Research

The sequencing of several mammalian genomes provides a basis for understanding the systemic functioning of living cells. The "omics" technologies have begun to produce vast amounts of context-specific biological data.

Thus, future developments in genomics, and the applications that are derived from genomics, will be dependent upon the scientific progress at the interface of three major disciplines; biology, engineering, and computer science. Our laboratory works in this interdisciplinary area of Bioinformatics and Systems Biology.

Bioinformatics characterizes the flow of information in living systems. This is schematically represented below.

Specific projects our laboratory is associated with in this area include,

Genome Annotation

• Design of a novel algorithm for generating protein family specific scoring matrices and applications of this scoring scheme in identifying orthologous and paralogous proteins in genomes.
• Design of nucleotide and protein profiles that will serve to develop a high throughput method to identifying genes in genome sequences. This has implications for expression profiling technology using oligonucleotides for assessing cell function.
• Design and development of high throughput pipeline for annotating genomes.

Protein Sequence-Structure Mapping

• Development of strategies for obtaining unique protein fragment structures that will serve as the basis set for modeling three-dimensional structures of all soluble proteins.
• Characterizing protein folds using fragment-based methods.
• Obtaining statistical potentials (pairwise atomic PDFs) for defining energy landscape of proteins.
• Using global optimization strategies for modeling structures of proteins from their primary sequences.

Functional Genomics

• Development of new methods for gene expression analysis.
• Reconstruction and biochemical analysis of transcriptional networks.
• Functional analysis of transcription factors.

Reconstruction and Modeling of Biochemical Pathways

• Reconstruction of disease networks pertaining to insulin resistance.
• Design and development of methods for analyzing cell signaling pathways from expression profile and proteomic data.
• Identification of protein partners in cell signaling pathways.
• Computational modeling of pathways.

Infrastructure for Biological Databases, Analysis Tools and Interfaces

• Extensions of the Biology Workbench (http://workbench.sdsc.edu) developed in my laboratory.
• Design of novel tools for expression profile and proteomic analysis in the Workbench.
• Creation of automated pipelines for genome, gene and protein analysis.
• Design and development of Laboratory Information Management Systems.
• Development of the Information Management System for Alliance for Cellular Signaling and LipidMaps projects.