Stefano Lonardi

University of California, Riverside — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

54h-index19.9kcitations272works2.92yr avg
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Research Topics

Genomics and Phylogenetic Studies(65), Algorithms and Data Compression(46), Chromosomal and Genetic Variations(34), RNA and protein synthesis mechanisms(28), Time Series Analysis and Forecasting(27)

Publications271 total

ASPred: identification of antigen apecific B-cell receptors from single V(D)J sequences using large language models 4171
The Journal of Immunology·2025Open Access
Prediction of DNA Methylation With Long-Range State-Space Models
IEEE Transactions on Computational Biology and Bioinformatics·2025
Impact of Single Point Mutations in the SARS-CoV-2 Spike Protein RBD on B-Cell Receptor Diversity and Cross-Reactivity 4525
The Journal of Immunology·2025Open Access
Fine-tuned protein language model identifies antigen-specific B cell receptors from immune repertoires
2025Open Access
Author response: A drug repurposing approach reveals targetable epigenetic pathways in Plasmodium vivax hypnozoites
2025Open Access
A drug repurposing approach reveals targetable epigenetic pathways in Plasmodium vivax hypnozoites
eLife·2025· 1 citedOpen Access
Predicting Antibody–Antigen Interactions with Structure-Aware LLMs: Insights from SARS-CoV-2 Variants
Journal of Chemical Information and Modeling·2025· 1 citedOpen Access
Kingdom-wide CRISPR guide design with ALLEGRO
Nucleic Acids Research·2025Open Access
TRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis
Genome biology·2025· 3 citedOpen Access
MSTmap Online: enhanced usability, visualization, and accessibility
Nucleic Acids Research·2025Open Access
RAmbler resolves complex repeats in human Chromosomes 8, 19, and X
Genome Research·2025· 2 citedOpen Access
Predicting differentially methylated cytosines in TET and DNMT3 knockout mutants via a large language model
Briefings in Bioinformatics·2025Open Access
Kingdom-Wide CRISPR Guide Design with ALLEGRO
2025Open Access
A Large Language Model Guides the Affinity Maturation of Variant Antibodies Generated by Combinatorial Optimization
2024· 1 citedOpen Access
Balanced Training Sets Improve Deep Learning-Based Prediction of CRISPR sgRNA Activity
ACS Synthetic Biology·2024· 4 citedOpen Access
Insights into the evolution, virulence and speciation of <i>Babesia MO1</i> and <i>Babesia divergens</i> through multiomics analyses
Emerging Microbes & Infections·2024· 10 citedOpen Access
Author response: A Drug Repurposing Approach Reveals Targetable Epigenetic Pathways in Plasmodium vivax Hypnozoites
2024Open Access
A Drug Repurposing Approach Reveals Targetable Epigenetic Pathways in Plasmodium vivax Hypnozoites
2024· 3 citedOpen Access
A drug repurposing approach reveals targetable epigenetic pathways in Plasmodium vivax hypnozoites
eLife·2024· 2 citedOpen Access
Predicting Differentially Methylated Cytosines in TET and DNMT3 Knockout Mutants via a Large Language Model
2024· 2 citedOpen Access
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Frequent Co-authors

Eamonn Keogh(16), Timothy J. Close(14), Steve Wanamaker(9), Jessica Lin(6), María Muñoz‐Amatriaín(6), Rachid Ounit(6), Chotirat Ann Ratanamahatana(6), Gary J. Muehlbauer(5), Nadia Ponts(5), Wei Li(4), Jaakko Tanskanen(4), Jaroslav Doležel(4), Alan H. Schulman(4), Robbie Waugh(4), Nils Stein(4), Jan T. Svensson(4), Prasanna R. Bhat(4), Yonghui Wu(4), Philip A. Roberts(4), Elena Y. Harris(4)