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

  3. 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]

  4. 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]

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

  6. 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]

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

  8. 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]

  9. 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]

  10. 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.

  11. 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]

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

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

  14. 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]

  15. 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]

  16. 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]

  17. 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]

  18. 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]