gene recognition papers (2000)

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2000

JF Abril, R Guigo (2000),
"gff2ps: visualizing genomic annotations",
Bioinformatics, 16(8):743-744.
V Bafna, DH Huson (2000),
"The conserved exon method for gene finding",
ISMB00.
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.
P Baldi, S Hampson, D Kibler, S Sandmeyer (2000),
"Analysis of yeast's ORF upstream regions by parallel processing, microarrays, and computational methods",
ISMB00.
Serafim Batzoglou, Lior Pachter, Jill Mesirov, Bonnie Berger, Eric S Lander (2000),
"Human and mouse gene structure: comparative analysis and application to exon prediction",
Proceedings of RECOMB'00,
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.
DL Black (2000),
"Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology",
Cell, 103(3):367-370.
WJ Bruno, I Holmes (2000),
"Finding regulatory elements using joint likelihoods for sequence and expression profile data",
ISMB00.
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.
Harmen Bussemaker, Hao Li, Eric Siggia (2000),
"Regulatory element detection using a probabilistic segmentation model",
ISMB00.
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]
D Cai, A Delcher, B Kao, S Kasif (2000),
"Modeling splice sites with Bayes networks",
Bioinformatics, 16(2):152-158.
JM Claverie (2000)
"Do we need a huge new centre to annotate the human genome?" (correspondence)
Nature, 403:12.
JM 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",
ISMB00.
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.
[ISIS is at http://isis.bit.uq.edu.au/a_splicers.html ]
RV Davuluri, Y Suzuki, S Sugano, MQ Zhang (2000),
"CART classification of human 5' UTR sequences",
Genome Research, 10:1807-1816.
[ PDF ]
David Elder (2000),
"Split gene origin and periodic introns",
Journal of Theoretical Biology, 207(4):455-472.
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.
I Goncalves, L DUret, D Mouchiroud (2000),
"Nature and structure of human genes that generate retropseudogenes",
Genome Research, 10:672-678.
[PDF]
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.
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 ]
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.
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.
Ian Holmes, William J Bruno (2000),
"Finding regulatory elements using joint likelihoods for sequence and expression profile data",
ISMB00.
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.
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.
IP Ioshikhes, MQ Zhang (2000),
"Large-scale human promoter mapping using CpG island",
Nature Genetics, 26:61-63.
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.
MV Katti, MK Sakharkar, PK Ranjekar, VS Gupta (2000),
"TRES: comparative promoter sequence analysis",
Bioinformatics, 16(8):739-740.
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]
S Lewis, M Ashburner, MG Reese (2000),
"Annotating eukaryote genomes",
Current Opinion in Structural Biology, 10(3):349-354.
Y Lou, E Splicer, S Hazard, Z Zhang (2000),
"Recognition of protein coding regions in human genomic DNA sequences,"
Journal of Computational Biology, in press.
L Marsay, M-F 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.
SM Mount (2000),
"Genomic sequence, splicing, and gene annotation",
American Journal of Human Genetics, 67:788-792.
Uwe Ohler (2000),
"Promoter prediction on a genomic scale - the Adh experience",
Genome Research, 10(4):539-542.
[ PDF]
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.
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.
http://atlas.swmed.edu/
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.
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.
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 ]
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]
Saurabh Sinha, Martin Tompa (2000),
"A statistical method for finding transcription factor binding data",
ISMB00.
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.
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.
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.
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.
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.
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.
M Tompa, S Saurabh (2000),
"A statistical method for finding transcription factor binding sites",
ISMB00.
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.
J Usuka, W Zhu, V Brendel (2000),
"Optimal spliced alignment of homologous cDNA to a genomic DNA template",
Bioinformatics, 16(3):203-211.
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.
Jaak Vilo, Alvis Brazma (2000),
"Mining for putative regulatory elements in the yeast genome using gene expression data",
ISMB00.
WW Wasserman, M Palumbo, W Thompson, JW Fickett, CE Lawrence (2000),
"Human-mouse genome comparisons to locate regulatory sites",
Nature Genetics, 26:225-227.
T Werner, E Wingender (2000),
"In memory of Dan S. Prestridge",
In Silico Biology (online publication), 1,0022.
[ html]
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.
CT Workman, GD Storm (2000),
"ANN-spec: a method for discovering transcription factor binding sites with improved specificity",
PSB00, 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 ]
J Zhu, MQ Zhang (2000),
"Cluster, function and promoter: analysis of yeast expression array",
PSB00, 5:476-487.
[ PDF ]
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.