Genetics, Genomics and Computational Biology
Laboratories in the area of Genetics, Genomics, and Computational Biology, GGCB, combine experimental data with computational approaches to address biological questions. Research in this focus area ranges from the molecular level to the cellular or even organismal levels. At the molecular level, X-ray and NMR structures are the basis for computations used to understand protein dynamics, protein-protein and protein-small molecule (e.g., drugs) interactions. At a higher level, genomic sequences are used to understand the structure and function of proteins and RNA molecules, and to understand the ancestral relationships between both genes and organisms. At an even higher level, high-throughput data describing gene and protein expression (transcriptomics and proteomics), protein-protein interactions, and metabolite levels (metabolomics) are used to describe living organisms as complex system (systems biology). GGCB laboratories use a wide range of computational approaches, including molecular dynamics, bioinformatics, machine learning, and network analysis.
Anderson, John
Professor of Biological Sciences
(Eukaryotic gene expression) Control of eukaryotic gene expression and replication; DNA structure; virus evolution.
Gribskov, Michael
Professor of Biological Sciences
My lab is interested in computational analysis of the evolution of protein families, the development of computational resource for molecular biology and genomics, Interoperation between electronic information resources, methods for comparing and identifying conserved RNA structures, and network and systems biological analysis of complex systems.
Kihara, Daisuke
Associate Professor of Biological Sciences
(Bioinformatics, computational biology) protein tertiary structure prediction/comparison, protein sequence analysis, evolution of protein families, metabolic/regulatory pathway analysis.
McCann, Maureen
Professor of Biological Sciences, Assitant Head, Director of the Energy Center, Discovery Park
(Plant cell and molecular biology; genomics) Plant extracellular matrix and cell differentiation
Qi, Yuan (Alan)
Assistant Professor of Computer Science,
Assistant Professor of Statistics,
Assistant Professor of Biological Sciences (by courtesy)
Machine learning, computational biology, and Bayesian statistics
Sherman, Louis
Professor of Biological Sciences
Dr. Sherman's research interests center on cyanobacteria and he has studied the processes of photosynthesis, nitrogen fixation and gene regulation. He has been particularly interested in the impact of environmental changes on gene transcription and the corresponding impact on cyanobacterial physiology
Cyanobacteria have become wonderful and versatile model organisms for the study of photosynthesis, nitrogen fixation and responses to environmental stresses. Current research can help answer questions involved with environmental concerns, alternative energy uses (i.e., solar energy), and health concerns such as microbial toxins and the design of new drugs. The genomic sequence of the model organism Synechocystis sp. PCC 6803 was completed a decade ago and the genomic sequences of 6 Cyanothece strains have now been completed. The lab has constructed microarrays for all of these strains and has been involved with high throughput experiments in proteomics and metabolomics. The unicellular Cyanothece strains show robust metabolic and circadian rhythms and performs photosynthesis and N2-fixation at different times of the day and night. This organism is key to a large project aimed at understanding the regulation of such processes and the assembly of membrane complexes. Strains in this genus have been shown to produce copious quantities of H2, organic acids, fatty acids, exopolysaccharides and polyhydroxyalkanoates and are now being analyzed in much greater detail. This analysis will help us determine how best to use specific strains for large-scale production of alternative energy compounds, such as H2, butanol or fatty acids.
Stein, Arnold
Professor of Biological Sciences
Dr. Stein's laboratory studies the fine structure of chromosomes to understand how chromosome abnormalities and rearrangements arise. Chromosome structural variants, which are characteristic of cancer cells and cells associated with other diseases, arise in part due to chromosome structure. The Stein lab has found that DNA sequence is involved in specifying chromosome fine structure. Particular periodic motifs interact preferentially with the protein cores of nucleosomes, the fundamental building blocks of chromosomes. Long-range variations in these motifs influence chromosome structure through a previously unrecognized code in the DNA. In this work, computer bioinformatics methods are used in addition to biochemical, biophysical, and molecular biology techniques.
Waddell, Peter
Assistant Professor of Biological Sciences
I develop methods of analysis/algorithms, work on their implementation, apply them to data and gather data relevant to particular problems. My lab is both wet lab, focusing on RNA/DNA extraction, cell culture plus mass sequencing, and dry lab, focusing on computer analysis of biological data, especially genomic data.
Wanner, Barry
Professor of Biological Sciences
(Molecular genetics) Molecular genetics; transmembrane signal transduction; cellular microbiology.