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
Dr. Babbitt initially trained as an evolutionary ecologist with a focus on functional morphology in avian and insect systems. During his postdoctoral studies, he transitioned to the field of molecular evolution and biophysics. He currently develops statistical methods for comparing molecular dynamics and conducts original investigations regarding the evolution of molecular dynamics in living systems. He also has more than ten years of experience as an aviculturist and zookeeper at the Columbus Zoo and Aquarium in Columbus, Ohio (working with large cats, hoofstock, and birds) and conducting reproductive research on captive birds at Disney's Discovery Island birdpark in Orlando, Florida.
For more information please visit the G.A. Babbitt Lab website.
585-475-6246
Currently Teaching
BIOG-140
Cell and Molecular Biology for Engineers I
3 Credits
This is the first course of a two-course sequence designed to introduce biomedical engineering students to the molecular and cellular basis of life with a particular emphasis on the integration of molecular systems that underscore human physiology. This course will start with the basic chemistry of biological macromolecules and then explore the cell starting from the nucleus and moving outward. Major topics will include: DNA replication; molecular basis of inheritance; the biology of RNA; gene expression; protein synthesis; the secretory pathways; and enzyme kinetics.
BIOL-798
Grad Biology Independent Study
1 - 4 Credits
This course is a faculty-directed, graduate level tutorial of appropriate topics that are not part of the formal curriculum.
ENVS-798
Advanced Environmental Science Independent Study
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-230
Bioinformatics Languages
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.
BIOL-498
Advanced Biology Independent Study
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-470
Statistical Analysis for Bioinformatics
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-495
Advanced Biology Research
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-301
Undergraduate Teaching Experience
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-298
Biology Independent Study
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-130
Introduction to Bioinformatics
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
Biology Research
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.
Latest News
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May 30, 2019
![Student types on computer.]()
RIT student develops tool to visualize molecular dynamics of proteins in virtual reality
Kyle Diller, a fifth-year computer science student from East Windsor, N.J., developed a plug-in application for the molecular visualization program UCSF ChimeraX. The application is currently under development at the University of California at San Francisco. Diller’s plug-in allows users to display an atomic structure as if it were a movie so they can see how the structure changes.
Select Scholarship
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.
Peer Reviewed/Juried Poster Presentation
Babbitt, G.A. "Triplet Codon Organization Optimizes the Impact of Synonymous Mutation on Nucleic Acid Molecular Dynamics." Proceedings of the Society for Molecular Biology and Evolution. Ed. SMBE. Austin, TX: SMBE.
Published Game, Application or Software
Babbitt, G.A., et al. DROIDS 1.2 - Free Software Project for Comparative Protein Dynamics. Software. GitHub. 2017.
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.
Babbitt G.A. and C.R. Cotter. “Functional conservation of nucleosome formation selectively biases presumably neutral molecular variation in yeast genomes.” Genome Biology andEvolution, (2010): n.p. Web.