Computational Biology Lab - Zespół Biologii Obliczeniowej IPI PAN

List of Selected Publications

2023

• Roura, Adria-Jaume, Paulina Szadkowska, Katarzyna Poleszak, Michal J. Dabrowski, Aleksandra Ellert-Miklaszewska, Kamil Wojnicki, Iwona A. Ciechomska, Karolina Stepniak, Bozena Kaminska, and Bartosz Wojtas. "Regulatory networks driving expression of genes critical for glioblastoma are controlled by the transcription factor c-Jun and the pre-existing epigenetic modifications." Clinical Epigenetics 15, no. 1 (2023): 29.
• Gupta, Ankur, Pawel Krupa, Oskar Engberg, Magdalena Krupa, Ankur Chaudhary, Mai Suan Li, Daniel Huster, and Sudipta Maiti. "Unusual Robustness of Neurotransmitter Vesicle Membranes against Serotonin-Induced Perturbations." The Journal of Physical Chemistry B 127, no. 9 (2023): 1947-1955.
• Rivas-Carrillo, Salvador Daniel, Evgeny E. Akkuratov, Hector Valdez Ruvalcaba, Angel Vargas-Sanchez, Jan Komorowski, Daniel San-Juan, and Manfred G. Grabherr. "MindReader: Unsupervised Classification of Electroencephalographic Data." Sensors 23, no. 6 (2023): 2971.

2022

• Garbulowski, Mateusz, Karolina Smolinska, Uğur Çabuk, Sara A. Yones, Ludovica Celli, Esma Nur Yaz, Fredrik Barrenäs, Klev Diamanti, Claes Wadelius, and Jan Komorowski. "Machine learning-based analysis of glioma grades reveals Co-enrichment." Cancers 14, no. 4 (2022): 1014.
• Yones, Sara A., Alva Annett, Patricia Stoll, Klev Diamanti, Linda Holmfeldt, Carl Fredrik Barrenäs, Jennifer RS Meadows, and Jan Komorowski. "Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data." Scientific Reports 12, no. 1 (2022): 7433.
• Sieradzan, Adam K., Cezary Czaplewski, Paweł Krupa, Magdalena A. Mozolewska, Agnieszka S. Karczyńska, Agnieszka G. Lipska, Emilia A. Lubecka et al. "Modeling the structure, dynamics, and transformations of proteins with the UNRES force field." Protein folding: Methods and protocols (2022): 399-416.

2021

• Karolina Stępniak, Magdalena A. Machnicka, Jakub Mieczkowski1, Anna Macioszek, Bartosz Wojtaś, Bartłomiej Gielniewski, Katarzyna Poleszak, Malgorzata Perycz, Sylwia K. Król, Rafał Guzik, Michał J. Dąbrowski, Michał Dramiński, Marta Jardanowska, Ilona Grabowicz, Agata Dziedzic, Hanna Kranas, Karolina Sienkiewicz, Klev Diamanti, Katarzyna Kotulska, Wiesława Grajkowska, Marcin Roszkowski, Tomasz Czernicki, Andrzej Marchel, Jan Komorowski, Bozena Kaminska and Bartek Wilczyński „Mapping chromatin accessibility and active regulatory elements reveals new pathological mechanisms in human gliomas”, Nature Communications 12, 3621 (2021). https://doi.org/10.1038/s41467-021-23922-2
• Grabowicz, I. E., Wilczyński, B., Kamińska, B., Roura, A. J., Wojtaś, B., & Dąbrowski, M. J. (2021). The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes. Scientific reports, 11(1), 1-15.
• Cavalli, M., Diamanti, K., Pan, G., Dabrowski, M. J., Komorowski, J., & Wadelius, C. (2021). A non-coding cancer mutation disrupting an HNF4α binding motif affects an enhancer regulating genes associated to the progression of liver cancer. Experimental Oncology, 43(1), 2-6.
• Gutkowska, Małgorzata, Magdalena Kaus‐Drobek, Marta Hoffman‐Sommer, Magdalena Małgorzata Pamuła, Anna Daria Leja, Małgorzata Perycz, Małgorzata Lichocka et al. "Impact of C‐terminal truncations in the Arabidopsis Rab escort protein (REP) on REP–Rab interaction and plant fertility." The Plant Journal (2021).

2020

• Teisseyre, Paweł, Jan Mielniczuk, and Michał J. Dąbrowski. "Testing the Significance of Interactions in Genetic Studies Using Interaction Information and Resampling Technique." In International Conference on Computational Science, pp. 511-524. Springer, Cham, 2020.
• Krupa, P., Karczyńska, A. S., Mozolewska, M. A., Liwo, A., & Czaplewski, C. (2020). UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations. Bioinformatics.
• Diamanti, K., Visvanathar, R., Pereira, M. J., Cavalli, M., Pan, G., Kumar, C., ... & Ahlström, H. (2020). Integration of whole-body [18 F] FDG PET/MRI with non-targeted metabolomics can provide new insights on tissue-specific insulin resistance in type 2 diabetes. Scientific reports, 10(1), 1-9.

2019

• Michal J. Dabrowski and Bartosz Wojtas. (2019). Global DNA Methylation Patterns in Human Gliomas and Their Interplay with Other Epigenetic Modifications. Special Issue of Epigenetics in Metabolic and Neurological Disorders. 20(14). 3478. (ISSN 1422-0067).
• Michal J. Dabrowski, Agata Dziedzic, Rafal Guzik, Michal Draminski, Bartosz Wojtas, Karolina Stepniak, Bartlomiej Gielniewski, Jacek Koronacki, Bozena Kaminska. (2019).Genome-wide mapping of DNA methylation variants affecting gene expression levels in gliomas with respect to their grade and IDH gene mutation status. 'Biology of Genomes' conference, Cold Spring Harbor Laboratory, 7-11.05.2019. Poster.
• Bartosz Wojtas, Michal J. Dabrowski, Agata Dziedzic, Michal Draminski, Rafal Guzik, Karolina Stepniak, Bartlomiej Gielniewski, Tomasz Czernicki, Pawel Nauman, Bartosz Czapski, Wieslawa Grajkowska, Katarzyna Kotulska, Bozena Kaminska. (2019). Mapping genome-wide DNA methylation patterns in gliomas in context of IDH gene mutation status and REST transcription factor binding. 'Biology of Genomes' conference, Cold Spring Harbor Laboratory, 7-11.05.2019.

2018

• Draminski M., Koronacki J. (2018). rmcfs: An R Package for Monte Carlo Feature Selection and Interdependency Discovery. Journal of Statistical Software vol. 85(12), doi:10.18637/jss.v085.i12.
• Dabrowski M.J., Draminski M., Diamanti K., Stepniak K., Mozolewska M.A., Teisseyre P., Koronacki J., Komorowski J., Kaminska B. & Wojtas B. (2018). Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival. Scientific Reports vol. 8, Article number: 4390, doi:10.1038/s41598-018-22829-1.

2017

• Draminski M., Koronacki J. (2017). rmcfs: An R Package for Monte Carlo Feature Selection and Interdependency Discovery. Accepted for publication in Journal of Statistical Software. Available as a vignette to rmcfs package.
• Karczyńska, A. S., Czaplewski, C., Krupa, P., Mozolewska, M. A., Joo, K., Lee, J., & Liwo, A. (2017). Ergodicity and model quality in template‐restrained canonical and temperature/Hamiltonian replica exchange coarse‐grained molecular dynamics simulations of proteins. Journal of computational chemistry, 38(31), 2730-2746.
• Ahmed, L., Rasulev, B., Kar, S., Krupa, P., Mozolewska, M. A., & Leszczynski, J. (2017). Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purpose. Nanoscale, 9(29), 10263-10276.
• Baltzer, N., Sundström, K., Nygård, J. F., Dillner, J., & Komorowski, J. (2017). Risk Stratification in Cervical Cancer Screening by Complete Screening History–Applying Bioinformatics to a General Screening Population. International Journal of Cancer.
• Koronacki, J., Dramiński, M. (2017). Empirical Model Building Revisited. Models and Reality: Festschrift for James Robert Thompson, Chicago, IL: T&NO Company.

2016

• Umer, H. M., Cavalli, M., Dąbrowski, M. J., Diamanti, K., Kruczyk, M., Pan, G., ... & Wadelius, C. (2016). A Significant Regulatory Mutation Burden at a High‐Affinity Position of the CTCF Motif in Gastrointestinal Cancers. Human mutation, 37(9), 904-913.
• Khaliq, Z., Leijon, M., Belák, S., & Komorowski, J. (2016). Identification of combinatorial host-specific signatures with a potential to affect host adaptation in influenza A H1N1 and H3N2 subtypes. BMC genomics, 17(1), 529.
• Diamanti, K., Umer, H. M., Kruczyk, M., Dąbrowski, M. J., Cavalli, M., Wadelius, C., & Komorowski, J. (2016). Maps of context-dependent putative regulatory regions and genomic signal interactions. Nucleic acids research, gkw800.
• Moghadam, B. T., Dąbrowski, M., Kamińska, B., Grabherr, M. G., & Komorowski, J. (2016). Combinatorial identification of DNA methylation patterns over age in the human brain. BMC bioinformatics, 17(1), 393.
• Bornelöv, S., & Komorowski, J. (2016). Selection of Significant Features Using Monte Carlo Feature Selection. In Challenges in Computational Statistics and Data Mining (pp. 25-38). Springer International Publishing.
• Dramiński, M., Dąbrowski, M. J., Diamanti, K., Koronacki, J., & Komorowski, J. (2016). Discovering networks of interdependent features in high-dimensional problems. In Big Data Analysis: New Algorithms for a New Society (pp. 285-304). Springer International Publishing.
• Mozolewska, M. A., Krupa, P., Zaborowski, B., Liwo, A., Lee, J., Joo, K., & Czaplewski, C. (2016). Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field. Journal of Chemical Information and Modeling, 56(11), 2263-2279.
• Krupa, P., Mozolewska, M. A., Wiśniewska, M., Yin, Y., He, Y., Sieradzan, A. K., ... & Ślusarz, R. (2016). Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. Bioinformatics, 32(21), 3270-3278.
• Nowakowska, E., Koronacki, J., & Lipovetsky, S. (2016). Dimensionality reduction for data of unknown cluster structure. Information Sciences, 330, 74-87.
• Dramiński, M. (2016). ADX Algorithm for Supervised Classification. In Challenges in Computational Statistics and Data Mining (pp. 39-52). Springer International Publishing.

2015

• Bornelöv, S., Komorowski, J., & Wadelius, C. (2015). Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription. BMC genomics, 16(1), 300.
• Khaliq, Z., Leijon, M., Belák, S., & Komorowski, J. (2015). A complete map of potential pathogenicity markers of avian influenza virus subtype H5 predicted from 11 expressed proteins. BMC microbiology, 15(1), 128.
• Dąbrowski, M. J., Bornelöv, S., Kruczyk, M., Baltzer, N., & Komorowski, J. (2015). ‘True’null allele detection in microsatellite loci: a comparison of methods, assessment of difficulties and survey of possible improvements. Molecular ecology resources, 15(3), 477-488.
• Nowakowska, E., Koronacki, J., & Lipovetsky, S. (2015). Clusterability assessment for Gaussian mixture models. Applied Mathematics and Computation, 256, 591-601.