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Andrew Dickson
I'm a postdoc in Dr. Taner Sen's lab at the USDA Agricultural Research Service in Albany, CA, working on efficient continued training of genomic sequence models.
I did my PhD in Applied Science and Technology at UC Berkeley (2020–2025), with concentrations in machine learning, bioinformatics, and biophysics.
Before that I did my BS in Electrical Engineering and Computer Science, also at Berkeley.
Email /
CV /
Projects /
Github
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FG nucleoporins feature unique patterns that distinguish them from other IDPs.
Peyro M, Soheilypour M, Nibber VS, Dickson AM, Mofrad MRK.
Biophys J, 2021
doi
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Nucleoporins’ exclusive amino acid sequence features regulate their transient interaction with and selectivity of cargo complexes in the nuclear pore.
Peyro M, Dickson A., Mofrad MRK.
Mol. Bio. of the Cell, 2021
doi
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Go Bench: Shared-Hub for Universal Benchmarking of Machine Learning-Based Protein Functional Annotations.
Dickson A., Asgari E, et. al.
Bioinformatics, 2022
doi
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Fine-tuning protein embeddings for functional similarity evaluation.
Dickson A, Mofrad MRK.
Bioinformatics, 2023
doi
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Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities.
Valiei A, Dickson A., Mofrad MRK, Amanian-D J.
npj Biofilms and Microbiomes, 2024
doi
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SIMBA-GNN: Simulation-augmented Microbiome Abundance Graph Neural Network.
Parsa M., Aminian-D. J. Dickson A., Mofrad MRK
npj Systems Biology and Applications, 2025
doi
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MetaBiome: a multiscale model integrating agent-based and metabolic networks to reveal spatial regulation in gut mucosal microbial communities.
Amanian-D J., Dickson A.*, et. al.
mSystems, 2025 [*Co-First Author]
doi
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Residue-level Protein Function Prediction with Interpretability Methods.
Dickson A., Mouline, S, Mofrad MRK
Bioinformatics, in press
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Bacteria-host interactions determine ecological outcomes in gut mucosal community models.
Dickson A., Mofrad MRK, Amanian-D J.
Manuscript submitted for publication, 2026
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STARP Primer: a web-based program of primer design for flexibly genotyping individual single nucleotide polymorphisms.
Long Y., Dickson A.*, et. al.
Manuscript submitted for publication, 2026 [*Co-First Author]
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Forecasting the future of American mass shootings with Bayesian agent-based model calibration.
Dickson AM, Bhatt M, Yu T, Mofrad MRK.
PNAS Nexus, 2026
doi
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Coupling Genome-Scale Representations with Generative Modeling for the Gut Microbiome.
Dickson A, Mofrad MRK.
Springer, 2025
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Talks
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Asgari E., Dickson A., et. al Fine-tuning of Language Model-Based Representation for Protein Functional Annotation. Intelligent Systems for Molecular Biology, 2020
Dickson A., Asgari E., et. al GO Bench: Shared-hub for Universal Benchmarking of Machine Learning-Based Protein Functional Annotations. Intelligent Systems for Molecular Biology, 2022
Dickson A., Mofrad MRK Fine-tuning Protein Embeddings for Generalizable Protein Annotation. Bioengineering Institute of California, 2023
Dickson A., Valiei A, Mofrad MRK, Agent Based Modeling of Invasion Scenarios in the Gut Microbiome. Biomedical Engineering Society, 2024
Mouline, S, Dickson A., Mofrad MRK, Identifying Functionally Important Residues: BERT Entropy and Interpretability Applied to Protein Function Prediction. Biomedical Engineering Society, 2024
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