CV
Biotech R&D - AI/ML - Comp Bio
With a PhD in Physics and over 4 years of industry experience in AI and biotech, I am committed to advancing science and technological innovation. I bring strong quantitative skills, paired with a solid track record in scientific communication, data visualization, and mentoring across disciplines. I’m passionate about contributing to projects that have a positive impact on society.
Skills
- Programming: Python, C/C++, NumPy, Pandas
- Machine Learning: PyTorch, scikit-learn, computer vision, active learning, diffusion models, large language models
- Protein Modeling and Design: protein language models (ESM2), structure prediction models (AlphaFold, OpenFold, Boltz), inverse folding models (ProteinMPNN), protein design workflows (RFdiffusion, BindCraft), BioEmu
- Drug Discovery Applications: antibody design, molecular property prediction, developability assessment, docking, in silico screening
- Computational Biology and Biophysics: molecular dynamics simulations, enhanced sampling, free energy calculations, GROMACS, ChimeraX, VMD, BioPython, MDAnalysis
- Parallel and Scientific Computing: CUDA, MPI, OpenMP, statistics, linear algebra, graph analysis, statistical physics
- MLOps and Research Infrastructure: AWS, Git, JIRA/Asana, experiment tracking (W&B), workflow automation, research tooling
Education
- Ph.D. in Computational Biophysics, University of Toronto, 2024
- M.Sc. in Computational Chemistry, University of Massachusetts Lowell, 2017
- B.S. in Applied Mathematics and Physics, Moscow Institute of Physics and Technology, 2014
Work Experience
- ML Scientist II, Fable Therapeutics; Toronto, ON, Canada — Apr 2025 – Now
- Develop and apply machine learning for antibody design and property optimization, including protein language models, structure-prediction and generative models, and active learning.
- Lead computational work that supports candidate screening, developability assessment, and hypothesis generation in preclinical discovery.
- Build and maintain discovery platform infrastructure—workflow automation, research tooling, and production pipeline improvements.
- Partner with experimental scientists and cross-functional teams on library design, in vitro result interpretation, and data-driven decision-making.
- ML Researcher, Neurooptic Dx; Toronto, ON, Canada — Sep 2024 – Mar 2025
- Contract-based consulting.
- Developed computer-vision and time-series models on facial video and micro eye movement data to estimate intoxication and impairment (patent pending).
- Managed three junior developers in building a machine learning pipeline for neurodiagnostic research.
- Junior AI Researcher, Denti.AI; Toronto, ON, Canada — Apr 2020 – Apr 2021
- Building algorithms for projecting 3D computer tomography scans to 2D panoramic images.
- Developing computer vision models for automated diagnostics from X-ray dental images and heuristic algorithms to improve AI predictions.
- Research Intern, Menten.AI; San Francisco, CA (Remote) — Dec 2019 – Dec 2020
- Benchmarking of classical vs. quantum combinatorial optimization methods for strategic decisions on technology adoption.
- Implementing GPU-accelerated combinatorial optimization algorithms.
- Development of an automated pipeline for drug target identification based on protein database.
- Graduate Research Assistant, University of Toronto; Toronto, ON, Canada — Sept 2017 – Sept 2024
- Delivering conference presentations and university lectures on advanced computational physics.
- Developing computational and ML pipelines for analysis of protein structural data, resulting in peer-reviewed publications.
- Running molecular simulations of complex protein systems (enzymes, cancer proteins) aimed to understand structure-dynamics-function paradigm.
- Graduate Research and Teaching Assistant, University of Massachusetts Lowell; Lowell, MA, USA — Sept 2015 – May 2017
- ML analysis of the simulated data to find the critical parameters of the dynamic process.
- Developing a CUDA-accelerated scientific software package for simulating microtubule dynamics, a critical chemotherapeutic target (peer-reviewed publication).
- Research Assistant, Moscow Institute of Physics and Technology; Moscow, Russia — Sept 2014 – May 2015
- Bioinformatics analysis of protein databases to extract clusters of protein contacts.
- Developing multiscale computational models of fibrin oligomers.
Publications
Jack B Maguire, Daniele Grattarola, Vikram Khipple Mulligan, Eugene Klyshko, Hans Melo (2021). "XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers." PLoS computational biology. 9 (17).
Evgenii Kliuchnikov, Eugene Klyshko, Maria S. Kelly, Artem Zhmurov, Ruxandra I. Dima, Kenneth A. Marx, Valeri Barsegov (2022). "Microtubule assembly and disassembly dynamics model: Exploring dynamic instability and identifying features of Microtubules’ Growth, Catastrophe, Shortening, and Rescue." Computational and Structural Biotechnology Journal. 20(1).
E Klyshko, JSH Kim, S Rauscher (2022). "LAWS: Local Alignment for Water Sites — tracking ordered water in simulations." Biophysical Journal. 122 (14), 2871-2883
Christopher J Nunn, Eugene Klyshko, Sid Goyal (2023). "petiteFinder: An automated computer vision tool to compute Petite colony frequencies in bakers yeast." BMC Bioinformatics 24, 50.
Klyshko E, Kim JS-H, McGough L, Valeeva V, Lee E, Ranganathan R, Rauscher S (2024) "Functional protein dynamics in a crystal." Nature Communications 15(1):3244
Talks and Posters
December 01, 2025
Invited talk · 2025 · Northeastern University Toronto, Toronto, ON, Canada — Invited industry–academic session for Northeastern University Toronto students on how generative AI is reshaping drug discovery, ML in biotech, and hybrid AI–experimental workflows.
January 15, 2025
Talk · 2025 · Department of Chemical and Physical Sciences, UTM (CC 3150), Mississauga, ON, Canada — Departmental colloquium on PhD thesis work: water in protein dynamics, allostery, simulations, and ties to structural biology (UTM Chemical & Physical Sciences).
April 27, 2024
Talk · 2024 · University of Toronto (Lash Miller Chemical Laboratories, 80 St. George St.), Toronto, ON, Canada — Talk on computational protein and water dynamics at the 21st Chemical Biophysics Symposium (graduate-led meeting, U of T St. George). [PDF]
July 10, 2023
Mentor · 2023 · Georgia Institute of Technology, Global Learning Center (IHPCSS 2023), Atlanta, GA, USA — Mentor at IHPCSS 2023 (Atlanta) on HPC in life sciences—molecular simulation, data analysis, and biophysical HPC.
May 24, 2023
Poster · 2023 · University of Calgary (MacEwan Hall), Calgary, AB, Canada — Poster on LAWS and ordered water at the BSC 8th annual meeting (Calgary); best poster award. [PDF]
February 19, 2023
Talk · 2023 · San Diego Convention Center, San Diego, CA, USA — Talk on LAWS (allosteric water networks in enzymes) at the BPS 67th annual meeting in San Diego; Biophysical Society travel grant. [PNG]
July 05, 2022
Poster · 2022 · Vancouver Convention Centre, Vancouver, BC, Canada — Poster on equilibrium dynamics in protein crystals and MD, at the WATOC 2022 congress in Vancouver. [PDF]
May 26, 2022
Poster · 2022 · University of Ottawa, Ottawa, ON, Canada — Poster on LAWS and ordered water in protein crystals at the joint BSC 7th annual meeting and IUPAB focused meeting in Ottawa. [PDF]
May 03, 2022
Poster · 2022 · University of Toronto Mississauga, Mississauga, ON, Canada — LAWS poster at the UTM GRC 2022 poster session; best poster award (same work as BSC 2022 in Ottawa later that month). [PDF]
July 20, 2021
Talk · 2021 · Virtual (Canadian Association of Theoretical Chemists, CATC), Online (Canada) — Speed talk on LAWS (local alignment for water sites) and crystallographic water in MD, at the virtual theoretical chemistry summer conference (VSTC3). [PDF]
February 19, 2020
Poster · 2020 · San Diego Convention Center, San Diego, CA, USA — Poster on EF–X, electric-field protein dynamics, and atomistic MD of a PDZ domain in a crystal, at the Biophysical Society annual meeting. [PDF]
July 08, 2019
Talk · 2019 · RIKEN Center, Kobe, Japan — Short contributed talk on research highlights at the International High Performance Computing summer school in Kobe, Japan. [PDF]
May 29, 2019
Poster · 2019 · University of Toronto Mississauga, Kaneff Building, Mississauga, ON, Canada — Poster on dimensionality reduction and conformational states of proteins at the Biophysical Society of Canada annual meeting (UTM). [PDF]
May 06, 2019
Workshop Poster · 2019 · McGill University, New Residence Hall, Montreal, QC, Canada — Workshop poster at the Physics and AI workshop, connecting ML with physical modeling. [PDF]
May 01, 2019
Talk · 2019 · University of Toronto Mississauga, IB150, Mississauga, Ontario, Canada — Graduate colloquium talk at the UTM research colloquium series on my physics graduate research.
March 05, 2019
Poster · 2019 · Baltimore Convention Center, Baltimore MD, USA — Poster on conformational states, dimensionality reduction, and clustering of protein ensembles at the Biophysical Society annual meeting. [PDF]
May 05, 2018
Poster · 2018 · University of Toronto, Earth Sciences Centre, Toronto, ON, Canada — Poster on protein and biophysics work at the Chemical Biophysics Symposium (U of T).
May 06, 2017
Poster · 2017 · Whitehead Institute, Cambridge MA, USA — Poster on microtubule and mitosis-related modeling at the 4th BAMM meeting in Cambridge, MA. [PDF]
May 07, 2016
Poster · 2016 · Whitehead Institute, Cambridge MA, USA — Poster on multiscale microtubule dynamics and mesoscale modeling at the BAMM regional cell-division meeting. [PDF]
Teaching
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