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Featured Publications: |
Faculty
in the Department of Computational Biology integrate disciplines
such as biological, biomedical, computational, physical, mathematical
and engineering sciences to formulate and solve critical biological
problems.
Faculty research areas include:
Bioinformatics
Cellular and Systems Biology
Genomics and Proteomics
Molecular Structural Biology
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 Sharlow ER, Close D, Shun T, Leimgruber S, Reed R,
Mustata G, Wipf P, Johnson J, O’Neil M, Gro¨gl M, Magill AJ, Lazo JS (2009) Identification of Potent Chemotypes Targeting Leishmania major Using a High-
Throughput, Low-Stringency, Computationally Enhanced, Small Molecule Screen. PLoS Negl Trop Dis 3(11): e540. doi:10.1371/journal.pntd.0000540 (PDF) |
 Molina G1, Vogt A1, Bakan A1, Dai W, de Oliveira PQ, Znosko W, Smithgall TE, Bahar I, Lazo JS, Day BW, Tsang M. (2009) “Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages.” Nat Chem Biol 5, 680-7. (PDF) 1Equal Contributions |
 Temiz NA, Camacho CJ (2009) “Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface.” Nucleic Acids Res 37, 4076-88. (PDF) |
 Gu Y, Shrivastava IH, Amara SG, Bahar I (2009) “Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter.” PNAS 106, 2589-94. (PDF) |
 Brower-Sinning R, Carter DM, Crevar CJ, Ghedin E, Ross TM, Benos PV (2009) “The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus.” Genome Biol 10, R18. (PDF) |
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Other Publications
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The
research, development, or application of computational
tools and approaches for expanding the use of biological,
medical, behavorial or health data, including those
to acquire, store, organize, archive, analyze,
or visualize such data (NIH working defintion).
Projects include genome annotation, genome assembly,
computational evolutionary biology, sequence analysis,
sequence alignment, and protein structure alignment. |
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Systems
biology seeks to integrate different levels of
information to understand how biological systems
function, with a goal of developing an understandable
model of the whole system. This is accomplished
by studying the relationships and interactions
between various parts of the system. Examples of
such systems are: cell signaling networks, metabolic
pathways, organelles, cells, physiological systems,
and organisms. |
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Genomics is the study of an organism’s genome. It consists of three main categories: functional genomics, structural genomics, and comparative genomics. Functional genomics generally refers to the high throughput determination of gene functions. Structural genomics is the systematic effort to to determine biomolecular structures, ultimately for an organism’s entire proteome. Comparative genomics uses evolutionary relationships between various organisms to understand genomic structure and function. Proteomics aims at quantifying the expression levels of all proteins in a given cell at a given time. While it was initially focused on 2D gel electrophoresis, it now refers to the functional characterization of the proteome. |
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Structural
biology is defined as the study of the architecture
and shape of biological macromolecules. Macromolecules
such as proteins and nucleic acids carry out most
of the functions of a cell. For the most part,
they are able to perform these functions by coiling
into a specific three-dimensional shape or native
structure. Structural biology is concerned with
the driving forces and interactions that determine
the structure and dynamics of biomolecules.
Computational structural biology aims at establishing
sequence-structure-function relations using fundamental
principles of physical sciences in theoretical models
and simulations of structure and dynamics. |
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