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Items: 37

1.

Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects.

Tiuryn J, Szczurek E.

Bioinformatics. 2019 Jul 15;35(14):i605-i614. doi: 10.1093/bioinformatics/btz334.

2.

The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost.

Gorecki P, Eulenstein O, Tiuryn J.

IEEE/ACM Trans Comput Biol Bioinform. 2019 May 28. doi: 10.1109/TCBB.2019.2919617. [Epub ahead of print]

PMID:
31150345
3.

Contribution of NtZIP1-Like to the Regulation of Zn Homeostasis.

Papierniak A, Kozak K, Kendziorek M, Barabasz A, Palusińska M, Tiuryn J, Paterczyk B, Williams LE, Antosiewicz DM.

Front Plant Sci. 2018 Feb 16;9:185. doi: 10.3389/fpls.2018.00185. eCollection 2018.

4.

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
5.

Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data.

Jankowski A, Tiuryn J, Prabhakar S.

Bioinformatics. 2016 Aug 15;32(16):2419-26. doi: 10.1093/bioinformatics/btw209. Epub 2016 Apr 19.

6.

Enhanceosome transcription factors preferentially dimerize with high mobility group proteins.

Jankowski A, Obara P, Mathur U, Tiuryn J.

BMC Syst Biol. 2016 Feb 4;10:14. doi: 10.1186/s12918-016-0258-3.

7.

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.

8.

GWAMAR: genome-wide assessment of mutations associated with drug resistance in bacteria.

Wozniak M, Tiuryn J, Wong L.

BMC Genomics. 2014;15 Suppl 10:S10. doi: 10.1186/1471-2164-15-S10-S10. Epub 2014 Dec 12.

9.

TACO: a general-purpose tool for predicting cell-type-specific transcription factor dimers.

Jankowski A, Prabhakar S, Tiuryn J.

BMC Genomics. 2014 Mar 19;15:208. doi: 10.1186/1471-2164-15-208.

10.

eCAMBer: efficient support for large-scale comparative analysis of multiple bacterial strains.

Wozniak M, Wong L, Tiuryn J.

BMC Bioinformatics. 2014 Mar 5;15:65. doi: 10.1186/1471-2105-15-65.

11.

A probabilistic model of neutral and selective dynamics of protein network evolution.

Dutkowski J, Tiuryn J.

J Comput Biol. 2013 Sep;20(9):631-42. doi: 10.1089/cmb.2012.0295. Epub 2013 Aug 9.

12.

Unrooted tree reconciliation: a unified approach.

Górecki P, Eulenstein O, Tiuryn J.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Mar-Apr;10(2):522-36. doi: 10.1109/TCBB.2013.22.

PMID:
23929875
13.

Bioinformatics and computational biology in Poland.

Bujnicki JM, Tiuryn J.

PLoS Comput Biol. 2013;9(5):e1003048. doi: 10.1371/journal.pcbi.1003048. Epub 2013 May 2. No abstract available.

14.

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers.

Jankowski A, Szczurek E, Jauch R, Tiuryn J, Prabhakar S.

Genome Res. 2013 Aug;23(8):1307-18. doi: 10.1101/gr.154922.113. Epub 2013 Apr 3.

15.

An approach to identifying drug resistance associated mutations in bacterial strains.

Wozniak M, Tiuryn J, Wong L.

BMC Genomics. 2012;13 Suppl 7:S23. doi: 10.1186/1471-2164-13-S7-S23. Epub 2012 Dec 13.

16.

CAMBer: an approach to support comparative analysis of multiple bacterial strains.

Wozniak M, Wong L, Tiuryn J.

BMC Genomics. 2011;12 Suppl 2:S6. doi: 10.1186/1471-2164-12-S2-S6. Epub 2011 Jul 27.

17.

CAMBerVis: visualization software to support comparative analysis of multiple bacterial strains.

Woźniak M, Wong L, Tiuryn J.

Bioinformatics. 2011 Dec 1;27(23):3313-4. doi: 10.1093/bioinformatics/btr561. Epub 2011 Oct 8.

PMID:
21984770
18.

Rhythmic diel pattern of gene expression in juvenile maize leaf.

Jończyk M, Sobkowiak A, Siedlecki P, Biecek P, Trzcinska-Danielewicz J, Tiuryn J, Fronk J, Sowiński P.

PLoS One. 2011;6(8):e23628. doi: 10.1371/journal.pone.0023628. Epub 2011 Aug 17.

19.

Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data.

Szczurek E, Markowetz F, Gat-Viks I, Biecek P, Tiuryn J, Vingron M.

BMC Bioinformatics. 2011 Jun 21;12:249. doi: 10.1186/1471-2105-12-249.

20.

Bi-billboard: symmetrization and careful choice of informant species results in higher accuracy of regulatory element prediction.

Dojer N, Biecek P, Tiuryn J.

J Comput Biol. 2011 Jun;18(6):809-19. doi: 10.1089/cmb.2010.0299. Epub 2011 May 12.

PMID:
21563976
21.

Introducing knowledge into differential expression analysis.

Szczurek E, Biecek P, Tiuryn J, Vingron M.

J Comput Biol. 2010 Aug;17(8):953-67. doi: 10.1089/cmb.2010.0034.

22.

MODEVO: exploring modularity and evolution of protein interaction networks.

Woźniak M, Tiuryn J, Dutkowski J.

Bioinformatics. 2010 Jul 15;26(14):1790-1. doi: 10.1093/bioinformatics/btq274. Epub 2010 May 27.

PMID:
20507893
23.

Phylogeny-guided interaction mapping in seven eukaryotes.

Dutkowski J, Tiuryn J.

BMC Bioinformatics. 2009 Nov 30;10:393. doi: 10.1186/1471-2105-10-393.

24.

Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments.

Szczurek E, Gat-Viks I, Tiuryn J, Vingron M.

Mol Syst Biol. 2009;5:287. doi: 10.1038/msb.2009.45. Epub 2009 Jul 7.

25.

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.

26.

Identification of functional modules from conserved ancestral protein-protein interactions.

Dutkowski J, Tiuryn J.

Bioinformatics. 2007 Jul 1;23(13):i149-58.

PMID:
17646291
27.

Library of local descriptors models the core of proteins accurately.

Drabikowski M, Nowakowski S, Tiuryn J.

Proteins. 2007 Nov 15;69(3):499-510.

PMID:
17623841
28.

Evolution of gene families based on gene duplication, loss, accumulated change, and innovation.

Wójtowicz D, Tiuryn J.

J Comput Biol. 2007 May;14(4):479-95.

PMID:
17572025
29.

Inferring phylogeny from whole genomes.

Górecki P, Tiuryn J.

Bioinformatics. 2007 Jan 15;23(2):e116-22.

PMID:
17237078
30.

URec: a system for unrooted reconciliation.

Górecki P, Tiuryn J.

Bioinformatics. 2007 Feb 15;23(4):511-2. Epub 2006 Dec 20.

PMID:
17182699
31.

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.

32.

A model for the evolution of paralog families in genomes.

Rudnicki R, Tiuryn J, Wójtowicz D.

J Math Biol. 2006 Nov;53(5):759-70. Epub 2006 Sep 19.

PMID:
16988827
33.

A new approach to the assessment of the quality of predictions of transcription factor binding sites.

Nowakowski S, Tiuryn J.

J Biomed Inform. 2007 Apr;40(2):139-49. Epub 2006 Jul 21.

34.

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.

35.

Alignment with context dependent scoring function.

Gambin A, Tiuryn J, Tyszkiewicz J.

J Comput Biol. 2006 Jan-Feb;13(1):81-101.

PMID:
16472023
36.

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.

37.

Contextual alignment of biological sequences (Extended abstract).

Gambin A, Lasota S, Szklarczyk R, Tiuryn J, Tyszkiewicz J.

Bioinformatics. 2002;18 Suppl 2:S116-27.

PMID:
12385993

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