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Journal of Bacteriology|July 25, 2022
Escherichia coli YigI is a Conserved Gammaproteobacterial Acyl-CoA Thioesterase Permitting Metabolism of Unusual Fatty Acid SubstratesMichael Schmidt, Theresa Proctor, Rucheng Diao, et al.Biorxiv : the Preprint Server for Biology|January 20, 2025
DNA methylation affects gene expression but not global chromatin structure in Escherichia coliWillow Jay Morgan, Haley M Amemiya, Lydia FreddolinoNucleic Acids Research|September 22, 2022
Genetic context effects can override canonical cis regulatory elements in Escherichia coliScott A Scholz, Chase D Lindeboom, Lydia FreddolinoBiorxiv : the Preprint Server for Biology|February 20, 2025
ShapeME: A tool and web front-end for de novo discovery of structural motifs underpinning protein-DNA interactionsJeremy W Schroeder, Michael B Wolfe, Lydia FreddolinoNucleic Acids Research|July 31, 2023
BioLiP2: an updated structure database for biologically relevant ligand-protein interactionsChengxin Zhang, Xi Zhang, Lydia Freddolino, et al.Journal of Bacteriology|July 14, 2025
DNA methylation affects gene expression but not global chromatin structure in Escherichia coliWillow 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
Escherichia coli 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.Pageof 9