals", in Computational Methods in Molecular Biology, eds. S Salzberg, D Searls, and S Kasif (Elsevier Science B.V). table of contents.
CB Burge, S Karlin (1998), "Finding the genes in genomic DNA", Current Opinion in Structural Biology, 8:346-354.
[abstract] [ Medline entry ]
promoter/TF

Tapan K Biswas, Godfrey S Getz (1998), "Position-specific inhibition of yeast mitochondrial transcription by a poly(T) sequence" Journal of Molecular Biology, 275(4):547-560.
[abstract
splicing

Volker Brendel, Jürgen Kleffe, Jose C Carle-Urioste, Virginia Walbot (1998), "Prediction of splice sites in plant pre-mRNA from sequence properties", Journal of Molecular Biology, 276(1):85-104 (Feb 13, 1998) [abstract]
T Chen (1998), "POMBE: A fission yeast gene-finding and exon-intron structure prediction system", Yeast, 14:701-710. [ Medline entry]
JM Claverie (1998), "Computer methods for exon detection", Molecular Biotechnology, 10:27-48.
translation

Thomas Dandekar, Katrin Beyer, Peer Bork, Mary-Rose Kenealy, Kostas Pantopoulos, Mathias Hentze, Vera Sonntag-Buck, Gilles Flouriot, Frank Gannon and Sonja Schreiber (1998), "Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches", Bioinformatics, 14(3):271-278.
[abstract] [ PDF ]
Barbara A Eckman, Jeffrey S Aaronson, Joseph A Borkowski, Wendy J Bailey, Keith O Elliston, Alan R Williamson, Richard A Blevins (1998), "The Merck Gene Index browser: an extensible data integration system for gene finding, gene characterization and EST data mining", Bioinformatics, 14(1):2-13.
[abstract] [ PDF ]
JW Fickett (1998), "Predictive methods using nucleotide sequences", in Bioinformatics: A practical guide to the analysis of genes and proteins , eds. AD Baxevanis and BFF Ouellette (John Wiley & Sons).
promoter/TF

Kornelie Frech, Kerstin Quandt and Thomas Werner (1998), "Muscle actin genes: A first step towards computational classification of tissue specific promoters", In Silico Biology (online publication), 1:0005.
[ html]
D Frishman, A Mironov, HW Mewes, M Gelfand (1998), "Combining diverse evidence for gene recognition in completely sequenced bacterial genomes", Nucleic Acids Research, 26(12):2941-2947. [ Medline entry]
X Guan, L Du (1998), "Domain identification by clustering sequence alignments", Bioinformatics, 14:783-788.
Roderic Guigo (1998), "Assembling genes from predicted exons in linear time with dynamic programming", Journal of Computational Biology, 5:681-702.
[ Medline entry ]
W Hayes, M Borodovsky (1998), "How to interpret anonymous genome? Machine learning approach to gene identification", Genome Research , 8:1154-1171.
Jian Jiang, Howard J Jacob (1998), "EbEST: an automatic tool using expressed sequence tags to delineate gene structure", Genome Research , 8(3):268-275.
[abstract]
Jurgen Kleffe, Klaus Hermann, Wolfgang Vahrson, Burghardt Wittig, Volker Brendel (1998), "GeneGenerator-a flexible algorithm for gene prediction and its application to maize sequences", Bioinformatics, 14(3):232-243.
[abstract] [abstract] [ PDF]
promoter/TF

NA Kolchanov, MP Ponomarenko, AE Kel, YV Kondrakhin, AS Frolov, FA Kolpakov, OV Kel, EA Ananko, EV Ignatieva, OA Podkolodnaya, IL Stepanenko, TI Merkulova, VN Babenko, DG Voroblev, SV Lavyushev, YV Ponomarenko, AV Kochetov, GB Kolesov, NL Podkolodny, L Milanesi, E Wingender, T Heinemeyer, VV Solovyev (1998), "Genexpress: a computer system for description, analysis and recognition of regulatory sequences in eukaryotic genome", Proceedings of the sixth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.95-104.
[ Medline entry]
A Krogh (1998), "Gene finding: putting the parts together", in Guide to Human Genome Computing , ed. Martin Bishop, 2rd edition (Academic Press).
A Krogh (1998), "An introduction to hidden Markov models for biological sequences", in Computational Methods in Molecular Biology, eds. S Salzberg, D Searls, S Kasif (Elsevier Science B.V). table of contents.
[ PDF ]
MT Laub, DW Smith (1998), "Finding intron/exon splice junctions using INFO, interruption finder and organizor", Journal of Computational Biology, 5(2):307-321.
splicing

HX Liu, MQ Zhang, AR Krainer (1998), "Identification of novel classes of exons splicing enhancers recognized by individual SR proteins", Gene and Development, 12:1998-2012.
[ PDF ]
splicing

M Long, SJ de Souza, C Rosenberg, W Gilbert (1998), "Relationship between 'proto-splice sites' and intron phases: evidence from dicodon analysis", Proceedings of the National Academy of Sciences, 95:219-223.
[ Medline entry ]
Alexander V Lukashin, Mark Borodovsky (1998), "GeneMark.hmm: new solutions for gene finding", Nucleic Acids Research, 26(4):1107-1115.
[abstract] [abstract]
Antonio Marin, Fransisco Gonzalez, Gabriel Gutierrez, Jose L Oliver (1998), "Gene lengths and GC content" (scientific correspondence), Nucleic Acids Research, 26:4540.
L Milanesi, I Rogozin (1998), "Prediction of human gene structure", in Guide to Human Genome Computing , ed. Martin Bishop, 2rd edition (Academic Press)
AA Mironov, MA Roytberg, PA Pevzner, MS Gelfand (1998), "Performance-guarantee gene predictions via spliced alignment", Genomics, 51(3):332-339.
[ Medline entry ] [PDF ]
Katsuhiko Murakami and Toshihisa Takagi (1998), "Gene recognition by combination of several gene-finding programs", Bioinformatics, 14(8):665-675.
[abstract] [ PDF ]
promoter/TF

L Pickert, I Reuter, F Klawonn, E Wingender (1998), "Transcription regulatory region analysis using signal detection and fuzzy clustering", Bioinformatics, 14(3):244-251.
[ abstract] [ PDF ]
promoter/TF

Ernesto Pérez-Rueda, Jay D Gralla, Julio Collado-Vides (1998), "Genomic position analyses and the transcription machinery", Journal of Molecular Biology, 275(2):165-170. [abstract]
splicing

Salvatore Rampone (1998), "Recognition of splice junctions on DNA sequences by BRAIN learning algorithm", Bioinformatics, 14(8):676-684.
[abstract] [ PDF ]
I Rigoutsos, A Floratos (1998), "Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm", Bioinformatics, 14:55-67.
promoter/TF

Emmanuelle Roulet, Igor Fisch, Thomas Junier, Philipp Bucher, Nicolas Mermod (1998), "Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA", In Silico Biology, 1:0004.
[ html]
Steven L Salzberg (1998) "Decision trees and Markov chains for gene finding ", in Computational Methods in Molecular Biology, eds. S Salzberg, D Searls, S Kasif (Elsevier Science B.V). table of contents.
Steven L Salzberg, Arthur L Delcher, Simon Kasif, Owen White (1998), "Microbial gene identification using interpolated Markov models", Nucleic Acids Research, 26(2):544-548.
[abstract] [abstract]
Steven L Salzberg, Arthur L Delcher, Kenneth H Fasman, John Henderson (1998), "A decision tree system for finding genes in DNA", Journal of Computational Biology, 5(4):667-680.
AA Salamov, T Nishikawa, MB Swindells (1998), "Assessing protein coding region integrity in cDNA sequencing projects", Bioinformatics, 14(5):384-390.
annotation

TF Smith (1998), "Functional genomics - bioinformatics is ready for the challenge", Trends in Genetics, 14(7):291-293.
Gary D Stormo (1998), "Information content and free energy in DNA-protein interactions", Journal of Theoretical Biology, 195(1):135-137.
Sing-Hoi Sze, Michael Roytberg, Mikhail Gelfand, Andrey Mironov, Tatiana Astakhova, Pavel Pevzner (1998), "Algorithms and software for support of gene identification experiments", Bioinformatics, 14(1):14-19.
[abstract] [ Medline entry] [ PDF ]
promoter/TF

Denis Thieffry, Heladia Salgado, Araceli M Huerta and Julio Collado-Vides (1998), "Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12", Bioinformatics, 14(5):391-400
[abstract] [ PDF ]
promoter/TF

T Tsunoda and T Takagi (1998), "Automatic extraction of position specific cooccurrence of transcriptionFactor bindings on promoters", Pacific Symposium on Biocomputing, 3:252-263.
[ Medline entry]
promoter/TF

J van Helden, B Andre, J Collado-Vides (1998), "Extracting regulatory sites from the upsteam region of yeast genes by computational analysis of oligonucleotide frequencies", Journal of Molecular Biology, 281:827-842.
A Wagner (1998), "A computational 'genome walk' technique to identify regulatory interactions in gene networks", Pacific Symposium on Biocomputing, 3:264-278.
[ Medline entry]
Takanori Washio, Junji Sasayama, Masaru Tomita (1998), "Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination", Nucleic Acids Research, 26(23):5456-5463.
[ PDF ]
expression

WW Wasserman, JW Fickett (1998), "Identification of regulatory regions which confer muscle-specific gene expression", Journal of Molecular Biology, 278(1):167-181.
[abstract]
similarity

Ying Xu, Edward C Uberbacher (1998), "Computational gene prediction using neural networks and similarity search", in Computational Methods in Molecular Biology, eds. S Salzberg, D Searls, S Kasif (Elsevier Science B.V). table of contents.
promoter/TF

T Yada, Y Totoki, M Ishikawa, K Asai, K Nakai (1998), "Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences", Bioinformatics, 14(4):317-325.
[ Medline entry]
Ming Yan, Zhe-Suai Lin, Chun-Ting Zhang (1998), "A new Fourier transform approach for protein coding measure based on the format of the Z curve", Bioinformatics, 14(8):685-690.
[abstract] [ PDF ]
CT Zhang, ZS Lin, M Yan, R Zhang (1998), "A novel approach to distinguish between intron-containing and intronless genes based on the format of Z curves", Journal of Theoretical Biology, 192(4):467-473.
[abstract]
promoter/TF

Michael Q Zhang (1998), "A discrimination study of human core-promoters", Pacific Symposium on Biocomputing, 3: 240-251.
[ Medline entry ]
promoter/TF

Michael Q Zhang (1998), "Identification of human gene core promoters in Silico", Genome Research , 8(3):319-326.
[ Medline entry ] [ PDF ]
Michael Q Zhang (1998), "Statistical features of human exons and their flanking regions", Human Molecular Genetics, 7(5):919-932.
[ abstract] [ Medline entry ] [ PDF]
Michael Q Zhang (1998), "Identification of protein coding regions in Arabidopsis thaliana genome based on quadratic discriminant analysis", Molecular Plant Biology, 37:803-806. [ Medline entry]
promoter/TF

X Zhang, TF Smith (1998), "Yeast 'operons'", Microbial & Comparative Genomics, 3(2):133-140.
[ Medline entry ]