Pawel Rubach – Researcher in Computer Science & Structural Bioinformatics

Biography

I am both a researcher and a practitioner. Throughout my career I have worked for or collaborated with several institutions.

Universities: Warsaw School of Economics (SGH) (alma mater) , Warsaw University of Technology , University of Warsaw , Texas Tech University , University of Virginia
NGOs: Stowarzyszenie Harcerskie , Stowarzyszenie 61 , Vicariato San Jose del Amazonas (Peru)
Banks: PKO Bank Polski
Telecommunications & R&D: Telekomunikacja Polska S.A. (Orange) , France Telecom R&D
Private sector: IGS Investment Fund , SMT Software , Scanway S.A.
Government: U.S. Air Force Research Laboratory

Research focus

My work focuses on developing and applying advanced computing — distributed systems, Big Data and AI — to both science and practical applications. Earlier in my career, via the employment at TP S.A. and then during my Fulbright scholarship at Texas Tech University, I had been involved in working with engineers and computer scientists developing modeling environments that integrate engineering tools and applications. As part of these activities, I contributed to the development of the SORCER project .

Since 2018 I have focused on computational methods for structural biology, in particular, on applying distributed computing and Big Data technologies to structural bioinformatics and the exploration of non-trivial protein topologies. I collaborate with Joanna Sulkowska’s Lab at the University of Warsaw and Wladek Minor Laboratory at the University of Virginia.

In my free time I love to travel and explore the world. I realize this often in collaboration with: ADVFactory.com (Krzysztof Samborski) and Przygody4x4

Education

Ph.D. in Computer Science (Distributed Computing), Warsaw University of Technology, 2010. Dissertation: Optimal Resource Allocation in Federated Metacomputing Environments .
Master of Science, Warsaw School of Economics (SGH), Quantitative Methods & Information Systems, 2003. Thesis: Komputerowe metody testowania wiedzy (Computerized Methods for Knowledge Testing) . Supervisor: Dr. Anna Rokicka-Broniatowska.
Specialization in Business Informatics, SGH.
Postgraduate Pedagogical Studies, SGH.

Employment / Academic Positions

Assistant Professor, SGH, Institute of Information Systems and Digital Economy (from 2003), 2003–2011 as Assistant.
Collaborator, Laboratory of Modeling of Biological Systems, Center for New Technologies, University of Warsaw (from 2018).
Postdoctoral Research Associate, University of Virginia, Charlottesville, USA (May 2024 – June 2025).
Fulbright Visiting Scholar, Texas Tech University, Lubbock, Texas, USA (Aug 2008 – May 2009).

Spoken Languages

🇵🇱 Polish • 🇬🇧 English • 🇪🇸 Spanish • 🇫🇷 French • 🇩🇪 German • 🇷🇺 Russian • 🇮🇹 Italian • 🇵🇹 Portuguese

Research Projects

AlphaKnot 2.0

Server & database for entanglement analysis in AlphaFold-predicted protein models.

AlphaLasso

Database of proteins with lasso-type motifs in AlphaFold models.

KnotProt 2.0

Database of proteins with knots, slipknots and knotoids.

Genus

Database of genus characteristics for proteins and RNA chains.

Topoly

Python package for polymer topology analysis — computing knot/link invariants.

Horda

Documentation of the HORDA computing cluster at CeNT, UW (Joanna Sulkowska's Group).

LSSCB

Documentation of the LSSCB computing cluster at CeNT, UW (Bartosz Trzaskowski's Group).

$Protein Diffraction logo$

Protein Diffraction

Integrated Resource for Reproducibility in Macromolecular Crystallography.

BioReproducibility

Interactive figures for structural biology research papers published at Minor Lab.

Important Links

Institute of Information Systems and Digital Economy (SGH)

Sułkowska Lab

Minor Lab

Publications

Download a list of my publications in the BIB format here

Teaching / Courses

Category: Teaching Coordination Teach + Coord Course taught personally / course only coordinated / both taught and coordinated.

Level: Bachelor / Master / Unified Until 2006 SGH offered only unified long-cycle studies which were later replaced with the current 2-cycle system.

Authorship: Authored indicates that the course and its content were originally created and proposed by me sometimes with the help of a team of colleagues from my Insitute.