gene recognition papers (2008)

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2008

promoter/TF

T Abeel, Y Saeys, E Bonnet, P Rouzé, Y Van de Peer (2008), "Generic eukaryotic core promoter prediction using structural features of DNA", Genome Research, 18:310-323.
M Akhtar, J Epps, E Ambikairajah (2008), "Signal processing in sequence analysis: advances in eukaryotic gene prediction", IEEE Journal of Selected Topics in Signal Processing, 2(3):310-321
[ abstract]
alternative-splicing

Tyler S Alioto, Roderic Guigo, Ernesto Picardi, Graziano Pesole (2008), "GenePC and ASPIC integrate gene predictions with expressed sequence alignments to predict alternative transcripts", Proceedings of the 6th Asia-Pacific Bioinformatics Conference eds. A Brazma, S Miyano, T Akutsu, pp.363-372 (Imperial College Press).
Sh A Atambayeva, VA Khailenko, AT Ivashchenko (2008), "Intron and exon length variation in Arabidopsis, rice, nematode, and human", Molecular Biology, 42(2):312-320.
[ abstract]
R.K. Azad (2008), "Genes in prokaryotic genomes and their computational prediction", in Computational Methods for Understanding Bacterial and Archaeal Genomes, eds. Y Xu, JP Gogarten, pp.?-? (Imperial College Press, London).
[from the publisher]
alternative-splicing

W Brad Barbazuk, Yan Fu, Karen M McGinnis (2008), "Genome-wide analyses of alternative splicing in plants: Opportunities and challenges", Genome Research, 18:1381-1392.
[ abstract]
Denis C Bauer, Timothy L Bailey (2008), "STREAM: Static Thermodynamic REgulAtory Model of transcription", Bioinformatics, 24(21):2544-2545.
[abstract]
promoter/TF

Evert-Jan Blom, Sacha AFT van Hijum, Klaas J Hofstede, Remko Silvis, Jos BTM Roerdink, Oscar P Kuipers (2008), "DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites", BMC Bioinformatics, 9:535
[abstract]
annotation

Michael R. Brent (2008), "Steady progress and recent breakthroughs in the accuracy of automated genome annotation", Nature Reviews Genetics, 9:62-73.
[abstract]
Rutger W. W. Brouwer, Oscar P. Kuipers, and Sacha A. F. T. van Hijum (2008), "The relative value of operon predictions", Briefings in Bioinformatics, 9: 367-375
[abstract]
promoter/TF

Debayan Datta, Hongyu Zhao (2008), "Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae ", Bioinformatics, 24(4):545-552.
[abstract]
promoter/TF

François Fauteux, Mathieu Blanchette, and Martina V. Strömvik (2008), "Seeder: discriminative seeding DNA motif discovery", Bioinformatics, 24(20):2303-2307.
[abstract]
promoter/TF

Shuji Fujita and Hideo Iba (2008), "Putative promoter regions of miRNA genes involved in evolutionarily conserved regulatory systems among vertebrates", Bioinformatics, 24:303-308.
[abstract]
F Gao, CT Zhang (2008), "Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes", BMC Bioinformatics, 9:79.
[abstract]
promoter/TF

Sumedha Gunewardena and Zhaolei Zhang (2008), "A hybrid model for robust detection of transcription factor binding sites", Bioinformatics, 24(4):484-491.
[abstract]
splicing

Klemens J Hertel (2008), "Combinatorial control of exon recognition", Journal of Biological Chemistry, 283(3):1211-1215.
[ abstract]
promoter/TF

Matthew S Hestand, Michiel van Galen, Michel P Villerius, Gert-Jan B van Ommen, Johan T den Dunnen, Peter AC 't Hoen (2008), "CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes", BMC Bioinformatics, 9:495
[abstract]
translation

Gang-Qing Hu, Xiaobin Zheng, Li-Ning Ju, Huaiqiu Zhu, Zhen-Su She (2008), "Computational evaluation of TIS annotation for prokaryotic genomes", BMC Bioinformatics, 9:160.
[abstract]
translation

Gang-Qing Hu, Xiaobin Zheng, Yi-Fan Yang, Philippe Ortet, Zhen-Su She, Huaiqiu Zhu (2008), "ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes", Nucleic Acids Research, 36(database issue):D114-D119.
T Kwan, D Benovoy, C Dias, S Gurd, C Provencher, P Beaulieu, TJ Hudson, R Sladek, J Majewski (2008), "Genome-wide analysis of transcript isoform variation in humans", Nature Genetics, 40(2):225-231.
Dean Laslett, Björn Canbäck (2008), "ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences", Bioinformatics, 24:172-175.
[abstract]
Qian-Ru Li, Anne-Ruxandra Carvunis, Haiyuan Yu, Jing-Dong J Han, Quan Zhong, Nicolas Simonis, Stanley Tam, Tong Hao, Niels J Klitgord, Denis Dupuy, Danny Mou, Ilan Wapinski, Aviv Regev, David E Hill, Michael E Cusick, Marc Vidal (2008), "Revisiting the Saccharomyces cerevisiae predicted ORFeome", Genome Research, 18(8):1294-1303.
[abstract]
promoter/TF

Kuo-Ching Liang , Xiaodong Wang and Dimitris Anastassiou (2008), "A profile-based deterministic sequential Monte Carlo algorithm for motif discovery", Bioinformatics, 24:46-55.
[abstract]
Qian Liu, Aaron J Mackey, David S Roos, Fernando C N Pereira (2008), "Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction", Bioinformatics, 24(5):597-605.
[abstract]
MD Maynard, J Chen, RK Stuart, JB Fan, B Ren (2008), "Genome-wide mapping of allele-specific protein-DNA interactions in human cells", Nature Methods, to appear.
alternative-splicing

Abigail M McGuire, Matthew D Pearson, Daniel E Neafsey, James E Galagan (2008), "Cross-kingdom patterns of alternative splicing and splice recognition", Genome Biology, 9:R50.
[ abstract]
promoter/TF

Patrick Ng, Uri Keich (2008), "GIMSAN: a Gibbs motif finder with significance analysis", Bioinformatics, 24(19):2256-2257.
[abstract]
Deng-Ke Niu (2008), "Exon definition as a potential negative force against intron losses in evolution", Biology Direct, 3:46.
[ abstract]
Jacques Oberto (2008), "BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence", Bioinformatics, 24(3):424-425.
[abstract]
promoter/TF

Jakub Orzechowski Westholm, Feifei Xu, Hans Ronne, Jan Komorowski (2008), "Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation", BMC Bioinformatics, 9:484
[abstract]
promoter/TF

Utz J Pape, Sven Rahmann, Martin Vingron (2008), "Natural similarity measures between position frequency matrices with an application to clustering" Bioinformatics, 24(3):350-357.
[abstract]
promoter/TF

Jason Persampieri, Deborah I. Ritter, Daniel Lees, Jessica Lehoczky, Qiang Li, Su Guo, Jeffrey H. Chuang (2008), "cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation", Bioinformatics, 24(20):2418-2419.
[abstract]
KS Pollard, D Serre, X Wang, H Tao, E Grundberg, TJ Hudson, AG Clark, K Frazer (2008), "A genome-wide approach to identifying novel-imprinted genes", Human Genetics, 122(6):625-634.
David J Reiss, Marc T Facciotti, Nitin S Baliga (2008), "Model-based deconvolution of genome-wide DNA binding", Bioinformatics, 24(3):396-403.
[abstract]
M Roy, N Kim, Y Xing, C Lee (2008), "The effect of intron length on exon creation ratios during the evolution of mammalian genomes", RNA, 14:2261-2273
promoter/TF

Geir Kjetil Sandve, Osman Abul, Finn Drabløs (2008), "Compo: composite motif discovery using discrete models", BMC Bioinformatics, 9:527
[abstract]
Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), "Using native and syntenically mapped cDNA alignments to improve de novo gene finding", Bioinformatics, 24(5):637-644.
[abstract]
promoter/TF

Michael Towsey, Peter Timms, James Hogan, Sarah A. Mathews (2008), "The cross-species prediction of bacterial promoters using a support vector machine", Computational Biology and Chemistry, 32(5):359-366.
[ abstract]
promoter/TF

ADJ van Dijk, CJF ter Braak, RG Immink, GC Angenent, RCHJ van Ham (2008), "Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control", Bioinformatics, 24:26-33.
[abstract]
promoter/TF

Xiaowo Wang, Jin Gu, Michael Q Zhang, Yanda Li (2008), "Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species", Bioinformatics, 24:165-171.
[abstract]
Peng Wei, Wei Pan (2008) "Incorporating gene networks into statistical tests for genomic data via a spatially correlated mixture model", Bioinformatics, 24(3):404-411.
[abstract]
promoter/TF

Edgar Wingender (2008), "The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation", Briefings in Bioinformatics, 9:326-332.
[abstract]
Kyoung-Jae Won, Iouri Chepelev, Bing Ren, Wei Wang (2008), "Prediction of regulatory elements in mammalian genomes using chromatin signatures", BMC Bioinformatics, 9:547
[abstract]
Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu (2008), "On application of directons to functional classification of genes in prokaryotes", Computational Biology and Chemistry, 32(3):176-184.
[ abstract]
promoter/TF

Wei-Sheng Wu, Wen-Hsiung Li (2008), "Systematic identification of yeast cell cycle transcription factors using multiple data sources", BMC Bioinformatics, 9:522
[abstract]
Jian-Yi Yang, Yu Zhou, Zu-Guo Yu, Vo Anh, Li-Qian Zhou (2008), "Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides", BMC Bioinformatics, 9:113.
[abstract]
Nancy R Zhang, Mary C Wildermuth and Terence P Speed (2008), "Transcription factor binding site prediction with multivariate gene expression data", Annals of Applied Statistics, 2(1):332-365.
[abstract]
promoter/TF

Guangyong Zheng, Kang Tu, Qing Yang, Yun Xiong, Chaochun Wei, Lu Xie, Yangyong Zhu, Yixue Li (2008), "ITFP: an integrated platform of mammalian transcription factors", Bioinformatics, 24(20):2416-2417.
[abstract]