Articles
- Karolina Stępniak, Magdalena A Machnicka, Jakub Mieczkowski, 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 pathological mechanisms in human gliomas
Nature Communications, 19 V 2021, doi: 10.1038/s41467-021-23922-2
- Ilona E Grabowicz, Bartek Wilczyński, Bożena Kamińska, Adria-Jaume Roura, Bartosz Wojtaś, Michał J Dąbrowski,
The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes
NAR Genomics and Bioinformatics, 02 VIII 2021, doi: 10.1038/s41598-021-95009-3
- Marlena Osipowicz, Bartek Wilczynski, Magdalena A Machnicka,
Careful feature selection is key in classification of Alzheimer’s disease patients based on whole-genome sequencing data
NAR Genomics and Bioinformatics, IX 2021, doi: 10.1093/nargab/lqab069
- Kinga Szyman, Bartek Wilczyński, Michał Dąbrowski,
K-mer Content Changes with Node Degree in Promoter–Enhancer Network of Mouse ES Cells
International journal of molecular sciences, I 2021, doi: 10.3390/ijms22158067
- Clémence Réda and Bartek Wilczyński,
Automated inference of gene regulatory networks using explicit regulatory modules
Journal of Theoretical Biology, Volume 486, 7 February 2020, doi:10.1016/j.jtbi.2019.110091
- B. Zawalski, I. Tuszyńska, B. Wilczyński,
QChromosomeVisualizer: A new tool for 3D visualization of long simulations of polymer-like chromosome models
Methods, in press, DOI: 10.1016/j.ymeth.2019.08.00
- R Zaborowski, B Wilczyński
BPscore: an effective metric for meaningful comparisons of structural chromosome segmentations
Journal of Computational Biology 26 (4), 305-314, 2019, DOI: 10.1089/cmb.2018.0162
- I. De Toma, I. E. Grabowicz, M. Fructuoso, D. Trujillano, B. Wilczynski and M. Dierssen
Overweighed mice show coordinated homeostatic and hedonic transcriptional response across brain
eNeuro 26 November 2018, ENEURO.0287-18.2018; DOI: 10.1523/ENEURO.0287-18.2018
- A. Frolova and B. Wilczynski
Distributed Bayesian networks reconstruction on the whole genome scale
PeerJ 6:e5692, 2018, doi:10.7717/peerj.5692
- A. Kikulska, T. Rausch, E. Krzywinska, M. Pawlak, B. Wilczynski, V. Benes, P. Rutkowski and T. Wilanowski
Coordinated expression and genetic polymorphisms in Grainyhead-like genes in human non-melanoma skin cancers
BMC Cancer, 2018, doi:10.1186/s12885-017-3943-8
- H. Niskanen, I. Tuszynska, R. Zaborowski, M. Heinäniemi, S. Ylä-Herttuala, B. Wilczynski and Minna U. Kaikkonen
Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions
Nucleic Acids Research, 2017, DOI: 10.1093/nar/gkx1214
- M. Pawlak, A. Kikulska, T. Wrzesinski, T. Rausch, Z. Kwias, B. Wilczynski, V. Benes, J. Wesoly, T. Wilanowski
Potential Protective Role of Grainyhead-like Genes in the Development of Clear Cell Renal Cell Carcinoma
Molecular Carcinogenesis, 2017, DOI: 10.1002/mc.22682
- Julia Herman-Izycka, Michal Wlasnowolski and Bartek Wilczynski
Taking promoters out of enhancers in sequence based predictions of tissue-specific mammalian enhancers
BMC Medical Genomics (Suppl 1):34, 2017, DOI: 10.1186/s12920-017-0264-3
- R. Archacki, R. Yatusevich, D. Buszewicz, K. Krzyczmonik, J. Patryn,
R. Iwanicka-Nowicka, P. Biecek, B. Wilczynski, M. Koblowska, A. Jerzmanowski, and S. Swiezewski
Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression
Nucl. Acids Res. first published online December 19, 2016 doi:10.1093/nar/gkw1273
- K. Rutowicz, M. Puzio, ,J. halibart-Puzio, M. Lirski, M. Kroteń, M. Kotliński, Ł. Kniżewski, B. Lange, A. Muszewska, K. Sniegowska-Świerk, J. Kościelniak, R. Iwanicka-Nowicka, K. Żmuda, K. Buza, F. Janowiak, I. Joessar, K. Laskowska-Kaszub, A. Fogtman, P. Zielenkiewicz, J. Tiuryn, H. Kollist, P. Siedlecki, K. Ginalski, S. Świeżewski, M. Koblowska, R. Archacki, B. Wilczyński, M. Rapacz, A. Jerzmanowski
A specialized histone H1 variant is required for adaptive responses to complex abiotic stress and related DNA methylation in Arabidopsis
Plant Physiology September 2015 pp.00493.2015
- Krisztian Buza, Bartek Wilczynski, and Norbert Dojer,
RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes
International Journal of Genomics, May 2015
- Y. Wei, S. Mondal, R. Mouawad, B. Wilczynski, R.W. Henry, D. Arnosti
Genome-Wide Analysis of Drosophila Rbf2 Protein Highlights Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis
G3 May 20, 2015 g3.115.019166
- M. Dabrowski, N. Dojer, I. Krystkowiak, B. Kaminska and B. Wilczynski
Optimally choosing PWM motif databases and sequence scanning
approaches based on ChIP-seq data
BMC Bioinformatics 2015, 16:140 doi:10.1186/s12859-015-0573-5
- Paweł Bednarz and Bartek Wilczyński
Supervised learning method for predicting chromatin boundary associated insulator elements
Journal of Bioinformatics and Computational Biology, December 2014, DOI:10.1142/S0219720014420062
- Lucia Ciglar, Charles Girardot, Bartek Wilczyński, Martina Braun and Eileen E. M. Furlong
Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis
Development, 141, 2633-2643, July 2014.
- A Podsiadło, M Wrzesień, W Paja, W Rudnicki, B Wilczyński
Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data
BMC Systems Biology, 7, (Suppl. 6), S16, 2013
- B. Wilczynski, YH.Liu, ZX.Yeo, EEM Furlong
Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state
PLoS Computational Biology, 2012. featured in Nat. Rev. Genetics
- S. Bonn, RP. Zinzen, C. Girardot, EH. Gustafson, A. Perez-Gonzalez, N. Delhomme, Y. Ghavi-Helm, B. Wilczyński, A. Riddell, EEM. Furlong
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
Nature Genetics, Volume 44, Number 2, pages 148–156, 2012, doi:10.1038/ng.1064
- Bartek Wilczynski, Torgeir R. Hvidsten
A computer scientist's guide to the regulatory genome
Fundamenta Informaticae, Volume 103, Issue 1-4, 2010, Pages 323-332
- Bartek Wilczynski, Eileen EM Furlong
Dynamic CRM occupancy reflects a temporal map of developmental progression
Molecular Systems Biology 6 Article number: 383 doi:10.1038/msb.2010.35
- Bartek Wilczynski, Eileen EM Furlong
Challenges for modeling global gene regulatory networks during development: Insights from Drosophila
Developmental Biology, 2010, Volume 340, Issue 2, 15 April 2010, Pages 161-169, DOI: 10.1016/j.ydbio.2009.10.032
- Bartek Wilczynski, Norbert Dojer, Mateusz Patelak and Jerzy Tiuryn
Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs
BMC Bioinformatics 2009 DOI: 10.1186/1471-2105-10-82
- Bartek Wilczynski, Jerzy Tiuryn
Reconstruction of Mammalian Cell Cycle Regulatory Network from Microarray Data using Stochastic Logical Networks
CMSB 2007, Edinburgh, LNBI 4695, pp. 121-135 DOI: 10.1007/978-3-540-75140-3_9
- B. Wilczyński, TR. Hvidsten, A.Kryshtafovych,
J. Tiuryn, J. Komorowski, K. Fidelis
Using
local gene expression similarities to discover regulatory binding
site modules
BMC Bioinformatics 2006, 7:505 DOI: 10.1186/1471-2105-7-505
- Bartek Wilczyński, Jerzy Tiuryn
Regulatory Network Reconstruction using Stochastic
Logical Networks
C. Priami (Ed.): CMSB 2006, LNBI 4210,
pp. 145-157, 2006. DOI: 10.1007/11885191_10
- Norbert Dojer, Anna Gambin, Bartek Wilczyński, Jerzy Tiuryn
Applying Dynamic Bayesian Networks to Perturbed
Gene Expression Data,
BMC Bioinfoirmatics, 2006,
7:249. DOI: 10.1186/1471-2105-7-249
- Anna Gambin, Katarzyna Bożek, Bartek Wilczyński, Jerzy Tiuryn,
Automated modeling of genetic control in
Arabidopsis thaliana,
Journal of Fruit and ornamental
plant research, 2006, Vol XIV, Supp. 1, pp. 163-171.
- T.R. Hvidsten, B. Wilczyński, A. Kryshtafovych, J. Tiuryn,
J. Komorowski and K. Fidelis,
Discovering regulatory binding site modules using
rule-based learning,
Genome Research 2005 15:
856-866. DOI: 10.1101/gr.3760605
Short papers and Application notes
- Hanna Kranas, Irina Tuszynska, and Bartek Wilczyński,
HiCEnterprise: identifying long range chromosomal contacts in Hi-C data
PeerJ, IV 2021, doi: 10.7717/peerj.10558
- Anna Macioszek and Bartek Wilczyński,
HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data
Int. J. Mol. Sci. 2021, 22(15), 8123; doi: 10.3390/ijms22158123
- B Wilczynski and J Tiuryn
FastBill: An Improved Tool for Prediction of Cis-Regulatory Modules
Journal of Computational Biology, 2016, ePub
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Paweł Daniluk, Bartek Wilczyński and Bogdan Lesyng
WeBIAS: a web server for publishing bioinformatics applications
BMC Research Notes 2015, 8:628
-
Alina Frolova, Bartek Wilczyński
Fast Parallel Bayesian Networks Reconstruction with BNFinder
Proceedings of the IWBBIO conference 2014 in Granada, Spain, pp.1179-1184
-
Norbert Dojer, Paweł Bednarz, Agnieszka Podsiadło, Bartek Wilczyński
BNFinder2: Faster Bayesian network learning and Bayesian classification
Bioinformatics (2013), 29(16), pages 2068-2070, first published online July 1, 2013 doi:10.1093/bioinformatics/btt323
- Paweł Bednarz and Bartek Wilczyński
Modeling cell populations in development using individual stochastic regulatory networks
SIMULTECH conference Rome July 2012 source code
- Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Knauff, Bartek Wilczynski, Michiel J.L. de Hoon
Biopython: freely available Python tools for computational molecular biology and bioinformatics
Bioinformatics 2009 source code
- Bartek Wilczynski, Norbert Dojer
BNFinder: Exact and efficient method for learning Bayesian networks
Bioinformatics 2008 source code
- Bartek Wilczynski
A Stochastic Extension of R.Thomas Regulatory Network Modelling
Banach Center Publications, 80 (2008), 271-276
In post-proceedings of Stochastic models in biological sciences, Warsaw, 2006
- B.Wilczyński, T.R. Hvidsten, A. Kryshtafovych, L. Stubbs, J. Komorowski, K. Fidelis,
A rule-based framework for gene regulation pathways discovery,
CSB 2003: 435-436, Stanford, 11-14. August, 2003,
Theses
