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J H Jackson & P
A Herring
Research on
Bacterial Genomics & Physiology
Information
Structure & Dynamics of Gene and Genome
Evolution
The major
research interest for the J-Lab is a study
of bacterial and archaeal genomes as information systems that determine
the
physiological states of an organism. The
larger goal is to model the dynamics of information evolution and
exchange in
prokaryotes, and to derive the theory base to explain the origin,
evolution
and function of genes and chromosomes. Our
goal is to discover and model gene-specific and
genome-specific
information that defines metabolic properties and physiological
behavior of
prokaryotes in adaptive response to their environment(s).
This research probes the limits of coding space, protein mobility, and
variation space, and seeks to understand the physiological consequences
of such limits.
This work utilizes
experimental methods for
genetic, molecular biological, biochemical and microbiological studies
in
combination with mathematical and computational methods for modeling
and
simulating the function of natural systems.
Integration of
Mathematics in Biology
An educational focus of major interest is the integration of
mathematics into the study of biology at the
undergraduate and graduate level. The teaching approach is to
prepare students to view organisms and their environments as biological
systems, to ask critical questions about how these systems work and
interact, and to design experiments that yield quantitative assessments
of systems behavior that will lead to construction of mathematical
models for simulation.
Selected publications
Jackson, J. H. Bioinformatics & Genomics. In Math & Bio 2010, Linking Undergraduate
Disciplines, L. Steen (editor). Mathematical Assoc. Am.
(2005).
Svetic, R. E., C. R. MacCluer, C. O. Buckley,
K. L. Smythe, & J. H. Jackson. A
metabolic force for gene clustering in bacteria.
Bull.
Math. Biol. 66:559-581
(2004).
Buckley, C.
O., D. Stephens, P. A. Herring, & J. H. Jackson.
%(G+C) variation and prediction by a model of
bacterial gene transfer and codon adaptation. OMICS: J. Integ. Biol. 6:259-272
(2002).
Jackson,
J.
H., S. H. Harrison, & P. A. Herring. A
theoretical limit to coding space in chromosomes
of bacteria. OMICS: J. Integ. Biol. 6:
115-121 (2002).
Herring, P.
A. and J. H. Jackson. Theoretical
indicators of enzyme reaction specificity from conserved information in
amino
acid side-chains. Micro. & Compar. Genomics 5:75-87 (2000).
Jackson, J. H., R. George,
& P. A. Herring. Vectors of Shannon
information from Fourier signals characterizing base periodicity in
genes and
genomes. Biochem. Biophys.
Res. Commun. 268:289-292
(2000).
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Brief Biographical Summaries
Advanced Study
Models at the Edges
Looking at Limits
Molecular size limits to protein
mobility contribute to subcellular organization of proteins in bacteria.
Chromosomal gene organization
contributes to subcellular protein organization
Natural limits to gene variation
reveal pathways of natural variation for bacterial genes.
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