CompBio: Special Focus on Information Processing in Biology

Increasingly, many aspects of biology can be viewed as involving the processing of information. Modern

information and computer science have played an important rolein such major biological accomplishments

as the sequencing of the human genome. On the other hand, biological ideas can inspire new concepts and

methods in information science. This project is motivated by these two observations. Progress in the field

of biological information processing will require interdisciplinary collaborations among computer scientists,

mathematicians, physicists, chemists, and biologists. The project is built around a series of workshops that

will enhance the interdisciplinary collaborations beginning to form and introduce outstanding junior people

to problems and topics at the forefront of research.

Intellectual Merit

The project will be organized around a series of workshops with four themes: (1) Algorithmic Approaches

to Biological Information Processing; (2) Computer Science, Engineering and Biology: Applications and

Analogies; (3) Biological Circuits and Cellular Signaling; (4) Proteomics. Two of these themes represent

approaches and two represent areas of application of these approaches. Under theme 1, planned workshops

are on Detecting and Processing Regularities in High Throughput Biological Data; Machine Learning Ap-

proaches for Understanding Gene Regulation; and Computational Tumor Modeling. Theme 2 workshops will

cover Nanotechnology and Biology; Control, Communication, and Computing in Biology; and The Mecha-

nism and Applications of the RNA Interference Process. For Theme 3, there will be workshops on Strategies

for Reverse Engineering Biological Circuits; Cell Communication and Information Processing in Developing

Tissues; Dynamics of Biological Networks; and Evolution of Gene Regulatory Networks. Theme 4 work-

shops will be on Information Processing by Protein Structures in Molecular Recognition; Proteome Network

Evolution; Functional Proteomics of Neurodegenerative Diseases; and Implications of Mathematical Models

of Infection and Molecular Modeling of Hepatitis B Virus. We expect that the workshops, scientific papers

and books coming out of the project will help to develop the long-term focus of the field, carefully define

problems and directions in computer science, mathematics, chemistry, andphysics of specific interest to and

designed in collaboration with biologists, and lead to new biological concepts that will in uence biological

and information science research in the future. In short, we expect the project to in uence the study of

biological information processing for years to come.

Broader Impacts

The ideas developed in this project will have impact on a myriad of fields and create cross-disciplinary

connections. A visitor program will encourage senior and junior researchers, including students, to participate

in collaborative research spawned by the workshops. Each workshop will have a fund for support of graduate

students and postdocs amd workshops will have a substantial educational component through talks of a

tutorial/expository nature. The topic lends itself well to undergraduate research and participating faculty

will coordinate topics with an undergraduate research program (REU program) already in existence. To give

the project widespread dissemination, each workshop will have awebsite with relevant references, problems,

and copies of presentations that can make it a resource for a large community. The project should significantly

in uence the careers of a large number of outstanding junior researchers and it should play an important

role in the training and development of scientists who are well-prepared to become leaders in the field of

biological information processing. The project is expected to have a long-term impact well beyond its four

year duration since the workshop, visitor, and dissemination components of the project will allow the ideas

developed to reach hundreds of people nationwide and worldwide.