Curriculum Vitae

· 4 min read

About Me

Passionate computational biologist working at the intersection of computer and life sciences. Enthusiast of using computational methods to solve complex biological problems.

Education

PhD in Computational Biology

École Polytechnique Fédérale de Lausanne (EPFL) | 2024-Present

  • PhD student in Laboratory of Protein and Cell Engineering (Barth Group)
  • Designing optogenetic therapy for vision restoration and de novo design of light-gated ion channels

MSc in Biotechnology

University of Gdańsk & Medical University of Gdańsk | 2021-2023

  • Thesis: Designing and studying physicochemical properties of peptides and peptidomimetics blocking PD-1/PD-L1 complex formation (Liwo Lab)
  • Master’s joint studies at the Intercollegiate Faculty of Biotechnology of UG & MUG
  • Graduated with the highest result (bardzo dobry)

BSc in Biotechnology

University of Gdańsk & Medical University of Gdańsk | 2018-2021

  • Thesis: Extending the functionality of the PyMOL plugin with the ability to simulate the dynamics of small molecules
  • Bachelor’s joint studies at the Intercollegiate Faculty of Biotechnology of UG & MUG
  • Graduated with the highest result (bardzo dobry)

Experience

Partnerships Officer

Polonium Foundation | 2023-

  • Volunteer connecting and promoting Polish scientists abroad
  • Co-organizer of ’Science: Polish Perspectives’ events in Berkeley, Paris and Milan

Bioinformatics Analyst

Oklahoma Medical Research Foundation | 2022-2024

  • Developing large-scale gene expression meta-analysis software (Wren Lab)
  • Polish-U.S. Fulbright Commission BioLAB Program

Intern

University of Cambridge | 2021

  • Internship at the Yusuf Hamied Department of Chemistry (Wales Group)
  • Combining the functionality of the UNRES and OPTIM software

Graduate Research Associate

University of Gdańsk | 2021-2022

  • Investigator in the project financed by Polpharma Scientific Foundation
    • Designing peptides and peptidomimetics acting as potential inhibitors of PD-1/PD-L1 complex formation
  • Investigator in the project financed by Polish National Science Centre
    • Introducing lipids to the coarse-grained UNRES force field by adapting potentials from the MARTINI force field

Microbiology Analyst

J.S. Hamilton Poland Sp. z o.o. | 2020-2022

  • Performing microbiological analyses in accordance with ISO/IEC 17025 standards

Research Articles

  1. Winnicki M.J. et al. “Biovdb: biological vector database for high-throughput gene expression meta-analysis”, Frontiers in Artificial Intelligence (2024)
  2. Wesołowski P. A. et al. “Energy landscapes for proteins described by the UNRES coarse-grained potential”, Biophysical Chemistry (2023)
  3. Bojko M. et al. “Design, synthesis and biological evaluation of PD-1 derived peptides as inhibitors of PD-1/PD-L1 complex formation for cancer therapy”, Bioorganic Chemistry (2022)
  4. Antoniak A. et al. “Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino-Acid Side Chains with lipids I. Aliphatic amino acids” (in preparation)

Presentations

AI revolution in protein structure prediction

Talk, Invited Speaker | Oklahoma Data Science Workshop | June 28, 2024 | Oklahoma City, OK, USA

  • Michał J. Winnicki

Exploring Earth’s Aerobiome Through Similarity Search Analysis

Poster | 2024 Galaxy Community Conference (GCC2024) | June 27, 2024 | Brno, Czech Republic

  • Michał J. Winnicki, Julia Jakiela, Anita Brzoza, Kacper Dudczak, Krystian Latos, Anna Lewkowicz, Barbara Szaflarska, Aleksander Szymczak

Designing and studying physicochemical properties of peptides and peptidomimetics blocking PD-1/PD-L1 complex formation

Talk | 13th Biotechnology Student’s Conference | June 7, 2024 | Gdańsk, Poland

  • Michał J. Winnicki

BioVDB: biological vector database for high-throughput gene expression meta-analysis

Poster | Oklahoma Geroscience Symposium 2023, Oklahoma Nathan Shock Center of Excellence | April 3, 2023 | Oklahoma City, OK, USA

  • Michał J. Winnicki, Chase A. Brown, Hunter L. Porter, Cory B. Giles, Jonathan D. Wren

BioVDB: biological vector database for high-throughput gene expression meta-analysis

Talk | MidSouth Computational Biology and Bioinformatics Society (MCBIOS 2023), University of Dallas | March 15, 2023 | Dallas, TX, USA

  • Michał J. Winnicki, Chase A. Brown, Hunter L. Porter, Cory B. Giles, Jonathan D. Wren

UNRES-MARTINI

Poster | 8th Polish-Korean Conference on Protein Folding | September 25, 2023 | Jastrzębia Góra, Poland

  • Anna M. Antoniak, Łukasz Dziadek, Paweł Krupa, Patryk A. Wesołowski, Michał J. Winnicki, Victoria Bielecki, Pamela Smardz, Agnieszka G. Lipska, Artur Giełdoń, Daria Heleniak, Aleksandra Drozd, Adam K. Sieradzan

Skills

Hard Skills

  • UNIX environment
  • Coarse-grained simulations (MARTINI, UNRES), All-atom simulations (Amber), QM calculations (Gaussian software), Schrödinger software (PyMOL)
  • AlphaFold, RoseTTaFold
  • PyTorch, Scikit-Learn, Docker
  • Python, R, Fortran 90/95

Soft Skills

  • Teamwork, Communication
  • Critical thinking, Problem-solving

Honors & Awards

  • 2023: QIAGEN Gdańsk Conference Award
  • 2023: MCBIOS Young Scientist Excellence Award
  • 2022-2024: Fulbright BioLAB Program stipend
  • 2022-2023: Mentee in elite BioLAB Mentoring Program
  • 2020-2021: The University of Gdańsk Rector’s scholarship

Memberships

  • MidSouth Computational Biology and Bioinformatics Society (MCBIOS)
  • Polish Astrobiology Society
  • Fulbrighter Network
  • Polonium Network
  • Boost Biotech Poland

Certificates

  • Mass Spectrometry (LabExperts): Course on the LC/MS system, including PCA analysis
  • Good Clinical Practice (Soft Communication): Standard ICH GCP E6 (R2)

Languages

  • Polish: Native
  • English: Fluent

Contact