gene recognition papers (2005)

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2005

promoter/TF

Irina Abnizova , Rene te Boekhorst , Klaudia Walter and Walter R Gilks "Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test", BMC Bioinformatics, 6:109.
[abstract]
splicing

Josep F. Abril, Robert Castelo, and Roderic Guigó (2005), "Comparison of splice sites in mammals and chicken", Genome Research, 15:111-119.
Alex Adai, Cameron Johnson, Sizolwenkosi Mlotshwa, Sarah Archer-Evans, Varun Manocha, Vicki Vance, Venkatesan Sundaresan (2005), "Computational prediction of miRNAs in Arabidopsis thaliana", Genome Research, 15:78-91.
JE Allen, SL Salzberg (2005), "JIGSAW: integration of multiple sources of evidence for gene prediction", Bioinformatics, 21(18):3596-3603.
[abstract]
promoter/TF

Shandar Ahmad, Akinori Sarai (2005), "PSSM-based prediction of DNA binding sites in proteins", BMC Bioinformatics, 6(1):33.
[abstract]
promoter/TF

Y Barash, G Elidan, T Kaplan, N Friedman (2005), "CIS: compound importance sampling method for protein-DNA binding site p-value estimation", Bioinformatics, 21(5):596-600.
[abstract]
Gill Bejerano, Adam C Siepel, W James Kent, David Haussler (2005), "Computational screening of conserved genomic DNA in search of functional noncoding elements", Nature Methods, 2:535-545.
[ abstract]
promoter/TF

I Ben-Gal, A Shani, A Gohr, J Grau, S Arviv, A Shmilovici, S Posch, I Grosse (2005), "Identification of transcription factor binding sites with variable-order Bayesian networks", Bioinformatics, 21(11):2657-2666.
[abstract]
promoter/TF

N Bluthgen, SM Kielbasa, H Herzel (2005), "Inferring combinatorial regulation of transcription in silico", Nucleic Acids Research, 33(1):272-279.
Paola Bonizzoni, Raffaella Rizzi, Graziano Pesole (2005), "ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences", BMC Bioinformatics, 6:244.
[abstract]
promoter/TF

Stefania Bortoluzzi, Alessandro Coppe, Andrea Bisognin, Cinzia Pizzi, Gian Antonio Danieli (2005), "A multistep bioinformatic approach detects putative regulatory elements in gene promoters", BMC Bioinformatics, 6:121.
[abstract]
Brona Brejova, Daniel G. Brown, Ming Li, Tomas Vinar (2005), "ExonHunter: a comprehensive approach to gene finding", Bioinformatics, 21(Suppl 1):i57-i65.
[abstract]
translation

JM Brockman, P Singh, D Liu, S Quinlan, J Salisbury, JH Graber (2005), "PACdb: PolyA Cleavage Site and 3'-UTR Database", Bioinformatics, 21(18):3691-3693.
[abstract]
promoter/TF

S Burden, YX Lin, R Zhang (2005), "Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences", Bioinformatics, 21:601-607.
[ abstract]
translation

Jun Cai, Jing Zhang, Ying Huang, and Yanda Li (2005), "ATID: a web-oriented database for collection of publicly available alternative translational initiation events", Bioinformatics, 21:4312-4314.
[ abstract]
A Carbone, F Kepes, A Zinovyev (2005), "Codon bias signatures, organisation of microorganisms in codon space and lifestyle", Molecular Biology and Evolution, 22(3):547-561.
[abstract]
promoter/TF

P Carninci, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schonbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group). "The transcriptional landscape of the mammalian genome", Science, 309(5740):1559-1563.
[abstract]
promoter/TF

K Cartharius, K Frech, K Grote, B Klocke, M Haltmeier, A Klingenhoff, M Frisch, M Bayerlein, T Werner (2005), "MatInspector and beyond: promoter analysis based on transcription factor binding sites", Bioinformatics, 21(13):2933-2942.
[abstract]
R Castelo, A Reymond, C Wyss, F Camara, G Parra, SE Antonarakis, R Guigo, E Eyras (2005), "Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes", Nucleic Acids Research, 33(6):1935-1939.
promoter/TF

Bob Y Chan, Dennis Kibler (2005), "Using hexamers to predict cis-regulatory motifs in Drosophila", BMC Bioinformatics, 6:262.
[abstract]
similarity

HL Chan, TW Lam, WK Sung, PW Wong, SM Yiu, X Fan (2005), "The mutated subsequence problem and locating conserved genes", Bioinformatics, 21(10):2271-2278.
[abstract]
D Charif, J Thioulouse, JR Lobry, G Perriere (2005), "Online synonymous codon usage analyses with the ade4 and seqinR packages", Bioinformatics, 21(4):545-547.
[abstract]
Sourav Chatterji, Lior Pachter (2005), "Large multiple organism gene finding by collapsed Gibbs sampling", Journal of Computational Biology, 12(6):599-608.
promoter/TF

D Che, S Jensen, L Cai, JS Liu (2005), "BEST: binding-site estimation suite of tools", Bioinformatics, 21(12):2909-2911.
[abstract]
alternative-splicing

FC Chen, TJ Chuang (2005), "ESTviewer: a web interface for visualizing mouse, rat, cattle, pig and chicken conserved ESTs in human genes and human alternatively spliced variants", Bioinformatics, 21(10):2510-2513.
[abstract]
annotation

Lifeng Chen, Hongfang Liu, Carol Friedman (2005), "Gene name ambiguity of eukaryotic nomenclatures", Bioinformatics, 21(2):248-256.
[abstract]
splicing

Te-Ming Chen, Chung-Chin Lu, and Wen-Hsiung Li (2005), "Prediction of splice sites with dependency graphs and their expanded bayesian networks", Bioinformatics, 21:471-482.
[ abstract]
promoter/TF

R Chowdhary, RA Ali, W Albig, D Doenecke, VB Bajic (2005), "Promoter modeling: the case study of mammalian histone promoters", Bioinformatics, 21(11):2623-2628.
[abstract]
similarity

Alexander Churbanov, Mark Pauley, Daniel Quest, Hesham Ali (2005), "A method of precise mRNA/DNA homology-based gene structure prediction", BMC Bioinformatics, 6:261.
[abstract]
expression

Steve W. Cole, Weihong Yan, Zoran Galic, Jesusa Arevalo, Jerome A. Zack (2005), "Expression-based monitoring of transcription factor activity: the TELiS database", Bioinformatics, 21:803-810.
[ abstract]
D Conklin, B Haldeman, Z Gao (2005), "Gene finding for the helical cytokines", Bioinformatics, 21(9):1776-1781.
[abstract]
promoter/TF

David L. Corcoran, Eleanor Feingold, Panayiotis V. Benos (2005), "FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting", Nucleic Acids Research, 33:W442-W446.
[ abstract]
splicing

S Degroeve, Y Saeys, B De Baets, P Rouze, Y Van de Peer (2005), "SpliceMachine: predicting splice sites from high-dimensional local context representations", Bioinformatics, 21(8):1332-1338.
[abstract]
annotation

M Delong, G Yao, Q Wang, A Dobra, EP Black, JT Chang, A Bild, M West, JR Nevins, H Dressman (2005), "DIG--a system for gene annotation and functional discovery", Bioinformatics, 21(13):2957-2959.
[abstract]
expression

T De Bie, P Monsieurs, K Engelen, B De Moor, N Cristianini, and K Marchal (2006), "Discovering transcriptional modules from motif, chip-chip and microarray data", Pacific Symposium on Biocomputing, 10:483-494.
Albert DG De Roos (2005), "Origins of introns based on the definition of exon modules and their conserved interfaces", Bioinformatics, 21:2-9.
[ abstract]
promoter/TF

Christoph Dieterich, Steffen Grossmann, Andrea Tanzer, Stefan Ropcke, Peter F Arndt, Peter F Stadler, Martin Vingron (2005), "Comparative promoter region analysis powered by CORG", BMC Genomics, 6:24.
promoter/TF

Thomas A Down, Tim JP Hubbard (2005), "NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence", Nucleic Acids Research, 33(5):1445-1453.
alternative-splicing

Gideon Dror, Rotem Sorek, Ron Shamir (2005), "Accurate identification of alternatively spliced exons using support vector machine", Bioinformatics, 21:897-901.
[ abstract]
annotation

François Enault, Karsten Suhre, Jean-Michel Claverie (2005), "Phydbac 'Gene Function Predictor' : a gene annotation tool based on genomic context analysis", BMC Bioinformatics, 6:247.
[abstract]
Eduardo Eyras , Alexandre Reymond , Robert Castelo , Jacqueline M Bye, Francisco Camara , Paul Flicek , Elizabeth J Huckle , Genis Parra, David D Shteynberg , Carine Wyss , Jane Rogers , Stylianos E Antonarakis, Ewan Birney , Roderic Guigo, Michael R Brent (2005), "Gene finding in the chicken genome", BMC Bioinformatics, 6:131.
[abstract]
promoter/TF

AV Favorov, MS Gelfand, AV Gerasimova, DA Ravcheev, AA Mironov, VJ Makeev (2005), "A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length", Bioinformatics, 21(10):2240-2245.
[abstract]
similarity

Andrew E Firth, Chris M Brown (2005), "Detecting overlapping coding sequences with pairwise alignments", Bioinformatics, 21:282-292.
[ abstract]
alternative-splicing

Liliana Florea, Valentina Di Francesco, Jason Miller, Russell Turner, Alison Yao, Michael Harris, Brian Walenz, Clark Mobarry, Gennady V. Merkulov, Rosane Charlab, Ian Dew, Zuoming Deng, Sorin Istrail, Peter Li, Granger Sutton (2005), "Gene and alternative splicing annotation with AIR", Genome Research, 15(1):54-66.
promoter/TF

K Florquin, Y Saeys, S Degroeve, P Rouze, Y Van de Peer (2005), "Large-scale structural analysis of the core promoter in mammalian and plant genomes", Nucleic Acids Research, 33(13):4255-4264.
expression

BJ Frey, N Mohammad, QD Morris, W Zhang, MD Robinson, S Mnaimneh, R Chang, Q Pan, E Sat, J Rossant, BG Bruneau, JE Aubin, BJ Blencowe, TR Hughes (2005), "Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs", Nature Genetics, 37(9):991-996.
expression

Brendan J. Frey, Quaid D. Morris, Naveed Mohammad, Mark Robinson, Wen Zhang, Timothy R. Hughes (2005), "GenRate - a generative model that finds and scores new gene structures in genome-wide microarray data", Proceedings of the Ninth International Conference on Research in Computational Molecular Biology , pp.?-?
expression

BJ Frey, QD Morris, W Zhang, N Mohammad, TR Hughes (2005), "Genrate: a generative model that finds and scores new genes and exons in genomic microarray data", Pacific Symposium on Biocomputing, 10:495-506.
Shigeo Fujimori, Takanori Washio, Masaru Tomita (2005), "GC-compositional strand bias around transcription start sites in plants and fungi", BMC Genomics, 6:26.
[ abstract]
promoter/TF

Mythily Ganapathi, Pragya Srivastava, Sushanta Kumar Das Sutar, Kaushal Kumar, Dipayan Dasgupta, Gajinder Pal Singh, Vani Brahmachari, Samir K Brahmachari (2005), "Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes", BMC Bioinformatics, 6:126.
[abstract]
Jianbo Gao, Yinhe Cao, Yan Qi, Jing Hu (2005), "Building innovative representations of DNA sequences to facilitate gene finding", IEEE Intelligent Systems, 20(6):34-39.
[ abstract]
promoter/TF

NI Gershenzon, IP Ioshikhes (2005), "Synergy of human Pol II core promoter elements revealed by statistical sequence analysis", Bioinformatics
promoter/TF

NI Gershenzon, GD Stormo, IP Ioshikhes (2005), "Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites", Nucleic Acids Research, 33(7):2290-2301.
promoter/TF

D Benjamin Gordon, Lena Nekludova, Scott McCallum, Ernest Fraenkel (2005), "TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs", Bioinformatics, 21:3164-3165.
G Gremme, V Brendel, ME Sparks, S Kurtz (2005), "Engineering a software tool for gene structure prediction in higher organisms", Information and Software Technology, 47(15):965-978.
[ abstract]
similarity

Samuel S. Gross, Michael R. Brent (2005), "Using multiple alignments to improve gene prediction", Proceedings of the Ninth International Conference on Research in Computational Molecular Biology , pp.?-?
promoter/TF

A Guo, K He, D Liu, S Bai, X Gu, L Wei, J Luo (2005), "DATF: a database of Arabidopsis transcription factors", Bioinformatics, 21(10):2568-2569.
annotation

Daniel H Haft, Jeremy D Selengut, Lauren M Brinkac, Nikhat Zafar, Owen White (2005), "Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics", Bioinformatics, 21:293-306.
[ abstract]
similarity

Xin He, Michael H. Goldwasser (2005), "Identifying conserved gene clusters in the presence of homology families", Journal of Computational Biology, 12(6):638-656.
Rose Hoberman, David Sankoff, Dannie Durand (2005), "The statistical analysis of spatially clustered genes under the maximum gap criterion", Journal of Computational Biology, 12(8):1083-1102.
promoter/TF

P Hong, XS Liu, Q Zhou, X Lu, JS Liu, WH Wong (2005), "A boosting approach for motif modeling using ChIP-chip data", Bioinformatics, 21(11):2636-2643.
alternative-splicing

Fang Rong Hsu, Hwan-You Chang, Yaw-Lin Lin, Yin-Te Tsai, Hui-Ling Peng, Ying Tsong Chen, Chia Yang Cheng, Min Yao Shih, Chia-Hung Liu, Chin-Feng Chen (2005), "AVATAR: A database for genome-wide alternative splicing event detection through analysis of large scale ESTs and mRNAs", Bioinformation, 1(1):16-18.
[abstract]
promoter/TF

Kei Iida, Motoaki Seki, Tetsuya Sakurai, Masakazu Satou, Kenji Akiyama, Tetsuro Toyoda, Akihiko Konagaya, and Kazuo Shinozaki (2005), "RARTF: database and tools for complete sets of Arabidopsis transcription factors", DAN Research, 12:247-256.
[ abstract]
Dean A Jackson (2005), "The amazing complexity of transcription factories", Briefings in Functional Genomics and Proteomics, 4(2):143-157.
[abstract]
E Jacob, R Sasikumar, KNR Nair (2005), "A fuzzy guided genetic algorithm for operon prediction", Bioinformatics, 21(8):1403-1407.
promoter/TF

Emmitt R Jolly, Chen-Shan Chin, Ira Herskowitz, Hao Li (2005), "Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis", BMC Bioinformatics, 6:275.
[abstract]
promoter/TF

Tommy Kaplan, Nir Friedman, Hanah Margalit (2005), "Predicting transcription factor binding sites using structural knowledge", Proceedings of the Ninth International Conference on Research in Computational Molecular Biology , pp.?-?
annotation

Jyotsna Kasturi, Raj Acharya (2005), "Clustering of diverse genomic data using information fusion", Bioinformatics, 21(4):423-429.
annotation

P Khatri, B Done, A Rao, A Done, S Draghici (2005), "A semantic analysis of the annotations of the human genome", Bioinformatics, 21(16):3416-3421.
promoter/TF

Szymon M Kielbasa, Didier Gonze, Hanspeter Herzel (2005), "Measuring similarities between transcription factor binding sites", BMC Bioinformatics, 6:237.
[abstract]
Jinsoo Kim, Jungmin Seo, Young Seek Lee, Sangsoo Kim (2005), "TFExplorer: integrated analysis database for predicted transcription regulatory elements", Bioinformatics, 21:548-550.
[ abstract]
promoter/TF

TH Kim, LO Barrera, M Zheng, C Qu, MA Singer, TA Richmond, Y Wu, RD Green, B Ren (2005), "A high-resolution map of active promoters in the human genome", Nature, 436(7052):876-880.
expression

Hisanori Kiryu, Taku Oshima, and Kiyoshi Asai (2005), "Extracting relations between promoter sequences and their strengths from microarray data", Bioinformatics, 21:1062-1068.
[ abstract]
expression

M Kloster, C Tang, NS Wingreen (2005), "Finding regulatory modules through large-scale gene-expression data analysis", Bioinformatics, 21:1172-1179.
[ abstract]
Alex V Kochetov (2005), "AUG codons at the beginning of protein coding sequences are frequent in eukaryotic mRNAs with a suboptimal start codon context", Bioinformatics, 21:837-840.
[ abstract]
promoter/TF

EA Kotelnikova, VJ Makeev, MS Gelfand (2005), "Evolution of transcription factor DNA binding sites", Gene, 347(2):255-263.
[ abstract]
Ekat Kritikou (2005), "Gene predictions - filling in the worm holes" (highlight), Nature Reviews Genetics, 6:429.
[ abstract]
Onkar C. Kulkarni, R. Vigneshwar, Valadi K. Jayaraman, and Bhaskar D. Kulkarni (2005), "Identification of coding and non-coding sequences using local Hölder exponent formalism", Bioinformatics, 21(20):3818-3823.
[abstract]
alternative-splicing

Christopher Lee, Qi Wang (2005), "Bioinformatics analysis of alternative splicing", Briefings in Bioinformatics, 6(1):23-33.
promoter/TF

Henry C.M. Leung, Francis Y.L. Chin, S.M. Yiu, Roni Rosenfeld, W.W. Tsang (2005), "Finding motifs with insufficient number of strong binding sites", Journal of Computational Biology, 12(6):686-701.
translation

Haifeng Li, Tao Jiang (2005), "A class of edit kernels for SVMs to predict translation initiation sites in eukaryotic mRNAs", Journal of Computational Biology, 12(6):702-718.
Heng Li, Jin-Song Liu, Zhao Xu, Jian Jin, Lin Fang, Lei Gao, Yu-Dong Li, Zi-Xing Xing, Shao-Gen Gao, Tao Liu, Hai-Hong Li, Yan Li, Li-Jun Fang, Hui-Min Xie, Wei-mou Zheng, Bai-lin Hao (2005), "Test data sets and evaluation of gene prediction programs on the rice genome", Journal of Computer Science and Technology, 20(4):446-453
[abstract] [PDF]
alternative-splicing

Y Lian, HR Garner (2005), "Evidence for the regulation of alternative splicing via complementary DNA sequence repeats", Bioinformatics, 21(8):1358-1364.
[abstract]
promoter/TF

Li-Hsieh Lin, Hsiao-Ching Lee, Wen-Hsiung Li, Bor-Sen Chen (2005), "Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification", BMC Bioinformatics, 6:258.
[abstract]
H Liu, H Han, J Li, L Wong (2005), "DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences", Bioinformatics, 21(5):671-673.
[abstract]
M Liu, A Grigoriev (2005), "Fast parsers for Entrez Gene", Bioinformatics, 21(14):3189-3190.
[abstract]
M Liu, S Wu, H Walch (2005), "Exon-domain correlation and its corollaries", Bioinformatics, 21(15):3213-3216.
[abstract]
expression

Yunlong Liu, Matthew P Vincenti, Hiroki Yokota (2005), "Principal component analysis for predicting transcription-factor binding motifs from array-derived data", BMC Bioinformatics, 6:276.
[abstract]
promoter/TF

S Mahony, D Hendrix, A Golden, TJ Smith, DS Rokhsar (2005), "Transcription factor binding site identification using the self-organizing map", Bioinformatics, 21(9):1807-1814.
[abstract]
WH Majoros, M Pertea, AL Delcher, SL Salzberg (2005), "Efficient decoding algorithms for generalized hidden Markov model gene finders", BMC Bioinformatics, 6(1):16.
[abstract]
WH Majoros, M Pertea, SL Salzberg (2005), "Efficient implementation of a generalized pair hidden Markov model for comparative gene finding", Bioinformatics, 21(9):1782-1788.
[abstract]
WH Majoros, SL Salzberg (2005), "An empirical analysis of training protocols for probabilistic gene finders", BMC Bioinformatics, 6:193.
Izabela Makalowska, Chiao-Feng Lin, Wojciech Makalowski (2005), "Overlapping genes in vertebrate genomes", Computational Biology and Chemistry , 29(1):1-12.
[ abstract]
promoter/TF

Y Makita, MJL De Hoon, N Ogasawara, S Miyano, K Nakai (2005), "Bayesian joint prediction of associated transcription factors in Bacillus subtilis", Pacific Symposium on Biocomputing, 10:507-518.
John S. Mattick (2005), "The functional genomics of noncoding RNA" (viewpoint), Science, 309(5740):1527-1528.
promoter/TF

Markey C McNutt, Ron Tongbai, Wenwu Cui, Irene Collins, Wendy J Freebern, Idalia Montano, Cynthia M Haggerty, GVR Chandramouli, Kevin Gardner (2005), "Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function", BMC Bioinformatics, 6:259.
[abstract]
promoter/TF

Manuel Middendorf, Anshul Kundaje, Mihir Shah, Yoav Freund, Chris Wiggins, Christina Leslie (2005), "Motif discovery through predictive modeling of gene regulation", Proceedings of the Ninth International Conference on Research in Computational Molecular Biology , pp.?-?
annotation

Tarjei S Mikkelsen, James E Galagan, Jill P Mesirov (2005), "Improving genome annotations using phylogenetic profile anomaly detection", Bioinformatics, 21:464-470.
[ abstract]
promoter/TF

Yoshiaki Minezaki, Keiichi Homma, and Ken Nishikawa (2005), "Genome-wide survey of transcription factors in prokaryotes reveals many bacteria-specific families not found in archaea", DNA Research, 12:269-280.
[ abstract]
promoter/TF

Richard Münch, Karsten Hiller, Andreas Grote, Maurice Scheer, Johannes Klein, Max Schobert, and Dieter Jahn (2005), "Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes", Bioinformatics, 21:4187-4189.
[ abstract]
alternative-splicing

AD Neverov, II Artamonova, RN Nurtdinov, D Frishman, MS Gelfand, AA Mironov (2005), "Alternative splicing and protein function", BMC Bioinformatics, 6:266.
[abstract]
Pernille Nielsen and Anders Krogh (2005), "Large-scale prokaryotic gene prediction and comparison to genome annotation", Bioinformatics, 21:4322-4329.
[ abstract]
Tatsunari Nishi, Toshimichi Ikemura, Shigehiko Kanaya (2005) "GeneLook: a novel ab initio gene identification system suitable for automated annotation of prokaryotic sequences", Gene, 346:115-125.
promoter/TF

Timothy R. O'Connor, Curtis Dyreson, and John J. Wyrick (2005), "Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences", Bioinformatics, 21:4411-4413.
[ abstract]
promoter/TF

RA O'Flanagan, G Paillard, R Lavery, AM Sengupta (2005), "Non-additivity in protein-DNA binding", Bioinformatics, 21(10):2254-2263.
[abstract]
promoter/TF

SK Palaniswamy, VX Jin, H Sun, RV Davuluri (2005), "OMGProm: a database of orthologous mammalian gene promoters", Bioinformatics, 21(6):835-836.
[abstract]
alternative-splicing

Q Pan, MA Bakowski, Q Morris, W Zhang, BJ Frey, TR Hughes, BJ Blencowe (2005), "Alternative splicing of conserved exons is frequently species-specific in human and mouse", Trends in Genetics, 21(2):73-77.
promoter/TF

D Papatsenko, M Levine (2005), "Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo", Proceedings of National Academy of Sciences, 102(14):4966-4971.
AA Philippakis, FS He, and ML Bulyk (2005), "ModuleFinder: a tool for computational discovery of Cis regulatory modules", Pacific Symposium on Biocomputing, 10:519-530.
promoter/TF

Rainer Pudimat, Ernst-Gunter Schukat-Talamazzini, Rolf Backofen (2005), "A multiple-feature framework for modelling and predicting transcription factor binding sites", Bioinformatics, 21(14):3082-3088.
[abstract]
promoter/TF

Chiara Sabatti, Lars Rohlin, Kenneth Lange, and James C. Liao (2005), "Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites", Bioinformatics, 21:922-931.
[ abstract]
promoter/TF

Eran Segal, Roded Sharan (2005), "A discriminative model for identifying spatial cis-regulatory modules", Journal of Computational Biology, 12(6):822-834.
promoter/TF

Dustin E Schones, Pavel Sumazin, Michael Q Zhang (2005), "Similarity of position frequency matrices for transcription factor binding sites", Bioinformatics, 21:307-313.
[ abstract]
promoter/TF

J Schug, WP Schuller, C Kappen, JM Salbaum, M Bucan, CJ Stoeckert Jr. (2005), "Promoter features related to tissue specificity as measured by Shannon entropy", Genome Biology, 6(4):R33.
alternative-splicing

AA Sharov, DB Dudekula, MS Ko (2005), "Genome-wide assembly and analysis of alternative transcripts in mouse", Genome Research, 15(5):748-754.
Michael E. Sparks and Volker Brendel (2005), "Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants", Bioinformatics, 21 (suppl 3):iii20-iii30.
[ abstract]
promoter/TF

M Stepanova, T Tiazhelova, M Skoblov, A Baranova (2005), "A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas", Bioinformatics, 21(9):1789-1796.
[abstract]
annotation

P Stothard, G Van Domselaar, S Shrivastava, A Guo, B O'Neill, J Cruz, M Ellison, DS Wishart (2005), "BacMap: an interactive picture atlas of annotated bacterial genomes", Nucleic Acids Research, 33(Database issue):D317-D320.
annotation

P Stothard, DS Wishart (2005), "Circular genome visualization and exploration using CGView", Bioinformatics, 21(4):537-539.
[abstract]
promoter/TF

P Sumazin, G Chen, N Hata, AD Smith, T Zhang, MQ Zhang (2005), "DWE: discriminating word enumerator", Bioinformatics, 21(1):31-38.
[abstract]
K Szafranski, R Lehmann, G Parra, R Guigo, G Glockner (2005), "Gene organization features in A/T-rich organisms", Journal of Molecular Evolution, 60(1):90-98.
promoter/TF

Kai Tan, Lee Ann McCue, Gary D Stormo (2005), "Making connections between novel transcription factors and their DNA motifs", Genome Research, 15:312-320.
translation

M Tech, N Pfeifer, B Morgenstern, P Meinicke (2005), "TICO: a tool for improving predictions of prokaryotic translation initiation sites", Bioinformatics, 21(17):3568-3569.
[abstract]
promoter/TF

M Tompa, N Li, TL Bailey, GM Church, B De Moor, E Eskin, AV Favorov, MC Frith, Y Fu, WJ Kent, VJ Makeev, AA Mironov, WS Noble, G Pavesi, G Pesole, M Regnier, N Simonis, S Sinha, G Thijs, J van Helden, M Vandenbogaert, Z Weng, C Workman, C Ye, Z Zhu (2005), "Assessing computational tools for the discovery of transcription factor binding sites", Nature Biotechnology, 23(1):137-144.
annotation

GH van Domselaar, P Stothard, S Shrivastava, JA Cruz, A Guo, X Dong, P Lu, D Szafron, R Greiner, DS Wishart (2005), "BASys: a web server for automated bacterial genome annotation", Nucleic Acids Research, 33(Web Server issue):W455-W459.
similarity

K Vandepoele, Y Van de Peer (2005), "Exploring the plant transcriptome through phylogenetic profiling", Plant Physiology, 137(1):31-42.
promoter/TF

Jan H Vogel, Anja von Heydebreck, Antje Purmann, Silke Sperling (2005), "Chromosomal clustering of a human transcriptome reveals regulatory background", BMC Bioinformatics, 6:230.
[abstract]
MB Wahl, U Heinzmann, K Imai(2005), "LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome", Bioinformatics, 21(8):1389-1392.
[abstract]
alternative-splicing

MB Wahl, U Heinzmann, K Imai (2005), "LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouse", Bioinformatics, 21(8):1393-1400.
[abstract]
X Wang, J Zhang, F Li, J Gu, T He, X Zhang, Y Li (2005), "MicroRNA identification based on sequence and structure alignment", Bioinformatics, 21(18):3610-3614.
[abstract]
C Wei, P Lamesch, M Arumugam, J Rosenberg, P Hu, M Vidal, MR Brent (2005), "Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions", Genome Research, 15(4):577-582.
promoter/TF

BP Westover, JD Buhler, JL Sonnenburg, JI Gordon (2005), "Operon prediction without a training set", Bioinformatics, 21:880-888.
[ abstract]
similarity

TD Wu, CK Watanabe (2005), "GMAP: a genomic mapping and alignment program for mRNA and EST sequences", Bioinformatics, 21(9):1859-1875.
[abstract]
promoter/TF

X Xie, J Lu, EJ Kulbokas, TR Golub, V Mootha, K Lindblad-Toh, ES Lander, M Kellis (2005), "Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals", Nature, 434(7031):338-345.
alternative-splicing

Yi Xing, Christopher Lee (2005), "Assessing the application of Ka/Ks ratio test to alternatively spliced exons", Bioinformatics, 21:3701-3703.
[ abstract]
promoter/TF

Y Xiong, T Liu, C Tian, S Sun, J Li, M Chen (2005), "Transcription factors in rice: a genome-wide comparative analysis between monocots and eudicots", Plant Molecular Biology, 59(1):191-203.
promoter/TF

R Yamashita, Y Suzuki, S Sugano, K Nakai (2005), "Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue-specificity", Gene, 350(2):129-136.
Jun Yan and Thomas G Marr (2005), "Computational analysis of 3'-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat", Genome Research, 15:369-375.
promoter/TF

Chen-Hsiang Yeang, Tommi Jaakkola (2005), "Moldeing the combinatorial functions of multiple transcription factors", Proceedings of the Ninth International Conference on Research in Computational Molecular Biology , pp.?-?
Changchuan Yin, Stephen S.T. Yau (2005), "A Fourier characteristic of coding sequences: origins and a non-Fourier approximation", Journal of Computational Biology, 12(9):1153-1165.
annotation

A Young, N Whitehouse, J Cho, C Shaw (2005), "OntologyTraverser: an R package for GO analysis", Bioinformatics, 21(2):275-276.
[abstract]
Weixiong Zhang, Jianhua Ruan, Tuan-hua David Ho, Youngsook You, Taotao Yu, Ralph S. Quatrano (2005), "Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana", Bioinformatics, 21(14):3074-3081.
[abstract]
promoter/TF

Xiaoyue Zhao, Haiyan Huang, Terence P. Speed (2005), "Finding short DNA motifs using permuted Markov models", Journal of Computational Biology, 12(6):894-906.
similarity

XH Zheng, F Lu, ZY Wang, F Zhong, J Hoover, R Mural (2005), "Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs", Bioinformatics, 21(6):703-710.
[abstract]
Yu Zheng, Brian P Anton, Richard J Roberts, Simon Kasif (2005), "Phylogenetic detection of conserved gene clusters in microbial genomes", BMC Bioinformatics, 6:243.
[abstract]
Huamin Zhou, Tyler Zarubin, Zhiliang Ji, Zheng Min, Wei Zhu, Jocelyn S. Downey, Shengcai Lin and Jiahuai Han (2005), "Frequency and distribution of AP-1 sites in the human genome", DNA Research, 12(2):139-150.
[ abstract]
Y Zhou, JA Young, A Santrosyan, K Chen, SF Yan, EA Winzeler (2005), "In silico gene function prediction using ontology-based pattern identification", Bioinformatics, 21(7):1237-1245.
[abstract]
expression

Min Zou, Suzanne D. Conzen (2005), "A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data", Bioinformatics, 21(1):71-79.
[abstract]