Clayton Kosonocky

Clayton Kosonocky

Austin, TX




2025 - 2025
I worked with Kevin K. Yang, Ava Amini, and Sarah Alamdari on developing new approaches for AI-driven protein design.
2023 -
I founded The BioML Society with my colleague Aaron Feller in Jaunary 2023. The BioML Society is a student-led research group focused on research, education, and outreach in applying machine learning for the biological sciences.

In Fall 2025, we launched the Charles W. Smith Jr. Graduate Fellowship in AI/ML for Biosciences, funding two doctoral students per year.

In Summer 2024, I organized a worldwide protein design competition with collaborators from The BioML Society and LEAH Labs. In this competition, we experimentally validated 12,000 protein binders that were created by teams from 42 different countries using AI-driven methods. This was covered in Nature and its manuscript will be pre-printed soon.

In Fall 2023, I designed and co-taught a lecture series on machine learning for biochemical applciations. This series went on to become an official course taught by Dr. Claus Wilke in Fall 2024.
2022 -
My PhD is focused on developing and applying AI-driven methods for small molecule discovery and protein design. I am co-advised by Andrew Ellington and Edward Marcotte.
2020 - 2022
I was a research associate at Beyond Meat where I worked on projects in analytical chemistry (GCMS, lipids), lab automation (liquid handlers, data processing, LIMS), and flavor chemistry.
2016 - 2020
BS in Chemical & Biological Engineering at the University of Colorado. Research on Organic Synthesis in Wei Zhang's lab and microfluidic simulations in Robert Davis' lab.



Publications

Mining patents with large language models elucidates the chemical function landscape | Digital Discovery 2024
Clayton Kosonocky, Claus Wilke, Edward Marcotte, Andrew Ellington
Using alternative SMILES representations to identify novel functional analogues in chemical similarity vector searches | Patterns 2023
Clayton Kosonocky, Aaron Feller, Claus Wilke, Andrew Ellington
Evolving to Evolve, Dan Tawfik’s Insights into Protein Engineering | Biochemistry 2023
Clayton Kosonocky, Andrew Ellington
Directed Evolution of a SelB Variant that Does Not Require a Selenocysteine Insertion Sequence Element for Function | ACS Synthetic Biology 2025
Satoshi Ishida, Arno Gundlach, Clayton Kosonocky, Andrew Ellington
Directed evolution of generalist biosensors for single ring aromatics | bioRxiv 2022
Hannah Cole, Clayton Kosonocky, Mason Schechter, Jimmy Gollihar, Andrew Ellington, Simon d'Oelsnitz
How our authors are using AI in manuscript writing | Patterns 2024
Yinqi Bai, Clayton Kosonocky, James Wang

Awards

  • Charles Smith, Jr. Graduate Fellowship in Molecular Biosciences, January 2026 - May 2026
  • Y Combinator AI Startup School 2025 invitation and travel grant
  • Graduate Continuing Research Fellowship, The University of Texas at Austin, June 2024 - May 2025