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Bio21: Teaching Biology with Bioinformatics


October 17-18th, 2003, Chapel Hill, North Carolina

Speakers

Stuart Brown, Ph.D., Research Computing Resource, NYU School of Medicine, New York, NY

Stuart M. Brown is an Associate Professor at the New York University School of Medicine, Department of Cell Biology and is the Director of the NYU Bioinformatics Core Facility. His research interests include bioinformatics, genomics, and molecular evolution. He teaches an annual Bioinformatics course for biomedical Ph.D. students and a Medical Genomics course for medical students. He also teaches bioinformatics short courses for graduate, undergraduate, and post-graduate audiences at many locations in the US. He holds a BS in Botany from the University of Michigan and a Ph.D. in Plant Molecular Biology from Cornell University. He is the author of “Bioinformatics: A Biologist’s Guide to Biocomputing and the Internet” and “Essentials of Medical Genomics.”


Debra Burhans, Ph.D., Assistant Professor/Director Bioinformatics, Canisius College, Buffalo, NY

Dr. Burhans directs the Bioinformatics Program at Canisius College in Buffalo, New York, where she also serves as an Assistant Professor in the Department of Computer Science. Canisius is a private, liberal arts college in the Jesuit tradition with an enrollment of approximately 3,000 full-time undergraduate students. Dr. Burhans has a strong background and interest in undergraduate education in computer science, bioinformatics, and interdisciplinary science. She received her B.S. in Mathematics from the University of Michigan and M.S. and Ph.D. in Computer Science from the State University of New York at Buffalo, where she was on the faculty as a Lecturer for four years. Dr. Burhans is part of a regional group of bioinformatics educators and researchers in Western New York and has participated in a number of bioinformatics education and outreach activities.


V. Celeste Carter, Ph.D., Biotechnology and Bioinformatics Program Director, Division of Biological and Health Sciences, Foothill College, CA

V. Celeste Carter received her Ph.D. in Microbiology from the Pennsylvania State University School of Medicine in 1982 under the direction of Dr. Satvir S. Tevethia. She moved to the University of California at Berkeley for postdoctoral studies in the laboratory of Dr. G. Steven Martin. She joined the Division of Biological and Health Sciences at Foothill College in 1994 to develop and head a Biotechnology Program, and has served for the past two years as a Program Director in the Division of Undergraduate Education at the National Science Foundation (NSF). Prior to her arrival at NSF, she was the recipient of a DUE-ATE award, which produced a set of case studies and associated laboratories with biotechnology industry partners. She was the acting lead program director for the Advanced Technological Education (ATE) Program during her second year, and worked on several other programs within NSF including: CCLI, Noyce, NSDL, TPC and GK-12 (DGE). She has recently returned to Foothill College to resume her position as Director for both the Biotechnology and Bioinformatics Programs.


Peter Cooper, Ph.D., National Center for Biotechnology Information, Bethesda, MD

Peter Cooper is a Staff Scientist with the National Center for Biotechnology Information (NCBI) at the National Library of Medicine. He has provided outreach and training programs on NCBI tools and databases for the scientific research and education community for the past five years. His background includes work in many biological disciplines including marine biology, biochemistry and molecular biology. He earned the Ph.D. in Marine Science from the College of William and Mary's School of Marine Science in 1996.


Joseph Day, Ph.D., Biotechnology Program Director, Lynnwood High School Lynnwood, WA

Dr. Day has worked in several areas related to molecular genetics and bioinformatics: as a forensic serologist using protein genetic markers at a crime lab in Illinois; at the University of Washington (UW), conducting population studies with various DNA population markers; and isolating proteins and cDNAs involved in HDL metabolism at the UW and in Seattle biotech companies. He draws on his diverse laboratory experience to establish a working research environment in the high school classroom and make his teaching relevant to the “real world.” He also coaches basketball.


Sam Donovan, Ph.D., BioQUEST Curriculum Consortium, University of Pittsburgh,
Department of Instruction and Learning, Pittsburgh, PA

Sam Donovan has been involved in many innovative projects in biology education. Some examples include the BioQUEST Curriculum Consortium, Student Biology Workbench, and Beagle Investigations Return with Darwinian Data (BIRDD). Currently, Dr. Donovan is the director of the BEDROCK initiative (Bioinformatics Education Dissemination: Reaching Out, Connecting and Knitting- together), a project to increase the use of bioinformatics in biology education. More information about BEDROCK is available at http://www.bioquest.org/bedrock/index.html


Betsey Dyer, Ph.D., Department of Biology, Wheaton College, Norton, MA

Betsey Dexter Dyer is a professor of biology at Wheaton College, Norton Massachusetts. In addition to genomics, her interests include field microbiology, cell evolution, and symbiosis. She teaches genetics and cell biology and often links those courses with Mark LeBlanc's computer science courses to teach genomics to undergraduates. She also co-supervises, with Dr. LeBlanc, a group of students who write software for searching and annotating DNA files. Their work can be seen at http://genomics.wheatoncollege.edu


Linnea Fletcher, Ph.D., Bio-Link Regional Director, and Biotechnology Program Director, Austin Community College, Austin, TX

Dr. Linnea Fletcher is the department chair for the Biotechnology Program at Austin Community College and also South Central Regional Bio-Link Director. For the past two years, Dr. Fletcher has been a visiting faculty member at the Dolan DNA Learning Center at the Cold Spring Harbor Laboratories, testing and assisting with DNA Interactive. Her two-year biotechnology program uses bioinformatics in every course and draws from a wide range of materials including Geospiza's Green Arrow Tutorials, Biology Workbench, and materials developed by the Dolan DNA Learning Center at Cold Spring Harbor Laboratories. This past year she partnered with Dr. Sandra Porter to teach a Chautauqua short course on Bioinformatics for four-year science faculty.


Martin Gollery, Associate Director of Bioinformatics, University of Nevada at Reno, Reno, NV

Martin Gollery is the Associate Director of Bioinformatics at the University of Nevada at Reno, the Chief Scientific Officer of Infoceutics, and the CEO of Tahoe Informatics. He has been the Director of Research at TimeLogic, a high school science teacher, an aerospace engineer, a photographer, and a wedding singer.

His research interests include the development of novel bioinformatics techniques to characterize Nucleic and Amino acid sequences that do not have homologous counterparts in existing database entries.  His specialty is modeling protein families and domains through the use of Hidden Markov Models.  Other research projects include the TLFAM series of databases, COGfam set of Clusters of Orthologous Genes, and the KinFam database representations of the various Kinase families, along with the design of microarrays and the analysis, storage, visualization and mining of microarray data.


Laurie Heyer, Ph.D., Department of Mathematics Davidson College, Davidson, NC

Assistant Professor Laurie Heyer joined Davidson College in 2000. She received her B.S. and M.S. from the University of Texas at Arlington, and was an Operations Research Analyst with a defense company before beginning doctoral work at the University of Colorado at Boulder. After receiving her Ph.D. in Applied Mathematics, she was a postdoctoral fellow in the Center for Computational and Experimental Genomics at the University of Southern California. Her primary interests are in mathematical modeling (especially of genomes and cellular processes), probability theory and operations research.  "Discovering Genomics, Proteomics & Bioinformatics", a textbook Professor Heyer has written with Professor Malcolm Campbell of the Department of Biology, is published by Cold Spring Harbor Press and Benjamin Cummings.


Uwe Hilgert, Ph.D., BioMedia Educator and Bioinformatics Manager, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

Dr. Uwe Hilgert is a microbiologist with many years of experience in college and pre-college science education. He is a fellow of the prestigious Alexander-von-Humboldt Foundation and the National Institute for Science Education, and works currently as science educator, web designer, and curriculum developer for the Dolan DNA Learning Center at Cold Spring Harbor Laboratory. He has developed a course for high school teachers and community college faculty called "Bioinformatics in the Classroom."


Dan Krane, Ph.D., Associate Professor Biological Sciences, Wright State University, Dayton, OH

Dan Krane (Ph.D. Penn State University) has taught in the Biological Sciences Department at Wright State for nearly 10 years, where he was recognized as Teacher of the Year in 1997. His research interests are primarily in the areas of molecular evolution and the way that gene frequencies change over the course of time in populations of organisms. As a graduate student he was the first to use phylogenetic reconstruction approaches to describe the evolutionary history of C repeats, a highly repeated DNA sequence that accounts for more than 10% of the rabbit genome. That work has been used as a model in his research laboratory and others that have since characterized analogous repeated sequences in several other mammalian genomes. He has published over thirty peer-reviewed papers in the areas of population genetics and molecular evolution. Prominent in that work has been the development of RAPD-PCR as a means of generating measures of genetic diversity that can serve as an indicator of exposure to environmental stressors.

In addition to his teaching, research, and writing, Dan is active as a court-appointed expert in forensic DNA profiling, and has testified in numerous high profile cases including the O. J. Simpson trial and the recent case in Wellesley, MA, in which a Harvard Medical School Professor was accused of murder. Dr. Krane's work to develop a comprehensive program in bioinformatics, led him to co-author a textbook, "Fundamental Concepts in Bioinformatics", with Micheal Raymer, published by Benjamin-Cummings, San Francisco. His second book, Molecular Evolution: A Primer, will be available in the Fall of 2004. Dr. Krane has published numerous papers regarding forensic DNA testing and has testified in over 40 criminal cases since 1991 as an expert for both the prosecution and defense in the areas of population genetics, molecular biology and bioinformatics. He is also the president and founder of Forensic Bioinformatic Services, Inc (bioforensics.com) where he has overseen the development and implementation of software designed to automatically and objectively review STR DNA testing results.


Mark LeBlanc, Ph.D., Computer Science, Wheaton College, Norton, MA

Mark LeBlanc is a professor of computer science at Wheaton College, Norton Massachusetts. The suite of software modules for DNA annotation and analysis at http://genomics.wheatoncollege.edu was written by undergraduates under his supervision. His interests include the application of linguistic analyses to the understanding of intergenic DNA sequences.


Loralyn Mears, Ph.D., Market Segment Manager ­ Life Sciences, Sun Microsystems

Loralyn Mears completed a Ph.D. in molecular biology at Case Western Reserve University, an M.Sc. in physiology at the University of Toronto and an Honours B.Sc. in biology at Queen's University in Canada. She previously worked for NetGenics in a variety of roles over a period of several years and later moved onto Sun Microsystems to help launch and establish Sun in life sciences. Loralyn is currently the Life Science Segment Manager of Market Development chartered to set the strategy for ISV partnerships and initiatives that will help to grow the industry for Sun.


Jeanette Mowery, Ph.D., Program Director Biotechnology Lab Technician Program, Madison Area Technical College, Madison, WI

Jeanette Mowery is the program director for the nationally recognized Biotechnology Laboratory Technician Program at the Madison Area Technical College in Madison, WI. Dr. Mowery, a protein biochemist with an industrial background, has helped develop courses in protein purification and has introduced bioinformatics tools for molecular modeling in her courses. She recently developed a bioinformatics course (running fall 2003) and a bioinformatics certificate program in collaboration with Eric Knapp, a faculty colleague in the computer information systems department of MATC.


Sandra Porter, Ph.D., Senior Scientist, Geospiza, Inc.

Sandra Porter is a senior scientist at Geospiza, Inc., a company that specializes in bioinformatics software and systems for data management and analysis. Dr. Porter's research interests include alternative splicing and polyadenylation along with methodologies for SNP detection and sequence assembly. Sandra has a long-standing interest in bioinformatics and education. Before joining Geospiza, Dr. Porter ran the biotechnology program at Seattle Central Community College and was the Northwest regional director for Bio-Link, an NSF-funded, Advanced Technology Education Center. In addition to research, Dr. Porter oversees a CCLI-EMD grant from the NSF to develop animated tutorials for classroom use in teaching biology with bioinformatics. Geospiza's tutorials and other materials are available at http://www.geospiza.com/outreach.


Gary Skuse, Ph.D., Director of Bioinformatics, Rochester Institute of Technology

Dr. Skuse is Director of Bioinformatics in the Department of Biological Sciences at the Rochester Institute of Technology. He also provides consulting services for a number of local, national, and international clients in the areas of human genetics, biotechnology and information management. Dr. Skuse, a native of Rochester, received his B.A. in Biology from the University of Rochester and Ph.D. in Biology (Developmental Genetics) from Syracuse University. He followed that with postdoctoral training in Molecular Virology at Harvard Medical School and more than a decade on the faculty of the University of Rochester School of Medicine and Dentistry. While at the University of Rochester Dr. Skuse studied the genetics of a common disease which predisposes affected individuals to tumors of the central and peripheral nervous system, namely neurofibromatosis type 1. As Director of Bioinformatics at RIT Dr. Skuse coordinated the development of BS and MS degree programs in Bioinformatics and is establishing partnerships with biotechnology companies which will provide training and employment opportunities for RIT students and graduates.


Christopher Smith, Ph.D., Program Manager, Integrative BioSciences / Integrative Computational Sciences, San Diego Supercomputer Center, University of California San Diego, CA

Christopher M. Smith, PhD., is a classically-trained biochemist turned computational biologist and educator. He is the curator of the CMS Molecular Biology Resource, and author of the Discovery Tools suite of instructional road-maps to bioinformatics tools. He has taught IT and bioinformatics concepts and practical use to health professionals, researchers, and high school, college and graduate students. His area’s of interest include evaluation of how computational tools are utilized in education and research, and the development of intuitive user-interfaces and educational portals to the plethora of online ‘bioinformatics’ tools available today.


Kenneth Tindall, Ph.D., North Carolina Biotechnology Center, Research Triangle Park, NC

Kenneth Tindall is the President of the North Carolina Genomics and Bioinformatics Consortium, a partnership comprised of industry, academic, and service organizations, which are interested in developing the infrastructure needed to support genomic technologies. Dr. Tindall is also the Senior Vice President for Science and Business Development at the North Carolina Biotechnology Center, Research Triangle Park, NC, where he oversees the Business and Technology Development Program, the Education and Training Program, and the Science and Technology Development Program.


Alex Tropsha, Ph.D., University of North Carolina, School of Pharmacy and Natural Products

Dr. Tropsha specializes in Biomolecular Informatics, the relationship between structures (organic or macromolecular) and their properties (activity or function). His research group has developed several important methodologies and software tools for Computer Assisted Drug Design (available at our Web server at http://mmlin1.pha.unc.edu/~jin/QSAR ). They have also developed a new approach to protein 3D structure analysis and prediction based on the principles of statistical geometry (Delaunay tessellation). This approach affords determination of key structural and sequence motifs responsible for protein function. Some of our methodologies have been implemented on the Protein Structure Workbench at http://mmlsun4.pha.unc.edu/3dworkbench.html.


Stefan Unger, Ph.D., Business Development Manager for Computational Biology in Global Education and Research, Science and Engineering. Sun Microsystems, Inc.

Dr. Stefan Unger is the Business Development Manager for Computational Biology in Sun's Global Education and Research Unit, Science and Engineering. He joined Sun in 2000. Unger joined Syntex Research in 1974 where he built and managed the Computer Aided Drug Design Group for 16 years, authoring several patents, and publications, and designing several drugs that were tested in the clinic. In 1990, he left Syntex to join Silicon Graphics, and held the position of Chemistry Market Manager. As VP Marketing and later as the CEO, Unger brought Oxford Molecular to the US in 1992. While he operated his own consulting firm, Unger worked with several life science software companies such as Apple Computers and IBM. He joined Frost & Sullivan International Market Research as Director of Drug Discovery Technologies in 1999. He authored reports on combinatorial chemistry libraries and proteomics, as well as several consulting projects. Unger held Post-Doctorial appointments at ETH, Zurich and Pomona College following receipt of his PhD in physical-organic chemistry from MIT.

 
 
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