Author

Matthew Aquilina

Harvard UniversityORCID 0000-0002-4039-1398Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Synthetic Biology· 2 Bioinformatics· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Assay:DNA methylation· 2 Research Focus:software / tool· 2 Approach:deep learning· 1 Approach:experimental assay· 1 Assay:imaging· 1 Approach:optimal transport· 1 Approach:statistical model· 1

Frequent Co-Authors

Florian KatzmeieriD· 2 shared William M. ShihiD· 2 shared Alan O’CallaghaniD· 1 shared Christopher M. WintersingeriD· 1 shared Corey BeckeriD· 1 shared Filip Bušić· 1 shared Giorgia IsinelliiD· 1 shared Huangchen Cui· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

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2 shared papersBioinformatics

Florian KatzmeierORCID

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Author profile →

4 papers

Recent·Most cited

OrthoSeq: A Design Workflow for Thermodynamically Orthogonal DNA Sequence-Pair Libraries

Florian Katzmeier, Matthew Aquilina, William Shih

OrthoSeq designs DNA sequence-pair libraries with thermodynamic orthogonality, outperforming sequential methods in library size under constraints.

bioRxiv · Aug 6, 2026 · PreprintBioinformatics

A computational framework for designing micron-scale crisscross DNA megastructures

Matthew Aquilina, Florian Katzmeier, Minke A. D. Nijenhuis, Siyuan S. Wang, Corey Becker, Yichen Zhao, Su Hyun Seok, Julie Finkel, Huangchen Cui, J H Lee, Seungwoo Lee, William M. Shih

This paper develops a computational framework to design crisscross DNA megastructures, optimizing handle assignment and expanding handle libraries to enable large-scale fabrication.

Nature Communications · Jul 17, 2026Peer-reviewedSynthetic Biology

Reusing excess staple oligonucleotides for economical production of DNA origami

Giorgia Isinelli, Christopher M. Wintersinger, Matthew Aquilina, Pascal Lill, Olivia J. Young, Jie Deng, William M. Shih, Yang C. Zeng

This paper demonstrates that reusing excess staple oligonucleotides with replenishment can reduce DNA origami production costs by up to 80%.

Nucleic Acids Research · Jun 6, 2025Peer-reviewedSynthetic Biology

GelGenie: an AI-powered framework for gel electrophoresis image analysis

Matthew Aquilina, Nathan J. W. Wu, Kiros Kwan, Filip Bušić, James Dodd, Laura Nicolás-Sáenz, Alan O’Callaghan, Peter Bankhead, Katherine E. Dunn

GelGenie is an AI framework that automatically identifies gel bands in electrophoresis images, outperforming existing software and matching manual analysis.

Nature Communications · May 5, 2025Peer-reviewedMolecular Biology