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",
in PSB98, 228-239.
[ Medline entry]
Stephane Audic and Jean-Michel Claverie (1998),
"Self-identification of protein-coding regions in microbial genomes",
Proceedings of the National Academy of Sciences, 95:10026-10031.
[ PDF ]
[SELFID is at http://igs-server.cnrs-mrs.fr/~audic/selfid.html ]
TL Bailey, M Gribskov (1998), "Methods and statistics for combining motif match scores", Journal of Computational Biology, 5:211-221.
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.
Stephane Audic and 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 ]
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.
[SPLICEPREDICTOR is at http://gremlin1.zool.iastate.edu/~volker/SplicePredictor.html ]
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 on Structural Biology, 8:346-354.
[abstract] [ Medline entry ]
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
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]
J.-M. Claverie (1998),
"Computer methods for exon detection",
Molecular Biotechnology, 10:27-48.
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).
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.
Jurgen Kleffe, Klaus Hermann, Wolfgang Vahrson, Burghardt Wittig and Volker Brendel (1998),
"GeneGenerator-a flexible algorithm for gene prediction and its application to maize sequences",
Bioinformatics, 14(3):232-243.
[abstract] [ PDF]
N.A. Kolchanov, M.P. Ponomarenko, A.E. Kel, Y.V. Kondrakhin, A.S. Frolov, F.A. Kolpakov, O.V. Kel, E.A. Ananko, E.V. Ignatieva, O.A. Podkolodnaya, I.L. Stepanenko, T.I. Merkulova, V.N. Babenko, D.G. Voroblev, S.V. Lavyushev, Y.V. Ponomarenko, A.V. Kochetov, G.B. Kolesov, N.L. Podkolodny, L. Milanesi, E. Wingender, T. Heinemeyer, V.V. Solvyev (1998),
"Genexpress: a computer system for description, analysis and recognition of regulatory sequences in eukaryotic genome",
in ISMB98 .
[ 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, and 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.
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 ]
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 and Mark Borodovsky (1998),
"GeneMark.hmm: new solutions for gene finding",
Nucleic Acids Research, 26(4):1107-1115.
[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 ]
L.Pickert, I.Reuter, F.Klawonn and E.Wingender (1998),
"Transcription regulatory region analysis using signal detection and fuzzy clustering",
Bioinformatics, 14(3):244-251.
[ abstract] [ PDF ]
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]
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.
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, and S. Kasif (Elsevier Science B.V). table of contents.
Steven L. Salzberg, Arthur L. Delcher, Simon Kasif and Owen White (1998),
"Microbial gene identification using interpolated Markov models",
Nucleic Acids Research, 26(2):544-548.
[abstract]
Steven L. Salzberg, Arthur L. Delcher, Kenneth H Fasman and John Henderson (1998),
"A decision tree system for finding genes in DNA",
Journal of Computational Biology, 5(4):667-680.
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 ]
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 ]
T Tsunoda and T Takagi (1998),
"Automatic extraction of position specific cooccurrence of transcriptionFactor bindings on promoters",
in PSB98, 252-263.
[ Medline entry]
A Wagner (1998),
"A computational 'genome walk' technique to identify regulatory interactions in gene networks",
in PSB98, 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 ]
W.W. Wasserman, J.W. Fickett (1998),
"Identification of regulatory regions which confer muscle-specific gene expression",
Journal of Molecular Biology, 278(1):167-181.
[abstract]
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, and S. Kasif (Elsevier Science B.V). table of contents.
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]
Michael Q Zhang (1998),
"A discrimination study of human core-promoters",
in PSB98,240-251.
[ Medline entry ]
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]
X Zhang, TF Smith (1998),
"Yeast 'operons'",
Microbial & Comparative Genomics, 3(2):133-140.
[ Medline entry ]