Author

Akio Shirali

Stanford UniversityORCID 0000-0003-0772-7117Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 1 Approach:deep learning· 1 Approach:experimental assay· 1 Assay:protein structure· 1 Research Focus:protein structure prediction· 1 Research Focus:software / tool· 1 Approach:transformer / foundation model· 1

Frequent Co-Authors

Jinho KimiD· 1 shared Julia VuiD· 1 shared Katie HaniD· 1 shared Nicholas MurphyiD· 1 shared Nils J. H. AvereschiD· 1 shared Petr KoubaiD· 1 shared Phillip KyriakakisiD· 1 shared Po‐Ssu HuangiD· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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1 shared paperBioengineering

Jinho KimORCID

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2 papers

Recent·Most cited

BioengineeringbioRxivPreprintAug 18, 2025

Conditional Protein Structure Generation with Protpardelle-1c

Tianyu Lu, Richard W. Shuai, Petr Kouba…·Po‐Ssu Huang

Protpardelle-1c is a protein structure generative model that improves motif scaffolding and multi-chain complex generation, achieving higher scores and faster sampling than existing models.

6 citations

protein structuredeep learning

𝕏 PostBluesky

BioengineeringbioRxivPreprintApr 24, 2025

Homology-Based Enzymatic Assembly of Modular T7 Phage Genome

Julia Vu, Zane Chan, Nicholas Murphy…·Phillip Kyriakakis

This paper introduces a method to assemble synthetic T7 phage genomes in vitro without restriction enzymes, enabling modular DNA insertion.

DOI 10.1101/2025.04.24.650493

experimental assay

𝕏 PostBluesky