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Items: 31

1.

Automated inference of gene regulatory networks using explicit regulatory modules.

Réda C, Wilczyński B.

J Theor Biol. 2020 Feb 7;486:110091. doi: 10.1016/j.jtbi.2019.110091. Epub 2019 Nov 30.

PMID:
31790679
2.

QChromosomeVisualizer: A new tool for 3D visualization of long simulations of polymer-like chromosome models.

Zawalski B, Tuszyńska I, Wilczyński B.

Methods. 2019 Aug 21. pii: S1046-2023(18)30481-X. doi: 10.1016/j.ymeth.2019.08.006. [Epub ahead of print]

PMID:
31445092
3.

BPscore: An Effective Metric for Meaningful Comparisons of Structural Chromosome Segmentations.

Zaborowski R, Wilczyński B.

J Comput Biol. 2019 Apr;26(4):305-314. doi: 10.1089/cmb.2018.0162. Epub 2019 Feb 27.

PMID:
30810370
4.

Overweight Mice Show Coordinated Homeostatic and Hedonic Transcriptional Response across Brain.

De Toma I, Grabowicz IE, Fructuoso M, Trujillano D, Wilczyński B, Dierssen M.

eNeuro. 2018 Jan 8;5(6). pii: ENEURO.0287-18.2018. doi: 10.1523/ENEURO.0287-18.2018. eCollection 2018 Nov-Dec.

5.

Distributed Bayesian networks reconstruction on the whole genome scale.

Frolova A, Wilczyński B.

PeerJ. 2018 Oct 19;6:e5692. doi: 10.7717/peerj.5692. eCollection 2018.

6.

Coordinated expression and genetic polymorphisms in Grainyhead-like genes in human non-melanoma skin cancers.

Kikulska A, Rausch T, Krzywinska E, Pawlak M, Wilczynski B, Benes V, Rutkowski P, Wilanowski T.

BMC Cancer. 2018 Jan 4;18(1):23. doi: 10.1186/s12885-017-3943-8.

7.

Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions.

Niskanen H, Tuszynska I, Zaborowski R, Heinäniemi M, Ylä-Herttuala S, Wilczynski B, Kaikkonen MU.

Nucleic Acids Res. 2018 Feb 28;46(4):1724-1740. doi: 10.1093/nar/gkx1214.

8.

Gender-related differences in long-term outcome among high-risk patients with myocardial infarction treated invasively.

Sarek J, Paczkowska A, Wilczyński B, Francuz P, Podolecki T, Lenarczyk R, Średniawa B, Kalarus Z, Kowalczyk J.

Postepy Kardiol Interwencyjnej. 2017;13(2):107-116. doi: 10.5114/pwki.2017.68048. Epub 2017 May 30.

9.

Taking promoters out of enhancers in sequence based predictions of tissue-specific mammalian enhancers.

Herman-Izycka J, Wlasnowolski M, Wilczynski B.

BMC Med Genomics. 2017 May 24;10(Suppl 1):34. doi: 10.1186/s12920-017-0264-3.

10.

Potential protective role of Grainyhead-like genes in the development of clear cell renal cell carcinoma.

Pawlak M, Kikulska A, Wrzesinski T, Rausch T, Kwias Z, Wilczynski B, Benes V, Wesoly J, Wilanowski T.

Mol Carcinog. 2017 Nov;56(11):2414-2423. doi: 10.1002/mc.22682. Epub 2017 Jun 15.

PMID:
28543713
11.

Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression.

Archacki R, Yatusevich R, Buszewicz D, Krzyczmonik K, Patryn J, Iwanicka-Nowicka R, Biecek P, Wilczynski B, Koblowska M, Jerzmanowski A, Swiezewski S.

Nucleic Acids Res. 2017 Apr 7;45(6):3116-3129. doi: 10.1093/nar/gkw1273.

12.

FastBill: An Improved Tool for Prediction of Cis-Regulatory Modules.

Wilczynski B, Tiuryn J.

J Comput Biol. 2017 Mar;24(3):193-199. doi: 10.1089/cmb.2016.0108. Epub 2016 Oct 6.

PMID:
27710048
13.

RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes.

Buza K, Wilczynski B, Dojer N.

Int J Genomics. 2015;2015:563482. doi: 10.1155/2015/563482. Epub 2015 Oct 19.

14.

WeBIAS: a web server for publishing bioinformatics applications.

Daniluk P, Wilczyński B, Lesyng B.

BMC Res Notes. 2015 Nov 2;8:628. doi: 10.1186/s13104-015-1622-x.

15.

A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis.

Rutowicz K, Puzio M, Halibart-Puzio J, Lirski M, Kotliński M, Kroteń MA, Knizewski L, Lange B, Muszewska A, Śniegowska-Świerk K, Kościelniak J, Iwanicka-Nowicka R, Buza K, Janowiak F, Żmuda K, Jõesaar I, Laskowska-Kaszub K, Fogtman A, Kollist H, Zielenkiewicz P, Tiuryn J, Siedlecki P, Swiezewski S, Ginalski K, Koblowska M, Archacki R, Wilczynski B, Rapacz M, Jerzmanowski A.

Plant Physiol. 2015 Nov;169(3):2080-101. doi: 10.1104/pp.15.00493. Epub 2015 Sep 8.

16.

Genome-Wide Analysis of Drosophila RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis.

Wei Y, Mondal SS, Mouawad R, Wilczyński B, Henry RW, Arnosti DN.

G3 (Bethesda). 2015 May 20;5(7):1503-15. doi: 10.1534/g3.115.019166.

17.

Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data.

Dabrowski M, Dojer N, Krystkowiak I, Kaminska B, Wilczynski B.

BMC Bioinformatics. 2015 May 1;16:140. doi: 10.1186/s12859-015-0573-5.

18.

Supervised learning method for predicting chromatin boundary associated insulator elements.

Bednarz P, Wilczyński B.

J Bioinform Comput Biol. 2014 Dec;12(6):1442006. doi: 10.1142/S0219720014420062.

PMID:
25385081
19.

Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis.

Ciglar L, Girardot C, Wilczyński B, Braun M, Furlong EE.

Development. 2014 Jul;141(13):2633-43. doi: 10.1242/dev.101956.

20.

Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data.

Podsiadło A, Wrzesień M, Paja W, Rudnicki W, Wilczyński B.

BMC Syst Biol. 2013;7 Suppl 6:S16. doi: 10.1186/1752-0509-7-S6-S16. Epub 2013 Dec 13.

21.

BNFinder2: Faster Bayesian network learning and Bayesian classification.

Dojer N, Bednarz P, Podsiadlo A, Wilczynski B.

Bioinformatics. 2013 Aug 15;29(16):2068-70. doi: 10.1093/bioinformatics/btt323. Epub 2013 Jul 1.

22.

Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state.

Wilczynski B, Liu YH, Yeo ZX, Furlong EE.

PLoS Comput Biol. 2012;8(12):e1002798. doi: 10.1371/journal.pcbi.1002798. Epub 2012 Dec 6.

23.

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.

Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyński B, Riddell A, Furlong EE.

Nat Genet. 2012 Jan 8;44(2):148-56. doi: 10.1038/ng.1064.

PMID:
22231485
24.

Dynamic CRM occupancy reflects a temporal map of developmental progression.

Wilczyński B, Furlong EE.

Mol Syst Biol. 2010 Jun 22;6:383. doi: 10.1038/msb.2010.35.

25.

Challenges for modeling global gene regulatory networks during development: insights from Drosophila.

Wilczynski B, Furlong EE.

Dev Biol. 2010 Apr 15;340(2):161-9. doi: 10.1016/j.ydbio.2009.10.032. Epub 2009 Oct 27. Review.

26.

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ.

Bioinformatics. 2009 Jun 1;25(11):1422-3. doi: 10.1093/bioinformatics/btp163. Epub 2009 Mar 20.

27.

Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs.

Wilczynski B, Dojer N, Patelak M, Tiuryn J.

BMC Bioinformatics. 2009 Mar 10;10:82. doi: 10.1186/1471-2105-10-82.

28.

BNFinder: exact and efficient method for learning Bayesian networks.

Wilczyński B, Dojer N.

Bioinformatics. 2009 Jan 15;25(2):286-7. doi: 10.1093/bioinformatics/btn505. Epub 2008 Sep 30.

29.

Using local gene expression similarities to discover regulatory binding site modules.

Wilczyński B, Hvidsten TR, Kryshtafovych A, Tiuryn J, Komorowski J, Fidelis K.

BMC Bioinformatics. 2006 Nov 17;7:505.

30.

Applying dynamic Bayesian networks to perturbed gene expression data.

Dojer N, Gambin A, Mizera A, Wilczyński B, Tiuryn J.

BMC Bioinformatics. 2006 May 8;7:249.

31.

Discovering regulatory binding-site modules using rule-based learning.

Hvidsten TR, Wilczyński B, Kryshtafovych A, Tiuryn J, Komorowski J, Fidelis K.

Genome Res. 2005 Jun;15(6):856-66.

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