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The Journal of Physical Chemistry. B|February 24, 2006
Coarse grained protein-lipid model with application to lipoprotein particlesAmy Y Shih, Anton Arkhipov, Lydia Freddolino, et al.
Elife|April 6, 2018
Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitryLydia Freddolino, Jamie Yang, Amir Momen-Roknabadi, et al.
Journal of Molecular Biology|April 17, 2026
ShapeME: A tool and web front-end for de novo discovery of structural motifs underpinning protein-DNA interactionsJeremy W Schroeder, Vivian Ramirez, Michael B Wolfe, et al.
Nano Letters|May 17, 2007
Disassembly of nanodiscs with cholateAmy Y Shih, Lydia Freddolino, Stephen G Sligar, et al.
The Journal of Physical Chemistry Letters|June 28, 2012
Structural Characterization of λ-Repressor Folding from All-Atom Molecular Dynamics SimulationsYanxin Liu, Johan Strümpfer, Lydia Freddolino, et al.
Msphere|June 26, 2024
Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio choleraeYulduz Rakibova, Drew T Dunham, Kimberley D Seed, et al.
Research Square|November 24, 2025
StoPred: Accurate Stoichiometry Prediction for Protein Complexes Using Protein Language Models and Graph AttentionQuancheng Liu, Chunxiang Peng, Wei Zheng, et al.
Microbiology and Molecular Biology Reviews : MMBR|July 31, 2020
A Thermosensitive, Phase-Variable Epigenetic Switch: pap RevisitedMario Zamora, Christine A Ziegler, Lydia Freddolino, et al.
Biorxiv : the Preprint Server for Biology|November 24, 2025
StoPred: Accurate Stoichiometry Prediction for Protein Complexes Using Protein Language Models and Graph AttentionQuancheng Liu, Chunxiang Peng, Wei Zheng, et al.
Methods in Molecular Biology (Clifton, N.J.)|July 19, 2024
High-Throughput Mapping of Chromosomal Conformations in E. coli Under Physiological Conditions Using Massively Multiplexed Mu TranspositionKhang Ho, Sonya K Royzenblat, Brady Wilkins, et al.
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