J H Jackson & P
Bacterial Genomics & Physiology
Structure & Dynamics of Gene and Genome
Mathematics in Biology
An educational focus of major interest to me is the integration of
mathematics into the study of biology at the
undergraduate and graduate level. My 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 measures
of systems behavior for construction of mathematical
models to simulate that behavior.
publications to contribute a
theory base relating evolution of genomic information and
physiology in bacteria.
research interest for the J-Lab is a study
of bacterial and archaeal genomes as information systems that determine
physiological states of an organism. A
larger goal is to model the dynamics of information evolution and
exchange in bacteria and archaea, and to derive a theory base to
explain the origin,
and function of genes and chromosomes. Our
goal is to discover and model gene-specific and
information that defines metabolic properties and physiological
behavior of bacteria 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.
seek to combine mathematical and computational methods to model
simulate the function of natural microbial systems.
Jackson, J. H. & C. R. MacCluer.
Hyperbolic saturation. Bull.
Math. Biol. 72:1315-1322
Jackson, J. H., T. M. Schmidt, & P. A.
Herring. A systems
appoach to model natural variation in reactive properties of bacterial
ribosomes. BMC Systems
Biology 2:62 (2008).
Jackson, J. H. Bioinformatics & Genomics.
In Math & Bio 2010, Linking
Disciplines, L. Steen (editor). Mathematical Assoc. Am.
Svetic, R. E., C. R. MacCluer, C.
K. L. Smythe, & J. H. Jackson. A
metabolic force for gene clustering in bacteria
Math. Biol. 66:559-581
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
H., S. H. Harrison, & P. A. Herring. A
theoretical limit to coding space in chromosomes
of bacteria. OMICS: J. Integ. Biol. 6:
A. and J. H. Jackson. Theoretical
indicators of enzyme reaction specificity from conserved information in
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
genomes. Biochem. Biophys.
Res. Commun. 268:289-292
Williamson, R. M., J. Hetherington, & J. H.
Jackson. Detection of fundamental principles and a level of order
for large-scale gene clustering on the Escherichia coli
chromosome. J. Molec. Evol.
Beginnings of chromosome evolution.
Brief Biographical Summaries
Coding Space Limit model
Limited Protein Mobility model
Natural Variation Space Limit model
Variable Translation Rate model
Edges and Limits
Coding entropy for genes in bacteria.
Organization of proteins in bacteria.
Visualization of limits to gene variation.
Ribosomal determinants of lifestyles.