Lab
Members
Research Team Leader
Tomasz obtained his M.Sc. in chemistry from Jagiellonian University in 2010 and a PhD in biological sciences from University College London (UK) in 2016. In years 2016-2019 he was a post-doctoral research associate in Rob Knight’s group at University of California San Diego (USA) and 2019-2022 was a group leader in bioinformatics at the Małopolska Centre of Biotechnology, Jagiellonian University in Kraków. He is working on the development and application of computational methods to better understand the function and dynamics of the human gut microbiome. He has contributed to the development of a suite of tools commonly used in microbiome analyses – QIIME 2 and Qiita – and he is also working on state-of-the-art machine learning and statistical methods to predict protein function (deepFRI) or to model the dysbiosis and dynamics of the microbiome. The goal of his group is to build a multi-level understanding of the microbiome from genes, through structures, to functions and therapies.
Postdoctoral Researchers
Rund Tawfiq earned her Ph.D. in Bioengineering from King Abdullah University of Science and Technology (KAUST) in 2025. Her research focuses on developing computational methods for protein function prediction and applying them to biological data. She is particularly interested in functional representations of biological samples and building bioinformatics tools that enable practical applications.
He obtained a BSc degree in computational & medical physics at Lodz University of Technology, Poland in 2011. His thesis was devoted to semiconductor lasers modelling. He completed his MSc and PhD degrees in theoretical physics at the University of Warsaw, Poland in 2013 and 2018, respectively. His research was focused on cosmology and particle physics. Both theses concerned dark matter in several extensions of the Standard Model of particle physics. Between 2016 and 2018, he supervised a scientific grant “Preludium” from National Science Center titled: “Models of Hot Dark Matter and their phenomenological consequences”. Between 2019 and 2023 he worked as a postdoctoral research associate in Structural and Functional Genomics lab at Małopolska Centre of Biotechnology. Since 2024 he is a postdoctoral researcher in dr Tomasz Kościółek’s research group at Sano.
His current research focus is on methods for protein structure and function prediction with special emphasis on their computational side. In general, he is interested in utilizing mathematical and machine learning techniques in science.
He received a Master’s in Bioinformatics and defended his doctoral degree in biomedical engineering at Wrocław University of Science and Technology. During his Ph.D. he developed bioinformatic tools for the identification of amyloidogenic regions in proteins as well as the first method for the prediction of amyloid interactions. He also studied amyloids in the human microbiome and their connection to the onset of neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. His research involves the development and application of state-of-the-art bioinformatic algorithms on large data sets, as well as the use of Machine learning approaches for biological big data
Adam Sułek earned his Ph.D. in Chemistry from the Jagiellonian University in 2022. His interdisciplinary research was conducted in collaboration with the Lukasiewicz Research Network – Kraków Institute of Technology and the Faculty of Mathematics and Computer Science at the Jagiellonian University. Adam’s research interests include molecular processes in tumor proliferation, computer-aided drug design, and structural biology.
Currently, he is working on a project that examines cell cycle dysregulation, specifically involving BRCA and CDK, which leads to uncontrolled cell proliferation. Another of his projects focuses on understanding protein thermostability and exploring the use of Protein Language Models in this field.
Students
Filip received a Bachelor’s Degree in Medical Biotechnology at Medial University of Silesia and a Master’s in Bioinformatics at Jagiellonian University in Kraków. During his Master’s, he worked with RNA-seq data, focusing on research reproducibility and in silico noise. Currently, he is engaged in research trying to uncover biological roles of proteins from the human gut microbiome by using state-of-the-art computational approaches. Passionate about synthetic biology, Filip was part of the JU-Krakow iGEM team that achieved First Runner-Up in 2024, where the team developed advanced detection methods for harmful golden algae.
Research Staff
Piotr is a computer scientist and data scientist with an interdisciplinary background in cognitive science and philosophy (PhD). At Sano, he supports the microbiomeGPT project by developing tools for metagenomic data processing, model training and evaluation. His research interests include computational intelligence, optimization methods, and the interdisciplinary (primarily logical) aspects of negation.
Sylwia holds a Bachelor’s and Master’s degree in Bioinformatics at the Jagiellonian University. Her Master’s thesis focused on the quantitative analysis of endogenous single-strand DNA breaks in mouse somatic and germ cells. In years 2023 – 2025, Sylwia served as the president of the Association of Bioinformatics Students In Silico and was the main organizer of the BioMeeting 2025 Conference. She is also the co-founder of the Bioinformatics Community PL organization, where she actively organizes meet-ups and other initiatives for bioinformatics professionals and enthusiasts eager to share knowledge, experience, and ideas about the future of this rapidly evolving field. Her main research interests are human microbiome studies and its impact on health and disease.