Publications

Bartosz Wilczyński

Number of publications: 46

2024

• Irina Tuszynska, Paweł Bednarz, Bartosz Wilczyński , Effective modeling of the chromatin structure by coarse-grained methods, Journal of Biomolecular Structure and Dynamics, 2024, p. 1-9. See in PBN

2021

• Marlena Osipowicz, Bartosz Wilczyński , Magdalena Machnicka , Careful feature selection is key in classification of Alzheimer’s disease patients based on whole-genome sequencing data, NAR Genomics and Bioinformatics, 3 (3) 2021, p. 1-8. See in PBN
• Anna Macioszek, Bartosz Wilczyński , HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data, International Journal of Molecular Sciences, 22 (15) 2021, p. 8123:1-13. See in PBN
• Hanna Kranas, Bartosz Wilczyński , Irina Tuszyńska, HiCEnterprise: identifying long range chromosomal contacts in Hi-C data, PeerJ, 9 2021, p. e10558: 1-9. See in PBN
• Kinga Szyman, Bartosz Wilczyński , MICHAŁ DĄBROWSKI, K-mer Content Changes with Node Degree in Promoter–Enhancer Network of Mouse ES Cells, International Journal of Molecular Sciences, 22 (15) 2021, p. 8067:1-15. See in PBN
• Karolina Stępniak, Magdalena Machnicka , Jakub Mieczkowski, Anna Macioszek, Bartosz Wojtaś, Bartłomiej Gielniewski, Katarzyna Poleszak, Małgorzata Perycz, sylwia Król, Rafał Guzik, Michał Dąbrowski, Michał Dramiński, Marta Jardanowska, Ilona Grabowicz, Agata Dziedzic, Hanna Kranas, Karolina Sienkiewicz, Klev Diamanti, Katarzyna Kotulska-Jóźwiak, Wiesława Grajkowska, Marcin Roszkowski, Tomasz Czernicki, Andrzej Marchel, Henryk Komorowski, Bożena Kamińska-Kaczmarek, Bartosz Wilczyński , Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas, Nature Communications, 12 (1) 2021, p. 1-17. See in PBN
• Ilona Grabowicz, Bartosz Wilczyński , Bożena Kamińska-Kaczmarek, Adria-Jaume Roura, Bartosz Wojtaś, Michał Dąbrowski, 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) 2021, p. 1-15. See in PBN

2020

• Clémence Réda, Bartosz Wilczyński , Automated inference of gene regulatory networks using explicit regulatory modules, Journal of Theoretical Biology, 486 2020, p. 110091:1-110091:53. See in PBN
• Bartłomiej Zawalski, Bartosz Wilczyński , Irina Tuszyńska, QChromosomeVisualizer: A new tool for 3D visualization of long simulations of polymer-like chromosome models, Methods, 181-182 2020, p. 80-85. See in PBN

2019

• Bartosz Wilczyński , Rafał Zaborowski, BPscore: An Effective Metric for Meaningful Comparisons of Structural Chromosome Segmentations, Journal of Computational Biology, 26 (4) 2019, p. 305-314. See in PBN

2018

• Agnieszka Kikulska, Tobias Rausch, Ewa Krzywinska, Magdalena Pawlak, Bartosz Wilczyński , Vladimir Benes, Tomasz Wilanowski, Piotr Rutkowski, Coordinated expression and genetic polymorphisms in Grainyhead-like genes in human non-melanoma skin cancers, BMC Cancer, 18 (23) 2018, p. 1-12. See in PBN
• Alina Frolova, Bartosz Wilczyński , Distributed Bayesian networks reconstruction on the whole genome scale, PeerJ, 6 (e5101) 2018, p. 1-20. See in PBN
• Henri Niskanen, Irina Tuszyńska, Rafał Zaborowski, Merja Heinäniemi, Seppo Ylä-Herttuala, Bartosz Wilczyński , Minna U Kaikkonen, Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions, Nucleic Acids Research, 46 (4) 2018, p. 1724–1740. See in PBN
• I. De Toma, Ilona Grabowicz, M Fructuoso, D. Trujillano, Bartosz Wilczyński , M Dierssen, Overweighed mice show coordinated homeostatic and hedonic transcriptional response across brain, eNeuro, 5 (6) 2018, p. e0287-18.2018 1–15. See in PBN

2017

• Rafał Archacki, Ruslan Yatusevich, Daniel Buszewicz, Katarzyna Krzyczmonik, Jacek Patryn, Roksana Iwanicka-Nowicka, Przemysław Biecek , Bartosz Wilczyński , Marta Koblowska, Andrzej Jerzmanowski, Szymon Świeżewski, Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression., Nucleic Acids Research, 45 (6) 2017, p. 3116–3129. See in PBN
• Magdalena Pawlak, Agnieszka Kikulska, Tomasz Wrzesinski, Tobias Rausch, Zbigniew Kwias, Bartosz Wilczyński , Vladimir Benes, Joanna Wesoły, Tomasz Wilanowski, Potential protective role of Grainyhead-like genes in the development of clear cell renal cell carcinoma, Molecular Carcinogenesis, 56 2017, p. 2414-2423. See in PBN
• Michal Wlasnowolski, Bartosz Wilczyński , Julia Herman-Iżycka, Taking promoters out of enhancers in sequence based predictions of tissue-specific mammalian enhancers, BMC Medical Genomics, 10 (1) 2017, p. 34-34. See in PBN

2016

• Jerzy Tiuryn , Bartosz Wilczyński , FastBill: An Improved Tool for Prediction of Cis-Regulatory Modules, Journal of Computational Biology, 2016. See in PBN

2015

• Katarzyna Żmuda, Jõesaar Indrek, Katarzyna Laskowska-Kaszub, Anna Fogtman, Hannes Kollist, Szymon Świeżewski, Paweł Siedlecki, Krzysztof Ginalski, Bartosz Wilczyński , Łukasz Kniżewski, Andrzej Jerzmanowski, Piotr Zielenkiewicz, Rafał Archacki, Marta Koblowska, Kinga Rutowicz, Marcin Puzio, Joanna Halibart-Puzio, Maciej Lirski, Magdalena Kroteń, Bartosz Lange, Katarzyna Śniegowska-Świerk, Janusz Kościelak, Krisztian Buza, Maciej Kotliński, Jerzy Tiuryn , Marcin Rapacz, Franciszek Janowiak, Anna Muszewska, Roksana Iwanicka-Nowicka, A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis., Plant Physiology, 2015. See in PBN
• Rima Mouawad, Bartosz Wilczyński , Yiliang Wei, R. William Henry, David N. Arnosti, SHAMBA MONDAL, Genome-Wide Analysis of Drosophila RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis, G3: Genes, Genomes, Genetics, 2015. See in PBN
• Norbert Dojer , MICHAŁ DĄBROWSKI, Bożena Kamińska, Izabella Krystkowiak, Bartosz Wilczyński , Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data, BMC Bioinformatics, 2015. See in PBN
• Krisztián Buza, Norbert Dojer , Bartosz Wilczyński , RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes, 2015. See in PBN
• Paweł Daniluk, Bogdan Lesyng, Bartosz Wilczyński , WeBIAS: a web server for publishing bioinformatics applications, BMC Research Notes, 2015. See in PBN

2014

• Martina Braun, Lucia Ciglar, Eileen EM Furlong, Charles Girardot, Bartosz Wilczyński , Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis, Development (Cambridge), 2014. See in PBN
• Paweł Bednarz, Bartosz Wilczyński , Supervised learning method for predicting chromatin boundary associated insulator elements, Journal of Bioinformatics and Computational Biology, 2014. See in PBN

2013

• Wiesław Paja, Agnieszka Podsiadlo, Witold Rudnicki, Bartosz Wilczyński , Mariusz Wrzesień, Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data, BMC Systems Biology, 24th International Conference on Genome Informatics (GIW), Singapore, Singapore, 16 December 2013 - 18 December 2013. See in PBN
• Bartosz Wilczyński , Agnieszka Podsiadlo, Wiesław Paja, Witold Rudnicki, Mariusz Wrzesień, Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data, BMC Systems Biology, 7 (Suppl 6) 2013, p. 1-7. See in PBN
• Paweł Bednarz, Norbert Dojer , Agnieszka Podsiadlo, Bartosz Wilczyński , BNFinder2: Faster Bayesian network learning and Bayesian classification, Bioinformatics, 2013. See in PBN

2012

• Paweł Bednarz, Bartosz Wilczyński , Modeling Cell Populations in Development using Individual Stochastic Regulatory Networks, 2012. See in PBN
• Eileen EM Furlong, Ya-Hsin Liu, Bartosz Wilczyński , Zhen-Xuan Yeo, Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State, PLoS Computational Biology, 2012. See in PBN
• Stefan Bonn, Nicolas Delhomme, Eileen E M Furlong, Yad Ghavi-Helm, Charles Girardot, E Hilary Gustafson, Alexis Perez-Gonzalez, Andrew Riddell, Bartosz Wilczyński , Robert P Zinzen, Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development, NATURE GENETICS, 2012. See in PBN

2010

• T.R. Hvidste, Bartosz Wilczyński , A Computer Scientist's Guide to the Regulatory Genome, Fundamenta Informaticae, 2010. See in PBN
• Eileen EM Furlong, Bartosz Wilczyński , Dynamic CRM occupancy reflects a temporal map of developmental progression, Molecular Systems Biology, 2010. See in PBN

2009

• Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Peter J. A. Cock, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartosz Wilczyński , Michiel J. L. de Hoon, Biopython: freely available Python tools for computational molecular biology and bioinformatics., Bioinformatics, 2009. See in PBN
• Norbert Dojer , Bartosz Wilczyński , BNFinder: Exact and efficient method for learning Bayesian networks, Bioinformatics, 2009. See in PBN
• Eileen Furlong, Bartosz Wilczyński , Challenges for modeling global gene regulatory networks during development: Insights from Drosophila, Developmental Biology, 2009. See in PBN
• Norbert Dojer , Mateusz Patelak, Jerzy Tiuryn , Bartosz Wilczyński , Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs, BMC Bioinformatics, 2009. See in PBN

2008

• Bartosz Wilczyński , A stochastic extension of R. Thomas regulatory network modelling, BANACH CENTER PUBLICATIONS, 80 2008, p. 271-276. See in PBN
• Bartosz Wilczyński , A Stochastic Extension of R.Thomas Regulatory Network Modelling, 2008. See in PBN

2007

• Jerzy Tiuryn , Bartosz Wilczyński , Reconstruction of Mammalian Cell Cycle Regulatory Network from Microarray Data using Stochastic Logical Networks, Lecture Notes in Computer Science, 2007. See in PBN

2006

• Norbert Dojer , Anna Gambin , A. Mizera, Jerzy Tiuryn , Bartosz Wilczyński , Applying Dynamic Bayesian Networks to Perturbed Gene Expression Data, BMC Bioinformatics, 2006. See in PBN
• Katarzyna Bozek, Anna Gambin , Jerzy Tiuryn , Bartosz Wilczyński , Automated modelling of genetic control in Arabidopsis thaliana, Journal of Fruit and Ornamental Plant Research, 2006. See in PBN
• Jerzy Tiuryn , Bartosz Wilczyński , Regulatory Network Reconstruction using Stochastic Logical Networks, Lecture Notes in Computer Science, 2006. See in PBN
• K. Fidelis, Tr. Hvidsten, J. Komorowski, A. Kryshtafovych, Jerzy Tiuryn , Bartosz Wilczyński , Using local gene expression similarities to discover regulatory binding site modules, BMC Bioinformatics, 2006. See in PBN

2005

• K. Fidelis, T. Hvidsten, J. Komorowski, Jerzy Tiuryn , A. Kryshtafovych, Bartosz Wilczyński , Discovering regulatory binding site modules using rule-based learning, Genome Research, 2005. See in PBN

Others

• Bartosz Wilczyński , Magdalena Machnicka , Machine learning and deep learning for the advancement of epigenomics, Epigenetics of the Immune System, , p. 217-237. See in PBN