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Journal of Bacteriology|July 14, 2025
DNA methylation affects gene expression but not global chromatin structure in <i>Escherichia coli</i>Willow Jay Morgan, Haley M Amemiya, Lydia FreddolinoNature Methods|February 8, 2022
CR-I-TASSER: assemble protein structures from cryo-EM density maps using deep convolutional neural networksXi Zhang, Biao Zhang, Lydia Freddolino, et al.Journal of Bacteriology|November 14, 2018
<i>Escherichia coli</i> Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect RoutesGrace M Kroner, Michael B Wolfe, Lydia FreddolinoProteins|August 31, 2023
Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15Wei Zheng, Qiqige Wuyun, Lydia Freddolino, et al.Nature Physics|February 8, 2011
Challenges in protein folding simulations: Timescale, representation, and analysisLydia Freddolino, Christopher B Harrison, Yanxin Liu, et al.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.Pageof 26