Katarzyna (Kasia) Sidorczuk

Academic CV and research profile of Katarzyna (Kasia) Sidorczuk, a BioGenies collaborator.

Biography

Hi! My name is Katarzyna Sidorczuk and I’m a bioinformatician interested in gut microbiome and use of machine learning for analysis of biological data.

During my PhD I worked with BioGenies and created multiple tools for prediction of peptide activity and protein localization. This led us to the work on negative data sampling for AMP prediction in which we showed that commonly used strategies introduce significance bias and leads to unreliable benchmarks.

Currently, I’m a postdoc in the Hildebrand group at the Quadram Institute, where I work with strain-resolved metagenomics. I’m interested in evolution of gut microbiota, how microbes are transferred between family members, and what are the factors that contribute to successful colonization and persistence.

Contact

Email GitHub ORCID

Conferences, workshops and training

13 conference and training events

2024-09-11 – 2024-09-13

Symposium of the Polish Bioinformatics Society

Warsaw, Poland
Talks, posters & participation (1)
  • Talk

    Strain-resolved metagenomics in analysis of gut microbiota dynamics within families

ECCB

2022-09-18 – 2022-09-21

European Conference on Computational Biology

Sitges, Spain
Talks, posters & participation (1)

  • Where do they come from, where do they go? Prediction of protein subplastid localization and origin with PlastoGram

ESCS

2022-09-18

European Student Council Symposium

Sitges, Spain
Talks, posters & participation (1)

  • Where do they come from, where do they go? Prediction of protein subplastid localization and origin with PlastoGram

Earlier activities (10)
2022 1
GCB

2022-09-06 – 2022-09-08

German Conference on Bioinformatics

Halle (Salle), Germany
Talks, posters & participation (1)

  • Where do they come from, where do they go? PlastoGram: a stacked model for prediction of protein subplastid localization and origin

2021 1
EYSF

2021-10-21 – 2021-10-22

EMBO Young Scientists' Forum (EYSF)

Warsaw, Poland
Talks, posters & participation (1)
  • Poster

    CancerGram: How to differentiate anticancer from antimicrobial peptides?

2020 2
IBID

2020-10-28 – 2020-10-29

International Biotech Innovation Days

Senftenberg, Germany
Talks, posters & participation (1)
  • Poster

    Prediction of antimicrobial peptides with AmpGram

DSS

2020-10-16

Data Science Summit

Warsaw, Poland
Talks, posters & participation (1)

  • Reproducible analytic workflows in R with drake and renv

2019 3

2019-09-26 – 2019-09-29

Why R? Conference

Warszawa, Poland
Talks, posters & participation (1)
  • Talk

    PepBay: Implementation of Bayesian inference in the analysis of peptide arrays

2019-09-19 – 2019-09-21

Symposium of the Polish Bioinformatics Society

Cracow, Poland
Talks, posters & participation (1)

  • In silico identification and phylogeny of components responsible for protein import into thylakoids of Paulinella photosynthetic species

SatRday

2019-05-17 – 2019-05-18

Conference for users of the R Language

Gdańsk, Poland
Talks, posters & participation (1)
  • Talk

    Bayesian inference in big data analysis

2018 3
PL in ML

2018-12-14 – 2018-12-17

Polish View on Machine Learning

Warsaw, Poland
Talks, posters & participation (1)
  • Poster

    PepBay: a Bayesian framework for analysis of peptide arrays

2018-09-05 – 2018-09-07

Symposium of the Polish Bioinformatics Society

Wrocław, Poland
Talks, posters & participation (1)
  • Poster

    Two protein import pathways into the cyanobacteria-derived, photosynthetic organelles of Paulinella chromatophora

IBID

2018-05-23 – 2018-05-25

International Biotech Innovation Days

Senftenberg, Germany
Talks, posters & participation (1)
  • Poster

    Protein import into the chromatophores of Paulinella photosynthetic species

Publications

29 publications listed · most recent first

Effect of dietary chickpea structures on the small intestine metabolome and microbiome: a randomised crossover trial

Nature Communications · 2026-09-15

Authors & citation details

Nadia J. Fernandes, Mingzhu Cai, Frederick J. Warren, Anthony Duncan, José Iván Serrano-Contreras, Katarzyna Sidorczuk, Andrés Bernal, Andrés Bernal, Katerina Petropoulou, Natalia Pérez‐Moral, Isabel García‐Pérez, Cathrina H. Edwards, Elaine C. Holmes, Julien Wist, Gary Steven Frost

Authorship: coauthor

https://doi.org/10.1038/s41467-026-77714-7
Earlier publications (26)
2026 4
Copper is an intestinal habitat filter affecting the gut microbiota interactions with Salmonella Typhimurium

Microbiome · 2026-03-28

Authors & citation details

Rafał Kolenda, Marwa M. Hassan, Ainhoa Arrieta-Gisasola, Rebecca Ansorge, Katarzyna Sidorczuk, Luke Acton, Gaetan J. A. Thilliez, Dave Baker, Michał Jan Burdukiewicz, Mark D. Stares, Hilary P. Browne, Gwénaëlle Le Gall, Mark P. Stevens, Trevor D. Lawley, Andreas J. Bäumler, Roberto La Ragione, Falk Hildebrand, Robert A. Kingsley

Authorship: coauthor

https://doi.org/10.1186/s40168-025-02322-4
Additional file 3 of Copper is an intestinal habitat filter affecting the gut microbiota interactions with Salmonella Typhimurium

Figshare · 2026-03-28

Authors & citation details

Rafał Kolenda, Marwa M. Hassan, Ainhoa Arrieta-Gisasola, Rebecca Ansorge, Katarzyna Sidorczuk, Luke Acton, Gaetan J. A. Thilliez, Dave Baker, Michał Jan Burdukiewicz, Mark D. Stares, Hilary P. Browne, Gwenaelle Le Gall, Mark P. Stevens, Trevor D. Lawley, Andreas J. Bäumler, Roberto La Ragione, Falk Hildebrand, Robert A. Kingsley

Authorship: coauthor

https://doi.org/10.6084/m9.figshare.31969200
2025 7
2024 2
2023 4
2022 2
2021 3
2020 3
2018 1