Computer Science Department
University of Illinois at Urbana-Champaign

CS498-SS Algorithms in Bioinformatics (Fall 2006)

Schedule (Anticipated)

  • Sections refer to (Jones & Pevzner) book, unless marked as "DEKM" (Durbin et al)
  • The lecture slides will be posted here on the day of the lecture.
  • The university calendar is here
Date Topic Readings
PHASE 1: ALGORITHMIC CONCEPTS FOR BIOINFORMATICS PROBLEMS
8/24 Thu Molecular Biology Primer. ppt
8/29 Tue Introduction to bioinformatics. ppt
8/31 Thu Enumerative algorithms. Restriction Mapping and Motif finding. ppt 4.1 - 4.6
9/05 Tue Enumerative algorithms continued.ppt4.7 - 4.9, 5.5
9/07 Thu Greedy algorithms. Genome rearrangement and breakpoints.ppt5.1 - 5.4
9/12 Tue Dynamic programming. Pairwise sequence alignment & local alignment. ppt6.3 - 6.9.
DEKM 2.1 - 2.3
9/14 Thu Dynamic programming. Gene prediction. ppt6.11 - 6.14
9/19 Tue Dynamic programming. RNA secondary structure. Energy minimization. pptDEKM 10.1 - 10.2 (parts)
9/21 Thu Graphs. DNA sequencing. ppt8.1 - 8.9
9/26 Tue Graphs. Protein sequencing. ppt8.10 - 8.15
9/28 Thu Combinatorial Pattern Matching. Repeat Finding. ppt9.1 - 9.7
10/03 Tue Clustering. Gene expression. ppt10.1 - 10.4
10/05 Thu Trees. Phylogeny reconstruction.ppt10.5 - 10.11
10/10 Tue HMM. ppt11.1 - 11.3
10/12 Thu Midterm examination
PHASE 2: BIOINFORMATICS IN ACTION
10/17 Tue Local sequence alignment. BLAST. pptAltschul et al. 1990
10/19 Thu Gene Finding. GeneMark.hmm. pptLukashin & Borodovsky
10/24 Tue Motif finding. Gibbs sampling. pptLawrence et al.
10/26 Thu Multiple alignment. pptBlanchette et al.
10/31 Tue Gene expression. Cancer microarrays. pptSegal et al.
11/02 Thu Cross species comparison & ChIP-chip data. Yeast regulation. ppt Harbison et al.
11/07 Tue Gene function prediction from microarray data. Classification. SVM. ppt Brown et al.
11/09 Thu Protein structure prediction. Neural networks. PSIPRED. pptJones
11/14 Tue Metabolic networks. pptJeong et al.
11/16 Thu Biological literature mining. pptLing et al.
11/28 Tue MicroRNA. pptLai et al.  Rhoades et al.
11/30 Thu Alternative Splicing. pptFlorea 06
12/05 Tue Class discussions
12/07 Thu Class discussions
12/12 Tue Final examination

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