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Bartosz Wilczyński

Liczba publikacji: 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, s. 1-9. Zobacz w 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, s. 1-8. Zobacz w 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, s. 8123:1-13. Zobacz w PBN
Hanna Kranas, Bartosz Wilczyński , Irina Tuszyńska, HiCEnterprise: identifying long range chromosomal contacts in Hi-C data, PeerJ, 9 2021, s. e10558: 1-9. Zobacz w 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, s. 8067:1-15. Zobacz w 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, s. 1-17. Zobacz w 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, s. 1-15. Zobacz w PBN

2020

Clémence Réda, Bartosz Wilczyński , Automated inference of gene regulatory networks using explicit regulatory modules, Journal of Theoretical Biology, 486 2020, s. 110091:1-110091:53. Zobacz w 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, s. 80-85. Zobacz w PBN

2019

Bartosz Wilczyński , Rafał Zaborowski, BPscore: An Effective Metric for Meaningful Comparisons of Structural Chromosome Segmentations, Journal of Computational Biology, 26 (4) 2019, s. 305-314. Zobacz w 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, s. 1-12. Zobacz w PBN
Alina Frolova, Bartosz Wilczyński , Distributed Bayesian networks reconstruction on the whole genome scale, PeerJ, 6 (e5101) 2018, s. 1-20. Zobacz w 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, s. 1724–1740. Zobacz w 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, s. e0287-18.2018 1–15. Zobacz w 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, s. 3116–3129. Zobacz w 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, s. 2414-2423. Zobacz w 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, s. 34-34. Zobacz w PBN

2016

Jerzy Tiuryn , Bartosz Wilczyński , FastBill: An Improved Tool for Prediction of Cis-Regulatory Modules, Journal of Computational Biology, 2016. Zobacz w 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. Zobacz w 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. Zobacz w 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. Zobacz w PBN
Krisztián Buza, Norbert Dojer , Bartosz Wilczyński , RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes, 2015. Zobacz w PBN
Paweł Daniluk, Bogdan Lesyng, Bartosz Wilczyński , WeBIAS: a web server for publishing bioinformatics applications, BMC Research Notes, 2015. Zobacz w 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. Zobacz w PBN
Paweł Bednarz, Bartosz Wilczyński , Supervised learning method for predicting chromatin boundary associated insulator elements, Journal of Bioinformatics and Computational Biology, 2014. Zobacz w 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 grudnia 2013 - 18 grudnia 2013. Zobacz w 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, s. 1-7. Zobacz w PBN
Paweł Bednarz, Norbert Dojer , Agnieszka Podsiadlo, Bartosz Wilczyński , BNFinder2: Faster Bayesian network learning and Bayesian classification, Bioinformatics, 2013. Zobacz w PBN

2012

Paweł Bednarz, Bartosz Wilczyński , Modeling Cell Populations in Development using Individual Stochastic Regulatory Networks, 2012. Zobacz w 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. Zobacz w 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. Zobacz w PBN

2010

T.R. Hvidste, Bartosz Wilczyński , A Computer Scientist's Guide to the Regulatory Genome, Fundamenta Informaticae, 2010. Zobacz w PBN
Eileen EM Furlong, Bartosz Wilczyński , Dynamic CRM occupancy reflects a temporal map of developmental progression, Molecular Systems Biology, 2010. Zobacz w 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. Zobacz w PBN
Norbert Dojer , Bartosz Wilczyński , BNFinder: Exact and efficient method for learning Bayesian networks, Bioinformatics, 2009. Zobacz w PBN
Eileen Furlong, Bartosz Wilczyński , Challenges for modeling global gene regulatory networks during development: Insights from Drosophila, Developmental Biology, 2009. Zobacz w PBN
Norbert Dojer , Mateusz Patelak, Jerzy Tiuryn , Bartosz Wilczyński , Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs, BMC Bioinformatics, 2009. Zobacz w PBN

2008

Bartosz Wilczyński , A stochastic extension of R. Thomas regulatory network modelling, BANACH CENTER PUBLICATIONS, 80 2008, s. 271-276. Zobacz w PBN
Bartosz Wilczyński , A Stochastic Extension of R.Thomas Regulatory Network Modelling, 2008. Zobacz w 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. Zobacz w PBN

2006

Norbert Dojer , Anna Gambin , A. Mizera, Jerzy Tiuryn , Bartosz Wilczyński , Applying Dynamic Bayesian Networks to Perturbed Gene Expression Data, BMC Bioinformatics, 2006. Zobacz w 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. Zobacz w PBN
Jerzy Tiuryn , Bartosz Wilczyński , Regulatory Network Reconstruction using Stochastic Logical Networks, Lecture Notes in Computer Science, 2006. Zobacz w 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. Zobacz w 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. Zobacz w PBN