gene recognition papers (2002)

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2002

DG Arques, J Lacan, CJ Michel (2002), "Identification of protein coding genes in genomes with statistical functions based on the circular code", Biosystems, 66:73-92.
promoter/TF

VB Bajic, A Chong, SH Seah, V Brusic (2002), "Intelligent system for vertebrate promoter recognition", IEEE Intelligent Systems, 17(4):64-70.
[ PDF]
promoter/TF

VB Bajic, SH Seah, A Chong, G Zhang, JLY Koh, V Brusic (2002), "Dragon promoter finder: recognition of vertebrate RNA polymerase II promoters", Bioinformatics, 18(1):198-199.
[PDF]
VB Bajic, S Tang, H Han, V Brusic, AG Hatzigeorgiou (2002), "Artificial neural networks based systems for recognition of genomic signals and regions: a review", Informatica, 26:389-400.
L Bao, Z Sun (2002), "Identifying genes related to drug anticancer mechanisms using support vector machine", FEBS Letters, 521(1-3):109-114.
MV Baytaluk, MS Gelfand, AA Mironov (2002), "Exact mapping of prokaryotic gene starts", Briefings in Bioinformatics, 3(2):181-194.
promoter/TF

M Blanchette, B Schwikowski, M Tompa (2002), "Algorithms for phylogenetic footprinting", Journal of Computational Biology, 9(2):211-223.
promoter/TF

M Blanchett, M Tompa (2002), "Discovery of regulatory elements by a computational method for phylogenetic footprinting", Genome Research, 12:739-748.
E Blanco, G Parra, R Guigo (2002), "Using geneid to identify genes", in Current Protocols in Bioinformatics , Vol. 1 eds. AD Baxevanis, DB Davison (John Wiley & Sons), pp.?-?.
annotation

Stephanie Bocs, Antoine Danchin, Claudine Medigue (2002), "Re-annotation of genome microbial CoDing-sequences: finding new genes and inaccurately annotated genes", BMC Bioinformatics, 3:5.
[ abstract]
V Brendel, W Zhu (2002), "Computational modeling of gene structure in Arabidopsis thaliana", Plant Mol. Biol., 48:49-58.
MR Brent (2002), "Predicting full-length transcripts", Trends in Biotechnology, 20(7):273-275.
Brona Brejova, Tomas Vinar (2002), "A better method for length distribution modeling in HMMs and its application to gene finding", in Combinatorial Pattern Matching, 13th Annual Symposium (CPM), 2373 volume of Lecture Notes in Computer Science, eds. A Apostolico, M Takeda, pp.190-202 (Springer).
alternative-splicing

D Brett, H Pospisil, J Valcarcel, J Reich, P Bork (2002), "Alternative splicing and genome complexity", Nature Genetics, 30(1):29-30.
promoter/TF

J Buhler, M Tompa (2002), "Finding motifs using random projections", Journal of Computational Biology, 9(2):225-242.
annotation

AA Camargo, SJ de Souza, RR Brentani, AJ Simpson (2002), "Human gene discovery through experimental definition of transcribed regions of the human genome", Current Opinion in Chemical Biology, 6(1):13-16.
P Carpena, P Bernaola-Galván, R Román-Roldán, JL Oliver (2002), "A simple and species-independent coding measure", Gene, 300(1-2):97-104.
[ abstract]
expression

Michele Caselle, Ferdinando Di Cunto, Paolo Provero (2002), "Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes", BMC Bioinformatics, 3:7.
[html]
promoter/TF

Hangil Chang (2002), "Development of an efficient method to search conserved noncoding sequences", Genome Informatics, 13:299-300.
promoter/TF

VV Chasov, AA Deev, IS Masulis, ON Ozoline (2002), "Distribution and functional significance of A/T tracts in promoter sequences of Escherichia coli", Molecular Biology (Molekulyarnaya Biologiya), 36(4):537-542.
translation

A Chong, G Zhang, VB Bajic (2002), "Information and sequence extraction around the 5'-end and translation initiation site of human genes", In Silico Biology, 2:0041.
[ html ]
alternative-splicing

F Clark, TA Thanaraj (2002), "Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human", Human Molecular Genetics, 11(4):451-464.
[ abstract]
T Clark, S Lee, LR Scott, SM Wang (2002), "Computational analysis of gene identification with SAGE", Journal of Computational Biology, 9(3):513-526.
translation

Darrell Conklin, Inge Jonassen, Rein Aasland, William R. Taylor (2002), "Association of nucleotide patterns with gene function classes: application to human 3' untranslated sequences", Bioinformatics, 18:182-189.
promoter/TF

TA Down, TJP Hubbard (2002), "Computational detection and location of transcription start sites in mammalian genomic DNA", Genome Research, 12(3):458-461.
E Eskin, PA Pevzner (2002), "Finding composite regulatory patterns in DNA sequences", Bioinformatics, 18:S354-S363.
splicing

W Fairbrother, RF Yeh, PA Sharp, CB Burge (2002), "Predictive identification of exonic splicing enhancers in human genes", Science, 297:1007-1013.
J Freudenberg, P Propping (2002), "A similarity-based method for genome-wide prediction of disease-relevant human genes", Bioinformatics, 18(supp 2):S110-S115.
Matthias Frisch, Kornelie Frech, Andreas Klingenhoff, Kerstin Cartharius, Ines Liebich, Thomas Werner (2002), "In Silico prediction of scaffold/matrix attachment regions in large genomic sequences", Genome Research, 12:349-354.
promoter/TF

Alexandre Gattiker, Elisabeth Gasteiger, Amos Bairoch (2002), "ScanProsite: a reference implementation of a PROSITE scanning tool", Applied Bioinformatics Journal, 1(2):51-52.
promoter/TF

Ulrich Gerland, J. David Moroz, Terence Hwa (2002), "Physical constraints and functional characteristics of transcription factor-DNA interaction", Proceedings of National Academy of Sciences, 99:12015-12020.
translation

JH Graber, GD McAllister, TF Smith (2002), "Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites", Nucleic Acids Research, 30(8):1851-1858.
[abstract]
promoter/TF

Marc S Halfon, Yonatan Grad, George M Church, Alan M Michelson (2002), "Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model", Genome Research, 12:1019-1028.
Paul M Harrison, Hedi Hegyi, Suganthi Balasubramanian, Nicholas M Luscombe, Paul Bertone, Nathaniel Echols, Ted Johnson, Mark Gerstein (2002), "Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22 ", Genome Research, 12:272-280.
translation

Artemis G. Hatzigeorgiou (2002), "Translation initiation start prediction in human cDNAs with high accuracy ", Bioinformatics, 18:343-350.
[abstract] [PDF]
promoter/TF

Jorng-Tzong Horng, Hsien-Da Huang, Shir-Ly Huang, Ueng-Cheng Yang and Yu-Chang Chang (2002), "Mining putative regulatory elements in gene promoter regions of Saccharomyces cerevisiae", In Silico Biology, 2:0026.
annotation

T. Hubbard, D. Barker, E. Birney1, G. Cameron, Y. Chen, L. Clark, T. Cox, J. Cuff, V. Curwen, T. Down, R. Durbin, E. Eyras, J. Gilbert, M. Hammond, L. Huminiecki, A. Kasprzyk, H. Lehvaslaiho, P. Lijnzaad, C. Melsopp, E. Mongin, R. Pettett, M. Pocock, S. Potter, A. Rust, E. Schmidt, S. Searle, G. Slater, J. Smith, W. Spooner, A. Stabenau, J. Stalker, E. Stupka, A. Ureta-Vidal, I. Vastrik and M. Clamp (2002), "The Ensembl genome database project", Nucleic Acids Research, 30(1):38-41.
[abstract]
Biju Issac, Harpreet Singh, Harpreet Kaur, GPS Raghava (2002), "Locating probable genes using Fourier transform approach", Bioinformatics, 18:196-197.
annotation

P Kapranov, SE Cawley, J Drenkow, S Bekiranov, RL Strausberg, SP Fodor, TR Gingeras (2002), "Large-scale transcriptional activity in chromosomes 21 and 22", Science, 296(5569):916-919.
U Keich, PA Pevzner (2002), "Finding motifs in the twilight zone", Proceedings of the sixth international conference on Research in Computational Molecular Biology, pp.195-204.
promoter/TF

Sunduz Keles, Mark van der Laan, Michael B Eisen (2002), "Identification of regulatory elements using a feature selection method", Bioinformatics, 18:1167-1175.
[PDF]
promoter/TF

OV Kel-Margoulis, TG Ivanova, E Wingender, AE Kel (2002), "Automatic annotation of genomic regulatory sequences by searching for composite clusters", Pacific Symposium on Biocomputing, 7:187-198.
promoter/TF

OV Kel-Margoulis, AE Kel, I Reuter, IV Deineko, E Wingender (2002), "TRANSCompel: a database on composite regulatory elements in eukaryotic genes", Nucleic Acids Research, 30(1):332-334.
translation

AV Kochetov, OA Sirnik, IB Rogosin, GV Glazko, ML Komarova, VK Shumny (2002), "Contextual features of higher plant mRNA 5'-untranslated regions", Molecular Biology (Molekulyarnaya Biologiya), 36(4):510-516.
alternative-splicing

Hiromi Kochiwa, Ryosuke Suzuki, Takanori Washio, Rintaro Saito, The RIKEN Genome Exploration Research Group Phase II Team, Hidemasa Bono, Piero Carninci, Yasushi Okazaki, Rika Miki, Yoshihide Hayashizaki, and Masaru Tomita (2002), "Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data", Genome Research, 12:1286-1293.
MJ Korenberg, ED Lipson, JR Green, JE Solomon (2002), "Parallel cascade recognition of exon and intron DNA sequences", Annals of Biomedical Engineering, 30(1):129-140.
AS Kutsenko, RZ Gizatullin, AN Al-Amin, F Wang, SM Kvasha, RM Podowski, YG Matushkin, A Gyanchandani, OV Muravenko, VG Levitsky, NA Kolchanov, AI Protopopov, VI Kashuba, LL Kisselev, W Wasserman, C Wahlestedt, ER Zabarovsky (2002), "NotI flanking sequences: a tool for gene discovery and verification of the human genome", Nucleic Acids Research, 30(14):3163-3170.
VA Kuznetsov, VV Pickalov, OV Senko, GD Knott (2002), "Analysis of the evolving proteomes: predictions of the number of protein domains in nature and the number of genes in eukaryotic organisms", Journal of Biological Systems, 10(4):381-407.
[PDF]
promoter/TF

Boris Lenhard and Wyeth W. Wasserman (2002), "TFBS: Computational framework for transcription factor binding site analysis", Bioinformatics, 18:1135-1136.
MJ Lercher, AO Urrutia, LD Hurst (2002), "Clustering of housekeeping genes provides a unified model of gene order in the human genome", Nature Genetics, 31(2):180-183.
W Li, P Bernaola-Galvan, F Haghighi, I Grosse (2002), "Applications of recursive segmentation to the analysis of DNA sequences", Computers & Chemistry, 26(5):491-510.
[ abstract]
promoter/TF

XS Liu, DL Brutlag, JS Liu (2002), "An algorithm for finding protein DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments", Nature Biotechnology, 20(8):835-839.
annotation

Ann E Loraine and Gregg A Helt (2002), "Visualizing the genome: techniques for presenting human genome data and annotations", BMC Bioinformatics, 3:19.
annotation

P Mackiewicz, M Kowalczuk, D Mackiewicz, A Nowicka, M Dudkiewicz, A Laszkiewicz, MR Dudek, S Cebrat (2002), "How many protein-coding genes are there in the Saccharomyces cerevisiae genome?", Yeast, 19(7):619-629.
expression

Václav Mach (2002), "PRESTA: associating promoter sequences with information on gene expression", Genome Biology, 3(9):research0050.
[html]
V Makarov (2002), "Computer programs for eukaryotic gene prediction", Briefings in Bioinformatics, 3(2):195-199.
Catherine Mathe, Marie-France Sagot, Thomas Schiex, Pierre Rouze (2002), "Current methods of gene prediction, their strengths and weaknesses", Nucleic Acids Research, 30:4103-4117.
[abstract] [html]
promoter/TF

Xavier Messeguer, Ruth Escudero, Domčnec Farré, Oscar Núńez, Javier Martínez, M.Mar Albŕ (2002), "PROMO: detection of known transcription regulatory elements using species-tailored searches", Bioinformatics, 18:333-334.
alternative-splicing

Barmak Modrek, Christopher Lee (2002), "A genomic view of alternative splicing", Nature Genetics, 30(1):13-19.
Burkhard Morgenstern, Oliver Rinner, Saďd Abdeddaďm, Dirk Haase, Klaus F. X. Mayer, Andreas W. M. Dress, and Hans-Werner Mewes (2002), "Exon discovery by genomic sequence alignment", Bioinformatics, 18:777-787.
Anton Nekrutenko, Kateryna D Makova, Wen-Hsiung Li (2002), "The K_A/K_S ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study", Genome Research, 12:198-202.
H Ogata, S Audic, C Abergel, PE Fournier, JM Claverie (2002) , "Protein coding palindromes are a unique but recurrent feature in Rickettsia", Genome Research, 12:808-816.
promoter/TF

U Ohler, GC Liao, H Niemann, GM Rubin (2002), "Computational analysis of core promoters in the Drosophila genome", Genome Biology, 3(12):research0087.
Guy Oshiro, Lisa M Wodicka, Michael P Washburn, John R Yates III, David J Lockhart, Elizabeth A Winzeler (2002), "Parallel identification of new genes in Saccharomyces cerevisiae", Genome Research, 12:1210-1220.
annotation

Ouzounis CA, Karp PD (2002), "The past, present and future of genome-wide re-annotation", Genome Biology, 3(2):comment2001.
translation

Y Ozawa, S Hanaoka, R Saito, T Washio, S Nakano, A Shinagawa, M Itoh, K Shibata, P Carninci, H Konno, J Kawai, Y Hayashizaki, M Tomita (2002), "Comprehensive sequence analysis of translation termination sites in various eukaryotes", Gene, 300(1-2):79-87.
[ abstract] [PDF ]
L Pachter, M Alexandersson, S Cawley (2002), "Application of generalized pair Hidden Markov Models to alignments and gene finding problems", Journal of Computational Biology, 9(2):389-400.
promoter/TF

DA Papatsenko, VJ Makeev, AP Lifanov, M Regnier, AG Nazina, C Desplan (2002), "Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers", Genome Research, 12(3):470-81.
Donald J Patterson, Ken Yasuhara, Walter L Ruzzo (2002), "Pre-mRNA secondary structure prediction aids splice site prediction", Pacific Symposium on Biocomputing, 7:223-234.
Vladimir Pavlovic, Ashutosh Garg, Simon Kasif (2002), "A Bayesian framework for combining gene predictions", Bioinformatics, 18:19-27.
M Pertea M, SL Salzberg (2002), "Computational gene finding in plants", Plant Mol Biol., 48(1-2):39-48.
Loďc Ponger and Dominique Mouchiroud (2002), "CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences", Bioinformatics, 18:631-633.
promoter/TF

Nikolaus Rajewsky, Nicholas D Socci, Martin Zapotocky, Eric D Siggia (2002), "The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons", Genome Research, 12:298-308.
annotation

A Reymond, AA Camargo, S Deutsch, BJ Stevenson, RB Parmigiani, C Ucla, F Bettoni, C Rossier, R Lyle, M Guipponi, S de Souza, C Iseli, CV Jongeneel, P Bucher, AJ Simpson, SE Antonarakis (2002)l "Nineteen additional unpredicted transcripts from human chromosome 21", Genomics, 79(6):824-832.
Sanja Rogic, BF Francis Ouellette, Alan K Mackworth (2002), "Improving gene recognition accuracy by combining predictions from two gene-finding programs", Bioinformatics, 18:1034-1045.
annotation

S Saha, AB Sparks, C Rago, V Akmaev, CJ Wang, B Vogelstein, KW Kinzler, VE Velculescu (2002), "Using the transcriptome to annotate the genome", Nature Biotechnology, 20(5):508-512.
A Sakurai, S Fujimori, H Kochiwa, S Kitamura-Abe, T Washio, R Saito, The RIKEN Genome Exploration Research Group Phase II Team, P Carninci, Y Hayashizaki, M Tomita (2002), "On biased distribution of introns in various eukaryotes", Gene, 300(1-2):89-95.
[ abstract]
J Shendure, GM Church (2002), "Computational discovery of sense-antisense transcription in the human and mouse genomes", Genome Biology, 3:1-14.
promoter/TF

S Sinha, M Tompa (2002), "Discovery of novel transcription factor binding sites by statistical overrepresentation", Nucleic Acids Research, 30(24):5549-5560.
SH Sze, MS Gelfand, PA Pevzner (2002), "Finding weak motifs in DNA sequences", Pacific Symposium on Biocomputing, 7:235-246.
alternative-splicing

Rotem Sorek, Gil Ast, Dan Graur (2002), "Alu-containing exons are alternatively spliced", Genome Research, 12:1060-1067.
LZ Strichman-Almashanu, RS Lee, PO Onyango, E Perlman, F Flam, MB Frieman, AP Feinberg (2002), "A genome-wide screen for normally methylated human CpG islands that can identify novel imprinted genes", Genome Research, 12(4):543-554.
annotation

AI Su, MP Cooke, KA Ching, Y Hakak, JR Walker, T Wiltshire, AP Orth, RG Vega, LM Sapinoso, A Moqrich, A Patapoutian, GM Hampton, PG Schultz, JB Hogenesch (2002), "Large-scale analysis of the human and mouse transcriptomes", Proceedings of the National Academy of Sciences, 99(7):4465-4470.
promoter/TF

G Thijs, K Marchal, M Lescot, S Rombauts, D de Moor, P Rouze, Y Moreau (2002), "A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes", Journal of Computational Biology, 9(2):447-?.
expression

Brian Tjaden, David R. Haynor, Sergey Stolyar, Carsten Rosenow, Eugene Kolker (2002), "Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis", Bioinformatics, 18:S337-S344.
promoter/TF

L Tsai, L Luo, Z Sun (2002), "Sequence-dependent flexibility in promoter sequences", Journal of Biomolecular Structure and Dynamics, 20(1):127-134.
promoter/TF

Erik van Nimwegen, Mihaela Zavolan, Nikolaus Rajewsky, Eric D Siggia (2002), "Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics", Proceedings of the National Academy of Sciences, 99:7323-7328.
promoter/TF

Eugenii E Vityaev, Yury L Orlov, Oleg V Vishnevsky, Mikhail A Pozdnyakov, Nikolay A Kolchanov (2002), "Computer system 'Gene Discovery' for promoter structure analysis ", In Silico Biology, 2:0024.
Y Wang, CT Zhang, P Dong (2002), "Recognizing shorter coding regions of human genes based on the statistics of stop codons", Biopolymers, 63:207-216.
[ PDF ]
promoter/TF

Thomas Werner (2002), "Finding and decrypting of promoters contributes to the elucidation of gene function", In Silico Biology, 2:0023.
alternative-splicing

Q Xu, B Modrek, C Lee (2002), "Genome-wide detection of tissue-specific alternative splicing in the human transcriptome", Nucleic Acids Research, 30:3754-3766.
Zhenyu Xuan, W Richard McCombie, Michael Q Zhang (2002), "GFScan: A gene family search tool at genomic DNA level", Genome Research, 12:1142-1149.
Edouard Yeramian, Serge Bonnefoy, Gordon Langsley (2002), "Physics-based gene identification: proof of concept for Plasmodium falciparum Bioinformatics, 18:190-193.
alternative-splicing

M Zavolan, E van Nimwegen, T Gaasterland (2002), "Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome", Genome Research, 12(9):1377-1385.
CT Zhang, J Wang, R Zhang (2002), "Using a Euclid distance discriminant method to find protein coding genes in the yeast genome", Computers & Chemistry, 26:195-206.
CT Zhang, R Zhang (2002), "Evaluation of gene-finding algorithms by a content-balancing accuracy index", Journal of Biomolecular Structure and Dynamics, 19:1045-1052.
[ PDF]
J Zhang, XF Shi (2002), "Tentative study of the coding sequences without 3-base periodicity" (in Chinese), Progress in Biochemistry and Biophysics, 29(2):267-272.
Michael Q. Zhang (2002), "Computational prediction of eukaryotic protein-coding genes", Nature Reviews Genetics, 3:698-709.
[abstract]
promoter/TF

MQ Zhang (2002), "Computational methods for promoter recognition", in Current Topics in Computational Molecular Biology, eds. T Jiang, Y Xu, MQ Zhang (MIT Press).
promoter/TF

Yu Zheng, Joseph D Szustakowski, Lance Fortnow, Richard J Roberts, Simon Kasif (2002), "Computational identification of operons in microbial genomes", Genome Research, 12:1221-1230.
similarity

Wei Zhu, Volker Brendel (2002), "Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictions", Bioinformatics, 18:761-762.