Author

Pascal Sturmfels

University of Washington

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biochemistry· 2 Bioinformatics· 1 Neuroscience· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 4 Research Focus:benchmarking· 3 Assay:bulk RNA-seq· 2 Approach:diffusion model· 2 Organism:human· 2 Assay:protein structure· 2 Approach:benchmark study· 1 Research Focus:database / resource· 1

Frequent Co-Authors

David A. BakeriD· 2 shared Frank DiMaioiD· 2 shared Magnus S. BaueriD· 2 shared Rafael I. BrentiD· 2 shared Rohith KrishnaiD· 2 shared Woody AherniD· 2 shared Alex KangiD· 1 shared Amir MotmaeniD· 1 shared

Activity by Year

2016-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 42 mutual co-author links

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2 shared papersBiochemistry

David A. BakerORCID

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Author profile →

5 papers

Recent·Most cited

De novo design of phosphotyrosine peptide binders

Magnus S. Bauer, Jason Z. Zhang, Kejia Wu, Gyu Rie Lee, Brian Coventry, Isabella M Silvestri, Kody A. Klupt, Jiuhan Shi, Rafael I. Brent, Xinting Li, Carolina Möller, Nicole Roullier, Dionne K. Vafeados, Indrek Kalvet, Rebecca Skotheim, , David A. Baker

This paper introduces RFD2-MI, a deep learning framework for designing phosphotyrosine peptide binders, showing high specificity and affinity for phosphorylated targets.

bioRxiv · Sep 29, 2025 · PreprintBiochemistry

Accelerating Biomolecular Modeling with AtomWorks andRF3

Nathaniel Corley, Simon V. Mathis, Rohith Krishna, Magnus S. Bauer, Tuscan R. Thompson, Woody Ahern, Maxwell W. Kazman, Rafael I. Brent, Kieran Didi, Andrew Kubaney, Ryan McHugh, Arnav Nagle, Andrew Favor, Meghana Kshirsagar, Pascal Sturmfels, , Frank DiMaio

AtomWorks, a modular atom-level data framework, trains structure prediction and design models; the resulting RF3 improves chirality handling and performs between AF3 and Boltz.

bioRxiv · Aug 14, 2025 · PreprintBiochemistry✦ In-depth digest

Unified AI framework to uncover deep interrelationships between gene expression and Alzheimer's disease neuropathologies

Nicasia Beebe-Wang, Safiye Çelik, Ethan Weinberger, Pascal Sturmfels, Philip L. De Jager, Sara Mostafavi, Su‐In Lee

The paper introduces MD-AD, a deep learning framework that identifies non-linear gene expression-neuropathology relationships in Alzheimer's disease using multi-cohort data, revealing sex-specific immune response patterns.

Nature Communications · Sep 10, 2021Peer-reviewedSystems Biology

Automated Brain Masking of Fetal Functional MRI

Saige E. Rutherford, Pascal Sturmfels, Mike Angstadt, Jasmine L. Hect, Jenna Wiens, Marion van den Heuval, Dustin Scheinost, Moriah E. Thomason, Chandra Sripada

The paper develops a CNN for automated fetal brain masking in rs-fMRI data, achieving good performance across different scanners and populations.

bioRxiv · Jul 13, 2019 · PreprintNeuroscience

The Lair: A resource for exploratory analysis of published RNA-Seq data

Harold Pimentel, Pascal Sturmfels, Nicolas Bray, Pall Melsted, Lior Pachter

The Lair provides tools to analyze published RNA-Seq data from the Short Read Archive, enabling accessible and extendable exploration without technical expertise.

bioRxiv · May 31, 2016Bioinformatics