Areas of Interest
The regulatory networks of bacteria play a key role in their information processing capabilities, coordinating and executing interactions with their environments. Quantitative, predictive models of these networks would be tremendously beneficial for facilitating the development of new antimicrobial therapies, enabling synthetic biology applications, and understanding bacterial evolution and ecology. Ultimately, the aim of my laboratory is to build a multiscale framework enabling modeling of bacterial regulatory networks at any level of detail, from atomistic to cellular. To this end, we develop and apply high-throughput experimental methods for measuring biomolecular interactions and cellular regulatory states in vivo, and for profiling the phenotypic consequences of regulatory changes. In tandem with these experimental approaches, we use molecular simulation and mathematical modeling to obtain high-resolution insight into the biomolecular interactions driving regulatory networks, and the systems-level effects of altering them.
Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom.
Amemiya HM, Schroeder J, Freddolino PL.
Transcription. 2021, in press.
Dynamic landscape of protein occupancy across the Escherichia coli chromosome.
Freddolino PL, Amemiya HM, Goss TJ, Tavazoie S.
PLoS Biol. 2021; 19: e3001306.
The leucine-responsive regulatory proteins/feast-famine regulatory proteins: an ancient and complex class of transcriptional regulators in bacteria and archaea.
Ziegler CA, Freddolino PL.
Crit Rev Biochem Mol Biol. 2021; 56: 373–400.
TNFRSF13B polymorphisms counteract microbial adaptation to natural IgA.
Platt JL, de Mattos Barbosa MG, Huynh D, Lefferts AR, Katta J, Kharas C, Freddolino PL, Bassis CM, Wobus CE, Geha R, Bram RJ, Nunez G, Kamada N, Cascalho M.
JCI Insight. 2021; 6: 148208.
Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome.
Zhang C, Zheng W, Cheng M, Omenn GS, Freddolino PL, Zhang Y.
J Proteome Res. 2021; 20: 1178–89.
Persistent epigenetic reprogramming of sweet taste by diet.
Vaziri A, Khabiri M, Genaw BT, May CE, Freddolino PL, Dus M.
Sci Adv. 2020; 6: eabc8492.
Principles of mRNA control by human PUM proteins elucidated from multi-modal experiments and integrative data analysis.
Wolfe MB, Schagat TL, Paulsen MT, Magnuson B, Ljungman M, Park D, Zhang C, Campbell ZT, Goldstrohm AC, Freddolino PL.
RNA. 2020; 26: 1680–1703.
For a list of publications at Google Scholar, click HERE