Bin Zhang, Genetics Department, Merck and Co., Inc., "Pathway and Gene Target Identification via Weighted Gene Co-Expression Network Analysis"

Pascal Braun, Center for Cancer Systems Biology, Dana Farber Cancer Institute, Harvard University, "Binary interactome mapping to study human disease"

Jinbo Xu, Toyota Technological Institute at Chicago, "Protein Threading by Nonlinearly Combining Evolutionary and Non-Evolutionary Information"

Christina Leslie, Computational Biology Program, Memorial Sloan-Kettering Cancer Center, "Deciphering microRNA-mediated regulation from perturbations in gene expression"

Jonathan Widom, Dept. of Biochemistry, Molecular Biology and Cell Biology Dept. of Chemistry , Northwestern University, "The Genomic Code for Nucleosome Positioning"

Carlos Sosa, Biomedical Informatics and Computational Biology, University of Minnesota, IBM, "Next Generation of Selected Bioinformatics Applications: Using Massively Parallel Supercomputers"

Stefan Kramer, Institute for Informatics, Technical University of Munich, Germany, "Data Mining in Reaction Databases: Towards Predicting Biodegradation Products and Pathways"

George Vasmatzis, Senior Associate Consultant, Mayo Clinic Cancer Center, "Differential transcriptomics for the prognosis and sub-typing of cancer"

Lynda B.M. Ellis, Laboratory Medicine and Pathology, University of Minnesota, "Improving Biodegradation Pathway Prediction"

Zoran Obradovic, Director, Center for Information Science and Technology, Temple University, "Functions of Intrinsically Disordered Proteins and Relationship with Human Disease Network"

Hirotada Mori, Nara Institute of Science and Technology, Nara 630-0101, Japan, Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017 Japan

Ying Xu, Department of Biochemistry and Molecular Biology, University of Georgia, "Computational Prediction of Functional Modules and Their Regulatory Networks in Microbial Organisms"

William W. Stead, Associate Vice Chancellor for, Strategy/Tranformation & CIO McKesson Foundation, Professor of Biomedical Informatics and Medicine, Vanderbilt University Medical Center, Chief Information Architect, Vanderbilt University, "Informatics: A Scientific Basis for Use of IT in Healthcare and Biomedicine"

Terri Attwood, Faculty of Life Sciences and School of Computer Science, University of Manchester, UK, "A taste of UTOPIA — a vision for the future of bioinformatics"

Anne Smith, School of Biology, University of St Andrews, Scotland, "Bayesian networks for analyzing complex biological systems"

Gavin Sherlock, Stanford University, "Towards a molecular description of adaptive evolution"

Ken A. Dill, Pharmaceutical Chemistry, University of California San Francisco, "Protein folding physics and computational modeling"

Peter Zandstra, Institute of Biomaterials and Biomedical Engineering, University of Toronto, "Spatial and temporal dynamics in stem cell self-renewal and differention"

Damian Gessler, National Center for Genome Resources, Santa Fe, New Mexico, "SSWAP: Simple Semantic Web Architecture and Protocol"

Wilma Olson, Rutgers University, "Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte-Carlo simulations"

Borya Shakhnovich, Harvard University, "The TATA box is not enough: the structure and conservation of TATA box promoters"

Trey Ideker, Department of Bioengineering, University of California, San Diego, "Protein Network Comparative Genomics"

Bioinformatics: Building Bridges

Yiannis Kaznessis, Department of Chemical Engineering and Materials Science, University of Minnesota, "Mathematical Models for Biological Engineering"

Alex Allardyce, ChemAxon, Budapest, Hungary, "ChemAxon Academic Package: Free end user applications and toolkits for cheminformatics"

Karin Remington, Candidate for CBCB Director, "Marine Metagenomics: Seawater to Sequence to Science"

Piet C. de Groen, Division of Gastroenterology and Hepatology, Mayo Clinic, "Objective Quality Control for Colonoscopy: Automated Extraction of Endoscopic Metrics from Video Files*"

Tony Dean, Biological Sciences, "The Biochemical Architecture of an Ancient Adaptive Landscape"
http://www.cbs.umn.edu/labs/deanlab/

Michael O'Connor, Genetics, Cell Biology

Ajay K. Royyuru, Computational Biology Center, IBM Thomas J. Watson Research Center, "Deep Computing in Biology: Challenges and Progress"

Mike Miller, Epidemiology, "Simulating Genetic Data for the Genetic Analysis Workshop"

Rui Kuang, Computer Science, "An optimization framework for applying discriminative classifiers to protein domain segmentation"

Lawrence P. Wackett, Department of Biochemistry, Molecular Biology, and Biophysics, and Biotechnology Institute,, University of Minnesota, "Computational Prediction of Chemical Fate in the Environment"
Download slides (pdf 1.4 MB)

David Odde, Biomedical Engineering, "Mechanisms of budding yeast mitosis: Integrated computational and experimental analysis"
Download slides (pdf 2.4 MB)

Nevin Young, Plant Pathology, "Sequencing the genome of the model legume plant, Medicago truncatula"
Download slides (pdf 1.15 MB)

Ananth Grama, Purdue University, "Comparative Analysis of Interaction Networks"

Terri Attwood, University of Manchester, "Text Mining — A Cure for Depression? (The Trials, Tribulations and Fantasies of a Database Curator)"

Gilad Lerman, UM, Mathematics, "Exploring Functional Landscapes of Proteins via Manifold Embeddings of the Gene Ontology"

Peter Swain, McGill University, "Stochasticity and designs of genetic networks"

Bioinformatics: Building Bridges

Naama Barkai, Weizmann Institute of Science, J. Berman’s guest

Claudia Neuhauser, UM, Dept. of Ecology, Evolution and Behavior, "The role of mathematics and computation in community ecology"
Download slides (pdf 981 KB)

Bud Mishra, Professor of Computer Science and Mathematics, Courant Institute, "Dude, Where is my genome? How to Build a Cheap Whole Genome Haplotypic Sequencer."
Download slides (pdf 5.64 MB)

Yu Zhang, Harvard University, Joint colloquium with CSE: bioinformatics position interview

Jan Ihmels, University of California, San Francisco, (J. Berman’s guest), "Modularity and Evolution of Transcription Networks"
Download slides (pdf 2.8 MB)

Benjamin Raphael, University of California, San Diego, Joint colloquium with CSE: bioinformatics position interview

Wei-Shou Hu, Chemical Engineering and Materials Science, "Unveiling the Regulatory Networks of Secondary Metabolism in Streptomyces"

Friedrich Srienc, Department of Chemical Engineering and Materials Science, BioTechnology Institute, "Design, construction, and performance of the most efficient E. coli bacterium"

Rui (Ray) Kuangi, Columbia University, Joint colloquium with CSE: bioinformatics position interview

Kevin Silverstein, Kathryn VandenBosch, Plant Biology, "Annotating the Medicago transcriptome: what to do with unknowns and ORFans"

Lisa Herron-Olson, Microbiologist, Syntiron LLC, "Data vaccination — Computational biology enhances infectious disease research"
Download slides (pdf 1.8 MB)

John Carlis, Computer Science, "What everybody knows but nobody says hurts interdisciplinary research"
Download slides (pdf 70 KB)

Tim Griffin, Biochemistry, Molecular Biology and Biophysics, "Proteomics: A Challenge for Technology and Information Science"
Download slides (pdf 545 KB)

David Selinger, Computational Biologist, Pioneer Information Management, DuPont Agriculture and Nutrition, "Industrial Science meets Renaissance Concepts"
Download slides (pdf 166 KB)

William Schuler, Department of Computer Science, "Toward machine understanding of unconstrained natural language text"
Download slides (pdf 49 KB)

Scott Fahrenkrug, Genetics Department of Animal Science, "Transcriptional crosstalk in isolated porcine islets responding to hyperglycemia and cytokine stress"
Download slides (pdf 1.2 MB)

George Karypis, Department of Computer Science, "Capturing the Right Signals: String Kernels for Protein Sequence Analysis"
Download slides (pdf 3.4 MB)

Vipin Kumar, Department of Computer Science, "Comparative Gene Expression Analysis: Data Analysis Issues and Solutions"
Download slides (pdf 121 KB)

Judith Berman, Depts of Genetics, Cell Biology & Development,, Microbiology, "Comparative Genomics Techniques for analyzing distantly related yeasts"
Download slides (pdf 1.64 MB)

Fumiaki Katagiri, Department of Plant Biology, "A systems approach to study plant disease resistance mechanisms"
Download slides (pdf 528 KB)

Lynda Ellis, Department of Laboratory Medicine and Pathology, "Databases for Microbes and Man"
Download slides (pdf 624 KB)

Yiannis Kaznessis, "How Can Biology Excite an Engineer: the Role of Computational Biology"
Download slides (pdf 4.4 MB)

Bob Elde, Dean of CBS, "What Do Biologists Need to Compute?"
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Bioinformatics: Building Bridges