2025

• K. Zielińska, K. I Udekwu, W. Rudnicki, A. Frolova, P. P. Łabaj. Healthy microbiome—moving towards functional interpretation, GigaScience, Volume 14, 2025, giaf015, https://doi.org/10.1093/gigascience/giaf015J.
• 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
• Brizola Toscan R, Lesiński W, Stomma P, Subramanian B, Łabaj PP and Rudnicki WR. Antimicrobial resistance in diverse urban microbiomes: uncovering patterns and predictive markers. Front. Genet. 16:1460508 (2025). doi: 10.3389/fgene.2025.1460508

2024

• 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
• W. Lesiński, A. Kitlas Golińska, W.R. Rudnicki. 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
• A. Polewko-Klim, P. Grablis, W. Rudnicki. 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

2023

• T. Niksa-Rynkiewicz, P. Stomma, A. Witkowska, D. Rutkowska, A. Słowik, K. Cpałka, J. Jaworek-Korjakowska, P. Kolendo. An Intelligent Approach to Short-Term Wind Power Prediction Using Deep Neural Networks. Journal of Artificial Intelligence and Soft Computing Research 13.3 (2023): 197-210.
• S. Gluch, T. Niksa-Rynkiewicz, D.Mikielewicz, P. Stomma. Application of Feed Forward Neural Networks for Modeling of Heat Transfer Coefficient During Flow Condensation for Low and High Values of
  Saturation Temperature”, DOI: 10.52202/069564-0036, 36th International Conference on Efficiency, Cost, Optimization, Simulation and Environmental Impact of Energy Systems (ECOS 2023), 25-30 June 2023, Las Palmas de Gran Canaria, Spain
• A. Tafazoli J. Mikros, F. Khaghani, M. Alimardani, M. Rafigh, M.
  Hemmati, S. Siamoglou, A. Kitlas Golińska, K. A. Kamiński. W. Miltyk,
  G. P. Patrinos. Pharmacovariome scanning using whole pharmacogene resequencing coupled with deep computational analysis and machine learning for clinical pharmacogenomics. Human Genomics 17, 62 (2023) (100 pkt. MEiN)
• A.Tafazoli, A. Kitlas Golińska, K. Mnich, A. Amirabadizadeh, J.C. Marquez, W. Miltyk. Toward Integration of Pharmacogenomic Tests into Daily Clinical Practice: A General Survey for Polish Healthcare Workers. Medical Science Monitor 2023; 29: e940119-1–e940119-8 DOI: 10.12659/MSM.940119 (140 pkt. MEiN)
• W. Lesiński, W. Rudnicki. A Robust Machine Learning Protocol for Prediction of Prostate Cancer Survival at Multiple Time-Horizons. In: Mikyška, J., de Mulatier, C., Paszynski, M., Krzhizhanovskaya, V.V., Dongarra, J.J., Sloot, P.M. (eds) Computational Science – ICCS 2023. ICCS 2023. Lecture Notes in Computer Science, vol 10475. Springer, Cham. https://doi.org/10.1007/978-3-031-36024-4_12 (140 pkt. MEiN)

2022

• 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. MEiN)
• A. Polewko-Klim, S. Zhu, W. Wu, Y. Xie, N. Cai, K. Zhang, Z. Zhu, T. Qing, Z. Yuan, K. Xu, T. Zhang, M. Lu, W. Ye, X. Chen, C. Suo, W.R. Rudnicki. Identification of Candidate Therapeutic Genes for More Precise Treatment of Esophageal Squamous Cell Carcinoma and Adenocarcinoma. Frontiers in Genetics 13:844542 (2022). DOI: 10.3389/fgene.2022.844542 (100 pkt. MEiN)
• B. Moszczuk, N. Krata, W. Rudnicki, B. Foroncewicz, D. Cysewski, L. Pączek, B. Kaleta, K. Mucha. Osteopontin—A Potential Biomarker for IgA Nephropathy: Machine Learning Application. Biomedicines 10: 734 (2022), DOI: 10.3390/biomedicines10040734 (100 pkt. MEiN)

2021

• 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 10(11): 3186 (2021), DOI: 10.3390/cells10113186 (140 pkt. MEiN)
• W. Lesiński, K. Mnich, W.R. Rudnicki. Prediction of alternative Drug Induced Liver Injury classifications using molecular descriptors, gene expression perturbation, and toxicology reports Frontiers in Genetics 12:661075 (2021), DOI: 10.3389/fgene.2021.661075 (100 pkt. MEiN)

• 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. MEiN)
• 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. MEiN)

2020

• K. Mnich, A. Polewko-Klim, A. Kitlas Golińska, W. Lesiński, W. R. Rudnicki, Super Learning with Repeated Cross Validation, 2020 International Conference on Data Mining Workshops (ICDMW), Sorrento, Italy, 2020, pp. 629-635, DOI: 10.1109/ICDMW51313.2020.00089
• 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)
• A. Kitlas Golińska, W. Lesiński, A. Przybylski, W. R. Rudnicki. Towards Prediction of Heart Arrhythmia Onset Using Machine Learning. In: Krzhizhanovskaya V. et al. (eds) Computational Science – ICCS 2020 . ICCS 2020. Lecture Notes in Computer Science 12140 (2020), 376-389. Springer, Cham. DOI: 10.1007/978-3-030-50423-6_28 (140 pkt. MNiSzW)
• K. Mnich, A. Kitlas Golińska, A. Polewko-Klim, W.R. Rudnicki. Bootstrap Bias Corrected Cross Validation Applied to Super Learning. In: Krzhizhanovskaya V. et al. (eds) Computational Science – ICCS 2020 . ICCS 2020. Lecture Notes in Computer Science 12139 (2020), 550-563. Springer, Cham. DOI: 10.1007/978-3-030-50420-5_41 (140 pkt. MNiSzW)
• A. Polewko-Klim, W. R. Rudnicki. Analysis of Ensemble Feature Selection for Correlated High-Dimensional RNA-Seq Cancer Data. In: Krzhizhanovskaya V. et al. (eds) Computational Science – ICCS 2020. ICCS 2020. Lecture Notes in Computer Science 12139 (2020), 525-538. Springer, Cham. DOI: 10.1007/978-3-030-50420-5_39 (140 pkt. MNiSzW)
• A. Polewko-Klim, W. R. Rudnicki. Data Integration Strategy for Robust Classification of Biomedical Data. In: Rocha Á., Adeli H., Reis L., Costanzo S., Orovic I., Moreira F. (eds) WorldCIST 2020: Trends and Innovations in Information Systems and Technologies . Advances in Intelligent Systems and Computing 1160 (2020), 596-606. Springer, Cham. DOI: 10.1007/978-3-030-45691-7_56 (20 pkt. MNiSzW)
• W. Lesiński, A. Polewko-Klim, W. R. Rudnicki. Identification of Clinical Variables Relevant for Survival Prediction in Patients with Metastatic Castration-Resistant Prostate Cancer. In: Rocha Á., Adeli H., Reis L., Costanzo S., Orovic I., Moreira F. (eds) WorldCIST 2020: Trends and Innovations in Information Systems and Technologies. Advances in Intelligent Systems and Computing 1160 (2020), 607-617. Springer, Cham. DOI: 10.1007/978-3-030-45691-7_57 (20 pkt. MNiSzW)
• K. Mnich, W.R. Rudnicki. All-relevant feature selection using multidimensional filters with exhaustive search. Information Sciences 524 (2020), 277-297. DOI: 10.1016/j.ins.2020.03.024 (200 pkt. MNiSzW)
• W.R. Rudnicki, R. Piliszek. Estimate of Covid-19 prevalence using imperfect data. (2020) medRxiv DOI: 10.1101/2020.04.14.20064840
• K. Niedzielewski, M.E. Marchwiany, R. Piliszek, M. Michalewicz, W. Rudnicki. Multidimensional Feature Selection and High Performance ParalleX. SN Computer Science 1 (2020), 1, 40. DOI: 10.1007/s42979-019-0037-5

2019

• among others: A. Golińska, W. Lesiński, A. Polewko-Klim, W. Rudnicki.
  Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach.
  Scientific Reports 9 (2019), 1-14. DOI: 10.1038/s41598-018-36873-4 (140 pkt. MNiSzW)
• M. Wrzesień, W. Treder, K. Klamkowski, W. Rudnicki.
  Prediction of the apple scab using machine learning and simple weather stations. Computers and Electronics in Agriculture 161 (2019), 252-259.
  DOI :  10.1016/j.compag.2018.09.026 (100 pkt. MNiSzW)
• R. Piliszek, K. Mnich, Sz. Migacz, P. Tabaszewski, A. Sułecki, A. Polewko-Klim, W. Rudnicki. MDFS: MultiDimensional Feature Selection in R. R Journal 11 (2019), 1, 198-210. DOI :  10.32614/RJ-2019-019 (100 pkt. MNiSzW)
• Sz. Migacz, K. Dutka, P. Gumienny, M. Marchwiany, D. Gront, W. Rudnicki. Parallel Implementation of a Sequential Markov Chain in Monte Carlo Simulations of Physical Systems with Pairwise Interactions. Journal of Chemical Theory and Computation 15 (2019), 5, 2797-2806. DOI :  10.1021/acs.jctc.8b01168 (140 pkt. MNiSzW)
• O. Aleksandrowicz, E. Brzosko, J. Kotowicz, B. Ostrowiecka, I. Tałałaj, A. Wróblewska. Spontaneous caudicle reconfiguration in Dactylorhiza fuchsii: A new self‑pollination mechanism for Orchideae. Plant Systematics and Evolution 305 (2019), 4, 269-280. DOI : 10.1007/s00606-019-01570-w (70 pkt. MNiSzW)
• E. Brzosko, E. Jermakowicz, A. Kostro-Ambroziak, J. Kotowicz, J. Kuprjanowicz, A. Lasoń, Ł. Mielczarek, P. Mirski, B. Ostrowiecka, I. Tałałaj, A. Wróblewska. Pollinators and visitors of the generalized food-deceptive orchid Dactylorhiza majalis in North-Eastern Poland. Biologia 74 (2019), 10, 1247-1257. DOI : 10.2478/s11756-019-00285-0 (40 pkt. MNiSzW)

2018

• M. L. Chodkiewicz, Sz. Migacz, W. Rudnicki, A. Makal, J. A. Kalinowski, N. W. Moriarty, R. W. Grosse-Kunstleved, P. Anfonine, P. D. Adams, P. M. Dominiak. DiSCaMB: a software library for aspherical atom model X-ray scattering factors calculations with CPU and GPU. Journal of Applied Crystallography 51 (2018), part 1, 193-199. DOI:  10.1107/S1600576717015825 (40 pkt. MNiSzW – nowe 100)
• A. Polewko-Klim, W. Lesiński, K. Mnich, R. Piliszek, W. Rudnicki. Integration of multiple types of genetic markers for neuroblastoma may contribute to improved prediction of the overall survival. Biology Direct 13 (2018), 1-22. DOI :  10.1186/s13062-018-0222-9 (35 pkt. MNiSzW – nowe 100)

2017

• among others: A. Golińska, W. Lesiński, A. Polewko-Klim, W. Rudnicki. Predicting human olfactory perception from chemical features of odor molecules. Science 355 (2017), 6327, 820-826. http://science.sciencemag.org/content/sci/suppl/2017/02/17/science.aal2014.DC1/Keller_SM.pdf. DOI: 10.1126/science.aal2014 (50 pkt. MNiSzW)
• among others: A. Golińska, W. Lesiński, A. Polewko-Klim, W. Rudnicki. Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data. Lancet Oncology 18 (2017), 1, 132-142. DOI: 10.1016/S1470-2045(16)30560-5 (50 pkt. MNiSzW)
• among others: A. Golińska, W. Lesiński, A. Polewko-Klim, W. Rudnicki. A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer. JCO Clinical Cancer Informatics 1 (2017), 1-15. DOI: 10.1200/CCI.17.00018
• among others: W. Rudnicki. A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. Cell Systems 5 (2017), 5, 485-497. DOI: 10.1016/j.cels.2017.09.004
• M. Bolesta, E. Brzosko, A. Gromotowicz, M. Gromotowicz, J. Kotowicz,  A. Orzechowska, J. Orzołek, B. Ostrowiecka, M. Wojdalska.Seed dispersal in six species of terrestrial orchids in Biebrza  National Park (NE Poland). Acta Societatis Botanicorum Poloniae 86 (2017), 3, 1-14. DOI :  10.5586/asbp.3557 (25 pkt. MNiSzW)
• E. Brzosko, E. Jermakowicz, J. Kotowicz, A. Wróblewska. Genetic diversity of orchid Malaxis monophyllos over Europen range as  an effect of population properties and postglacial colonization. Polish Journal of Ecology 65 (2017), 1, 69-86. DOI :  10.3161/15052249PJE2017.65.1.007 (15 pkt. MNiSzW)
• P. Mirski, E. Brzosko, I. Jędrzejczyk, J. Kotowicz, B. Ostrowiecka, A.  Wróblewska. Genetic structure of dioecious and trioecious Salix myrsinifolia  populations at the border of geographic range. Tree Genetics & Genomes 13 (2017), 1, 1-16. DOI :  10.1007/s11295-016-1096-6 (35 pkt. MNiSzW)

2016

• P. Trędak, W. Rudnicki, J. A. Majewski. Efficient implementation of the many-body Reactive Bond Order (REBO) potential on GPU. Journal of Computational Physics 321 (2016), 556-570. DOI: 10.1016/j.jcp.2016.05.061 (45 pkt. MNiSzW)

• W. Paja, M. Wrzesień, R. Niemiec, W. Rudnicki. Application of all-relevant feature selection for the failure analysis of parameter-induced simulation crashes in climate models. Geoscientific Model Development 9 (2016), 3, 1065-1072. DOI: 10.5194/gmd-9-1065-2016 (45 pkt. MNiSzW)