Fall 2003

Bioinformatics Seminar Series

Thursday, September 11, 2003
4:00 PM
North Lecture Hall - (3rd Floor Med Sci II)
"Bioinformatics Challenges for the HUPO Plasma Proteome Project"
Gil Omenn, M.D., Ph.D.
Professor, Department of Human Genetics
The University of Michigan, Ann Arbor, MI

Reading Materials for 511 Students:

Plasma Proteome Project topics at www.hupo.org from the Bethesda Workshop 16-17 July

Thursday, September 18, 2003
4:00 PM
5330 Med Sci I
"Toward a physically accurate statistical energy function for protein folding and binding studies. The power of combining structural knowledge with physical principles."
Yaoqi Zhou, Ph.D.
Assistant Professor, Department of Physiology and Biophysics
University at Buffalo, State University of New York

Reading Materials for 511 Students:

HONGYI ZHOU AND YAOQI ZHOU, "Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction" Protein Science (2002), 11:2714–2726.

Thursday, October 2, 2003
4:00 PM
5330 Med Sci I
"MiMI: Effective Integration of Protein Data."
Hosagrahar Jagadish, Ph.D.
Professor, Department of Electrical Engineering & Computer Science
University of Michigan, Ann Arbor, MI

Reading Materials for 511 Students:

http://bioinfo.mshri.on.ca/cgi-bin/bind/dataman
http://dip.doe-mbi.ucla.edu/

Thursday, October 16, 2003
4:00 PM
5330 Med Sci I
"Bioinformatics issues with database searching using genomic and proteomic data."
Akhilesh Pandey, M.D., Ph.D.
Assistant Professor, Department of Biological Chemistry
Johns Hopkins School of Medicine, Baltimore, MD

Thursday, October 23, 2003 - CANCELLED
4:00 PM
5330 Med Sci I
John Weinstein, M.D., Ph.D.
Head, Genomics and Bioinformatics Group
National Cancer Institute

Thursday, October 30, 2003
4:00 PM
5330 Med Sci I
"Structural genomics of RNA using NMR."
Hashim Al-Hashimi, Ph.D.
Assistant Professor, Department of Chemistry
Assistant Research Scientist, Biophysics Research Division
The University of Michigan, Ann Arbor, MI

Thursday, November 6, 2003
4:00 PM
5330 Med Sci I
"How enzymes work as illustrated by haloalkane dehalogenase."
Jiali Gao, Ph.D.
Professor, Department of Chemistry
University of Minnesota, Minneapolis, MN

Reading Materials for 511 Students:

• Combined QM/MM Study of the Mechanism and Kinetic Isotope Effect of the Nucleophilic Substitution Reaction in Haloalkane Dehalogenase
• Dynamics of an Enzymatic Substitution Reaction in Haloalkane Dehalogenase
• Supporting Information for:
  Dynamics of an Enzymatic Substitution Reaction in Haloalkane Dehalogenase

Thursday, November 20, 2003
4:00 PM
5330 Med Sci I
"Novel Quantum Mechanical Approaches for Drug Design and Discovery."
Kenneth Merz, Ph.D.
Professor, Department of Chemistry
The Pennsylvania State University, University Park, PA

Thursday, December 4, 2003 - Room Change
4:00 PM
LRC 2903
"Multi-criteria differential expression analysis of microarray data."
Al Hero, Ph.D.
Professor, Department of Biomedical Engineering
Professor, Department of Electrical Engineering & Computer Science
Professor, Department of Statistics
University of Michigan, Ann Arbor, MI

Thursday, December 11, 2003 - Room Change
4:00 PM
LRC 2903
"Novel Chemical Proteomics Technologies for Probing Organelles and Post-translational Modifications."
Yingming Zhao, Ph.D.
Assistant Professor, Department of Biochemistry
Assistant Professor, Department of Pharmacology
The University of Texas Southwestern Medical Center at Dallas, Dallas, TX

Thursday, December 18, 2003
4:00 PM
5330 Med Sci I
Mike Snyder, Ph.D.
Professor and Chairman, Department of Molecular Cellular and Developmental Biology
Professor, Department of Molecular Biophysics & Biochemistry
Yale University, New Haven, CT

Winter 2004

Seminars are in 2903 LRC unless otherwise noted.

Thursday, January 22, 2004
4:00 PM
2903 LRC (Second Floor of Taubman Medical Library)
"Identification of co-regulated genes through sequence analysis, poorman's microarray?"
Zhaohui Steve Qin, Ph.D.
Assistant Professor, Department of Biostatistics
The University of Michigan, Ann Arbor, MI

Reading Material for 511 Students:

• Qin ZS, McCue LA, Thompson W, Mayerhofer L, Lawrence CE & Liu JS (2003). Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. Nature Biotech, 21, 435-39.

Thursday, January 29, 2004
4:00 PM
2903 LRC (Second Floor of Taubman Medical Library)
"Prediction of protein structure and function on a genomic scale."
Jeff Skolnick, Ph.D.
Director, Center of Excellence in Bioinformaitcs
University at Buffalo, Buffalo, NY

Reading Material for the 511 Students:

• Jeffrey Skolnick, Jacquelyn S. Fetrow, Andrzej Kolinski
  Structural genomics and its importance for gene function analysis
  Nature Biotechnology 18, 283 - 287 (01 Mar 2000)
  
• Long Lu, Adrian K. Arakaki, Hui Lu, and Jeffrey Skolnick
  Multimeric Threading-Based Prediction of Protein–Protein Interactions on a Genomic Scale: Application to the Saccharomyces cerevisiae Proteome
  Genome Res. 2003 13: 1146-1154.
  
• J. Skolnick, Y. Zhang, A. K. Arakaki, A. Kolinski, M. Boniecki, A. Szilagyi, D. Kihara
  Touchstone: A Unified Approach to Protein Structure Prediction.
  Proteins: Structure, Function and Genetics, CASP5 Proceedings (special issue), 53, 469-479 (2003)
  

Thursday, February 5, 2004
4:00 PM
2903 LRC (Second Floor of Taubman Medical Library)
"Integrative Functional Genomics: Protein interaction and genetic interaction mapping of a TGF-beta signaling network in C. elegans"
Muneesh Tewari, M.D., Ph.D.
Dana Farber Cancer Institute,
Harvard Medical School, Boston, MA

• Hui Ge, Albertha J.M. Walhout and Marc Vidal
  Integrating ‘omic’ information: a bridge between genomics and systems biology.
  TRENDS in Genetics Vol.19 No.10 (October 2003): 551-560
  

Thursday, February 12, 2004 - Cancelled
4:00 PM
Catherine Fenselau, Ph.D.
Professor, Department of Chemistry and Biochemistry
University of Maryland, College Park, MD

Thursday, March 4, 2004
4:00 PM
2903 LRC
"How Aventis Pharmaceuticals applies proteomics to drug discovery: challenges and future directions"
Matthew Davison, Ph.D.
Head of US Proteomics
Aventis Pharmaceuticals, Bridgewater, NJ

Thursday, March 11, 2004
3:00 PM - Time Change
West Lecture Hall (3rd Floor of Medical Science II)- Room Change
"Mad Cow Disease: Mad Cows, Prions & Protein Folding"
Fred Cohen, M.D., D.Phil.
Professor, Department of Cellular & Molecular Pharmacology
University of California, San Francisco, CA

Thursday, March 18, 2004
4:00 PM
2903 LRC
"Integrated gloabl profiling of cancer"
Samir Hanash, M.D., Ph.D.
Professor, Department of Pediatrics
The University of Michigan, Ann Arbor, MI

Thursday, March 25, 2004
4:00 PM
2903 LRC
"The sequence capacity of protein structures"
Ron Elber, Ph.D.
Professor, Department of Computer Science
Cornell University, Ithaca, NY

Thursday, April 1, 2004
4:00 PM
2903 LRC
"Large-Scale Functional Analysis of the Yeast Genome"
Anuj Kumar, Ph.D.
Assistant Professor, Department of Molecular, Cellular & Developmental Biology
Assistant Research Scientist, Life Sciences Institute
The University of Michigan, Ann Arbor, MI

Thursday, April 8, 2004
Kenneth Pienta, M.D. - Cancelled
Professor, Department of Surgery
Professor, Internal Medicine Department
The University of Michigan, Ann Arbor, MI

Thursday, April 15, 2004
4:00 PM
Mark Gerstein, Ph.D. - Cancelled
Albert L Williams Associate Professor of Biomedical Informatics, Molecular Biophysics and Biochemistry and Computer Science
Yale University, New Haven, CT

Thursday, April 22, 2004
4:00 PM
William Sellers, M.D. - Cancelled
Assistant Professor of Medicine
Dana Farber Cancer Institute,
Harvard Medical School, Boston, MA