gene recognition papers (2001)

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2001

annotation

Michael Ashburner, Catherine A. Ball, Judith A. Blake, Heather Butler, J. Michael Cherry, John Corradi, Kara Dolinski, Janan T. Eppig, Midori Harris , David P. Hill, Suzanna Lewis, Brad Marshall , Chris Mungall, Leonore Reiser, Sue Rhee, Joel E. Richardson, John Richte, Martin Ringwald, Gerald M. Rubin, Gavin Sherlock , J. Yoon (The Gene Ontology Consortium) (2001), "Creating the gene ontology resource: design and implementation", Genome Research, 11(8):1425-1433.
J Besemer, A Lomsadze, M Borodovsky (2001) , "GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions", Nucleic Acids Research, 29:2607-2618.
[abstract]
similarity

MJ Betts, R Guigo, P Agarwal, RB Russel (2001), "Exon structure conservation despite low sequence similarity: a relic of dramatic events in evolution?" EMBO Journal , 20(19):5354-5360.
alternative-splicing

Michael Brudno, Mikhail S Gelfand, Sylvia Spengler, Manfred Zorn, Inna Dubchak, and John G. Conboy (2001), "Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing", Nucleic Acids Research, 29:2338-2348.
[PDF]
splicing

Chris Burge (2001), "Chipping away at the transcriptome", Nature Genetics, 27:4-6.
Chris Burge, M Das, E Park, J Colinas, J Pelletier (2001), "Assessment of the total number of human transcription units", Genomics, 77:71-78.
splicing

M Burset, IA Seledtsov, VV Solovyev (2001), "SpliceDB: Database of canonical and non-canonical mammalian splice sites." Nucleic Acid Research, 29(1):255-259.
expression

HJ Bussemaker, H Li, ED Siggia (2001), "Regulatory element detection using correlation with expression", Nature Genetics, 27:167-171.
[ PDF]
annotation

Camargo AA, Samaia HP, Dias-Neto E, Simao DF, Migotto IA, 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, Sonati MF, Tajara EH, Valentini SR, Alberto FL, Amaral ME, Aneas I, Arnaldi LA, de Assis AM, Bengtson MH, Bergamo NA, Bombonato V, de Camargo ME, Canevari RA, Carraro DM, Cerutti JM, Correa ML, Correa RF, Costa MC, Curcio C, Hokama PO, Ferreira AJ, Furuzawa GK, Gushiken T, Ho PL, Kimura E, Krieger JE, Leite LC, Majumder P, Marins M, Marques ER, Melo AS, Melo MB, Mestriner CA, Miracca EC, Miranda DC, Nascimento AL, Nobrega FG, Ojopi EP, Pandolfi JR, Pessoa LG, Prevedel AC, Rahal P, Rainho CA, Reis EM, Ribeiro ML, da Ros N, de Sa RG, Sales MM, Sant'anna SC, dos Santos ML, da Silva AM, da Silva NP, Silva WA Jr, da Silveira RA, Sousa JF, Stecconi D, Tsukumo F, Valente V, Soares F, Moreira ES, Nunes DN, Correa RG, Zalcberg H, Carvalho AF, Reis LF, Brentani RR, Simpson AJ, de Souza SJ, Melo M (2001), "The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome", Proceedings of National Academy of Sciences , 98(21):12103-12108.
H Caron, B van Schaik, M van der Mee, F Baas, G Riggins, P van Sluis, M-C Hermus, R van Asperen, K Boon, PA Voute, S Heisterkamp, A van Kampen, R Versteeg (2001), "The human transcriptome map: clustering of highly expressed genes in chromosomal domains", Science, 291:1289-1292.
S Castellano, N Morozova, M Morey, MJ Berry, F Serras, M Corominas, R Guigo (2001), "in silico identification of novel selenoproteins in the Drosophila melanogaster genome", EMBO Reports, 2(8):697-702.
SE Cawley, AI Wirth, TP Speed (2001), "Phat - a gene finding program for Plasmodium falciparum", Molecular and Biochemical Parasitology, 118(2):167-174.
T Chen (2001), "Gene-finding via tandem mass spectrometry", Proceedings of the fifth international conference on Research in Computational Molecular Biology, pp.87-94.
expression

Derek Y Chiang, Patrick O Brown, Michael B Eisen (2001), "Discovery of regulatory elements from microarray data using genome mean expression profiles", Bioinformatics, 17:S49-S55.
Jean-Michel Claverie (2001), "What if there are only 30,000 human genes?" Science, 1291:1255-1257.
LV Danilova, K Yu Gorbunov, MS Gelfand, VA Lyubetskii (2001), "Algorithm of regulatory signal recognition in DNA sequences", Molecular Biology (Molekulyarnaya Biologiya), 35(6):841-848.
M Das, CB Burge, E Park, J Colinas, J Pelletier (2001), "Assessment of the total number of human transcription units", Genomics, 77(1-2):71-78.
Duncan Davidson, Richard Baldock (2001), "Bioinformatics beyond sequence mapping gene function in the embryo", Nature Reviews Genetics, 2:409-417.
promoter/TF

R V Davuluri, I Grosse, MQ Zhang (2001), "Computational identification of promoters and first exons in the human genome", Nature Genetics, 29:412-417.
Sean R Eddy (2001), "Non-coding RNA genes and the modern RNA world", Nature Reviews Genetics, 2:919-929.
MD Ermolaeva, O White, SL Salzberg (2001), "Prediction of operons in microbial genomes", Nucleic Acids Research, 29(5):1216-1221.
Martin C Frith, Ulla Hansen, Zhiping Weng (2001), "Detection of cis -element clusters in higher eukaryotic DNA ", Bioinformatics, 17: 878-889.
promoter/TF

Wataru Fujibuchi, John SJ Anderson, David Landsman (2001), "PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches", Nucleic Acids Research, 29:3988-3996.
AV Gerasimova, DA Rodionov, AA Mironov, MS Gelfand (2001), "Computer analysis of regulatory signals in bacterial genomes. Fnr binding sites", Molecular Biology (Molekulyarnaya Biologiya), 35(6):853-861.
promoter/TF

Ulrich Gerland, Terence Hwa (2001), "On the selection and evolution of regulatory DNA motifs", arXiv preprint, physics/0112039. [ abstract]
alternative-splicing

Brenton R Graveley (2001), "Alternative splicing: increasing diversity in the proteomic world", Trends in Genetics, 17(2):100-107.
AN Gorban, A Yu Zinovyev, TG Popova (2001), "Statistical approaches to automated gene identification without teacher", Institut des Hautes Etudes Scientifiques Preprint. IHES M/01/34.
[ PDF ]
promoter/TF

Debraj GuhaThakurta, Gary D Stormo (2001), "Identifying target sites for cooperatively binding factors", Bioinformatics, 17:608-621.
[ PDF ]
promoter/TF

Sridhar Hannenhalli, Samuel Levy (2001), "Promoter prediction in the human genome", Bioinformatics, 17:S90-S96.
promoter/TF

Artemis G Hatzigeorgiou, Petko Fiziev, Martin Reczko (2001), "DIANA-EST: a statistical analysis", Bioinformatics, 17: 913-919.
promoter/TF

R Hehl, E Wingender (2001), "Database-assisted promoter analysis", Trends in Plant Science, 6(6):251-255.
promoter/TF

R Hershberg, G Bejerano, A Santos-Zavaleta, H Margalit (2001), "PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites", Nucleic Acids Research, 29(1):277
annotation

JB Hogenesch, KA Ching, S Batalov, AI Su, JR Walker, Y Zhou, SA Kay, PG Schultz, MP Cooke (2001), "A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes", Cell, 106(4):413-415.
alternative-splicing

Gang Ken Hu, Steven J Madore, Brian Moldover, Tim Jatkoe, David Balaban, Jeffrey Thomas, and Yixin Wang (2001), "Predicting splice variant from DNA chip expression data", Genome Research, 11:1237-1245.
promoter/TF

R Hu, B Wang (2001), "Statistically significant strings are related to regulatory elements in the promoter regions of Saccharomyces cerevisiae", Physica A, 290(3-4):464-474.
annotation

Iliopoulos I, Tsoka S, Andrade MA, Janssen P, Audit B, Tramontano A, Valencia A, Leroy C, Sander C, Ouzounis CA (2001), "Genome sequences and great expectations", Genome Biology, 2(1):interactions0001.
expression

LM Jakt, L Cao, KSE Cheah, DK Smith (2001), "Assessing clusters and motifs from gene expression data", Genome Research, 11:112-113.
[ PDF]
alternative-splicing

Zhengyan Kan, Eric C Rouchka, Warren R Gish, David J States (2001), "Gene structure prediction and alternative splicing analysis using genomically aligned ESTs ", Genome Research, 11(5):889-900.
[abstract] [related web page at http://stl.wustl.edu/~zkan/TAP/ ]
promoter/TF

AE Kel, OV Kel-Margoulis, PJ Farnham, SM Bartley, E Wingender, MQ Zhang (2001), "Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors", Journal of Molecular Biology, 309(1):99-120.
Szymon M Kielbasa, Jan O Korbel, Dieter Beule, Johannes Schuchhardt, Hanspeter Herzel (2001), "Combining frequency and positional information to predict transcription factor binding sites", Bioinformatics, 17:1019-1026.
NA Kolchanov, OA Podkolodnaya, EA Ananko, EV Ignatieva, NL Podkolodnyi, VM Merkulov, IL Stepanenko, MA Pozdnyakov, OE Belova, DA Grigorovich, AN Naumochkin (2001), "Transcription regulation of eukaryotic genes: description in the TRRDatabase", Molecular Biology (Molekulyarnaya Biologiya), 35(6):794-801.
similarity

Ian Korf, Paul Flicek, Daniel Duan, Michael R Brent "Integrating genomic homology into gene structure prediction", Bioinformatics, 17:S140-S148.
M Kozak (2001), "Extensively overlapping reading frames in a second mammalian gene", EMBO Report, 2(9):768-769.
translation

M Kozak (2001), "New ways of initiating translation in eukaryotes?" Molecular and Cellular Biology, 21(6):1899-1907.
Eileen Kraemer, Jian Wang, Jinhua Guo, Samuel Hopkins, and Jonathan Arnold (2001), "An analysis of gene-finding programs for Neurospora crassa ", Bioinformatics, 17:901-912.
promoter/TF

William Krivan, Wyeth W Wasserman (2001), "A predictive model for regulatory sequences directing liver-specific transceiption", Genome Research, 11(9):1559-1566.
J Lacan, CJ Michel (2001), "Analysis of a circular code model", Journal of Theoretical Biology, 213:159-170.
annotation

C Lee, K Irizarry (2001), "The GeneMine system for genome/proteome annotation and collaborative data-mining", IBM Systems Journal, 40:592-603.
promoter/TF

VG Levitsky, AV Katokhin (2001), "Computer analysis and recognition of Drosophila melanogaster gene promoters", Molecular Biology (Molekulyarnaya Biologiya), 35(6):826-832.
promoter/TF

Victor G Levitsky, Olga A Podkolodnaya, Nikolay A Kolchanov, Nikolay L Podkolodny (2001), "Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis", Bioinformatics, 17: 998-1010.
promoter/TF

Samuel Levy, Sridhar Hannenhalli, and Christopher Workman (2001), "Enrichment of regulatory signals in conserved non-coding genomic sequence", Bioinformatics, 17:871-877.
promoter/TF

JD Lieb, X Liu, D Botstein, PO Brown (2001), "Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association", Nature Genetics, 28(4):327-334.
LP Lim, CB Burge (2001), "A computational analysis of sequence features involved in recognition of short introns", Proceedings of National Academy of Sciences , 98:11193-11198.
X Liu, DL Brutlag, JS Liu (2001), "BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-existing genes", Pacific Symposium on Biocomputing, 6:127-138.
annotation

Izabela Makalowska, Joseph F Ryan, Andreas D Baxevanis (2001), "GeneMachine: gene prediction and sequence annotation ", Bioinformatics, 17:843-844.
promoter/TF

IS Masulis, VV Chasov, EG Kostyanitsyna, Yu A Purtov, ON Ozoline "Sequence-determined conformational changes downstream of the promoter DNA on transcription complex formation", Molecular Biology (Molekulyarnaya Biologiya), 35(6):849-852.
similarity

Andrey A Mironov, Pavel S Novichkov, and Mikhail S Gelfand (2001), "Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors", Bioinformatics, 17:13-15.
alternative-splicing

B Modrek, A Resch, C Grasso, C Lee (2001), "Genome-wide analysis of alternative splicing using human expressed sequence data", Nucleic Acids Research, 29:2850-2859.
David Mount (2001), Bioinformatics: Sequence and Genome , Chapter 8, Gene Prediction. (Cold Spring Harbor Laboratory Press).
KR Muller, S Mika, G Ratsch, K Tsuda, B Scholkopf (2001), "An introduction to kernel-based learning algorithms", IEEE Transactions on Neural Networks, 12(2):181-201.
PS Novichkov, MS Gelfand, AA Mironov (2001), "Gene recognition in eukaryotic DNA by comparison of genomic sequences", Bioinformatics,17:1011-1018.
[ abstract]
promoter/TF

Uwe Ohler, Heinrich Niemann (2001), "Identification and analysis of eukaryotic promoters: recent computational approaches", Trends in Genetics, 17(2):56-60.
promoter/TF

Uwe Ohler, Heinrich Niemann, Guo-chun Liao, Gerald M Rubin (2001), "Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition", Bioinformatics, 17:S199-S206.
Justin M O'Sullivan, J Bernard Davenport, Mick F Tuite (2001), "Codon reassignment and the evolving genetic code: problems and pitfalls in post-genome analysis", Trends in Genetics, 17(1):20-22.
L Pachter, M Alexandersson, S Cawley (2001), "Applications of generalized pair hidden Markov models to alignment and gene finding problems Proceedings of the fifth international conference on Research in Computational Molecular Biology, pp.241-248.
Marco Pagni, Christian Iseli, Thomas Junier, Laurent Falquet, Victor Jongeneel, Philipp Bucher (2001), "trEST, trGEN and Hits: access to databases of predicted protein sequences ", Nucleic Acids Research, 29:148-151.
P Pavlidis, TS Furey, M Liberto, D Haussler, WN Grundy (2001), "Promoter region-based classification of genes", Pacific Symposium on Biocomputing, 6:151-163.
promoter/TF

LA Pennacchio, EM Rubin (2001), "Genomic strategies to identify mammalian regulatory sequences", Nature Reviews Genetics, 2(2):100-109.
[abstract]
splicing

M Pertea, X Lin, SL Salzberg (2001), "GeneSplicer: a new computational method for splice site prediction", Nucleic Acids Research, 29(5):1185-1190.
[abstract]
OA Podkolodnaya, VG Levitsky, NL Podkolodnyi (2001), "Locus control regions: description in the LCR-TRRDatabase", Molecular Biology (Molekulyarnaya Biologiya), 35(6): 802-809.
MA Pozdnyakov, EE Vityaev, EA Ananko, EV Ignatieva, OA Podkolodnaya, NL Podkolodnyi, SV Lavryushev, NA Kolchanov (2001), "Comparative analysis of methods recognizing potential transcription factor binding sites", Molecular Biology (Molekulyarnaya Biologiya), 35(6):818-825.
promoter/TF

Martin G Reese (2001), "Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome", Computers & Chemistry, 26(1):51-56.
Elena Rivas, Sean R Eddy (2001), "Noncoding RNA gene detection using comparative sequence analysis", BMC Bioinformatics, 2:8.
[ abstract ]
Sanja Rogic, Alan K Mackworth, Francis BF Ouellette (2001), "Evaluation of gene-finding programs on mammalian sequences ", Genome Research, 11(5):817-832.
[abstract] [ PDF ] [related web page at http://www.cse.ucsc.edu/~rogic/evaluation.html ]
Sanja Rogic, Alan K Mackworth, Francis BF Ouellette (2001), "Evaluation of gene-finding programs on mammalian sequences", Genome Research, 11(5):817-832.
[supplement material: http://www.cs.ubc.ca/~rogic/evaluation/]
Igor B Rogozin, Alexey V Kochetov, Fyodor A Kondrashov, Eugene V Koonin, Luciano Milanesi (2001), "Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a `weak' context of the start codon ", Bioinformatics, 17: 890-900.
John S Chuang, Dan Roth (2001), "Gene recognition based on DAG shortest paths", Bioinformatics, 17:S56-S64.
Meena K Sakharkar, Tin Wee Tan, Sandro J de Souza (2001), "Generation of a database containing discordant intron positions in eukaryotic genes (MIDB)", Bioinformatics, 17:671-675.
promoter/TF

M Scherf, A Klingenhoff, K Frech, K Quandt, R Schneider, K Grote, M Frisch, V Gailus-Durner, A Seidel, R Brack-Werner, T Werner (2001), "First pass annotation of promoters on human chromosome 22", Genome Research, 11(3):333-340.
Thomas Schiex, Annick Moisan, and Pierre Rouz� (2001), "EUGENE: an eukaryotic gene finder that combines several sources of evidence", in Lecture Notes in Computer Science , Vol 2066, pp. ?-? (Computational Biology, eds. O Gascuel, M-F Sagot) (Springer).
[webpage from the published: http://link.springer.de/link/service/series/0558/">]
annotation

Shoemaker DD, Schadt EE, Armour CD, He YD, Garrett-Engele P, McDonagh PD, Loerch PM, Leonardson A, Lum PY, Cavet G, Wu LF, Altschuler SJ, Edwards S, King J, Tsang JS, Schimmack G, Schelter JM, Koch J, Ziman M, Marton MJ, Li B, Cundiff P, Ward T, Castle J, Krolewski M, Meyer MR, Mao M, Burchard J, Kidd MJ, Dai H, Phillips JW, Linsley PS, Stoughton R, Scherer S, Boguski MS. (2001), "Experimental annotation of the human genome using microarray technology", Nature, 409(6822):922-927.
M Skovgaard, LJ Jensen, S Brunak, D Ussery, A Krogh (2001), "On the total number of genes and their length distribution in complete microbial genomes", Trends in Genetics, 17:425-428.
V Solovyev (2001), "Statistical approaches in Eukaryotic gene prediction", in Handbook of Statistical Genetics, eds. DJ Balding, C Cannings, M Bishop (John Wiley & Sons) pp. 83-128.
annotation

Lincoln Stein (2001), "Genome annotation: from sequence to biology", Nature Reviews Genetics, 2:493-503.
Baris E Suzek, Maria D Ermolaeva, Mark Schreiber, Steven L Salzberg (2001), "A probabilistic method for identifying start codons in bacterial genomes ", Bioinformatics, 17:1123-1130.
promoter/TF

Yutaka Suzuki, Tatsuhiko Tsunoda, Jun Sese, Hirotoshi Taira, Junko Mizushima-Sugano, Hiroko Hata, Toshio Ota, Takao Isogai, Toshihiro Tanaka, Yusuke Nakamura, Akira Suyama, Yoshiyuki Sakaki, Shinichi Morishita, Kousaku Okubo, and Sumio Sugano (2001), "Identification and characterization of the potential promoter regions of 1031 kinds of human genes", Genome Research, 11:677-684.
JE Tabaska, R Davuluri, MQ Zhang (2001), "A novel 3'-terminal exon recognition algorithm", Bioinformatics, 17:602-607.
[abstract] [PDF]
promoter/TF

Goro Terai, Toshihisa Takagi, Kenta Nakai (2001), "Prediction of co-regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related species", Genome Biology, 2(11):research0048.
[html]
alternative-splicing

TA Thanaraj, F Clark (2001), "GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions", Nucleic Acids Research, 29(12):2581-2593.
[PDF]
expression

G Thijs, K Marchal, M Lescot, S Rombauts, B de Moor, P Rouze, Y Moreau (2001), "A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes", Proceedings of the fifth international conference on Research in Computational Molecular Biology, pp.305-312.
promoter/TF

Gert Thijs, Magali Lescot, Kathleen Marchal, Stephane Rombauts, Bart De Moor, Pierre Rouz�, and Yves Moreau (2001), "A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling ", Bioinformatics , 17:1113-1122.
[PDF]
promoter/TF

M Tompa (2001), "Identifying functional elements by comparative DNA sequence analysis", Genome Research, 11(7):1143-1144.
OV Vishnevsky, EE Vityaev (2001), "Analysis and recognition of erythroid-specific gene promoters basing on degenerate oligonucleotide motifs", Molecular Biology (Molekulyarnaya Biologiya), 35(6):833-840.
EE Vityaev, Yu L Orlov, OV Vishnevsky, AS Belenok, NA Kolchanov (2001), "Computer system 'gene discovery' to search for patterns in eukaryotic regulatory nucleotide sequences", Molecular Biology (Molekulyarnaya Biologiya), 35(6):810-817.
J Wang, CT Zhang (2001), "Identification of protein-coding genes in the genome of Vibrio cholerae with more than 98% accuracy using occurrence frequencies of single nucleotides", European Journal of Biochemistry, 268(15):4261-4268.
similarity

Sarah J Wheelan, Deanna M Church, James M Ostell (2001), "Spidey: a tool for mRNA-to-genomic alignments", Genome Research, 11:1952-1957.
[abstract]
similarity

T Wiehe, S Gebauer-Jung, T Mitchell-Olds, R Guigo (2001), "SGP-1: prediction and validation of homologous genes based on sequence alignments", Genome Research, 11(9):1574-1583.
[ abstract]
Gane Ka-Shu Wong, Douglas A Passey, Jun Yu (2001), "Most of the human genome is transcribed", Genome Research, 11: 975-1977.
Tetsushi Yada, Yasushi Totoki, Toshihisa Takagi, and Kenta Nakai (2001), "A novel bacterial gene-finding system with improved accuracy in locating start codons", DNA Research, 8(3):97-106.
[ abstract]
similarity

Ru-Fang Yeh, Lee P Lim, Christopher B Burge (2001), "Computational inference of homologous gene structures in the human genome ", Genome Research, 11(5): 803-816.
[abstract] [ PDF ] [supplement material: http://genes.mit.edu/genomescan/ (genomescan)]
promoter/TF

Theresa Zhang, Michael Zhang (2001) "Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes", Bioinformatics, 17:1232-1233.
promoter/TF

Joel Zupicich, Steven E Brenner, William C Skarnes (2001), "Computational prediction of membrane-tethered transcription factors", Genome Biology, 2(12):research0050.
[html]