CH. 01 / ABOUT

Mateusz Jaskolowski, PhD.

Postdoctoral Fellow · University of Cambridge · SNSF Postdoc Mobility Fellow

I design and screen synthetic nanobody libraries for diverse protein targets, including challenging membrane proteins, combining structural biology, phage display, and machine learning. I also bring long-standing, end-to-end cryo-EM experience, from grid preparation and microscope operation to data collection, processing, model building, and structural analysis.

Portrait of Mateusz Jaskolowski, outdoors in warm afternoon light.
FIG. 1: Outdoor Portrait · 2024

§ Gdańsk · Education

I grew up in Poland and studied biotechnology at the Intercollegiate Faculty of Biotechnology, jointly run by the University of Gdańsk and the Medical University of Gdańsk. That is where I first encountered proteins as objects you could study, build, and redesign. The interest stuck.

§ Chicago · Early Training

The Kossiakoff lab at the University of Chicago was where I first worked full-time in research, completing the practical part of my MSc as a research assistant. I spent just over a year raising synthetic Fabs against the Ebola virus nucleoprotein by phage display and solving crystal structures of the resulting complexes. The work produced a US patent and my first publications.

§ Zürich · Doctoral Work

During nine years at ETH Zürich in Nenad Ban's group, I worked first as a PhD student and then as a postdoc, mostly at the cryo-electron microscope. The focus was the mitochondrial ribosome and its assembly, the human ribosome, and the cotranslational factors that act on each protein while it is still emerging from the exit tunnel.

§ Cambridge · Current

Since October 2024 I have been at the University of Cambridge on an SNSF Postdoc Mobility Fellowship, split between Paul Miller's group (Pharmacology) and Pietro Sormanni's (Chemistry). By analysing large collections of nanobody sequences, I identify patterns associated with stability and developability, then build and use a sequence-level model to design a set of three next-generation synthetic nanobody libraries for phage-display discovery.

§ Outlook

I want to connect library design, experimental discovery, and structural biology more tightly, so that a useful binder becomes not just a hit, but a tool for understanding how a protein works.

§ Outside the Lab

I read fantasy and science fiction, cycle, and train at the gym. I am also slowly writing a fantasy novel. In fiction, the experiments always work.

Current Focus
  • Sequence-informed design of nanobody libraries
  • Models for nanobody structure and CDR conformation prediction
  • Phage-display discovery of nanobodies against membrane-protein targets
  • Experimental and computational integration
At a Glance
~12
Years in research
4
Countries
13
Publications
1
Patent
Current Affiliations
  • Miller Group, Dept. of Pharmacology
  • Sormanni Group, Dept. of Chemistry
Current Funding
  • SNSF Postdoc Mobility Fellowship
CH. 02 / INVESTIGATIONS

Research.

Cryo-EM Phage Display Protein Engineering Membrane-Protein Biochemistry Applied Machine Learning
IV
Computational Nanobody Engineering
2024–present · University of Cambridge
Sequence-informed design of three next-generation synthetic nanobody libraries for phage-display discovery, applicable to both soluble and membrane-protein targets. In parallel, I contribute to a nanobody structure-prediction project that began with self-distillation and was later extended with sequence- and disulphide-encoded conformational priors.
Current open-source tool: NbFrame →
III
Cotranslational Protein Processing
2021–2024 · ETH Zürich, Ban Lab
Separate cryo-EM studies of ribosome complexes with TRAP, NAC, MetAP1, NatD, and the N-myristoylation machinery. Together, these factors shape protein fate during synthesis.
Representative paper: TRAP complex in ER protein biogenesis →
II
Ribosome Architecture & Biogenesis
2015–2021 · ETH Zürich, Ban Lab
Cryo-EM studies of mitochondrial large-subunit biogenesis, human ribosome assembly intermediates, and trypanosomal mitoribosome structure.
Representative paper: mitoribosomal maturation →
I
Synthetic Fabs Against Ebola
2014–2015 · University of Chicago, Kossiakoff Lab
Phage-display-derived synthetic Fabs against the Ebola virus nucleoprotein, alongside early contributions to structure-guided antibody engineering.
Patent →
CH. 03 / OPEN-SOURCE WORK

Open-source work.

NbFrame
Python 3.10+ Apache-2.0 PyPI
Predict whether a nanobody's CDR3 is kinked or extended from sequence alone.

NbFrame is a lightweight Python library for nanobody CDR3 conformation classification. Given an amino-acid sequence, it predicts loop geometry: kinked versus extended, without requiring a 3D structure.

View on GitHub
CH. 04 / PUBLICATIONS

Selected work.

A selected record of structural biology, protein engineering, and computational nanobody work. An asterisk denotes equal contribution.

Selected Peer-Reviewed Work
Mechanism of cotranslational modification of histones H2A and H4 by MetAP1 and NatD. StructuralPeer-reviewed
Yudin, D., Jaskolowski, M.*, Fan, Z., et al.
Science Advances 11 · 2025 · DOI
NAC controls cotranslational N-terminal methionine excision in eukaryotes. StructuralPeer-reviewed
Gamerdinger, M., Jia, M., Schloemer, R., Rabl, L., Jaskolowski, M., et al.
Science · 2023 · DOI
Molecular basis of the TRAP complex function in ER protein biogenesis. StructuralPeer-reviewed
Jaskolowski, M.*, Jomaa, A., Gamerdinger, M., et al.
Nature Structural & Molecular Biology · 2022 · DOI
Structural Insights into the Mechanism of Mitoribosomal Large Subunit Biogenesis. StructuralPeer-reviewed
Jaskolowski, M.*, Ramrath, D.J.F., Bieri, P., et al.
Molecular Cell · 2020 · DOI
Current Methods Work
Disulphide and sequence-encoded conformational priors guide nanobody structure prediction. MethodsPreprint
Ali, M., Jaskolowski, M., Greenig, M., et al.
bioRxiv · 2026 · View preprint
Improving nanobody structure prediction with self-distillation. MethodsConference
Ali, M., Greenig, M., Jaskolowski, M., et al.
NeurIPS 2025 · MLSB Workshop · bioRxiv
Patents
Recombinant antibodies that recognize the C-terminal domains of Ebola virus nucleoprotein. PatentActive
Derewenda, Z.S., Engel, D.A., Kossiakoff, A., Davydova, E.K., Jaskolowski, M.
US Patent 10,640,549 B2 · 2020 · Google Patents

Full publication record: Google Scholar · ORCID.

CH. 05 / TIMELINE

Journey.

2024–present
Cambridge, United Kingdom
Postdoctoral Fellow, SNSF Postdoc Mobility Fellow
Designing three synthetic nanobody libraries from scratch with ML. The libraries support discovery against soluble and membrane-protein targets; my current phage-display work focuses on the latter. Miller group (Pharmacology) and Sormanni group (Chemistry).
2015–2024
Zürich, Switzerland
PhD Student → Postdoctoral Researcher, Ban Lab, ETH Zürich
Nine years at the cryo-electron microscope. Mitoribosome assembly, human ribosome biogenesis, and the cotranslational machinery that processes each protein as it comes out of the ribosome.
2014–2015
Chicago, United States
Master's Research, Kossiakoff Lab, University of Chicago
Synthetic antibodies against the Ebola virus nucleoprotein, raised by phage display. One US patent and my first publications came out of those fourteen months.
Sep–Dec 2013
Glasgow, United Kingdom
Erasmus Exchange, University of Glasgow
One semester on Erasmus at the start of the MSc. First time studying abroad. It turned out not to be the last.
2010–2015
Gdańsk, Poland
BSc + MSc Biotechnology, Intercollegiate Faculty of Biotechnology
Where I first got interested in proteins, and where I started working in a lab.
Pre-2010
Ciechanów, Poland
Home town
A small town in northern Mazovia, about ninety kilometres north of Warsaw. The place where I grew up and went to school.
CH. 06 / GET IN TOUCH

Contact.

I welcome research collaborations, speaking invitations, and conversations about protein discovery. For selected industry work, the consulting address is the quickest route.

General Contact
Dr. Mateusz Jaskolowski
Miller Group, Department of Pharmacology
University of Cambridge
Tennis Court Road
Cambridge CB2 1PD, United Kingdom
Consulting
I take on selected projects with biotech and pharmaceutical teams, including nanobody and antibody discovery, computational library design, ML integration, cryo-EM workflows, and structure-driven design.