Jonathan Allen

Lawrence Livermore National Laboratory — United States

Computer Science · Physical Sciences

42h-index19.8kcitations198works1.42yr avg
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Research Topics

Computational Drug Discovery Methods(43), Genomics and Phylogenetic Studies(19), Protein Structure and Dynamics(19), Machine Learning in Materials Science(17), Nanowire Synthesis and Applications(11)

Publications198 total

Author response for "SLAB: Simultaneous Labeling And Binding affinity prediction for protein-ligand structures"
2025
Author response for "SLAB: Simultaneous Labeling And Binding affinity prediction for protein-ligand structures"
2025
Author response for "SLAB: Simultaneous Labeling And Binding affinity prediction for protein-ligand structures"
2025
ChemBERTa-3: An Open Source Training Framework for Chemical Foundation Models
Zenodo (CERN European Organization for Nuclear Research)·2025Open Access
ChemBERTa-3: An Open Source Training Framework for Chemical Foundation Models
Zenodo (CERN European Organization for Nuclear Research)·2025Open Access
ChemBERTa-3: An Open Source Training Framework for Chemical Foundation Models
Zenodo (CERN European Organization for Nuclear Research)·2025Open Access
ChemBERTa-3: An Open Source Training Framework for Chemical Foundation Models
2025· 2 citedOpen Access
ChemBERTa-3: An Open Source Training Framework for Chemical Foundation Models
2025· 2 citedOpen Access
SLAB: Simultaneous Labeling And Binding affinity prediction for protein-ligand structures
2025Open Access
Harnessing Machine Learning for Agnostic Biodetection
Health Security·2025Open Access
Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification
mSystems·2025· 4 citedOpen Access
Protein-ligand binding affinity prediction using multi-instance learning with docking structures
Frontiers in Pharmacology·2025· 5 citedOpen Access
Leveraging a Multi-Disciplinary Approach to Appraise the Permian’s Southern Delaware Basin
2025
HDBind: encoding of molecular structure with hyperdimensional binary representations
Scientific Reports·2024· 6 citedOpen Access
GENTANGLE: integrated computational design of gene entanglements
Bioinformatics·2024· 2 citedOpen Access
Addressing the dynamic nature of reference data: a new nt database for robust metagenomic classification
2024· 3 citedOpen Access
Enhancing Docking Accuracy with PECAN2, a 3D Atomic Neural Network Trained without Co-Complex Crystal Structures
Machine Learning and Knowledge Extraction·2024· 2 citedOpen Access
Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies
PLoS ONE·2024Open Access
PRIMED for the Future: Purposing Raw Intake for Machine Learning-Enabled Detection
2023Open Access
GENTANGLE: integrated computational design of gene entanglements
2023· 1 citedOpen Access
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Frequent Co-authors

Steven L. Salzberg(10), Mihaela Pertea(9), Lincoln J. Lauhon(9), Shea N. Gardner(7), Crystal Jaing(7), Owen White(6), Claire M. Fraser(6), Tom Slezak(6), Bernard Suh(5), Samuel V. Angiuoli(5), James B. Thissen(5), Derek Jones(5), Monica K. Borucki(5), Malcolm J. Gardner(4), Jane M. Carlton(4), Shamira J. Shallom(4), J. Craig Venter(4), Brian J. Haas(4), Jennifer R. Wortman(4), Martin Shumway(4)