Papers

2026
Uncovering Cas9 PAM diversity through metagenomic mining and machine learning
Tao Fang, Lea Bogensperger, Lilith Feer, Ahmed Allam, Valentyn Bezshapkin, Zsolt Balázs, Christian von Mering, Shinichi Sunagawa, Michael Krauthammer, Gerald Schwank
Nature Communications
2026-02-08
Summary: We expanded the known diversity of Cas9 protospacer adjacent motifs, increasing the range of adressable genomic targets in CRISPR-Cas9 based genome editing.
My Role: Assembled and preprocessed expanded phage dataset, which contained more than 50% of protospacer adjacent motifs used in downstream analysis.
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2025
Scikit-bio: a fundamental Python library for biological omic data analysis
Matthew Aton, Daniel McDonald, Jorge Cañardo Alastuey, Raeed Azom, Paarth Batra, Valentyn Bezshapkin, Evan Bolyen, Alexander Cagle, J Gregory Caporaso, Justine W Debelius, Kestrel Gorlick, Nirmitha Hamsanipally, Lars Hunger, Aryan Keluskar, Disen Liao, Yang Young Lu, Jose A Navas-Molina, Anders Pitman, Jai Ram Rideout, Anton Sazonov, Bharath Sathappan, Karen Schwarzberg Lipson, Igor Sfiligoi, Chris Tapo, Yoshiki Vázquez-Baeza, Zijun Wu, Zhenjiang Zech Xu, Mingsong Sam Ye, Jianshu Zhao, Rob Knight, James T Morton, Qiyun Zhu
Nature Methods
2025-12-11
Summary: Developed multi-platform Python package for omics data analysis, installed 1.5M times worldwide.
My Role: Contributed to the development of the package in 2024-2025, provided training materials and tutorials for the package.
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2024
Predictors of outcomes of patients ≥ 80 years old admitted to intensive care units in Poland – a post-hoc analysis of the VIP2 prospective observational study
Paweł Melchior Pasieka, Michał Kurek, Wojciech Skupnik, Evan Skwara, Valentyn Bezshapkin, Jakub Fronczek, Anna Kluzik, Bartosz Kudliński, Szymon Białka, Dorota Studzińska
Anaesthesiology Intensive Therapy
2024-03-29
Summary: We identified frailty and frailty-related phenotypes as significant predictors of mortality in elderly ICU patients, highlighting the need for early frailty assessment in geriatric critical care.
My Role: Developed and implemented statistical methodology to analyze prospective clinical data and interpret results.
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Determinants of the microbiome spatial variability in chronic rhinosinusitis
J Szaleniec, Valentyn Bezshapkin, A Krawczyk, K Kopera, B Zapała, T Gosiewski, T Kosciolek
Rhinology
2024-02-01
Summary: We demonstrated that the middle nasal meatus is not universally representative of the sinus microbiome in chronic rhinosinusitis, as sampling site heterogeneity is patient-specific and cannot be predicted from ostial patency. The lack of identifiable driving factors suggests a revision of current treatment strategies.
My Role: Developed and implemented analysis pipeline in QIIME 2. Evaluated, interpreted and visualized results in the manuscript. Co-authored a grant proposal for further research, awarded 500,000 USD in funding.
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2023
Diagnostic accuracy of bimanual palpation in bladder cancer patients undergoing cystectomy: A prospective study
Anna K Czech, Katarzyna Gronostaj, Jakub Fronczek, Jakub Frydrych, Valentyn Bezshapkin, Mikolaj Przydacz, Przemyslaw Dudek, Lukasz Curylo, Tomasz Wiatr, Jerzy Gasowski, Piotr L Chlosta
Urologic Oncology: Seminars and Original Investigations
2023-05-03
Summary: We demonstrated that bimanual palpation remains a valuable diagnostic tool in bladder cancer, demonstrating 80% accuracy in T-staging of cancer.
My Role: Developed a statistical methodology to analyze prospective clinical data and interpret diagnostic concordance metrics.
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Comprehensive functional annotation of metagenomes and microbial genomes using a deep learning-based method
Mary Maranga, Pawel Szczerbiak, Valentyn Bezshapkin, Vladimir Gligorijevic, Chris Chandler, Richard Bonneau, Ramnik J Xavier, Tommi Vatanen, Tomasz Kosciolek
mSystems
2023-04-27
Summary: We advanced functional understanding of the human gut microbiome by developing a deep learning-integrated metagenomic workflow that achieved 99% gene annotation coverage across a 1.9M gene catalogue.
My Role: Engineered an HPC-optimized bioinformatics pipeline to automate de novo genome reconstruction and functional profiling, and contributed to data analysis, interpretation and visualization.
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2022
Treatment with multi-species probiotics changes the functions, not the composition of gut microbiota in postmenopausal women with obesity: a randomized, double-blind, placebo-controlled study
Mariusz Kaczmarczyk, Monika Szulińska, Igor Łoniewski, Matylda Kręgielska-Narożna, Karolina Skonieczna-Żydecka, Tomasz Kosciolek, Valentyn Bezshapkin, Paweł Bogdański
Frontiers in Cellular and Infection Microbiology
2022-03-11
Summary: We evaluated probiotic treatment response in postmenopausal women with obesity, highlighting that the composition of gut microbiota does not change after probiotic intervention and its composition does not predict treatment response. However, the statistical power of the study was limited.
My Role: Conducted amplicon sequencing data processing and analysis, applied statistical methods to evaluate the impact of probiotic intervention.
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