computational gene recognition

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+ 2008

  1. 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.

  2. 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]

  3. 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).

  4. 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]

  5. 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]

  6. Denis C Bauer, Timothy L Bailey (2008), "STREAM: Static Thermodynamic REgulAtory Model of transcription", Bioinformatics, 24(21):2544-2545.
    [abstract]

  7. annotation
    Michael R. Brent (2008), "Steady progress and recent breakthroughs in the accuracy of automated genome annotation", Nature Reviews Genetics, 9:62-73.
    [abstract]

  8. 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]

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

  10. 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]

  11. F Gao, CT Zhang (2008), "Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes", BMC Bioinformatics, 9:79.

  12. 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]

  13. 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.

  14. 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.

  15. Dean Laslett, Björn Canbäck (2008), "ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences", Bioinformatics, 24:172-175.
    [abstract]

  16. 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]

  17. 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]

  18. 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]

  19. 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.

  20. promoter/TF
    Patrick Ng, Uri Keich (2008), "GIMSAN: a Gibbs motif finder with significance analysis", Bioinformatics, 24(19):2256-2257.
    [abstract]

  21. 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]

  22. 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]

  23. Jacques Oberto (2008), "BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence", Bioinformatics, 24(3):424-425.
    [abstract]

  24. David J Reiss, Marc T Facciotti, Nitin S Baliga (2008), "Model-based deconvolution of genome-wide DNA binding", Bioinformatics, 24(3):396-403.
    [abstract]

  25. 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]

  26. 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]

  27. 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]

  28. 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]

  29. 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]

  30. 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]

  31. 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]

  32. 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]

  33. 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]