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Items: 1 to 20 of 28


i-BLESS is an ultra-sensitive method for detection of DNA double-strand breaks.

Biernacka A, Zhu Y, Skrzypczak M, Forey R, Pardo B, Grzelak M, Nde J, Mitra A, Kudlicki A, Crosetto N, Pasero P, Rowicka M, Ginalski K.

Commun Biol. 2018 Oct 31;1:181. doi: 10.1038/s42003-018-0165-9. eCollection 2018.


Predicting proteome dynamics using gene expression data.

Kuchta K, Towpik J, Biernacka A, Kutner J, Kudlicki A, Ginalski K, Rowicka M.

Sci Rep. 2018 Sep 14;8(1):13866. doi: 10.1038/s41598-018-31752-4.


The NFκB subunit RELA is a master transcriptional regulator of the committed epithelial-mesenchymal transition in airway epithelial cells.

Tian B, Widen SG, Yang J, Wood TG, Kudlicki A, Zhao Y, Brasier AR.

J Biol Chem. 2018 Oct 19;293(42):16528-16545. doi: 10.1074/jbc.RA118.003662. Epub 2018 Aug 30.


Respiratory Syncytial Virus Infection Changes Cargo Composition of Exosome Released from Airway Epithelial Cells.

Chahar HS, Corsello T, Kudlicki AS, Komaravelli N, Casola A.

Sci Rep. 2018 Jan 10;8(1):387. doi: 10.1038/s41598-017-18672-5.


A Conserved Structural Signature of the Homeobox Coding DNA in HOX genes.

Fongang B, Kong F, Negi S, Braun W, Kudlicki A.

Sci Rep. 2016 Oct 14;6:35415. doi: 10.1038/srep35415.


Comparison between Timelines of Transcriptional Regulation in Mammals, Birds, and Teleost Fish Somitogenesis.

Fongang B, Kudlicki A.

PLoS One. 2016 May 18;11(5):e0155802. doi: 10.1371/journal.pone.0155802. eCollection 2016.


G-Quadruplexes Involving Both Strands of Genomic DNA Are Highly Abundant and Colocalize with Functional Sites in the Human Genome.

Kudlicki AS.

PLoS One. 2016 Jan 4;11(1):e0146174. doi: 10.1371/journal.pone.0146174. eCollection 2016.


Systematic Determination of Human Cyclin Dependent Kinase (CDK)-9 Interactome Identifies Novel Functions in RNA Splicing Mediated by the DEAD Box (DDX)-5/17 RNA Helicases.

Yang J, Zhao Y, Kalita M, Li X, Jamaluddin M, Tian B, Edeh CB, Wiktorowicz JE, Kudlicki A, Brasier AR.

Mol Cell Proteomics. 2015 Oct;14(10):2701-21. doi: 10.1074/mcp.M115.049221. Epub 2015 Jul 24.


Analysis of the TGFβ-induced program in primary airway epithelial cells shows essential role of NF-κB/RelA signaling network in type II epithelial mesenchymal transition.

Tian B, Li X, Kalita M, Widen SG, Yang J, Bhavnani SK, Dang B, Kudlicki A, Sinha M, Kong F, Wood TG, Luxon BA, Brasier AR.

BMC Genomics. 2015 Jul 18;16:529. doi: 10.1186/s12864-015-1707-x.


Inferring genome-wide functional modulatory network: a case study on NF-κB/RelA transcription factor.

Li X, Zhu M, Brasier AR, Kudlicki AS.

J Comput Biol. 2015 Apr;22(4):300-12. doi: 10.1089/cmb.2014.0299.


Correcting positional correlations in Affymetrix® genome chips.

Homouz D, Chen G, Kudlicki AS.

Sci Rep. 2015 Mar 13;5:9078. doi: 10.1038/srep09078.


Probabilistic approach to predicting substrate specificity of methyltransferases.

Szczepińska T, Kutner J, Kopczyński M, Pawłowski K, Dziembowski A, Kudlicki A, Ginalski K, Rowicka M.

PLoS Comput Biol. 2014 Mar 20;10(3):e1003514. doi: 10.1371/journal.pcbi.1003514. eCollection 2014 Mar.


Modulation of gene expression regulated by the transcription factor NF-κB/RelA.

Li X, Zhao Y, Tian B, Jamaluddin M, Mitra A, Yang J, Rowicka M, Brasier AR, Kudlicki A.

J Biol Chem. 2014 Apr 25;289(17):11927-44. doi: 10.1074/jbc.M113.539965. Epub 2014 Feb 12.


The precise timeline of transcriptional regulation reveals causation in mouse somitogenesis network.

Fongang B, Kudlicki A.

BMC Dev Biol. 2013 Dec 5;13:42. doi: 10.1186/1471-213X-13-42.


The 3D organization of the yeast genome correlates with co-expression and reflects functional relations between genes.

Homouz D, Kudlicki AS.

PLoS One. 2013;8(1):e54699. doi: 10.1371/journal.pone.0054699. Epub 2013 Jan 31.


The optimal exponent base for emPAI is 6.5.

Kudlicki A.

PLoS One. 2012;7(3):e32339. doi: 10.1371/journal.pone.0032339. Epub 2012 Mar 5.


Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome.

Wlodarski T, Kutner J, Towpik J, Knizewski L, Rychlewski L, Kudlicki A, Rowicka M, Dziembowski A, Ginalski K.

PLoS One. 2011;6(8):e23168. doi: 10.1371/journal.pone.0023168. Epub 2011 Aug 9.


Comparison of pattern detection methods in microarray time series of the segmentation clock.

Dequéant ML, Ahnert S, Edelsbrunner H, Fink TM, Glynn EF, Hattem G, Kudlicki A, Mileyko Y, Morton J, Mushegian AR, Pachter L, Rowicka M, Shiu A, Sturmfels B, Pourquié O.

PLoS One. 2008 Aug 6;3(8):e2856. doi: 10.1371/journal.pone.0002856.


The crystallographic fast Fourier transform. Recursive symmetry reduction.

Kudlicki A, Rowicka M, Otwinowski Z.

Acta Crystallogr A. 2007 Nov;63(Pt 6):465-80. Epub 2007 Oct 17.


High-resolution timing of cell cycle-regulated gene expression.

Rowicka M, Kudlicki A, Tu BP, Otwinowski Z.

Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):16892-7. Epub 2007 Sep 7.

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