gene recognition papers (2000)

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2000

annotation

JF Abril, R Guigo (2000), "gff2ps: visualizing genomic annotations", Bioinformatics, 16(8):743-744.
JP Alimi, O Poirot, F Lopez, JM Claverie (2000) , "Reverse transcriptase-polymerase chain reaction validation of 25 'Orphan' genes from Escherichia coli K-12 MG1655", Genome Research, 10:959-966.
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G. (2000), "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium", Nature Genetics, 25:25-29
V Bafna, DH Huson (2000), "The conserved exon method for gene finding", Proceedings of the eighth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp. 3-12.
VB Bajic (2000), "Comparing the success of different prediction software in sequence analysis: a review", Briefings in Bioinformatics, 1(3):214-228.
[ PDF ]
P Baldi (2000), "On the convergence of a clustering algorithm for protein-coding regions in microbial genomes", Bioinformatics, 16(4):367-371.
[ PDF ]
Pierre Baldi, Søren Brunak, Yves Chauvin, Claus A. F. Andersen, Henrik Nielsen (2000), "Assessing the accuracy of prediction algorithms for classification: an overview", Bioinformatics, 16:412-424.
similarity

Serafim Batzoglou, Lior Pachter, Jill P Mesirov, Bonnie Berger, Eric S Lander (2000), "Human and mouse gene structure: comparative analysis and application to exon prediction", Genome Research, 10:950-958.
[abstract]
P Bernaola-Galvan, I Grosse, P Carpena, JL Oliver, R Roman-Roldan, HE Stanley (2000), "Finding borders between coding and noncoding DNA regions by an entropic segmentation method", Physical Review Letters, 85(6):1342-1345.
[abstract] [PDF]
A Bhattacharya, S Bhattacharya, A Joshi, S Ramachandran, R Ramaswamy (2000), "Identification of parasitic genes by computational methods", Parasitology Today, 16(3):127-131.
alternative-splicing

DL Black (2000), "Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology", Cell, 103(3):367-370.
M Borodovsky, A Melikyan, FL Chernousko, AM Shmatkov (2000), "Application of a hidden Markov model and dynamic programming to gene recognition in DNAs of bacteria and viruses", International Journal of Computer and Systems Sciences, 39:155-161.
splicing

M Burset, IA Seledtsov, VV Solovyev (2000), "Analysis of canonical and non-canonical splice sites in mammalian genomes", Nucleic Acids Research, 28(21):4364-4375.
promoter/TF

Harmen Bussemaker, Hao Li, Eric Siggia (2000), "Regulatory element detection using a probabilistic segmentation model", Proceedings of the eighth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.67-74.
promoter/TF

Harmen Bussemaker, Hao Li, Eric Siggia (2000), "Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis ", Proceedings of the National Academy of Sciences, 97:10096-10100.
[abstract] [ PDF]
splicing

D Cai, A Delcher, B Kao, S Kasif (2000), "Modeling splice sites with Bayes networks", Bioinformatics, 16(2):152-158.
annotation

Jean-Michel Claverie (2000) "Do we need a huge new centre to annotate the human genome?" (correspondence) Nature, 403:12.
Jean-Michel Claverie (2000) "From bioinformatics to computational biology", Genome Research, 10:1277-1279.
M Craven, D Page, J Shavlik (2000), "A probabilistic learning approach to whole-genome operon prediction", Proceedings of the eighth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp. 116-127.
alternative-splicing

Larry Croft, Soeren Schandorff, Francis Clark, Kevin Burrage, Peter Arctander, John S Mattick (2000), "ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome", Nature Genetics, 24:340-341.
[supplement material: http://isis.bit.uq.edu.au/a_splicers.html (ISIS)]
RV Davuluri, Y Suzuki, S Sugano, MQ Zhang (2000), "CART classification of human 5' UTR sequences", Genome Research, 10:1807-1816.
[ PDF ]
annotation

de Souza SJ, Camargo AA, Briones MR, Costa FF, Nagai MA, Verjovski-Almeida S, Zago MA, Andrade LE, Carrer H, El-Dorry HF, Espreafico EM, Habr-Gama A, Giannella-Neto D, Goldman GH, Gruber A, Hackel C, Kimura ET, Maciel RM, Marie SK, Martins EA, Nobrega MP, Paco-Larson ML, Pardini MI, Pereira GG, Pesquero JB, Rodrigues V, Rogatto SR, da Silva ID, Sogayar MC, de Fatima Sonati M, Tajara EH, Valentini SR, Acencio M, Alberto FL, Amaral ME, Aneas I, Bengtson MH, Carraro DM, Carvalho AF, Carvalho LH, Cerutti JM, Correa ML, Costa MC, Curcio C, Gushiken T, Ho PL, Kimura E, Leite LC, Maia G, Majumder P, Marins M, Matsukuma A, Melo AS, Mestriner CA, Miracca EC, Miranda DC, Nascimento AN, Nobrega FG, Ojopi EP, Pandolfi JR, Pessoa LG, Rahal P, Rainho CA, da Ros N, de Sa RG, Sales MM, da Silva NP, Silva TC, da Silva W Jr, Simao DF, Sousa JF, Stecconi D, Tsukumo F, Valente V, Zalcbeg H, Brentani RR, Reis FL, Dias-Neto E, Simpson AJ (2000), "Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags", Proceedings of the National Academy of Sciences, 97(23):12690-12693.
David Elder (2000), "Split gene origin and periodic introns", Journal of Theoretical Biology, 207(4):455-472.
promoter/TF

L Florea, M Li, C Riemer, B Giardine, W Miller, R Hardison (2000), "Validating computer programs for functional genomics in gene regulatory regions", Current Genomics, 1(1):11-27.
X Gai, S Lal, L Xing, V Brendel, V Walbot (2000), "Gene discovery using the maize genome database ZmDB", Nucleic Acids Research, 28:94-96.
MS Gelfand, EV Koonin, AA Mironov (2000), "Predication of transcriptio regulatory sites in archaea by a comparative genomic approach", Nucleic Acids Research, 28(3):695-705. "Comparative analysis of regulatory patterns in bacterial genomes", Briefings in Bioinformatics, 1(4):357-371.
I Goncalves, L DUret, D Mouchiroud (2000), "Nature and structure of human genes that generate retropseudogenes", Genome Research, 10:672-678.
[PDF]
similarity

O Gotoh (2000), "Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps", Bioinformatics, 16(3):190-202.
[abstract]
I Grosse, H Herzel, SV Buldyrev, HE Stanley (2000), "Species independence of mutual information in coding and noncoding DNA", Physical Review E, 61(5):5624-5629.
[ abstract ] [ PDF ]
similarity

R Guigo, M Burset, P Agarwal, JF Abril, RF Smith, JW Fickett (2000), "Sequence similarity based gene prediction", in Genomics and Proteomics: Functional and Computational Aspects , ed. S Suhai (Plenum).
R Guigo, P Agarwal, JF Abril, M Burset, JW Fickett (2000), "An assessment of gene prediction accuracy in large DNA sequences", Genome Research, 10(10):1631-1642.
S Hampson, P Baldi, D Kibler, S Sandmeyer (2000), "Analysis of yeast's ORF upstream regions by parallel processing, microarrays, and computational methods", Proceedings of the eighth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp. 190-201.
promoter/TF

RC Hardison (2000), "Conserved noncoding sequences are reliable guides to regulatory elements", Trends in Genetics, 16(9):369-372.
M Hirosawa, K Ishikawa, T Nagase, O Ohara (2000), "Detection of spurious interruptions of protein-coding regions in cloned cDNA sequences by GeneMark analysis", Genome Research, 10(9):1333-1341.
expression

Ian Holmes, William J Bruno (2000), "Finding regulatory elements using joint likelihoods for sequence and expression profile data", Proceedings of the eighth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp. 202-210.
D Holste, I Grosse, SV Buldyrev, HE Stanley, H Herzel (2000), "Optimization of coding potentials using positional dependence of nucleotide frequencies", Journal of Theoretical Biology, 206(4):525-537.
PM Hooper, H Zhang, DS Wishart (2000), "Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment", Bioinformatics, 16(5):425-438.
promoter/TF

YJ Hu, S Sandmeyer, C McLaughlin, D Kibler (2000), "Combinatorial motif analysis and hypothesis generation on a genomic scale", Bioinformatics, 16(3):222-232.
JD Hughes, PW Estep, S Tavazoie, GM Church (2000), "Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae", Journal of Molecular Biology, 296:1205-1214.
promoter/TF

IP Ioshikhes, MQ Zhang (2000), "Large-scale human promoter mapping using CpG island", Nature Genetics, 26:61-63.
expression

Lars Juhl Jensen, Steen Knudsen (2000), "Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation", Bioinformatics, 16(4):326-333.
[ PDF ]
CV Jongeneel (2000), "Searching the expressed sequence tag (EST) databases: panning for genes", Briefings in Bioinformatics, 1:76-92.
CV Jongeneel (2000), "The need for a human gene index" (editorial), Bioinformatics, 16(12):1059-1061.
promoter/TF

MV Katti, MK Sakharkar, PK Ranjekar, VS Gupta (2000), "TRES: comparative promoter sequence analysis", Bioinformatics, 16(8):739-740.
promoter/TF

A Klingenhoff, K Frech, T Werner (2000), "Regulatory modules shared within gene classes as well as across gene classes can be detected by the same in silico", In Silico Biology (online publication), 1:0020
[ html]
A Krogh (2000), "Using database matches with HMMGene for automated gene detection in Drosophila", Genome Research, 10(4):523-528.
[PDF]
annotation

S Lewis, M Ashburner, MG Reese (2000), "Annotating eukaryote genomes", Current Opinion in Structural Biology, 10(3):349-354.
[ abstract]
promoter/TF

L Marsay, MF Sagot (2000), "Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification", Journal of Computational Biology, 7(3/4):345-362.
annotation

SM Mount (2000), "Genomic sequence, splicing, and gene annotation", American Journal of Human Genetics, 67:788-792.
translation

Tetsuo Nishikawa, Toshio Ota , Takao Isogai (2000), "Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences", Bioinformatics, 16(11):960-967.
H Ogata, S Audic, V Barbe, F Artiguenave, PE Fournier, D Raoult, JM Claverie (2000), "Selfish DNA in protein coding genes of Rickettsia", Science, 290:347-350 .
promoter/TF

Uwe Ohler (2000), "Promoter prediction on a genomic scale - the Adh experience", Genome Research, 10(4):539-542.
[ PDF]
promoter/TF

Uwe Ohler, G Stemmer, S Harbeck, H Niemann (2000), "Stochastic segment models of eukaryotic promoter regions", Pacific Symposium on Biocomputing, 5:380-391.
G Parra, E Blanco, R Guigo (2000), "GeneID in Drosophila", Genome Research, 10(4):511-515.
[ PDF ]
SG Penn, DR Rank, DK Hanzel, DL Barker (2000), "Mining the human genome using microarrays of open reading frames", Nature Genetics, 26(3):315-318.
promoter/TF

RC Perier, V Praz, T Junier, C Bonnard, P Bucher (2000), "The eukaryotic promoter database (EPD)", Nucleic Acids Research, 28:302-303.
M Pertea, SL Salzberg, MJ Gardner (2000), "Finding genes in Plasmodium falciparum chromosome 3", Nature, 404:34.
[ PDF ]
A Pertsemlidis, A Pande, B Miller, P Schilling, MH Wei, MI Lerman, JD Minna, HR Garner (2000), "PANORAMA: an integrated web-based sequence analysis tool and its role in gene discovery", Genomics, 70:300-306.
[supplement material: http://atlas.swmed.edu/ (PANORAMA) ]
translation

G Pesole, G Grillo, A Larizza, S Liuni (2000), "The untranslated regions of eukaryotic mRNAs: structure, function, evolution and bioinformatic tools for their analysis", Briefings in Bioinformatics, 1(3):236-249.
annotation

MG Reese G Hartzell, NL Harris, U Ohler, JF Abril, SE Lewis (2000), "Genome annotation assessment in Drosophila melanogaster", Genome Research, 10(4):483-501.
MG Reese, D Kulp, H Tammana, D Haussler (2000), "Genie - gene finding in Drosophila melanogaster", Genome Research, 10(4):529-538.
[ PDF]
F Rodolphe, C Mathe (2000), "Translation conditional models for protein coding sequences", Journal of Computational Biology, 7(1-2):249-260.
IB Rogozin, GV Glozko, MV Glazkov (2000), "Computer prediction of sites associated with various elements of the nuclear matrix", Briefings in Bioinformatics, 1:33-44.
promoter/TF

E Roulet, P Bucher, R Schneider, E Wingender, Y Dusserre, T Werner, N Mermod (2000), "Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites", Journal of Molecular Biology, 297(4):833-48.
MK Sakharkar, P Kangueane, TW Woon, TW Tan, PR Kolatkar, M Long, SJ de Souza (2000), "IE-Kb: intron exon knowledge base", Bioinformatics, 16(12):1151-1152.
AA Salamov, VV Solovyev (2000), "Ab initio gene finding in Drosophila genomic DNA", Genome Research, 10(4);516-522.
[ PDF ]
promoter/TF

Matthias Scherf, Andreas Klingenhoff, Thomas Werner (2000), "Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach", Journal of Molecular Biology, 297:599-606.
[ PDF]
DB Searls (2000), "Bioinformatics tools for whole genomes", Annual Review of Genomics and Human Genetics, 1:251-279.
[ PDF]
Colin Semple (2000), "Gene prediction: the end of the beginning" (meeting report), Genome Biology , 1(2):reports4012.1-4012.3.
[PDF]
promoter/TF

Saurabh Sinha, Martin Tompa (2000), "A statistical method for finding transcription factor binding data", Proceedings of the eighth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp. 344-354.
D Slavov, M Hattori, Y Sakaki, A Rosenthal, N Shimizu, S Minoshima, J Kudoh, ML Yaspo, J Ramser, R Reinhardt, C Reimer, K Clancy, A Rynditch, K Gardiner (2000), "Criteria for gene identification and features of genome organization: analysis of 6.5 Mb of DNA sequence from human chromosome 21, Gene, 247:215-232.
alternative-splicing

S Stamm, J Zhu, K Nakai, P Stoilov, O Stoss, MQ Zhang (2000), "A alternative exon database (AEDB) and its statistical analysis", DNA & Cell Biology, 19:739-756.
promoter/TF

GD Stormo (2000), "DNA binding sites: representation and discovery", Bioinformatics, 16(1):16-23.
GD Stormo (2000), "Gene-finding approaches for eukaryotes", Genome Research, 10(4):394-397.
translation

Y Suzuki, D Ishihara, M Sasaki, H Nakagawa, H Hata, T Tsunoda, M Watanabe, T Komatsu, T Ota, T Isogai, A Suyama, S Sugano (2000), "Statistical analysis of the 5' untranslated region of human mRNA using 'oligo-capped' cDNA libraries", Genomics, 64:286-297.
splicing

TA Thanaraj (2000), "Positional characterisation of false positives from computational prediction Of human splice sites", Nucleic Acids Research, 28(3):744-754.
[ abstract]
TA Thanaraj, AJ Robinson (2000) . "Prediction of exact boundaries of exons", Briefings in Bioinformatics, 1(4):343-356.
annotation

TA Thanaraj, AJ Robinson, J Muilu, J-J Riethovan (2000), "Paradigm shifts in the approaches for gene annotation", Briefings in Bioinformatics, 1(4):324-330.
EC Thayer, C Bystroff, D Baker (2000), "Detection of protein coding sequences using a mixture model for local protein amino acid sequence", Journal of Computational Biology, 7(1-2):317-327.
splicing

J Usuka, V Brendel (2000), "Gene structure prediction by spliced alignment of genomic DNA with protein sequences: Increased accuracy by differential splice site scoring", Journal of Molecular Biology, 297:1075-1085.
splicing

J Usuka, W Zhu, V Brendel (2000), "Optimal spliced alignment of homologous cDNA to a genomic DNA template", Bioinformatics, 16(3):203-211.
[abstract]
promoter/TF

J van Helden (2000), "A web site for the computational analysis of yeast regulatory sequences", Yeast, 16(2):177-187.
promoter/TF

J van Helden, AF Rios, J Collado-Vides (2000), "Discoverying regulatory elements in non-coding sequences by analysis of spaced dyads", Nucleic Acids Research, 28(8):1808-1818.
expression

Jaak Vilo, Alvis Brazma, Inge Jonassen, Alan Robinson, Esko Ukkonen (2000), "Mining for putative regulatory elements in the yeast genome using gene expression data", Proceedings of the eighth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp. 384-394.
promoter/TF

WW Wasserman, M Palumbo, W Thompson, JW Fickett, CE Lawrence (2000), "Human-mouse genome comparisons to locate regulatory sites", Nature Genetics, 26:225-227.
promoter/TF

T Werner, E Wingender (2000), "In memory of Dan S. Prestridge", In Silico Biology (online publication), 1:0022.
[ html]
similarity

T Wiehe, R Guigo, W Miller (2000), "Genome sequence comparisons: hurdles in the fast lane to functional genomics", Briefings in Bioinformatics, 1(4):381-388.
promoter/TF

CT Workman, GD Storm (2000), "ANN-spec: a method for discovering transcription factor binding sites with improved specificity", Pacific Symposium on Biocomputing, 5:464-475.
[ PDF ]
CT Zhang, J Wang (2000), "Recognition of protein coding genes in the yeast genome at better than 95% accuracy based an the Z curve", Nucleic Acids Research, 28(14):2804-2814.
MQ Zhang (2000), "Discriminant analysis and its application in DNA sequence motif recognition", Briefings in Bioinformatics, 1(4):331-342.
[ PDF ]
expression

J Zhu, MQ Zhang (2000), "Cluster, function and promoter: analysis of yeast expression array", Pacific Symposium on Biocomputing, 5:476-487.
[ PDF ]
translation

A Zien, G Ratsch, S Mika, B Scholkopf, T Lengauer, KR Muller (2000), "Engineering support vector machine kernels that recognize translation initiation sites", Bioinformatics, 16(9):799-807.