Department of Biomedical Informatics
State University of New York at Buffalo
2002 Searle Scholar
The Big Picture: from genotype to phenotype
How does the genome of an organism specify its behaviour and
A fundamental biological challenge is to understand how the linear information in an organism's genome is processed to produce the resulting behavior or phenotype. Genes, made up of DNA, are transcribed into RNA, and translated into proteins which together form the vast majority of functional elements in an organism. Evolutionary processes ensure that these functional elements interact with their environment in a manner that is beneficial to the organism, using a variety of molecules to catalyse reactions, recognise cellular signals, build cellular structures, and to perform a host of other diverse biological functions.
Our research elucidates these processes by developing computational algorithms to model, annotate, and understand the relationships between the sequences, structures, functions, and interactions of proteins, DNA, RNA, and metabolites, at both the molecular and the genomic/systems levels. The goal is to develop a coherent picture of the mechanistic basis (wiring diagram) of molecular and organismal structure, function, networks, and evolution within a fundamental scientific framework.
Our specific aims are to develop novel methods to:
We expect that the biological role of every protein can eventually be deduced from its three dimensional structure in the context of its environment in the cell. This information will enable us to probe that organism's cellular pathways with an exquisite degree of sensitivity and also help us understand and treat infectious and inherited disease in an increasingly efficient and rational manner. The development of algorithms and tools to understand organismal genomes will have practical utility for pharmacogenomics and genetic engineering, and will be of use to the general research community to pose and answer ever more precise biological questions.
Understanding organismal biology from a genomic perspective requires expertise in several scientific disciplines, including computing science, mathematics, physics, chemistry, and biology. The problems that need to be solved generally involve exploration of large search spaces and finding objects of interest within those spaces, as well as managing the large amount of data produced and making predictions from analysis of the data. Thus our research has significance in not only answering biological questions, but is also relevant for solving problems of a similar nature in other scientific disciplines.
Long term goals
Our research involves integrating knowledge from the fields of computing science, mathematics, biology, physics, and chemistry to:
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