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.
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.
Differential processing and localization of human Nocturnin controls metabolism of mRNA and nicotinamide adenine dinucleotide cofactors.
Abshire ET, Hughes KL, Diao R, Pearce S, Gopalakrishna S, Trievel RC, Rorbach J, Freddolino PL, Goldstrohm AC.
J Biol Chem. 2020; 295: 15112–33.
A Thermosensitive, Phase-Variable Epigenetic Switch: pap Revisited.
Zamora M, Ziegler CA, Freddolino PL, Wolfe AJ.
Microbiol Mol Biol Rev. 2020; 84: e00030-17.
A Well-Mixed E. coli Genome: Widespread Contacts Revealed by Tracking Mu Transposition.
Walker DM, Freddolino PL, Harshey RM.
Cell. 2020; 180: 703–16.
Unique repression domains of Pumilio utilize deadenylation and decapping factors to accelerate destruction of target mRNAs.
Arvola RM, Chang CT, Buytendorp JP, Levdansky Y, Valkov E, Freddolino PL, Goldstrohm AC.
Nucleic Acids Res. 2020; 48: 1843–71.
For a list of publications at Google Scholar, click HERE