Author

Matthew F. Allan

Harvard UniversityORCID 0000-0001-8182-7402Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:experimental assay· 2 Approach:deep learning· 1 Organism:human· 1 Research Focus:protein structure prediction· 1 Research Focus:software / tool· 1 Assay:structural biology· 1 Approach:transformer / foundation model· 1

Frequent Co-Authors

Silvi RouskiniD· 3 shared Yves J. Martin des TailladesiD· 3 shared Albéric A. de LajarteiD· 2 shared Casper L’Esperance-KerckhoffiD· 2 shared Federico Fuchs WightmaniD· 2 shared Justin ArudaiD· 2 shared Scott L. GroteiD· 2 shared Alex Kashi· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 39 mutual co-author links

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3 shared papersMolecular Biology

Silvi RouskinORCID

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3 papers

Recent·Most cited

BiochemistryScience AdvancesPeer-reviewedFeb 25, 2026

Diverse Database and Machine Learning Model to narrow the generalization gap in RNA structure prediction

Albéric A. de Lajarte, Yves J. Martin des Taillades, Justin Aruda…·Silvi Rouskin

The paper introduces a diverse RNA structure database and a deep learning model, eFold, which improves RNA secondary structure prediction by emphasizing structural diversity over database size.

18 citationstop 1%

humanstructural biology

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Molecular BiologyNucleic Acids ResearchPeer-reviewedJul 14, 2025

SEISMICgraph: a web-based tool for RNA structure data visualization

Federico Fuchs Wightman, Grant Yang, Yves J. Martin des Taillades…·Lauren D. Hagler

SEISMICgraph is a web-based tool for visualizing RNA structure data from chemical probing experiments, enabling comparison across sequences and conditions.

4 citations

experimental assaysoftware / tool

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Molecular BiologybioRxivPreprintApr 29, 2024

Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA

Matthew F. Allan, Justin Aruda, Jesse S. Plung…·Silvi Rouskin

The paper introduces SEARCH-MaP and SEISMIC-RNA to discover and quantify long-range RNA base pairs in coronaviruses, revealing their role in ribosomal frameshifting.

16 citations

experimental assay

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