Papers related to potential term projects for Bioinformatics I


Machine learning techniques

  • Predicting the in vivo signature of human gene regulatory sequences
  • GPCRpred: and SVM-based method for prediction of families and subfamilies of G-protein coupled receptors
  • Distinguishing regulatory DNA from neutral sites
  • Into the heart of darkness: large-scale clustering of human non-coding DNA


    Genome alignments

  • Human-mouse alignments with BLASTZ
  • LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
  • MCALIGN: Stochasitc alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution


    Predicting expression patterns

  • Identification of regulatory regions which confer muscle-specific gene expression
  • oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes


    Bioinformatic analysis of protein families

  • PRED-GPCR: GPCR recognition and family classification server
  • ConPredII: consensus prediction method for obtaining transmembrane topology models with high reliability
  • Identification of regulatory regions which confer muscle-specific gene expression


    Prediction of regulatory sites

  • Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences


    Human variation

  • On the number of new world founders: A population genetic portrait of the peopling of the americas