Although this event is now over, please feel free to browse the links below
to familiarize yourself with the many valuable resources coming out of this workshop.
BEDROCK Project Home Page
NSF Home Page
HHMI Home Page
Cornell Theory Center Homepage

Workshop Announcement
Travel Directions


October 9 - 12, 2003

Cornell Theory Center
Frank H.T. Rhodes Hall
Cornell University

Photo Album


This short course will focus on several different ways that the analysis of molecular data is being applied to solve current biological problems in areas such as medicine, agriculture, conservation, and evolution. The relationships between evolutionary theory and the analysis of molecular sequence and structure data will be addressed. A wide range of sub-disciplines that use bioinformatic analysis will be drawn upon. The focus will be on learning about the causal bases for bioinformatic analyses
along with a philosophy of education: problem posing, problem-
solving, and peer review/publication (BioQUEST's three P's ).

The laboratory sessions deal with medical, cell biology, and conservation examples. The lectures relate to: Evolutionary Bioinformatics: Orthology, Paralogy, Xenology, Phylogenetic Probes and Phylogenetic Profiling; BioQUEST's Curricular Philosophy: Problem Posing, Problem Solving and Peer Review / Publication; and, Theoretical, mathematical and computational aspects that complicate bioinformatics: homoplasies, computational complexity, numerous tree topologies, scoring multiple sequence alignments, long branch attraction problems, rate variations. The discussions focus on how to analyze data, how to implement bioinformatics investigations across the curriculum, and how to develop sustained collaboration. For more details, visit the BEDROCK home page and follow the links to past workshops.

The workshop is designed for:

  • Biologists who are interested in implementing bioinformatics across their biology curriculum by incorporating bioinformatics into a variety of courses, using a problem-solving approach, and who enjoy collaborative learning such as has been developed and diffused by the BioQUEST Curriculum Consortium.
  • Mathematicians and computer scientists who are already involved in teaching bioinformatics or computational molecular biology are welcome to come and interact with biologists so that they can develop a better idea of what questions biologists outside of genomics have with respect to teaching and learning elements of bioinformatics appropriate to their sub-discipline of biology.
This short course serves several purposes:
As a learning resource for faculty across the biological sciences who are interested in developing their understanding of the biological (as compared to the computational or mathematical) aspects of bioinformatic analyses.
As a forum for undergraduate teachers of bioinformatics to collaborate in the development of biology or bioinformatics courses and/or curricula.
As an opportunity for developing undergraduate research programs in bioinformatics.


    Workshop Leaders

    John R. Jungck
    Tia Johnson
    Tony Weisstein

Beloit College, Wisconsin
Department of Biology

    Rama Viswanathan
Beloit College, Wisconsin
Chemistry and Math & Computer Science Departments
    Sam Donovan University of Pittsburgh
Department of Instruction and Learning
    Gregory B. Martin

Professor, Department of Plant Pathology
Cornell University

Martin received his PhD from Michigan State University and held faculty positions in Agronomy at Purdue University. His research at Cornell since 1998 focuses on plant molecular biology, plant genomics, bacterial genomics, plant pathology, plant disease resistance, signal transduction, and gene expression profiling.

    Alan Collmer

Professor, Department of Plant Pathology
Cornell University

Collmer received his PhD from Cornell, held faculty positions in Botany at the University of Maryland, returning to Cornell in 1994. His research focuses on bacterial genomics, mechanisms, pathogenic microbiology, and protein secretion.

    Qi Sun

Senior Research Associate
Computational Biology Service Unit, Cornell University

After receiving a PhD in Genetics from the California Institute of Technology, Sun completed a postdoctoral fellowship at Harvard Medical School. He has focused on computational support for biology research projects since joining the Cornell Theory Center in 2001.

    Jaroslaw Pillardy

Senior Research Associate
Computational Biology Service Unit, Cornell University

Pillardy received his Ph.D. in theoretical chemistry at Warsaw University, Warsaw, Poland. After teaching for five years at Warsaw University, he came to Cornell University's chemistry department in 1996. His current research is in the fields of protein structure prediction, molecular force field design and optimization, global optimization and crystal structure prediction.

    Dave Schneider

Computational Biologist
USDA Agricultural Research Service

Dave Schneider has worked on computational problems arising in chemistry, physics, engineering and biology for the past 15 years at IBM, the Center for Supercomputing Research and Development at the University of Illinois at Urbana-Champaign, the Theory Center at Cornell University, and the USDA Agricultural Research Service. Currently he is involved in a large interdisciplinary research project focusing on the regulation of gene and protein expression in Pseudomonas syringae, an important plant pathogen. Schneider is presently working on his Ph.D. in physics from Jagellonian University in Krakow, Poland.


For more information please
contact Tia Johnson or
Sue Risseeuw


Sponsored by a grant from the National Science Foundation (DUE/CCLI-ND)