Computer Science Department
University of Illinois at Urbana-Champaign

CS591-BIO Advanced seminar in biomedical informatics (Spring 2007)

Date Speaker Topic
1/19 Fri - Organizational meeting
1/26 Fri Saurabh SinhaCounting position weight matrices in a sequence & an application to discriminative motif finding. (ISMB 2006) ppt
2/02 FriChengXiang Zhai Statistical LAnguage Models for Biomedical Literature Retrieval ppt
2/08 ThuFred Wright (UNC) Hypothesis Tests of Functional Categories in Microarray Data A New Approach
2/12 MonMarti Hearst (Berkeley) New Search Tools for Full Text BioScience Journal Articles
2/23 FriRichard Leduc (UIUC) A Probabilistic Scoring Scheme for Automated Protein Identification and Characterization in Top Down Proteomic Experiments
3/02 FriMao-Feng Ger (UIUC) Glutamate Receptor Ion Channels and their relatives in Bacteria and Archaea
3/09 FriMatthew Hudson (UIUC)
3/16 FriEleftheria (Elina) Athanasopoulou (ECE, UIUC)http://decision.csl.uiuc.edu/~aelina/
3/23 Fri
3/30 FriZ. Lewis Liu (USDA) Towards genomics on inhibitor stress tolerance of ethanologenic yeast Saccharomyces cerevisiae
4/06 FriFeida Zhu (UIUC) Efficient discovery of Frequent Approximate Sequential Patterns
4/13 FriXu Ling (UIUC)Generating Gene Summaries from Biomedical Literature: A Study of Semi-Structured Summarization
4/20 FriPing Ma (UIUC) Statistical Analysis of Histone Acetylation
4/27 FriOlga Vitek (Purdue). Host: Ping Ma.

Tentative list of papers to be presented

  • Priors on TF class improve motif discovery. Hartemink. ISMB 06.
  • Forensic inference in disasters. Xing. ISMB 06.
  • RNA secondary structure prediction. Batzoglou. ISMB 06.
  • Unsupervised feature filtering of biological data. Horn. ISMB 06.
  • Stat Mech modeling of TF occupancy. Bussemaker. ISMB 06.
  • Quantification of TF expression from Arabidopsis images. Ohler. ISMB 06.
  • De novo cis-regulatory module elicitation for eukaryotic genomes. Gupta and Liu, PNAS 2005.
  • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Siepel et al. Genome Research 2005.

Tentative list of Speakers


  • UIUC: S. Rodriguez/Y. Kee, J. Kim (confirmed), A. Ivan (confirmed), S. Zhong, Dong Xin.
  • External: X. Li (host: Zhong),


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