BioE 494  Introduction to Bioinformatics Methods
Instructor: Yang Dai (yangdai@uic.edu)

Office Locations
     East Campus :  SEO120 (first floor of SEO. I am here during the office hours)
     West Campus :

       Room W125
    Medical Sciences Building
    835 S. Wolcott Ave
       Tel : (312)413-1487

        Look for the sign of
      CLIMB Clinical Laboratory for Interfacial Molecular Bioengineering
      I am here except teaching time and office hours

Syllabus
Grading   Policy
    homework 40%, project 20%, two exams 40%
    mid-term exam on 10/22, final exam on 11/26
    final project presentation on 12/03, 12/05, 12/10, 12/12

note1 (including homework1)
note2
note3(including homework2)
note4 (homework3 is added, due on 10/03/02)
application (LP for cancer diagnosis)
  appli1.ppt
  wdbc.data
  article0(O.L. Mangasarian, W.N. Street and W.H. Wolberg, "Breast cancer diagnosis and prognosis via linear programming".
                 Operations Research, 43(4), pages 570-577, 1995
             for  more information visit http://www.cs.wisc.edu/~olvi/uwmp/mpml.html)
note5 (including homework4, due on 10/10/02)
note6
applications (IP)
  appli2.ppt
  article1 (J. Borneman et al., "Probe selection algorithms with applications in the analysis of  microbial communities",
                       Bioinformatics, vol. 17, S39-S48,2001)
   article2 (A. Caprara and G. Lancia, "Structural Alignment of Large-Size Proteins via Lagrangian Relaxation",
                    Proceedings of 6th RECOMB, ACM Conference on Computational Molecular Biology, ACM,  press, 2002.)
                 I failed to transfer this file to pdf. If you don't have a ps viewer, you can download from here

   article3 (O. Eriksson, Y. Zhou, and A. Elofsson, "Side chain-positioning as an integer programming problem",
                    1st Workshop on Algorithms in BioInformatics, BRICS, University of Aarhus, Denmark, August 28-31, 2001)
note7
note8
note9(including homework5, due  10/22/02)
Branch-and-Bound (demo)
The range for the mid-term exam is  note1-note9
    article4 (R. H. Lathrop and T. F. Smith, "Global optimum protein threading with gapped alighment and empirical pair score functions",
               Journal of Molecular Biology, (1996) 255 pp. 641-665)
note10
note11
   article5(D. R. Westhead et al., "A comparison of heuristic search algorithms for molecular docking",
                  J. Computer Aided Molecular Design, vol. 11, pp.193-207,1997)
   article6(C. D. Rosin et al., "A comparison of global and local search methods in drug docking",
                Proceedings of the Seventh International Conference on Genetic Algorithms (ICGA97)).
   article7(P. V. Pevzner and S-H. Sze, "Combinatorial Approaches to Finding Subtle Signals in DNA Sequences,"
                 Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology (ISMB), pp. 269-278, 2000. )
    article8(J. D. Szustakowski, J. & Weng, Z, "Structural alignment using a genetic algorithm",
                 Proteins: Structure, Function and Genetics, 38:428-440,  2000)
    article9(Brown el at., "Knowledge-based analysis of microarray gene expression data by using support vector machines",
                Proceedings of the National Academy of Sciences, Vol. 97, Issue 1, 262-267, January 4, 2000
                      related material see http://www.cse.ucsc.edu/research/compbio/genex/genex.html)
    article10(T. Akutsu et al, "Algorithms for inferring qualitative models of biological network"
                Proceedings of  thePacific Symposium on Biocomputing, 2000, 290-301.
    article11(Michihiro Kuramochi, George Karypis,"Gene Classification using Expression Profiles: A Feasiblity Study".
                 Proceedings of  2nd IEEE International Symposium on Bioinformatics and Bioengineering,
                   Bethesda, Maryland, USA, 191-200.
NEOS Server privides information on the state-of-the-art in optimization software. Maintained at Argonne National Laboratory.
note12(some of the figures are missing)
note13(some of the figure are missing)
note14