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Nucleic Acids Research|July 31, 2023
BioLiP2: an updated structure database for biologically relevant ligand-protein interactionsChengxin Zhang, Xi Zhang, Lydia Freddolino, 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.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.Biorxiv : the Preprint Server for Biology|June 29, 2026
Whole-proteome structure/function prediction in Uropathogenic <i>E. coli</i> reveals previously missed host-microbe and microbe-phage interaction pathwaysChunxiang Peng, Henry Schreiber, Chengxin Zhang, et al.Nature Methods|January 3, 2024
Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics dataWei Zheng, Qiqige Wuyun, Yang Li, et al.Nature Communications|September 16, 2023
Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure predictionYang Li, Chengxin Zhang, Chenjie Feng, et al.Annual Review of Cell and Developmental Biology|May 8, 2012
Beyond homeostasis: a predictive-dynamic framework for understanding cellular behaviorLydia Freddolino, Saeed TavazoieThe Journal of Physical Chemistry. B|May 5, 2017
Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy LandscapesMorteza Khabiri, Lydia FreddolinoBiorxiv : the Preprint Server for Biology|January 9, 2026
The Algorithm for Reversible Jump Inference of MotifsAli M Farhat, Lydia FreddolinoMolecular Microbiology|February 19, 2025
Polyphosphate: The "Dark Matter" of Bacterial Chromatin StructureLisa R Racki, Lydia FreddolinoPageof 26