Gregory Babbitt Headshot

Gregory Babbitt

Associate Professor
Thomas H. Gosnell School of Life Sciences
College of Science
Bioinformatics Program Faculty

585-475-6246
Office Location

Gregory Babbitt

Associate Professor
Thomas H. Gosnell School of Life Sciences
College of Science
Bioinformatics Program Faculty

Education

BA, Ohio Wesleyan University; MS, Ph.D., University of Florida

Bio

I am a computational biologist with a focused interest in the development of modern statistical tools for comparative molecular dynamic simulation applied to the function and evolution of proteins and their interactions with other molecules in the cell. I am also broadly interested in the evolution of complex and stochastic biophysical process, across all scales, from the molecular to the ecological. For more information please visit our software project website

585-475-6246

Areas of Expertise

Currently Teaching

BIOL-470
3 Credits
This course is an introduction to the probabilistic models and statistical techniques used in computational molecular biology. Examples include Markov models, such as the Jukes-Cantor and Kimura evolutionary models and hidden Markov models, and multivariate models use for discrimination and classification.
BIOL-230
3 Credits
This is an introductory course in scripting languages focusing on the Perl programming language, the R statistical analysis program, and their application to biological data. We will investigate the use of Perl and R for processing sequence and "-omics" data, managing a variety of biological data types, and providing effective Web and graphical interfaces to existing tools for analysis of these data.
ENVS-798
1 - 4 Credits
This course is a faculty-directed tutorial of appropriate topics that are not part of the formal curriculum. The level of study is appropriate for student in the Environmental Science graduate program.
BIOL-298
1 - 4 Credits
This course is a faculty-directed tutorial of appropriate topics that are not part of the formal curriculum. The level of study is appropriate for student in their first three years of study.
BIOL-495
1 - 4 Credits
This course is a faculty-directed student project or research involving laboratory or field work, computer modeling, or theoretical calculations that could be considered of an original nature. The level of study is appropriate for students in their final two years of study.
BIOL-498
1 - 4 Credits
This course is a faculty-directed tutorial of appropriate topics that are not part of the formal curriculum. The level of study is appropriate for student in their final two years of study.
BIOL-301
1 - 4 Credits
This course allows students to assist in a class or laboratory for which they have previously earned credit. The student will assist the instructor in the operation of the course. Assistance by the student may include fielding questions, helping in workshops, and assisting in review sessions. In the case of labs, students may also be asked to help with supervising safety practices, waste manifestation, and instrumentation.
BIOL-798
1 - 4 Credits
This course is a faculty-directed, graduate level tutorial of appropriate topics that are not part of the formal curriculum.
BIOL-130
3 Credits
This course will explore topics in the field of bioinformatics including tools and resources used by the discipline, including direct experience with the common user environment.
BIOL-295
1 - 4 Credits
This course is a faculty-directed student project or research involving laboratory work, computer modeling, or theoretical calculations that could be considered of an original nature. The level of study is appropriate for students in their first three years of study.

Select Scholarship

Published Game, Application or Software
GA, Babbitt. DROIDS 3.0 - software for comparative protein dynamics. Software. https://github.com/gbabbitt/DROIDS-3.0-comparative-protein-dynamics. 2019.
Babbitt, G.A., et al. DROIDS 1.2 - Free Software Project for Comparative Protein Dynamics. Software. GitHub. 2017.
Journal Paper
E.G, Ryen, et al. "Ecological Foraging Models as Inspiration for Optimized Recycling Systems in the Circular Economy." RESOURCES CONSERVATION AND RECYCLING. 135 (2018): 48-57. Print.
G.A., Babbitt, et al. "DROIDS 1.2 – a GUI-based Pipeline for GPU-accelerated Comparative Protein Dynamics." BIOPHYSICAL JOURNAL 114. (2018): 1009-1017. Print.
G.A., Babbitt, et al. "Triplet codon organization optimizes the impact of synonymous mutation on nucleic acid molecular dynamics." JOURNAL OF MOLECULAR EVOLUTION 86. (2018): 91-102. Print.
Ryen, E.G., et al. "Ecological Foraging Models as Inspiration for Optimized Recycling Systems in the Circular Economy." Resources, Conservation & Recycling. (2017): 1-10. Web.
Babbitt, G.A., et al. "Triplet-Based Codon Organization Optimizes the Impact of Synonymous Mutation on Nucleic Acid Molecular Dynamics." Journal of Molecular Evolution. (2018): 1-12. Web.
GA, Babbitt. "Can all heritable biology really be reduced to a single dimension?" GENE 578. 2 (2016): 162-168. Print.
GA, Babbitt. "Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid." NUCLEIC ACIDS RESEARCH 42. 17 (2014): 10915-10926. Print.
GA, Babbitt. "Codons support the maintenance of intrinsic DNA polymer flexibility over evolutionary timescales." GENOME BIOLOGY AND EVOLUTION 5. 4 (2012): 954-965. Web.
GA, Babbitt. "Functional conservation of nucleosome formation selectively biases presumably neutral molecular variation in yeast genomes." GENOME BIOLOGY AND EVOLUTION 3. (2011): 15-22. Web.
Invited Article/Publication
GA, Babbitt. "Chromatin Evolving." American Scientist - cover story. (2011). Print.
Published Article
Kim Y., J.H. Lee, and G.A. Babbitt. “The enrichment of TATA box and the scarcity of depleted-proximal-nucleosome in the promoters of duplicated yeast genes.” Journal of Molecular Evolution, 70.1 (2010): 69-73. Print. «
Babbitt, G.A., M.Y. Tolstorukov, and Y. Kim. “The molecularevolution of nucleosome positioning through sequence-dependent deformationof the DNA polymer. Special issue - currentperspective in nucleosome positioning.” Journal of Biomolecular Structure and Dynamics, 27.6 (2010): 765-780. Print. «
Babbitt, G.A. “Relaxed Selection Against Accidental Blinding of Transcription Factors with Conserved Chromatin Contexts.” GENE, 466 (2010): 43-48. Print.