Laboratory Web Site
4213 Scott Hall
Dr. Gatti's research involves Computational Biology, Scientific Computing, and Matlab Programming.
Dr. Gatti's laboratory is involved in the development of new computational tools to study enzyme mechanisms and metabolic pathways, and to identify coevolving elements inside protein structures. An overview of his research includes:
1. X-ray crystallography of:
a. chaperones of F1F0 ATPase
b. enzymes involved in polysaccharide biosynthesis
c. metallo beta lactamases
d. prolyl hydroxylase
2. QM/MM and metadynamics simulations of enzymatic reactions
3. Simulation and analysis of coevolution in proteins
4. Simulation and analysis of cell metabolism using Flux Balance Analysis
5. Computational Biology
- Gatti D.L. "Foundations of Computational Biology with MATLAB." MathWorks, Natick, MA, US, 2017. (https://www.mathworks.com/academia/courseware/foundations-of-computational-biology.html)
Written for graduate students in the Chemical and Biological Sciences, Foundations of Computational Biology with MATLAB is an e-book in which MATLAB is introduced and progressively developed as a programming and visualization tool in a variety of applications ranging from data analysis and simulation to the development of complex mathematical models in biology.
Reports of Original Work
- Zhu F., Gatti DL., Yang, KH., "Nodal versus total axonal strain and the role of cholesterol in traumatic brain injury.", J. Neurotrauma 33, 859-870, 2016.
- Lipovich L., Hou, Z., Ji H., Sinkler C., McGowen M., Sterner KN., Weckle A., Sugalski AB., Pipes L., Gatti DL., Mason CE., Sherwood CC., Hof PR., Kuzawa CW., Grossman LI., Goodman M., Wildman DE. "High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans" J Comp Neurol. 524, 288-308, 2015.
- Gatti, DL. "Tools for the Simulation and Detection of Coevolving Positions in Multiple Sequence Alignments" Current Biotechnology, 4, 16-25, 2015.
- Gatti, DL. "Assessing the contribution of coevolving residues to the stability of proteins by computational means." Current Topics in Biochemical Research, 16, 67-79, 2014.
- Clark GW, Ackerman SH, Tillier ER, Gatti DL. "Multidimensional mutual information methods for the analysis of covariation in multiple sequence alignments." BMC Bioinformatics, 15, 157-163, 2014.
- Ackerman SH, Gatti DL. “Biapenem inactivation by B2 metallo β-lactamases: energy landscape of the hydrolysis reaction.” PLoS One. 8, Issue 1 | e55136, 2013.
- Ackerman SH, Tillier ER, Gatti DL. “Accurate simulation and detection of coevolution signals in multiple sequence alignments.” PLoS One. 7, Issue 10 | e47108, 2012.
- Gatti DL. “Biapenem inactivation by B2 metallo β-lactamases: energy landscape of the post-hydrolysis reactions.” PLoS One. 7, Issue 1 | e30079, 1-17, 2012.
- Acin-Perez R., Gatti D.L., Bai Y, Manfredi G. “Protein phosphorylation and prevention of cytochrome oxidase inhibition by ATP: coupled mechanisms of energy metabolism regulation.” Cell Metab. 13, 712-9, 2011.
- Ackerman S.H, and Gatti D.L. “The contribution of co-evolving residues to the stability of KDO8P synthase”, PLoS ONE, 6, Issue 3 | e17459, 1-14, 2011.
- Tao P, Schlegel HB, Gatti D.L. “Common basis for the mechanism of metallo and non-metallo KDO8P synthases.” J Inorg Biochem. 104, 1267-75, 2010.
- Meulemans A, Seneca S, Pribyl T, Smet J, Alderweirld V, Waeytens A, Lissens W, Van Coster R, De Meirleir L, di Rago JP, Gatti D.L., Ackerman SH. “Defining the pathogenesis of the human ATP12p W94R mutation using a saccharomyces cerevisiae yeast model.” J Biol Chem. 285, 4099-109, 2010.
- Tao P, Gatti D.L., Schlegel HB. “The energy landscape of 3-deoxy-D-manno-octulosonate 8-phosphate synthase.” Biochemistry. 48, 11706-14, 2009.
- Ludlam A, Brunzelle J, Pribyl T, Xu X, Gatti D.L, Ackerman SH. “Chaperones of F1-ATPase.” J Biol Chem. 284, 17138-46, 2009
- Kona F, Tao P, Martin P, Xu X, Gatti D.L. “Electronic structure of the metal center in the Cd(2+), Zn(2+), and Cu(2+) substituted forms of KDO8P synthase: implications for catalysis.” Biochemistry. 48, 3610-30, 2009.