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Items: 32

1.

Cigarette Smoke Condensate Exposure Changes RNA Content of Extracellular Vesicles Released from Small Airway Epithelial Cells.

Corsello T, Kudlicki AS, Garofalo RP, Casola A.

Cells. 2019 Dec 17;8(12). pii: E1652. doi: 10.3390/cells8121652.

2.

Maximum parsimony interpretation of chromatin capture experiments.

Homouz D, Kudlicki AS.

PLoS One. 2019 Nov 25;14(11):e0225578. doi: 10.1371/journal.pone.0225578. eCollection 2019.

4.

Coevolution of Residues Provides Evidence of a Functional Heterodimer of 5-HT2AR and 5-HT2CR Involving Both Intracellular and Extracellular Domains.

Fongang B, Cunningham KA, Rowicka M, Kudlicki A.

Neuroscience. 2019 Aug 1;412:48-59. doi: 10.1016/j.neuroscience.2019.05.013. Epub 2019 Jun 1.

PMID:
31158438
5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

Correcting positional correlations in Affymetrix® genome chips.

Homouz D, Chen G, Kudlicki AS.

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

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

PMID:
17940325
24.

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.

25.

SCEPTRANS: an online tool for analyzing periodic transcription in yeast.

Kudlicki A, Rowicka M, Otwinowski Z.

Bioinformatics. 2007 Jun 15;23(12):1559-61. Epub 2007 Mar 30.

PMID:
17400726
26.

Valosin-containing protein (p97) is a regulator of endoplasmic reticulum stress and of the degradation of N-end rule and ubiquitin-fusion degradation pathway substrates in mammalian cells.

Wójcik C, Rowicka M, Kudlicki A, Nowis D, McConnell E, Kujawa M, DeMartino GN.

Mol Biol Cell. 2006 Nov;17(11):4606-18. Epub 2006 Aug 16.

27.

Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes.

Tu BP, Kudlicki A, Rowicka M, McKnight SL.

Science. 2005 Nov 18;310(5751):1152-8. Epub 2005 Oct 27. Erratum in: Science. 2006 Feb 17;311(5763):954.

28.

Coordinate transformations in modern crystallographic computing.

Rowicka M, Kudlicki A, Zelinka J, Otwinowski Z.

Acta Crystallogr A. 2004 Nov;60(Pt 6):542-9. Epub 2004 Oct 26.

PMID:
15507736
29.

The crystallographic fast Fourier transform. IV. FFT-asymmetric units in the reciprocal space.

Kudlicki A, Rowicka M, Otwinowski Z.

Acta Crystallogr A. 2004 Mar;60(Pt 2):146-52. Epub 2004 Feb 17.

PMID:
14966326
30.

The crystallographic fast Fourier transform. III. Centred lattices.

Rowicka M, Kudlicki A, Otwinowski Z.

Acta Crystallogr A. 2003 Mar;59(Pt 2):183-92. Epub 2003 Feb 26.

PMID:
12604858
31.

The crystallographic fast Fourier transform. II. One-step symmetry reduction.

Rowicka M, Kudlicki A, Otwinowski Z.

Acta Crystallogr A. 2003 Mar;59(Pt 2):172-82. Epub 2003 Feb 26.

PMID:
12604857
32.

The crystallographic fast Fourier transform. I. p3 symmetry.

Rowicka M, Kudlicki A, Otwinowski Z.

Acta Crystallogr A. 2002 Nov;58(Pt 6):574-9. Epub 2002 Nov 1.

PMID:
12388876

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