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.
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, in press.
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, in press.
A Thermosensitive, Phase-Variable Epigenetic Switch: pap Revisited.
Zamora M, Ziegler CA, Freddolino PL, Wolfe AJ.
Microbiol Mol Biol Rev. 2020; 84: e00030-17.
Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons.
Wei X, Zhang C, Freddolino PL, Zhang Y.
Bioinformatics. 2020, in press.
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.
Rapid metabolic shifts occur during the transition between hunger and satiety in Drosophila melanogaster.
Wilinski D, Winzeler J, Duren W, Persons JL, Holme KJ, Mosquera J, Khabiri M, Kinchen JM, Freddolino PL, Karnovsky A, Dus M.
Nat Commun. 2019; 10: 4052.
High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription.
Scholz SA, Diao R, Wolfe MB, Fivenson EM, Lin XN, Freddolino PL.
Cell Syst. 2019; 8: 212–25.
For a list of publications at Google Scholar, click HERE