gene recognition papers (2004)

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2004

promoter/TF

Stein Aerts, Gert Thijs, Michal Dabrowski, Yves Moreau, Bart De Moor (2004), "Comprehensive analysis of the base composition around the transcription start site in Metazoa", BMC Genomics, 5(1):34.
JE Allen, M Pertea, SL Salzberg (2004), "Computational gene prediction using multiple sources of evidence", Genome Research, 14(1):142-148.
[ abstract]
annotation

Luiz G. P. Almeida, Roger Paixão, Rangel C. Souza, Gisele C. da Costa, Frank J. A. Barrientos, M. Trindade dos Santos, Darcy F. de Almeida, Ana Tereza R. Vasconcelos (2004), "A System for Automated Bacterial (genome) Integrated Annotation-SABIA", Bioinformatics, 20(16):2832-2833.
[abstract]
annotation

F Al-shahrour, R Diaz-Uriarte, J Dopazo (2005), "FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes", Bioinformatics, 20:578-580.
alternative-splicing

Gil Ast (2004), "How did alternative splicing evolve?" Nature Reviews Genetics, 5:773-782.
[abstract]
Rajeev K. Azad, Mark Borodovsky (2004), "Effects of choice of DNA sequence model structure on gene identification accuracy", Bioinformatics, 20:993-1005.
[abstract]
Rajeev K. Azad, Mark Borodovsky (2004), "Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the HMM theory", Briefings in Bioinformatics, 5(2):118-130.
annotation

T Beissbarth, T Speed (2004), "GOstat: find statistically overrepresented Gene Ontologies within group of genes", Bioinformatics, 20:1464-1465.
promoter/TF

Eugene Berezikov, Victor Guryev, Ronald H.A. Plasterk, and Edwin Cuppen (2004), "CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting", Genome Research, 14(1):170-178.
[ abstract]
Paul Bertone, Viktor Stolc, Thomas E. Royce, Joel S. Rozowsky, Alexander E. Urban, Xiaowei Zhu, John L. Rinn, Waraporn Tongprasit, Manoj Samanta, Sherman Weissman, Mark Gerstein,3{dagger} Michael Snyder (2004), "Global identification of human transcribed sequences with genome tiling arrays", Science, 306(5705):2242-2246.
[abstract]
Therese Biedl, Brona Brejova, Erik D Demaine, Angele M Hamel, Alejandro Lopez-Ortiz, Tomas Vinar (2004), "Finding hidden independent sets in interval graphs", Theoretical Computer Science, 310(1-3):287-307.
[ abstract]
Ewan Birney, Michele Clamp, Richard Durbin (2004), "GeneWise and genomewise", Genome Research, 14:988-995.
[ abstract]
Michael A. Brasch, James L. Hartley, and Marc Vidal (2004), "ORFeome cloning and systems biology: standardized mass production of the parts from the parts-list" (perspectives), Genome Research, 14:2001-2009.
similarity

Volker Brendel, Liqun Xing, and Wei Zhu (2004), "Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus", Bioinformatics, 20:1157-1169.
[abstract]
similarity

Brona Brejova, Daniel G. Brown, Tomas Vinar (2004), "Optimal spaced seeds for homologous coding regions", Journal of Bioinformatics and Computational Biology, 1(4):595-610.
MR Brent, R Guigo (2004), "Recent advances in gene structure prediction", Current Opinion in Structural Biology, 14(3):264-272.
promoter/TF

Martha L Bulyk, Abigail M McGuire, Nobuhisa Masuda, George M Church (2004), "A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli", Genome Research, 14(2):201-208.
[ abstract]
annotation

Vanina Castelli, Jean-Marc Aury, Olivier Jaillon, Patrick Wincker, Christian Clepet, Manuella Menard, Corinne Cruaud, Francis Quétier, Claude Scarpelli, Vincent Schächter, Gary Temple, Michel Caboche, Jean Weissenbach, and Marcel Salanoubat (2004), "Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation", Genome Research, 14(3):406-413.
[abstract]
splicing

Robert Castelo and Roderic Guigo (2004), "Splice site identification by idlBNs", Bioinformatics, 20:i69-i76.
Andre RO Cavalcanti, Laura F Landweber (2004), "Gene Unscrambler for detangling scrambled genes in ciliates", Bioinformatics, 20(5):800-802.
[ abstract]
alternative-splicing

Trees-Juen Chuang, Feng-Chi Chen, Meng-Yuan Chou (2004), "A comparative method for identification of gene structures and alternatively spliced variants", Bioinformatics, 20:3064-3079.
[ abstract]
promoter/TF

Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, Wheeler R, Wong B, Drenkow J, Yamanaka M, Patel S, Brubaker S, Tammana H, Helt G, Struhl K, Gingeras TR (2004), "Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs", Cell, 116(4):499-509.
annotation

Kushal Chakrabarti and Lior Pachter (2004), "Visualization of multiple genome annotations and alignments with the K-BROWSER", Genome Research, 14:716-720.
[abstract]
similarity

Sourav Chatterji, Lior Pachter (2004), "Multiple organism gene finding by collapsed Gibbs sampling", Proceedings of the Eighth International Conference on Research in Computational Molecular Biology , pp.?-?
expression

G Chen, N Hata, MQ Zhang (2004), "Transcription factor binding element detection using functional clustering of mutant expression data", Nucleic Acids Research, 32(8):2362-2371.
Nansheng Chen, Daniel Lawson, Keith Bradnam, Todd W. Harris, and Lincoln D. Stein (2004), "WormBase as an integrated platform for the C. elegans ORFeome", Genome Research, 14:2155-2161.
promoter/TF

Francis Y.L. Chin, Henry C.M. Leung, S.M. Yiu, T.W. Lam, Roni Rosenfeld, W.W. Tsang, David K. Smith, Y.Jiang (2004), "Finding motifs for insufficient number of sequences with strong binding to transcription factor", Proceedings of the Eighth International Conference on Research in Computational Molecular Biology , pp.?-?
promoter/TF

CH Choi, G Kalosakas, KO Rasmussen, M Hiromura, AR Bishop, A Usheva (2004), "DNA dynamically directs its own transcription initiation", Nucleic Acids Research, 32(4):1548-1590.
L. Coin and R. Durbin (2004), "Improved techniques for the identification of pseudogenes", Bioinformatics, 20:i94-i100.
promoter/TF

GE Crawford, IE Holt, JC Mullikin, D Tai, R Blakesley, G Bouffard, A Young, C Masiello, ED Green, TG Wolfsberg, FS Collins, National Institutes Of Health Intramural Sequencing Center (2004), "Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites", Proceedings of National Academy of Sciences, 101(4):992-997.
S Cruveiller, K Jabbari, O Clay, G Bernardi (2004), "Incorrectly predicted genes in rice?", Gene, 333:187-188.
annotation

Val Curwen, Eduardo Eyras, T. Daniel Andrews, Laura Clarke, Emmanuel Mongin, Steven M.J. Searle, and Michele Clamp (2004), "The ensembl automatic gene annotation system", Genome Research, 14:942-950.
promoter/TF

D Das, N Banerjee, MQ Zhang (2004), "Interacting models of cooperative gene regulation", Proceedings of National Academy of Sciences, 101(46):16234-16239.
Vincent Daubin, Howard Ochman (2004), "Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli", Genome Research, 14:1036-1042.
promoter/TF

MJL de Hoon, S Imoto, K Kobayashi, N Ogasawara, S Miyano (2004), "Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information", Pacific Symposium on Biocomputing, 9:276-287(2004)
similarity

Colin Dewey, Jia Qian Wu, Simon Cawley, Marina Alexandersson, Richard Gibbs, Lior Pachter (2004), "Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat", Genome Research, 14:661-664.
[abstract] [supplement material]
expression

Thomas Dickmeis, Charles Plessy, Sepand Rastegar, Pia Aanstad, Ralf Herwig, Frédéric Chalmel, Nadine Fischer, and Uwe Strähle (2004), "Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the Zebrafish embryo ", Genome Research, 14(2):228-238.
[ abstract]
promoter/TF

Christoph Dieterich, Sven Rahmann, and Martin Vingron (2004), "Functional inference from non-random distributions of conserved predicted transcription factor binding sites", Bioinformatics, 20:i109-i115.
S Dike, VS Balija, LU Nascimento, Z Xuan, J Ou, T Zutavern, LE Palmer, G Hannon, MQ Zhang, WR McCombie (2004), "The mouse genome: Experimental examination of gene predictions and transcriptional start sites", Genome Research, 14(12):2424-2429.
annotation

Li Ding, Aniko Sabo, Nicolas Berkowicz, Rekha R. Meyer, Yoram Shotland, Mark R. Johnson, Kymberlie H. Pepin, Richard K. Wilson, and John Spieth (2004), "EAnnot: A genome annotation tool using experimental evidence", Genome Research, 14:2503-2509.
promoter/TF

Denis Dupuy, Qian-Ru Li, Bart Deplancke, Mike Boxem, Tong Hao, Philippe Lamesch, Reynaldo Sequerra, Stephanie Bosak, Lynn Doucette-Stamm, Ian A. Hope, David E. Hill, Albertha J.M. Walhout, and Marc Vidal (2004), "A first version of the Caenorhabditis elegans promoterome", Genome Research, 14: 2169-2175.
splicing

E. Eden and S. Brunak (2004), "Analysis and recognition of 5' UTR intron splice sites in human pre-mRNA", Nucleic Acids Research, 32(3):1131-1142.
[abstract]
alternative-splicing

Eduardo Eyras, Mario Caccamo, Val Curwen, and Michele Clamp (2004), "ESTGenes: Alternative Splicing From ESTs in Ensembl", Genome Research, 14:976-987.
[abstract]
splicing

WG Fairbrother, D Holste, CB Burge, PA Sharp (2004), "Single nucleotide polymorphism-based validation of exonic splicing enhancers", PLoS Biology, 2(9):E268.
splicing

WG Fairbrother, GW Yeo, R Yeh, P Goldstein, M Mawson, PA Sharp, CB Burge (2004), "RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons", Nucleic Acids Research, 32:W187-W190.
promoter/TF

Peter C FitzGerald, Andrey Shlyakhtenko, Alain A Mir, Charles Vinson (2004), "Clustering of DNA sequences in human promoters", Genome Research, 14:1562-1574.
Trevor W Fox, Alex Carreira (2004), "A digital signal processing method for gene prediction with improved noise suppression", EURASIP Journal on Applied Signal Processing, 2004(1):108-114.
[ abstract]
annotation

Terrence S. Furey, Mark Diekhans, Yontao Lu, Tina A. Graves, Lachlan Oddy, Jennifer Randall-Maher, LaDeana W. Hillier, Richard K. Wilson, and David Haussler (2004), "Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing", Genome Research, 14:2034-2040.
[abstract]
Feng Gao, Chun-Ting Zhang (2004), "Comparison of various algorithms for recognizing short coding sequences of human genes", Bioinformatics, 20(5):673-681.
[ abstract]
alternative-splicing

C Grasso, B Modrek, Y Xing, C Lee (2004), "Genome-wide detection of alternative splicing in expressed sequences using partial order multiple sequence alignment graphs", Pacific Symposium on Biocomputing, 9:29-41.
promoter/TF

Debraj GuhaThakurta, Lawrence A. Schriefer, Robert H. Waterston, Gary D. Stormo (2004), "Novel transcription regulatory elements in Caenorhabditis elegans muscle genes", Genome Research, 14:2457-2468.
alternative-splicing

S. Gupta, D. Zink, B. Korn, M. Vingron, S. A. Haas (2004), "Genome wide identification and classification of alternative splicing based on EST data", Bioinformatics, 20(16):2579-2585.
[ abstract]
promoter/TF

CT Harbison, DB Gordon, TI Lee, NJ Rinaldi, KD Macisaac, TW Danford, NM Hannett, JB Tagne, DB Reynolds, J Yoo, EG Jennings, J Zeitlinger, DK Pokholok, M Kellis, PA Rolfe, KT Takusagawa, ES Lander, DK Gifford, E Fraenkel, RA Young (2004), "Transcriptional regulatory code of a eukaryotic genome", Nature, 431(7004):99-104.
similarity

Xin He, Michael H. Goldwasser (2004), "Identifying conserved gene clusters in the presence of orthologous groups", Proceedings of the Eighth International Conference on Research in Computational Molecular Biology , pp.?-?
Aubrey Hill, Eric Sorscher (2004), "Common structural patterns in human genes", Bioinformatics, 20:1632-1635.
[ abstract]
annotation

R Hoffmann, A Valencia (2004), "A gene network for navigating the literature" (letter), Nature Genetics, 36:664.
http://www.ihop-net.org/UniPub/iHOP/
LD Hurst, C Pal, MJ Lercher (2004), "The evolutionary dynamics of eukaryotic gene order", Nature Reviews Genetics, 5(4):299-310.
expression

Jan Ihmels, Sven Bergmann, and Naama Barkai (2004), "Defining transcription modules using large-scale gene expression data", Bioinformatics, 20:1993-2003.
[ abstract]
K Jabbari, S Cruveiller, O Clay, J Le Saux, G Bernardi (2004), "The new genes of rice: a closer look", Trends in Plant Science, 9(6):281-285.
promoter/TF

ST Jensen, XS Liu, Q Zhou, JS Liu (2004), "Computational discovery of gene regulatory binding motifs: a Bayesian perspective", Statistical Science, 19(1):188-204.
[abstract]
Zackary I Johnson, Sallie W Chisholm (2004), "Properties of overlapping genes are conserved across microbial genomes", Genome Research, 14:2268-2272.
annotation

Cliff A. Joslyn, Susan M. Mniszewski, Andy Fulmer, and Gary Heaton (2004), "The Gene Ontology Categorizer", Bioinformatics, 20:i169-i177.
Aaron Kaluszka and Cynthia Gibas (2004), "Interactive gene-order comparison for multiple small genomes", Bioinformatics, 20:3662-3664.
annotation

Dione Kampa, Jill Cheng, Philipp Kapranov, Mark Yamanaka, Shane Brubaker, Simon Cawley, Jorg Drenkow, Antonio Piccolboni, Stefan Bekiranov, Gregg Helt, Hari Tammana, and Thomas R. Gingeras (2004), "Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22", Genome Research, 14(3):331-342.
[abstract]
alternative-splicing

Z Kan, J Castle, JM Johnson, NF Tsinoremas (2004), "Detection of novel splice forms in human mouse using cross-species approach", Pacific Symposium on Biocomputing, 9:42-53.
annotation

Shintaro Katayama, Mutsumi Kanamori, Yoshihide Hayashizaki (2004), "Integrated analysis of the genome and the transcriptome by FANTOM", Briefings in Bioinformatics, 5(3):249-258.
promoter/TF

M Kato, N Hata, N Banerjee, B Futcher, MQ Zhang (2004), "Identifying combinatorial regulation of transcription factors and binding motifs", Genome Biology, 5(8):R56.
promoter/TF

A Kel, Y Tikunov, N Voss, E Wingender (2004), "Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods", Bioinformatics, 20(10):1512-1516.
promoter/TF

Sündüz Keles, Mark J. van der Laan, Chris Vulpe (2004), "Regulatory motif finding by logic regression", Bioinformatics, 20(16):2799-2811.
[ abstract]
Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. Lander (2004), "Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery", Journal of Computational Biology, 11(2-3):319-355.
M Kiriakidou, PT Nelson, A Kouranov, P Fitziev, C Bouyioukos, Z Mourelatos, A Hatzigeorgiou (2004), "A combined computational-experimental approach predicts human microRNA targets", Genes & Devepment, 18(10):1165-1178.
[ abstract]
promoter/TF

Diana Kolbe, James Taylor, Laura Elnitski, Pallavi Eswara, Jia Li, Webb Miller, Ross Hardison, and Francesca Chiaromonte (2004), "Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat ", Genome Research, 14:700-707.
[abstract]
promoter/TF

A Krishnamachari, Vijnan moy Mandal, Karmeshu "Study of DNA binding sites using the Rényi parametric entropy measure", Journal of Theoretical Biology, 227(3):429-436.
Philippe Lamesch, Stuart Milstein, Tong Hao, Jennifer Rosenberg, Ning Li, Reynaldo Sequerra, Stephanie Bosak, Lynn Doucette-Stamm, Jean Vandenhaute, David E. Hill, and Marc Vidal (2004), "C. elegans ORFeome version 3.1: increasing the coverage of ORFeome resources with improved gene predictions", Genome Research, 14:2064-2069.
[ abstract]
promoter/TF

Laurence Lavie, Esther Maldener, Brook Brouha, Eckart U. Meese, Jens Mayer (2003), "The human L1 promoter: Variable transcription initiation sites and a major impact of upstream flanking sequence on promoter activity", Genome Research, 14:2253-2260.
promoter/TF

R Lavigne, WD Sun, G Volckaert (2004), "PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes", Bioinformatics, 20(5):629-635.
Chesley M. Leslin, Alex Abyzov, and Valentin A. Ilyin (2004), "Structural exon database, SEDB, mapping exon boundaries on multiple protein structures", Bioinformatics, 20:1801-1803.
[ abstract]
translation

Haifeng Li, Tao Jiang (2004), "A class of edit kernels for SVMs to predict translation initiation sites in eukaryotic mRNAs", Proceedings of the Eighth International Conference on Research in Computational Molecular Biology , pp.?-?
translation

Jinyan Li, Huiqing Liu, Limsoon Wong (2004), "Techniques for recognition of translational initiation sites", in Practical Bioinformatician, ed. Limsoon Wong (World Scientific).
translation

Huiqing Liu, Hao Han, Jinyan Li, Limsoon Wong (2004), "Using amino acid patterns to accurately predict translation initiation sites", In Silico Biology, 4:0022.
promoter/TF

Yueyi Liu, X. Shirley Liu, Liping Wei, Russ B. Altman, and Serafim Batzoglou (2004), "Eukaryotic regulatory element conservation analysis and identification using comparative genomics", Genome Research, 14(3):451-458.
[abstract]
promoter/TF

Yueyi Liu, Liping Wei, Serafim Batzoglou, Douglas L. Brutlag, Jun S. Liu and X. Shirley Liu (2004), "A suite of web-based programs to search for transcriptional regulatory motifsA suite of web-based programs to search for transcriptional regulatory motifs", Nucleic Acids Research, 32:W204-W207.
DD Long, I Grosse, KA Marx (2004), "Coding and non-coding DNA thermal stability differences in eukaryotes studied by melting simulation, base shuffling and DNA nearest neighbor frequency analysis", Biophysical Chemistry, 110(1-2):25-38.
[ abstract]
promoter/TF

F Long (2004), "Genome-wide prediction and analysis of function-specific transcription factor binding sites", In Silico Biology, 4:0033.
promoter/TF

F Long, H Liu, C Hahn, P Sumazin, MQ Zhang, A Zilberstein (2004), "Genome-wide prediction and analysis of function-specific transcription factor binding sites", In Silico Biology, 4(3):0033.
WH Majoros, M Pertea, SL Salzberg (2004), "TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders", Bioinformatics, 20(16):2878-2879.
[ abstract]
WH Majoros, SL Salzberg (2004), "An empirical analysis of training protocols for probabilistic gene finders", BMC Bioinformatics, 5(1):206.
promoter/TF

Leonardo Marino-Ramirez, John L Spouge, Gavin C Kanga, David Landsman (2004), "Statistical analysis of over-represented words in human promoter sequences", Nucleic Acids Research, 32(3):949-958.
[PDF]
promoter/TF

Manuel Martínez-Bueno, Antonio J. Molina-Henares, Eduardo Pareja, Juan L. Ramos, Raquel Tobes (2004), "BacTregulators: a database of transcriptional regulators in bacteria and archaea", Bioinformatics, 20(16):2787-2791.
[ abstract]
Lakshmi K Matukumalli, John J Grefenstette, Tad S Sonstegard, Curtis P Van Tassell (2004), "EST-PAGE--managing and analyzing EST data", Bioinformatics, 20(2): 286-288.
Alice C. McHardy, Alexander Goesmann, Alfred Pühler, and Folker Meyer (2004), "Development of joint application strategies for two microbial gene finders", Bioinformatics, 20:1622-1631.
[ abstract]
expression

David N. Messina, Jarret Glasscock, Warren Gish, and Michael Lovett (2004), "An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression", Genome Research, 14:2041-2047.
[abstract]
The MGC Project Team (2004), "The status, quality, and expansion of the NIH full-length cDNA project: the mammalian gene collection (MGC)", Genome Research, 14:2121-2127.
[ abstract]
promoter/TF

M Morley, CM Molony, TM Weber, JL Devlin, KG Ewens, RS Spielman, VG Cheung (2004), "Genetic analysis of genome-wide variation in human gene expression", Nature, 430(7001):743-747.
annotation

Lisa Mullan (2004), "Genomes, genomes everywhere - but where to browse?", Briefings in Bioinformatics, 5(4):365-369.
translation

Afshin Nadershahi, Scott C Fahrenkrug, Lynda BM Ellis (2004), "Comparison of computational methods for identifying translation initiation sites in EST data", BMC Bioinformatics, 5(1):14.
expression

VH Nagaraj, RA O'Flanagan, AR Bruning, JR Mathias, AK Vershon, AM Sengupta (2005), "Combined analysis of expression data and transcription factor binding sites in the yeast genome", BMC Genomics, 5(1):59.
promoter/TF

Craig E Nelson, Bradley M Hersh, Sean B Carroll (2004), "The regulatory content of intergenic DNA shapes genome architecture", Genome Biology, 5:R25.
[html]
Daniel Nicorici and Jaakko Astola (2004), "Segmentation of DNA into coding and noncoding regions based on recursive entropic segmentation and stop-codon statistics", EURASIP Journal on Applied Signal Processing, 2004(1):81-91.
[ abstract]
C Nikolaou, Y Almirantis (2004), "Measuring the coding potential of genomic sequences through a combination of triplet occurrence patterns and RNY preference", Journal of Molecular Evolution, 59(3):309-316.
promoter/TF

U Ohler, S Yekta, LP Lim, DP Bartel, CB Burge (2004), "Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification", RNA, 10(9):1309-1322.
promoter/TF

Robert Osada, Elena Zaslavsky, Mona Singh (2004), "Comparative analysis of methods for representing and searching for transcription factor binding sites", Bioinformatics, 20:3516-3525.
HY Ou, FB Guo, CT Zhang (2004), "GS-finder: a program to find bacterial gene start sites with a self-training method", International Journal of Biochemistry & Cell Biology, 36:536-545.
[supplement material: http://tubic.tju.edu.cn/GS-Finder/ (GS-finder)]
Masaaki Oyama, Chiharu Itagaki, Hiroko Hata, Yutaka Suzuki, Tomonori Izumi, Tohru Natsume, Toshiaki Isobe, and Sumio Sugano (2004), "Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs", Genome Research, 14:2048-2052.
[ abstract]
expression

alternative-splicing

Q Pan, O Shai, C Misquitta, W Zhang, AL Saltzman, N Mohammad, T Babak, H Siu, TR Hughes, QD Morris, BJ Frey, BJ Blencowe (2004), "Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform", Molecular Cell, 16(6):929-941.
John Parkinson, Alasdair Anthony, James Wasmuth, Ralf Schmid, Ann Hedley, Mark Blaxter (2004), "PartiGene-constructing partial genomes", Bioinformatics, 20(9):1398-1404.
promoter/TF

Giulio Pavesi, Giancarlo Mauri, Graziano Pesole (2004), "In silico representation and discovery of transcription factor binding sites", Briefings in Bioinformatics, 5(3):217-236.
Tu Minh Phuong, Doheon Lee, Kwang Hyung Lee (2004), "Regression trees for regulatory element identification", Bioinformatics, 20(5):750-757.
[ abstract]
promoter/TF

A Prakash, M Blanchette, S Sinha, M Tompa (2004), "Motif discovery in heterogeneous sequence data", Pacific Symposium on Biocomputing, 9:348-359.
promoter/TF

Moshe Pritsker, Yir-Chung Liu, Michael A. Beer, Saeed Tavazoie (2004), "Whole-genome discovery of transcription factor binding sites by network-level conservation", Genome Research, 14(1):99-108.
[ abstract]
Antony Rodriguez, Sam Griffiths-Jones, Jennifer L. Ashurst, and Allan Bradley (2004), "Identification of mammalian microRNA host genes and transcription units", Genome Research, 14:1902-1910.
PR Romero, PD Karp (2004), "Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases ", Bioinformatics, 20(5):709-717.
[ abstract]
annotation

Jeffrey A. Rosenfeld, Indra N. Sarkar, Paul J. Planet, David H. Figurski, Rob DeSalle (2004), "ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms", Bioinformatics, 20:3462-3465.
Jean-François Rual, Tomoko Hirozane-Kishikawa, Tong Hao, Nicolas Bertin, Siming Li, Amélie Dricot, Ning Li, Jennifer Rosenberg, Philippe Lamesch, Pierre-Olivier Vidalain, Tracey R. Clingingsmith, James L. Hartley, Dominic Esposito, David Cheo, Troy Moore, Blake Simmons, Reynaldo Sequerra, Stephanie Bosak, Lynn Doucette-Stamm, Christian Le Peuch, Jean Vandenhaute, Michael E. Cusick, Joanna S. Albala, David E. Hill, and Marc Vidal (2004), "Human ORFeome version 1.1: a platform for reverse proteomics", Genome Research, 14:2128-2135.
[ abstract]
annotation

Eric E Schadt, Stephen W Edwards, Debraj GuhaThakurta, Dan Holder, Lisa Ying, Vladimir Svetnik, Amy Leonardson, Kyle W Hart, Archie Russell, Guoya Li, Guy Cavet, John Castle, Paul McDonagh, Zhengyan Kan, Ronghua Chen, Andrew Kasarskis, Mihai Margarint, Ramon M Caceres, Jason M Johnson, Christopher D Armour, Philip W Garrett-Engele, Nicholas F Tsinoremas, Daniel D Shoemaker (2004), "A comprehensive transcript index of the human genome generated using microarrays and computational approaches", Genome Biology, 5:R73.
Todd E. Scheetz, Jennifer J. Laffin, Brian Berger, Sara Holte, Susan A. Baumes, Robert Brown, II, Shereen Chang, Justin Coco, Jim Conklin, Keith Crouch, Micca Donohue, Greg Doonan, Chris Estes, Mari Eyestone, Katrina Fishler, Jack Gardiner, Lankai Guo, Brad Johnson, Catherine Keppel, Rikki Kreger, Mark Lebeck, Rudy Marcelino, Vladan Miljkovich, Mindee Perdue, Ling Qui, Joshua Rehmann, Rebecca S. Reiter, Bridgette Rhoads, Kelly Schaefer, Christina Smith, Ivana Sunjevaric, Kurtis Trout, Ning Wu, Clayton L. Birkett, Jared Bischof, Barry Gackle, Allen Gavin, A. Jason Grundstad, Brian Mokrzycki, Chris Moressi, Brian O'Leary, Kevin Pedretti, Chad Roberts, Natalie L. Robinson, Michael Smith, Dylan Tack, Nishank Trivedi, Tamara Kucaba, Tom Freeman, Jim J.-C. Lin, Maria F. Bonaldo, Thomas L. Casavant, Val C. Sheffield, and M. Bento Soares (2004), "High-throughput gene discovery in the rat", Genome Research, 14:733-741.
[ abstract]
annotation

Stephen M.J. Searle, James Gilbert, Vivek Iyer, and Michele Clamp (2004), "The Otter annotation system", Genome Research, 14:963-970. [ abstract]
Marie Semon, Laurent Duret (2004), "Evidence that functional transcription units cover at least half of the human genome", Trends in Genetics, 20:229-232.
[ abstract] [PDF]
promoter/TF

KT Takusagawa, DK .Gifford (2004), "Negative information for motif discovery" Pacific Symposium on Biocomputing, 9:360-371.
alternative-splicing

H Sakai, O Maruyama (2004), "Extensive search for discriminative features of alternative splicing", Pacific Symposium on Biocomputing, 9:54-65.
alternative-splicing

Tetsuo Shibuya, Hisashi Kashima, Akihiko Konagaya (2004), "Efficient filtering methods for clustering cDNAs with spliced sequence alignment", Bioinformatics, 20(1):29-39.
[ abstract]
H. Shmuely, E. Dinitz, I. Dahan, J. Eichler, D. Fischer, B. Shaanan (2004), "Poorly conserved ORFs in the genome of the archaea Halobacterium sp. NRC-1 correspond to expressed proteins", Bioinformatics, 20:1248-1253.
[ abstract]
A. Siepel, D. Haussler (2004), "Computational identification of evolutionarily conserved exons", Proceedings of the Eighth International Conference on Research in Computational Molecular Biology , pp.?-?
promoter/TF

N Simonis, J van Helden, GN Cohen, SJ Wodak (2004), "Transcriptional regulation of protein complexes in yeast", Genome Biology, 5(5):R33.
promoter/TF

N Simonis, SJ Wodak, GN Cohen, J Van Helden (2004), "Combining pattern discovery and discriminant analysis to predict gene co-regulation", Bioinformatics, 20(15):2370-2379.
[abstract]
promoter/TF

Saurabh Sinha, Mathieu Blanchette and Martin Tompa (2004), "PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences", BMC Bioinformatics, 5:170.
annotation

Sogayar MC, Camargo AA, Bettoni F, Carraro DM, Pires LC, Parmigiani RB, Ferreira EN, de Sa Moreira E, do Rosario D de O Latorre M, Simpson AJ, Cruz LO, Degaki TL, Festa F, Massirer KB, Sogayar MC, Filho FC, Camargo LP, Cunha MA, De Souza SJ, Faria M Jr, Giuliatti S, Kopp L, de Oliveira PS, Paiva PB, Pereira AA, Pinheiro DG, Puga RD, S de Souza JE, Albuquerque DM, Andrade LE, Baia GS, Briones MR, Cavaleiro-Luna AM, Cerutti JM, Costa FF, Costanzi-Strauss E, Espreafico EM, Ferrasi AC, Ferro ES, Fortes MA, Furchi JR, Giannella-Neto D, Goldman GH, Goldman MH, Gruber A, Guimaraes GS, Hackel C, Henrique-Silva F, Kimura ET, Leoni SG, Macedo C, Malnic B, Manzini B CV, Marie SK, Martinez-Rossi NM, Menossi M, Miracca EC, Nagai MA, Nobrega FG, Nobrega MP, Oba-Shinjo SM, Oliveira MK, Orabona GM, Otsuka AY, Paco-Larson ML, Paixao BM, Pandolfi JR, Pardini MI, Passos Bueno MR, Passos GA, Pesquero JB, Pessoa JG, Rahal P, Rainho CA, Reis CP, Ricca TI, Rodrigues V, Rogatto SR, Romano CM, Romeiro JG, Rossi A, Sa RG, Sales MM, Sant'Anna SC, Santarosa PL, Segato F, Silva WA Jr, Silva ID, Silva NP, Soares-Costa A, Sonati MF, Strauss BE, Tajara EH, Valentini SR, Villanova FE, Ward LS, Zanette DL; Ludwig-FAPESP Transcript Finishing Initiative (2004), "A transcript finishing initiative for closing gaps in the human transcriptome", Genome Research, 14(7):1413-1423.
expression

Dirk Steinhauser, Björn H Junker, Alexander Luedemann, Joachim Selbig, Joachim Kopka (2004), "Hypothesis-driven approach to predict transcriptional units from gene expression data", Bioinformatics, 20:1928-1939.
[ abstract]
annotation

AI Su, T Wiltshire, S Batalov, H Lapp, KA Ching, D Block, J Zhang, R Soden, M Hayakawa, G Kreiman, MP Cooke, JR Walker, JB Hogenesch (2004), "A gene atlas of the mouse and human protein-encoding transcriptomes", Proceedings of National Academy of Sciences, 101(16):6062-6067.
alternative-splicing

CW Sugnet, WJ Kent, M Ares Jr., D Haussler (2004), "Transcriptome genome conservation of alternative splicing events in humans and mice", Pacific Symposium on Biocomputing, 9:66-77.
promoter/TF

Yutaka Suzuki, Riu Yamashita, Matsuyuki Shirota, Yuta Sakakibara, Joe Chiba, Junko Mizushima-Sugano, Kenta Nakai, and Sumio Sugano (2004), "Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions", Genome Research, 14:1711-1718.
promoter/TF

Mahlet G. Tadesse, Marina Vannucci, and Pietro Liò (2004), "Identification of DNA regulatory motifs using Bayesian variable selection", Bioinformatics, 20(16):2553-2561.
[abstract]
Daiya Takai, Peter A Jones (2004), "Origins of didirectional promoters: computational analyses of intergenic distance in the human genome", Molecular Biology and Evolution, 21(3):463-467.
Aaron E Tenney, Randall H Brown, Charles Vaske, Jennifer K Lodge, Tamara L Doering, Michael R Brent (2004), "Gene prediction and verification in a compact genome with numerous small introns", Genome Research, 14:2330-2335.
promoter/TF

Nathan D. Trinklein, Shelley Force Aldred, Sara J. Hartman, Diane I Schroeder, Robert P Otillar, Richard M Myers (2004), "An abundance of bidirectional promoters in the human genome", Genome Research, 14(1):62-66.
[ abstract]
Jacques van Helden (2004), "Metrics for comparing regulatory sequences on the basis of pattern counts", Bioinformatics, 20(3):399-406.
[ abstract]
Vamsi Veeramachaneni, Wojciech Makalowski, Michal Galdzicki, Raman Sood, and Izabela Makalowska (2004), "Mammalian overlapping genes: the comparative perspective", Genome Research, 14(2):280-286.
[ abstract]
promoter/TF

Wyeth W Wasserman, Albin Sandelin (2004), "Applied bioinformatics for the identification of regulatory elements", Nature Reviews Genetics, 5:276-287.
[ abstract]
splicing

Michael Weir and Michael Rice (2004), "Ordered partitioning reveals extended splice-site consensus information ", Genome Research, 14(1):67-78. [ abstract]
alternative-splicing

Fang Wen, Fei Li, Huiyu Xia, Xin Lu, Xuegong Zhang, Yanda Li (2004), "The impact of very short alternative splicing on protein structures and functions in the human genome", Trends in Genetics,
[ abstract]
Stefan Wiemann, Dorit Arlt, Wolfgang Huber, Ruth Wellenreuther, Simone Schleeger, Alexander Mehrle, Stephanie Bechtel, Mamatha Sauermann, Ulrike Korf, Rainer Pepperkok, Holger Sültmann, and Annemarie Poustka (2004), "From ORFeome to biology: a functional genomics pipeline", Genome Research, 14:2136-2144.
promoter/TF

E Wingender (2004), "TRANSFAC, TRANSPATH and CYTOMER as starting points for an ontology of regulatory networks", In Silico Biology, 4(1):55-61.
Jia Qian Wu, David Shteynberg, Manimozhiyan Arumugam, Richard A. Gibbs, Michael R. Brent (2004), "Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing", Genome Research, 14:665-671.
[abstract]
promoter/TF

Wen Xue, Jin Wang, Zhirong Shen, and Huaiqiu Zhu (2004), "Enrichment of transcriptional regulatory sites in non-coding genomic region", Bioinformatics, 20(4):569-575.
[abstract]
Yukimitsu Yabuki, Yuri Mukai, Mark B. Swindells, and Makiko Suwa (2004), "GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures", Bioinformatics, 20(4):596-598.
[abstract]
splicing

G Yeo, CB Burge (2004), "Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals", Journal of Computational Biology, 11(2-3):377-394.
splicing

G Yeo, S Hoon, B Venkatesh, CB Burge (2004), "Variation in sequence and organization of splicing regulatory elements in vertebrate genes", Proceedings of National Academy of Sciences, 101(44):15700-15705.
alternative-splicing

G Yeo, D Holste, G Kreiman, CB Burge (2004), "Variation in alternative splicing across human tissues", Genome Biology, 5(10):R74.
expression

Lap Kun Yeung, Lap Keung Szeto, Alan Wee-Chung Liew, Hong Yan (2004), "Dominant spectral component analysis for transcriptional regulations using microarray time-series data", Bioinformatics, 20(5):742-749.
[ abstract]
promoter/TF

Han Yu, Andrew S. Yoo, and Iva Greenwald (2004), "Cluster Analyzer for Transcription Sites (CATS): a C++-based program for identifying clustered transcription factor binding sites", Bioinformatics, 20:1198-1200.
R Zhang, HY Ou, CT Zhang (2004), "DEG: a database of essential genes", Nucleic Acids Research, 32:D271-D272.
[supplement material: http://tubic.tju.edu.cn/deg/ (DEG: database of essential genes)]
Theresa Zhang, Peter Haws, Qiang Wu (2004), "Multiple variable first exons: a mechanism for cell- and tissue-specific gene regulation", Genome Research, 14(1):79-89. [ abstract]
alternative-splicing

CL Zheng, TM Nair, M Gribskov, YS Kwon, HR Li, XD Fu (2004), "A database designed to computationally aid an experimental approach to alternative splicing", Pacific Symposium on Biocomputing, 9:78-88.
promoter/TF

Qing Zhou, Jun S. Liu (2004), "Modeling within-motif dependence for transcription factor binding site predictions", Bioinformatics, 20:909-916.
[ abstract]
translation

Huai-Qiu Zhu, Gang-Qing Hu, Zheng-Qing Ouyang, Jin Wang, and Zhen-Su She (2004), "Accuracy improvement for identifying translation initiation sites in microbial genomes", Bioinformatics, 20:3308-3317.
Qingsong Zhu, Youping Deng, Phaneendra Vanka, Susan J Brown, Subbaratnam Muthukrishnan, and Karl J. Kramer (2004), "Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome", Bioinformatics, 20: 161-169.
[ abstract]