CS591-BIO Advanced seminar in biomedical informatics (Fall 2006)

Tentative list of papers to be presented

De novo cis-regulatory module elicitation for eukaryotic genomes. Gupta and Liu, PNAS 2005.
A genomic code for nucleosome positioning. Segal et al. Nature 2006 (Assigned to Lyndsy Kron.).
Extensive low-affinity transcriptional interactions in the yeast genome. Amos Tanay. Genome Research 2006 (Assigned to Abhilasha Chaudhary.)
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Blanchette et al. Genome Research 2006. (Assigned to Manish Agarwal.)
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Siepel et al. Genome Research 2005.
Identification and Characterization of Multi-Species Conserved Sequences. Marguilies et al. Genome Research 2003. (Assigned to Kranthi Varala.)
Combinatorial microRNA target predictions. Rajewsky et al. Nature Gen. 2005.

Speakers presenting their research (tentative)

UIUC: Bruce Schatz, Xin He.
External: J. Zhou, M. Hearst, W. Xiao.

Date

Speaker

Topic

8/25 Fri

Organizational meeting

9/01 Fri

Jaebum Kim

A probabilistic framework for annotation of insertions and deletions in a multiple alignment

9/08 Fri

Xu Ling

Genome Scan for cis-regulatory DNA motifs associated with social regulation in honeybee.

9/15 Fri

Jing Jiang

Tokenization and Synonym Expansion -- Some Challenges in Biomedical Information Retrieval

9/22 Fri

Manish Agarwal

Blanchette et al. ppt

9/29 Fri

Abhilasha Chaudhary

Tanay

10/06 Fri

Kranthi Varala

Marguilles et al.

10/13 Fri

Bruce Schatz

Analysis Environments for scientists ppt

10/20 Fri

Charu Gupta Kumar

10/27 Fri

Lyndsy Kron

Segal et al.

11/03 Fri

Jay Mashl

Large scale conformational changes of potassium channels

11/10 Fri

Lei Liu

11/17 Fri

Andra Ivan

Computational discovery of cis regulatory modules without knowledge of binding motifs

12/01 Fri

Xin He

A Statistical Approach to Literature-based Microarray Data Annotation.

12/08 Fri

Guixian Lin

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