Author

Prashant Vaidyanathan

Microsoft Research (United Kingdom)ORCID 0000-0002-9722-7089Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Synthetic Biology· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 1 Organism:E. coli· 1 Approach:large language model· 1 Research Focus:software / tool· 1 Approach:statistical model· 1

Frequent Co-Authors

Alexander Vahid· 1 shared Andrew PhillipsiD· 1 shared Bryan BartleyiD· 1 shared Carlo Spaccasassi· 1 shared Chris John MyersiD· 1 shared Colin Gravill· 1 shared David TraniD· 1 shared Douglas Michael DensmoreiD· 1 shared

Activity by Year

2019-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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1 shared paperBioinformatics

Alexander Vahid

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3 papers

Recent·Most cited

Ontology-driven software engineering using LLMs for knowledge graphs in engineering biology

İhsan Tolga Medeni, Metehan Ünal, Roberto Galizi, Bryan Bartley, Jacob Beal, Chris John Myers, Prashant Vaidyanathan, Göksel Mısırlı

The paper presents an ontology-driven approach using LLMs to create software libraries for knowledge graphs in engineering biology, demonstrating it with the SBOL3 Ontology and sbol-script library.

bioRxiv · Jun 1, 2026 · PreprintSynthetic Biology

Algorithms for the selection of fluorescent reporters

Prashant Vaidyanathan, Evan Appleton, David Tran, Alexander Vahid, George McDonald Church, Douglas Michael Densmore

The paper presents algorithms and an open-source tool to optimize fluorophore panels for maximal signal and minimal bleed-through in fluorescent measurements.

Communications Biology · Jan 26, 2021Peer-reviewedBioinformatics

Scalable dynamic characterization of synthetic gene circuits

Neil Dalchau, Paul K. Grant, Prashant Vaidyanathan, Carlo Spaccasassi, Colin Gravill, Andrew Phillips

This paper presents a method to dynamically characterize synthetic gene circuits using time-series data and parameter inference, enabling scalable analysis of complex circuits in E. coli.

bioRxiv · Aug 15, 2019 · PreprintSynthetic Biology