Kinga Zielińska, Klas I Udekwu, Witold Rudnicki, Alina Frolova, Paweł P Łabaj, Healthy microbiome—moving towards functional interpretation, GigaScience, Volume 14, 2025, giaf015, https://doi.org/10.1093/gigascience/giaf015 Abstract Background Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often…
New paper in Research in Autism!
J. Karwowska, A. Polewko-Klim, B. Panasiuk, B. Stasiewicz-Jarocka, A. Tafazoli, E. Dobrowolska, K. Jarząbek, R. Posmyk, N. Wawrusiewicz-Kurylonek. Replication of rs10099100 Association with Autism Spectrum Disorder Risk in a Polish‐Origin Cohort. Research in Autism (Research in Autism Spectrum Disorders) 123 (2025), 202542. DOI: 10.1016/j.reia.2025.202542 Abstract Background The genetic basis of autism spectrum disorders (ASD) remains unidentified and unclear. The aim of our study was to conduct replication analyses of previously…
New paper in Frontiers in Genetics!
Brizola Toscan R, Lesiński W, Stomma P, Subramanian B, Łabaj PP and Rudnicki WR (2025) Antimicrobial resistance in diverse urban microbiomes: uncovering patterns and predictive markers. Front. Genet. 16:1460508. doi: 10.3389/fgene.2025.1460508 Antimicrobial resistance (AMR) is a growing global health concern, driven by urbanization and anthropogenic activities. This study investigated AMR distribution and dynamics across microbiomes from six U.S. cities, focusing on resistomes, viromes, and mobile genetic elements (MGEs). Using metagenomic…
New paper!
P. Stomma, W. R. Rudnicki. HCS—hierarchical algorithm for simulation of omics datasets, Bioinformatics, Volume 40, Issue Supplement_2, September 2024, Pages ii98–ii104, https://doi.org/10.1093/bioinformatics/btae392 Analysis of the omics data with the help of machine learning (ML) methods is limited by small sample sizes and a large number of variables. One possible approach to deal with such data is using algorithms for feature selection and reducing the dataset to include only those variables…
New paper!
Lesiński, W., Golińska, A.K., Rudnicki, W.R. (2024). Modelling of Drug-Induced Liver Injury with Multiple Machine Learning Algorithms. In: Nguyen, NT., et al. Advances in Computational Collective Intelligence. ICCCI 2024. Communications in Computer and Information Science, vol 2166. Springer, Cham. https://doi.org/10.1007/978-3-031-70259-4_33 Motivation: Drug-induced liver injury (DILI) is one of the primary problems in drug development. The current study aims to build predictive models using the physical and chemical properties of compounds causing DILI….
New paper!
Polewko-Klim, A., Grablis, P., Rudnicki, W. (2024). EnsembleFS: an R Toolkit and a Web-Based Tool for a Filter Ensemble Feature Selection of Molecular Omics Data. In: Franco, L., de Mulatier, C., Paszynski, M., Krzhizhanovskaya, V.V., Dongarra, J.J., Sloot, P.M.A. (eds) Computational Science – ICCS 2024. ICCS 2024. Lecture Notes in Computer Science, vol 14835. Springer, Cham. https://doi.org/10.1007/978-3-031-63772-8_7 The development of more complex biomarker selection protocols based on the machine learning (ML) approach, with additional processing of…
New paper in International Journal of Molecular Sciences!
R. Piliszek, A. A. Brożyna, W. R. Rudnicki. Computational Analysis Identifies Novel Biomarkers for High-Risk Bladder Cancer Patients. International Journal of Molecular Sciences 23.13: 7057 (2022), DOI: 10.3390/ijms23137057 (140 pkt. MNiSzW) In the case of bladder cancer, carcinoma in situ (CIS) is known to have poor diagnosis. However, there are not enough studies that examine the biomarkers relevant to CIS development. Omics experiments generate data with tens of thousands of…
New paper in Frontiers in Genetics!
Polewko-Klim A, Zhu S, Wu W, Xie Y, Cai N, Zhang K, Zhu Z, Qing T, Yuan Z, Xu K, Zhang T, Lu M, Ye W, Chen X, Suo C and Rudnicki WR. Identification of Candidate Therapeutic Genes for More Precise Treatment of Esophageal Squamous Cell Carcinoma and Adenocarcinoma. Frontiers in Genetics 2022 13:844542. doi: 10.3389/fgene.2022.844542 The standard therapy administered to patients with advanced esophageal cancer remains uniform, despite its…
New paper!
Moszczuk, B.; Krata, N.; Rudnicki, W.; Foroncewicz, B.; Cysewski, D.; Pączek, L.; Kaleta, B.; Mucha, K. Osteopontin—A Potential Biomarker for IgA Nephropathy: Machine Learning Application. Biomedicines 2022, 10, 734. https://doi.org/10.3390/biomedicines10040734 Abstract Many potential biomarkers in nephrology have been studied, but few are currently used in clinical practice. One is osteopontin (OPN). We compared urinary OPN concentrations in 80 participants: 67 patients with various biopsy-proven glomerulopathies (GNs)—immunoglobulin A nephropathy (IgAN, 29),…
New paper in Cells!
M. Pac, N. Krata, B. Moszczuk, A. Wyczałkowska-Tomasik, B. Kaleta, B. Foroncewicz, W. Rudnicki, L. Pączek,K. Mucha NR3C1 Glucocorticoid Receptor Gene Polymorphisms Are Associated with Membranous and IgA Nephropathies Cells 2021, 10(11), 3186 https://doi.org/10.3390/cells10113186 Abstract: Glomerular diseases (GNs) are responsible for approximately 20% of chronic kidney diseases. Glucocorticoid receptor gene (NR3C1) single nucleotide polymorphisms (SNPs) are implicated in differences in predisposition to autoimmunity and steroid sensitivity. The aim of this…
New paper in Frontiers in Genetics!
W. Lesiński, K. Mnich, W.R. Rudnicki. Prediction of alternative Drug Induced Liver Injury classifications using molecular descriptors, gene expression perturbation, and toxicology reportsFrontiers in Genetics 12:661075 (2021), DOI: 10.3389/fgene.2021.661075 (100 pkt. MNiSzW) Motivation: Drug-induced liver injury (DILI) is one of the primary problems in drug development. Early prediction of DILI, based on the chemical properties of substances and experiments performed on cell lines, would bring a significant reduction in the…
New paper in Journal of Medical Systems!
A. Polewko-Klim, K. Mnich, W.R. Rudnicki. Robust Data Integration Method for Classification of Biomedical Data. Journal of Medical Systems 45(4):45 (2021), DOI: 10.1007/s10916-021-01718-7 (100 pkt. MNiSzW) Wczesna diagnoza jest kluczowa dla wyboru i zwiekszenia skuteczność leczenia nowotworów. W niniejszej pracy, wykorzystując szereg zaawansowanych metod uczenia maszynowego, przedstawiliśmy i porównaliśmy różne modele predykcyjne, w tym model hybrydowy, których celem jest określanie klinicznego punktu końcowego pacjenta (KPKP) na podstawie danych klinicznich i…
New paper in Biology Direct!
W. Lesiński, K. Mnich, A. Kitlas Golińska, W.R. Rudnicki. Integration of human cell lines gene expression and chemical properties of drugs for Drug Induced Liver Injury prediction. Biology Direct 16:2 (2021). DOI: 0.1186/s13062-020-00286-z (100 pkt. MNiSzW) Motivation Drug-induced liver injury (DILI) is one of the primary problems in drug development. Early prediction of DILI can bring a significant reduction in the cost of clinical trials. In this work we examined…
Our new paper is out!
A. Polewko-Klim, W. Lesiński, A. Kitlas Golińska, K. Mnich, M. Siwek, W. R. Rudnicki. Sensitivity analysis based on the Random Forest machine learning algorithm identifies candidate genes for regulation of innate and adaptive immune response of chicken. Poultry Science 99 (2020), 12, 6341-6354. DOI: 10.1016/j.psj.2020.08.059 (140 pkt. MNiSzW) Spożywanie zdrowej żywności m.in. produktów drobiarskich ma wielkie znaczenie dla zdrowia ludzi. Zwalczanie chorób drobiu to jeden z największych problemów jego producentów….