Lydia Freddolino, PhD
1150 W. Medical Center Dr.
Ann Arbor, MI 48109-0600
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About
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.
Links
Freddolino Lab
Qualifications
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Postdoctoral fellowColumbia University, Systems Biology, United States
2011 - 2014
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Postdoctoral researcherPrinceton University, Molecular Biology, United States
2009 - 2011
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PhDUniversity of Illinois at Urbana-Champaign, Urbana, IL, United States
2004 - 2009
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BSCalifornia Institute of Technology, Pasadena, CA, United States
2000 - 2004
Research Overview
* Interplay of protein occupancy, chromosomal structure, and gene regulation in bacteria
* New mechanisms of bacterial transcriptional regulation
* High-performance methods for protein structure prediction
* Functions and physiological roles of poorly annotated proteins
Recent Publications
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Abbondanzieri EA, Badrinarayanan AB, Barillà D, Bell SD, Blombach F, Bouet JY, Bulgheresi S, Cao QAD, Dame RT, Dekker C, Demuysere M, Espéli O, Fogg PCM, Freddolino PL, Ganji M, Gerson TM, Grainger DC, Hamoen LW, Harju J, Hocher A, Hustmyer CM, Kaljevic JK, Karney MK, Kleckner N, Laloux G, Landick R, Lioy VS, Liu WL, Liu CL, Mäkelä J, Meyer AS, Noy A, Pineau MP, Premrajka K, Racki LR, Rashid FZM, Schnetz K, Schwab S, Tišma M, van der Sijs AI, van Heesch T, van Raaphorst R, Vreede J, Walker AW, Walter JC, Weber SC, Wiggins PA, Wing HJ, Xiao J, Zhang Z. Molecular Microbiology, 2025 Feb 1; 123 (2): 89 - 100.Journal ArticleFuture Directions of the Prokaryotic Chromosome Field
DOI:10.1111/mmi.15347 PMID: 39977301 -
Chen Z, Seman M, Fyodorova Y, Farhat A, Ames A, Levashkevich A, Biswas S, Huang F, Freddolino L, Biteen JS, Ragunathan K. Nucleic Acids Research, 2024 Oct 14; 52 (18): 10731 - 10746.Journal ArticleTracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions
DOI:10.1093/nar/gkae692 PMID: 39142658 -
Rakibova Y, Dunham DT, Seed KD, Freddolino L. mSphere, 2024 Aug 14; 9 (7): e0001124 - e0001124.Journal ArticleNucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae.
DOI:10.1128/msphere.00011-24 -
Zhang C, Freddolino L. Briefings in Bioinformatics, 2024 Aug 14; 25 (4):Journal ArticleA large-scale assessment of sequence database search tools for homology-based protein function prediction
DOI:10.1093/bib/bbae349 -
Zhang C, Freddolino L. PLoS Biology, 2024 Aug 14; 22 (7 JULY):Journal ArticleFURNA: A database for functional annotations of RNA structures
DOI:10.1371/journal.pbio.3002476 -
Haugen RJ, Barnier C, Elrod ND, Hua LUO, Jensen MK, Ping JI, Smibert CA, Lipshitz HD, Wagner EJ, Freddolino PL, Goldstrohm AC. RNA, 2024 Aug 14; 30 (7): 866 - 890.Journal ArticleRegulation of the Drosophila transcriptome by Pumilio and the CCR4–NOT deadenylase complex
DOI:10.1261/rna.079813.123 -
Royzenblat SK, Freddolino L. EcoSal Plus, 2024 Aug 14; eesp00012022 - eesp00012022.Journal ArticleSpatio-temporal organization of the E. coli chromosome from base to cellular length scales.
DOI:10.1128/ecosalplus.esp-0001-2022 -
Zhang Z, Cai Y, Zhang B, Zheng W, Freddolino L, Zhang G, Zhou X. Briefings in Bioinformatics, 2024 Mar 1; 25 (2):Journal ArticleDEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting
DOI:10.1093/bib/bbae113 PMID: 38517699
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