Fall 2002

Bioinf/ Biochem 511 Seminar Series

September 12, 2002
Dr. Christopher Hogue
Department of Chemistry, University of Toronto
Samuel L. Lunenfeld Research Institute
"The Blueprint Initiative - Archiving Molecular Interactions Worldwide"

Papers for 511 students to read for this seminar include:

• A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Module
  
• Functional Organization of the Yeast Proteome By Systematic Analysis of Protein Complexes
• Integrating Interactomes
  
• Systematic Identification of Protein Complexes In Saccharomyces Cerevisiae By Mass Spectrometry

October 3, 2002
Dr. Jeffrey de Wet
Pfizer Global Research and Development
"Bioinformatics, Biological Information, and Education: The View from the Client Side"

October 10, 2002
Dr. Patrick Nelson
LS&A Mathematics Department, The University of Michigan, Ann Arbor, MI
"Topics In HIV Modeling"
Papers for 511 students to read include:

• Mathematical Analysis of HIV-1 Dynamics In Vivo
  
• Effect of Drug Efficacy and the Eclipse Phase of the Viral Life Cycle On Estimates of HIV Viral Dynamic Parameters

October 31, 2002
Dr. Richard Miller
Department of Pathology and Institute of Gerontology, The University of Michigan, Ann Arbor, MI
"Gene Expression Analysis of Decelerated Aging In Mice"

Papers for 511 students to read include:

• Gene Expression Profile of Aging and Its Retardation by Caloric Restriction
  
• Interpretation, Design, and Analysis of Gene Array Expression Experiments
  
• Significance Analysis of Microarrays Applied To the Ionizing Radiation Response
  
• Extending the Lifespan of Long-lived Mice

November 14, 2002
Dr. Vamsi Mootha
Whitehead Institute/MIT Center for Genome Research
"Integrative Genomics Approaches to Human Disease"

Papers for 511 students to read include:

• Directed Proteomic Analysis of the Human Nucleolus

December 5, 2002
Dr. Richard Neubig
Department of Pharmacology, The University of Michigan, Ann Arbor, MI
"Regulators of G protein signaling as novel drug targets"

Papers for 511 students to read incluce:

• Regulators of G-Protein Signalling as New Central Nervous System Drug Targets
• High-Affinity Activators of CFTR Chloride Conductance Identified by Hgh-Throughput Screening of 60,000 Diverse Compounds
• Integration of Virtual and High-Throughput Screening

Winter 2003

Bioinf/ Biochem 511 Seminar Series

January 16, 2003
Dr. David Lubman
LS&A Chemistry Department, The University of Michigan, Ann Arbor, MI
"2-D Liquid Separations of Proteins From Cancer Cell Lysates"

Reading material for 511 students:

• A 2-D Liquid Separations/Mass Mapping Method for
  Interlysate Comparison of Ovarian Cancers

January 30, 2003
Dr. Eberhard O. Voit
Biometry and Epidemiology, Medical University of South Carolina
"Metabolic Pathway Analysis, Round 3."

Reading materials for 511 students:

• Biochemical systems analysis of genome-wide expression data
• Dynamic Profiling and Canonical Modeling: Powerful Partners in Metabolic Pathway Identification
• Metabolic modeling: a tool of drug discovery in the post-genomic era
  

February 13, 2003
Dr. Arul Chinnaiyan
Departments of Pathology and Urology Surgery, University of Michigan
"The Three B's of Prostate Cancer: Biology, Biomarkers, and Bioinformatics."

Reading materials for 511 students:

• The polycomb group protein EZH2 is involved in progression of prostate cancer
• The silence of the genes
• Delineation of prognostic biomarkers in prostate cancer
• Meta-Analysis of Microarrays: Interstudy Validation of Gene Expression Profiles Reveals Pathway Dysregulation in Prostate Cancer
  

February 20, 2003
Dr. Eva Feldman
Department of Neurology, The University of Michigan, Ann Arbor, MI
"Diabetes and Bioinformatics: Perfect Partners."

March 6, 2003 - Postponed
Dr. Sharon Kardia
Department of Epidemiology, The University of Michigan, Ann Arbor, MI

March 20, 2003
Dr. Trey Ideker
Whitehead Institute, MIT/Pfizer
"Digesting large molecular interaction networks into manageable pieces"

Reading materials for 511 students:

• Discovering regulatory and signalling circuits in molecular interaction networks
• Damage Recovery Pathways in Saccharomyces cerevisiae Revealed by Genomic Phenotyping and Interactome Mapping
• Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network

April 3, 2003
Dr. Julian Adams
LS&A Molecular, Cellular, and Developmental Biology, The University of Michigan, Ann Arbor, MI
"Chromosomes as variables: genomic rearrangements during evolution in microbes"

Reading materials for 511 students:

• Adams, J. S. Puskas-Rozsa, J. Simlar and C. M. Wilke, "Adaptation and major chromosomal changes in populations of Saccharomyces cerevisiae", Current Genetics 22 (1992): 13-19.
• Genetic architecture of thermal adaptation in Escherichia coli
• Characteristic genome rearrangements accompany experimental evolution of S. cerevisiae
  

April 10, 2003 - Cancelled
Dr. Jeffrey Skolnick
Director, Buffalo Center of Excellence In Bioinformatics, University of Buffalo

April 17, 2003
Dr. Sharon Kardia
Department of Epidemiology, The University of Michigan, Ann Arbor, MI
"Chromosomal patterns of gene expression"

Reading materials for 511 students:

• The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains
• A Preliminary Transcriptome Map of Non-Small Cell Lung Cancer

Bioinformatics, Proteomics and Functional Genomics Seminar

March 13, 2003
Dr. Kathleen Cho
Int Med-Molecuar Med & Genetics Department of Pathology, University of Michigan
"Ovarian Cancer- New Insights from Gene Expression Profiling"

March 27, 2003
Dr. Craig Logsdon
Department of Molecular & Integrative Physiology, The University of Michigan
"Expression profiling reveals early events in acute pancreatitis"

April 24, 2003
Dr. Kunliang Guan
Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI
"Protein phosphorylation in cell growth and neuronal axon guidance"