Bioinformatics Papers

• April 8:
  • Steve Hampson: Extracting Regulatory Sites from the Upstream Region of Yeast Genes by Computational Analysis of Oligonucleotide Frequencies. Jacques van Helden, B. Andre and J. Collado-Vides. JMB (1998) 281,827-842
• April 15:
  • Dennis Kibler: Molecular Classification fo Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring. T.R. Golub, D. K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J.P. Mesirov, H. Coller, M. L. Loh, J. R. Downing, M. A. Caligiuri, C. D. Bloomfield, E. S. Lander. Science, vol 286 October 1999.
• April 22:
  • Bob Chan: Multiclass cancer diagnosis using tumor gene expression signatures. S. Ramaswamy, P. Tamayo, R. Rifkin, S. Mukherjee, C-H. Yeang, M. Angelo, C. Ladd, M. Reich, E. Latulippe, J. P. Mesirov, T. Poggio, W. Gerald, M. Loda, E. S. Lander, and T. R. Golub. PNAS December 18, no. 26, 15149-15154.
  • Jennifer Miok Rhough: Beyond Synexpression Relationships: Local Clustering of Time-shifted and Inverted Gene Expression Patterns Expression Profiles Identifies New, Biologically Relevant Interactions. J. Qian, M. Dolled-Filhart, J Lin, M. Gertstein (Yale) JMB 2001 314, 1053-1066.
• April 29:
  • Sean Lee: Multi-alphabet consensus algorithm for identification of low specificity protein-DNA interactions. Anatoly Ulyanov and Gary Stormo. Nucleic Acids Research, vol 23, no 8 (1995) 1434-1440.
  • Gianluca Pollastri: Machine Learning Structural and Functional Proteomics. P.Baldi, G.Pollastri. IEEE Intelligent Systems (Intelligent Systems in Biology II), March/April 2002. Download at: ftp://promoter.ics.uci.edu/Papers/2002_IEEE.pdf
• May 13:
  • Gianluca Pollastri: Prediction of Contact Maps by Recurrent Neural Network Architectures and Hidden Context Propagation from All Four Cardinal Corners. G.Pollastri, P.Baldi. Bioinformatics (ISMB2002 special issue), in press. Download at ftp://promoter.ics.uci.edu/Papers/2002_ISMB.pdf
  • Son Dang: Hidden Markov models that use predicted secondary structures for fold recognition. Hargbo J, Elofsson. PROTEINS-STRUCTURE FUNCTION AND GENETICS. v36 (1): 68-76 JUL 1 1999.
• May 20:
  • Li Zhang: Support Vector Machine Classifciation of Microarray data. S. Murherjee, P. Tamayou, D. Slonim, A. Verri, T. Golub, J. P. Mesirov, and T. Poggio. A.I. Memo No 1677 MIT.
  • Karalyn Ramon: Genome-wide transcript profiled in aging and calorically restricted D. melanogaster. : S. Pletcher et al. Current Biology, Vol.12, 1-20, April 30, 2002.
• May 27: (Memorial Day) Class?
• June 3:
  • Hilda Yu: Predicted highly expressed genes of diverse prokaryotic genomes. Karlin, S., Mrazek, J.: Jour. of Bacteriology 182: 5238-5250 (2000) (available on pub med)
  • Steve Hampson Ribosome Binding Sites: Probability Matrices and Weight Matrices. Kibler and Hampson. METMBS-2002. (available on my web page)
• June 10 Last Presentations