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. We also wrote a review on experimentally validated methods in AI-driven protein design that was published in Current Opinion in Structural Biology.
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 the manuscript can be found on bioRxiv.

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.

Selected Publications

Closing the loop: Experimentally validated methods in artificial intelligence-driven protein design Current Opinion in Structural Biology 2026 Clayton Kosonocky, Sarah Alamdari, Kevin Yang, Ava Amini
Validation and analysis of 12,000 AI-driven CAR-T designs in the Bits to Binders competition bioRxiv 2026 Clayton Kosonocky, Alex Abel, Aaron Feller, Amanda Cifuentes Rieffer, Phillip Woolley, Jakub Lála, Daryl Barth, Tynan Gardner, Bits to Binders Competitors, Stephen Ekker, Andrew Ellington, Wesley Wierson, Edward Marcotte
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

Recent Talks and Posters

  • Primer on AI Protein Design: Applications and Validation — YouTube, August 2026
  • Invited Talk, RAND Journal Club — Virtual, August 2026
  • The Scientist webinar on the Bits to Binders Competition — Virtual, June 2026
  • Invited Talk, NVIDIA Digital Biology Team — Virtual, June 2026
  • AI Is Designing the Next Cancer Fighter — Hidden Layers Podcast, May 2026
  • Invited Talk, Kevin Drew Lab Meeting — University of Illinois Chicago, May 2026
  • Guest Lecture, BCH 339N Systems Biology and Bioinformatics — UT Austin, February 2026
  • Presentation to DARPA — UT Austin, February 2026
  • Talk at BioML Mixer — UT Austin, February 2026
  • Invited Talk at Texas Health Catalyst — Capital Factory, December 2025
  • Fourth Year PhD Seminar — UT Austin, September 2025
  • Invited Talk at Rowan Scientific Demo Day — Rowan Scientific, August 2025
  • Internship Introduction Talk — Microsoft Research New England, June 2025
  • Interdisciplinary Life Sciences Department Recruitment Talk — UT Austin, February 2025
  • Life Sciences Tech Showcase Pitch — UT Austin, March 2025
  • BATBridge Seminar — UT Austin, February 2025
  • Plastics Working Group Lecture on AI-driven Protein Design — UT Austin, December 2024
  • Bits to Binders Kickoff Event — Virtual, August 2024
  • Texas Health Catalyst Advertisement — Capital Factory, July 2024
  • Molecular Machine Learning Conference Poster Presentation — MILA, June 2024
  • Interdisciplinary Life Sciences Department Recruitment Talk — UT Austin, February 2024
  • Interdisciplinary Life Sciences Department Retreat Poster Presentation — UT Austin, August 2023
  • BioML Seminar Series, Lecture 8 — UT Austin, May 2023
  • BioML Seminar Series, Lecture 1 — UT Austin, May 2023
  • Pandemic Preparedness Workshop Talk — UT Austin, May 2023
  • BioTACOS Seminar — UT Austin, May 2023
  • Guest Lecture, BCH 339J Chemical and Synthetic Biology — UT Austin, April 2023

Awards

Misc