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Biorxiv : the Preprint Server for Biology|October 31, 2023
Explainable protein function annotation using local structure embeddingsAlexander Derry, Russ B AltmanProtein Science : a Publication of the Protein Society|December 15, 2022
COLLAPSE: A representation learning framework for identification and characterization of protein structural sitesAlexander Derry, Russ B AltmanProceedings of the National Academy of Sciences of the United States of America|August 20, 2025
Protein functional site annotation using local structure embeddingsAlexander Derry, Alp Tartici, Russ B AltmanPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing|December 10, 2021
Training data composition affects performance of protein structure analysis algorithmsAlexander Derry, Kristy A Carpenter, Russ B AltmanBioinformatics (Oxford, England)|June 26, 2025
Unsupervised learning reveals landscape of local structural motifs across protein classesAlexander Derry, Haim Krupkin, Alp Tartici, et al.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing|December 5, 2019
A Literature-Based Knowledge Graph Embedding Method for Identifying Drug Repurposing Opportunities in Rare DiseasesDaniel N Sosa, Alexander Derry, Margaret Guo, et al.Nature Communications|February 9, 2022
Protein sequence design with a learned potentialNamrata Anand, Raphael Eguchi, Irimpan I Mathews, et al.Clinical Pharmacology and Therapeutics|November 15, 2017
Challenges for Training Translational Researchers in the Era of Ubiquitous DataRuss B AltmanCurrent Opinion in Drug Discovery & Development|July 2, 2003
Genetic sequence data for pharmacogenomicsRuss B AltmanPageof 31