gene recognition papers (1999)

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1999

You may find some relevant presentations at The Second Georgia Tech International Conference on Bioinformatics, both the lectures and the posters

Y Almirantis (1999), "A standard deviation based quantification differentiates coding from non-coding DNA sequences and gives insight to their evolutionary history", Journal of Theoretical Biology, 196(3):297-308.
[abstract] [ Medline entry ]
promoter/TF

VN Babenko, PS Kosarev, OV Vishnevsky, VG Levitsky, VV Basin, AS Frolov (1999), "Investigating extended regulatory regions of genomic DNA sequences", Bioinformatics, 15:644-653.
JH Badger, GJ Olsen (1999), "CRITICA: coding region identification tool invoking comparative analysis", Molecular Biology and Evolution, 16:512-524.
[ Medline entry ] [ PDF ]
R Baldock (1999), "Gene expression databases", in Genetics Databases , ed. M Bishop, pp.53-80 (Academic Press)
J Besemer, M Borodovsky (1999), "Heuristic approach to deriving models for gene finding", Nucleic Acids Research, 27:3911-3920.
M Borodovsky , WS Hayes, AV Lukashin (1999), "Statistical predictions of coding regions in prokaryotic genomes by using inhomogeneous Markov models", in Organization of Prokaryotic Genomes, ed. RL Charlebois (ASM Press), pp.11-33.
P Bucher (1999), "Gene feature identification", Genetics Databases , ed. M Bishop (Academic Press)
Hélène Chiapello, Emmanuelle Ollivier, Claudine Landès-Devauchelle, Patrick Nitschké, Jean-Loup Risler (1999), "Codon usage as a tool to predict the cellular location of eukaryotic ribosomal proteins and aminoacyl-tRNA synthetases", Nucleic Acids Research, 27(14):2848-2851.
[ Medline entry ] [ PDF ]
Deanna M Church, Alan J Buckler (1999), "Gene identification by exon amplification", Methods in Enzymology, 303:83-99.
translation

Mark E. Dalphin, Peter A. Stockwell, Warren P. Tate and Chris M. Brown(1999), "TransTerm, the translational signal database, extended to include full coding sequences and untranslated regions", Nucleic Acids Research, 27(1):293-294.
[ PDF ]
AL Delcher, D Harmon, S Kasif, O White, SL Salzberg (1999), "Improved microbial gene identification with GLIMMER", Nucleic Acids Research, 27(23):4636-4641.
[abstract]
Michael Deutsch, Manyuan Long (1999), "Intron-exon structures of eukaryotic model organisms", Nucleic Acids Research, 27(5):3219-3228.
[ Medline entry] [ PDF ]
Kyle Durick, John Mendlein, Kleanthis G Xanthopoulos (1999), "Hunting with traps: genome-wide strategies for gene discovery and functional analysis", Genome Research, 9(11):1019-1025.
Volker A. Erdmann, Maciej Szymanski, Abraham Hochberg, Nathan de Groot and Jan Barciszewski (1999), "Collection of mRNA-like non-coding RNAs", Nucleic Acids Research, 27(1):192-195.
[ PDF ]
Daniel Fischer, David Eisenberg (1999), "Finding families for genomic ORFans", Bioinformatics, 15(9):759-762.
D Frishman, Andrei Mironov, Mikhail Gelfand (1999), "Starts of bacterial genes: estimating the reliability of computer predictions", Gene, 234:257-265.
[ abstract] [ Medline entry ] [ PDF]
Katheleen Gardiner (1999), "Saturation identification of coding sequences in genomic DNA", Methods in Enzymology, 303:144-161.
alternative-splicing

MS Gelfand, I Dubchak, I Dralyuk, M Zorn (1999), "ASDB: database of alternatively spliced genes", Nucleic Acids Research, 27(1):301-302.
[ Medline entry] [ PDF ]
promoter/TF

David Ghosh (1999), "Object oriented transcription factors database (ooTFD)", Nucleic Acids Research, 27(1):315-317.
translation

Joel H Graber, Charles R Cantor, Scott C Mohr, Temple F Smith (1999), "Genomic detection of new yeast pre-mRNA 3'-end-processing signals", Nucleic Acids Research, 27(3):888-894.
[ Medline entry]
translation

Joel H Graber, Charles R Cantor, Scott C Mohr, Temple F Smith (1999), "In silico detection of control signals: mRNA 3'-end-processing sequences in diverse species", Proceedings of the National Academy of Sciences , 96(24):14055-14060.
Roderic Guigo (1999), "DNA composition, codon usage and exon prediction", in Genetics Databases , ed. M Bishop (Academic Press)
[ PDF ]
alternative-splicing

Jens Hanke, Dave Brett, Inga Zastrow, Atakan Aydin, Sebastian Delbruck, Gerrit Lehmann, Fredrich Luft, Jens Reich, Peer Bork (1999), "Alternative splicing of human genes: more the rule than the exception?", Trends in Genetics, 15(10):389-390.
Sridhar S Hannenhalli, William S. Hayes, Artemis G. Hatzigeorgiou and James W. Fickett (1999), "Bacterial start site prediction", Nucleic Acids Research, 27(17):3577-3582.
promoter/TF

T Heinemeyer, X Chen, H Karas, AE Kel, OV Kel, I Liebich, T Meinhardt, I Reuter, F Schacherer, E Wingender (1999), "Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms", Nucleic Acids Research, 27(1):318-322.
GZ Hertz, GD Stormo (1999), "Identifying DNA and protein patterns with statistically significant alignments of multiple sequences", Bioinformatics, 15:563-577.
Laurence D Hurst, Clair FA Brunton, Nicholas GC Smith (1999), "Small introns tend to occur in GC-rich regions in some but not all vertebrates", Trends in Genetics, 15(11):437-439.
promoter/TF

Ilya Ioshikhes, Edward N Trifonov, Michael Zhang (1999), "Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure", Proceedings of the National Academy of Sciences , 96:2891-2895.
[ Medline entry] [ PDF]
Chungfan Kim, Akihiko Konagaya, Kiyoshi Asai (1999), "A generic criterion for gene recognitions in genomic sequences", Genome Informatics, 10:13-22.
promoter/TF

Andreas Klingenhoff, Komelie French, Kerstin Quandt, Thomas Werner (1999), "Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity", Bioinformatics, 15(3):180-186.
promoter/TF

Steen Knudsen (1999), "Promoter2.0: for the recognition of PolII promoter sequences", Bioinformatics,15(5):356-361.
[ abstract] [ PDF ]
translation

Alex V. Kochetov, Mikhail P. Ponomarenko, Anatoly S. Frolov, Lev L. Kisselev and Nikolay A. Kolchanov (1999), "Prediction of eukaryotic mRNA translational properties", Bioinformatics, 15:704-712.
NA Kolchanov, MP Ponomarenko, AS Frolov, EA Ananko, FA Kolpakov, EV Ignatieva, OA Podkolodnaya, TN Goryachkovskaya, IL Stepanenko, TI Merkulova, VV Babenko, Yu V Ponomarenko, AV Kochetov, NL Podkolodny, DV Vorobiev, SV Lavryushev, DA Grigorovich, Yu V Kondrakhin, L Milanesi, E Wingender, V Solovyev, GC Overton (1999), "Integrated databases and computer systems for studying eukaryotic gene expression", Bioinformatics, 15:669-686.
promoter/TF

NA Kolchanov, EA Ananko, OA Podkolodnaya, EV Ignatieva, IL Stepanenko, OV Kel-Margoulis, AE Kel, TI Merkulova, TN Goryachkovskaya, TV Busygina, FA Kolpakov, NL Podkolodny, AN Naumochkin and AG Romashchenko (1999), "Transcription Regulatory Regions Database (TRRD): its status in 1999", Nucleic Acids Research, 27(1):303-306.
[ PDF ]
annotation

M Kowalczuk, P Mackiewicz, A Gierlik, MR Dudek, S Cebrat (1999), "Total number of coding open reading frames in the yeast genome", Yeast, 15(11):1031-1034.
Kyrpides NC, Ouzounis CA (1999), "Transcription in archaea", Proceedings of the National Academy of Sciences , 96(15):8545-8550.
annotation

Kyrpides NC, Ouzounis CA (1999), "Whole-genome sequence annotation: 'Going wrong with confidence'", Molecular Microbiology, 32(4):886-887.
promoter/TF

RF Lascaris, WH Mager, RJ Planta (1999), "DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequence", Bioinformatics, 15(4):267-277.
[ abstract] [ PDF ]
promoter/TF

G Lavorgna, A Guffanti, G Borsani, A Ballabio, E Boncinelli (1999), "TargetFinder: searching annotated sequence databases for target genes of transcription factors", Bioinformatics, 15(2):172-173.
splicing

E Lemoine, D Merceron, J Sallantin, EM Nguifo (1999), "Improving the efficiency of a user-driven learning system with reconfigurable hardware. application to DNA splicing", Pacific Symposium on Biocomputing, 4: 290-301.
[ Medline entry]
W Li (1999), "Statistical properties of open reading frames in complete genome sequences", Computers & Chemistry (informatics and the genome issue), 23(3-4):283-301.
[ abstract] [ Medline entry ] [ PDF ]
translation

Izabela Makalowska, Erik S. Ferlanti, Andreas D. Baxevanis and David Landsman (1999), "Histone Sequence Database: sequences, structures, post-translational modifications and genetic loci", Nucleic Acids Research, 27(1):323-324.
alternative-splicing

ME Mangan, KS Frazer (1999), "An extensive list of genes that produce alternative transcripts in the mouse", Bioinformatics, 15(2):170-171.
Luciano Milanesi, Dino D'Angelo and Igor B. Rogozin (1999), "GeneBuilder: interactive in silico prediction of gene structure", Bioinformatics, 15:612-621.
alternative-splicing

AA Mironov, JW Fickett, MS Gelfand (1999), "Frequent alternative splicing of human genes", Genome Research, 9:1288-1293.
[ PDF ]
promoter/TF

AA Mironov, EV Koonin, MA Roytberg, MS Gelfand (1999), "Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes", Nucleic Acids Research, 27(14):2981-2989.
[ Medline entry] [ PDF ]
A Mironov, PA Pevzner (1999), "SST versus EST in gene recognition", Microbial and Comparative Genomics, 4:254-260
Richard J Mural (1999), "Current status of computational gene finding: a perspective", Methods in Enzymology, 303:77-83.
Yasukazu Nakamura, Takashi Gojobori and Toshimichi Ikemura(1999), "Codon usage tabulated from the international DNA sequence databases; its status 1999", Nucleic Acids Research, 27(1):292-294.
[ PDF ]
promoter/TF

Uwe Ohler, Stefan Harbeck, Heinrich Niemann, Elmar Noth, Martin G Reese (1999), "Interpolated Markov chains for eukaryotic promoter recognition", Bioinformatics, 15(5):362-369.
[ abstract ] [ PDF ]
N Pavy, S Rombauts, P Dehais, C Mathe, DVV Ramana, P Loroy, P Rouze (1999), "Evaluating of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences", Bioinformatics, 15(11):887-899.
[abstract]
promoter/TF

AG Pedersen, P Baldi, Y Chauvin, S Brunak (1999), "The biology of eukaryotic promoter prediction - a review", Computers & Chemistry (informatics and the genome issue), 23(3-4):191-207.
[ PDF ]
promoter/TF

Rouaida Cavinb Perier, Thomas Junier, Claude Bonnard, Philipp Bucher (1999), "The Eukaryotic Promoter Database (EPD): recent developments", Nucleic Acids Research, 27(1):307-309.
[ PDF ]
promoter/TF

Dan S Prestridge (1999), "Computer software for eukaryotic promoter analysis", ? [ html]
Y Quentin, C Voiblet, F Martin, G Fichant (1999), "Protein-coding region discovery in organisms under-represented in databases", Computers & Chemistry (informatics and the genome issue), 23(3-4):209-217.
[ Medline entry] [ PDF]
Raghavan S, Ouzounis CA (1999), "Novel coding regions in four complete archaeal genomes", Nucleic Acids Research, 27(22):4405-4408.
R Ramakrishna, R Srinivasan (1999), "Gene identification in bacterial and organellar genomes using GeneScan", Computers & Chemistry, 23(2):165-174.
[ abstract]
promoter/TF

H Salgado, A Santos, U Garza-Ramos, J van Helden, E Diaz, J Collado-Vides (2000), "RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli", Nucleic Acids Research, 27(1):59-60.
SL Salzberg, M Pihaela, AL Delcher, MJ Gardner, H Tettelin (1999), "Interpolated Markov models for eukaryotic gene finding", Genomics,59:24-31.
AM Shmatkov, AA Melikyan, FL Chernousko, M Borodovsky (1999), "Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes", Bioinformatics, 15(11):874-886.
Victor V Solovyev, Asaf A. Salamov (1999), "INFOGENE: a database of known gene structures and predicted genes and proteins in sequences of genome sequencing projects", Nucleic Acids Research, 27(1):248-250.
[ Medline entry] [ PDF ]
translation

JE Tabaska, MQ Zhang (1999), "Detection of polyadenylation signals in human DNA sequences", Gene, 231(1-2):77-86.
[ Medline entry]
TA Thanaraj (1999), "A clean data set of EST-confirmed splice sites from homo sapiens and standards for clean-up procedures", Nucleic Acids Research, 27(13):2627-2637. [ abstract ] [ EST-confirmed human splice sites ]
annotation

Tsoka S, Promponas V, Ouzounis CA (1999), "Reproducibility in genome sequence annotation: the Plasmodium falciparum chromosome 2 case", FEBS Letters, 451(3):354-355.
promoter/TF

Tatsuhiko Tsunoda and Toshihisa Takagi (1999), "Estimating transcription factor bindability on DNA", Bioinformatics, 15:622-630.
splicing

L Vignal, F Lisacek, J Quinqueton, Y d'Aubenton-Carafa, C Thermes (1999), "A multi-agent system simulating human splice site recognition", Computers & Chemistry (informatics and the genome issue), 23(3-4):219-231.
Alexander E Vinogradov (1999), "Intron-genome size relationship on a large evolutionary scale", Journal of Molecular Evolution, 49:376-384.
promoter/TF

A Wagner (1999), "Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes", Bioinformatics, 15(10):776-784.
promoter/TF

T Werner (1999), "Models for prediction and recognition of eukaryotic promoters", Mammalian Genome, 10:168-175.
promoter/TF

TG Wolfsberg, AE Gabrielian, MJ Campbell, RJ Cho, JL Spouge, D Landsman (1999), "Candidate regulatory sequence elements for cell cycle-dependent transcription in saccharomyces cerevisiae", Genome Research, 9(8):775-792.
[ Medline entry]
promoter/TF

MQ Zhang (1999), "Promoter analysis of co-regulated genes in the yeast genome", Computers & Chemistry (informatics and the genome issue), 23(3-4):233-250.
[ Medline entry]
promoter/TF

J Zhu, MQ Zhang (1999), "SCPD: a promoter database of yeast Saccharomyces cerevisiae", Bioinformatics, 15:607-611.
[ PDF]