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Items: 1 to 50 of 114

1.

Chromatin changes trigger laminin genes dysregulation in aging kidneys.

Denisenko O, Mar D, Trawczynski M, Bomsztyk K.

Aging (Albany NY). 2018 May 29;10(5):1133-1145. doi: 10.18632/aging.101453.

2.

DNA methylation yields epigenetic clues into the diabetic nephropathy of Pima Indians.

Bomsztyk K, Denisenko O, Wang Y.

Kidney Int. 2018 Jun;93(6):1272-1275. doi: 10.1016/j.kint.2018.02.015.

PMID:
29792271
3.

Engineering a multicellular vascular niche to model hematopoietic cell trafficking.

Kotha SS, Hayes BJ, Phong KT, Redd MA, Bomsztyk K, Ramakrishnan A, Torok-Storb B, Zheng Y.

Stem Cell Res Ther. 2018 Mar 23;9(1):77. doi: 10.1186/s13287-018-0808-2.

4.

Genome-wide co-localization of active EGFR and downstream ERK pathway kinases mirrors mitogen-inducible RNA polymerase 2 genomic occupancy.

Mikula M, Skrzypczak M, Goryca K, Paczkowska K, Ledwon JK, Statkiewicz M, Kulecka M, Grzelak M, Dabrowska M, Kuklinska U, Karczmarski J, Rumienczyk I, Jastrzebski K, Miaczynska M, Ginalski K, Bomsztyk K, Ostrowski J.

Nucleic Acids Res. 2016 Dec 1;44(21):10150-10164. Epub 2016 Sep 1.

5.

Regulation of ribosomal RNA expression across the lifespan is fine-tuned by maternal diet before implantation.

Denisenko O, Lucas ES, Sun C, Watkins AJ, Mar D, Bomsztyk K, Fleming TP.

Biochim Biophys Acta. 2016 Jul;1859(7):906-13. doi: 10.1016/j.bbagrm.2016.04.001. Epub 2016 Apr 7.

6.

SYSTEM-WIDE MAPPING OF ACTIVATED CIRCUITRY IN EXPERIMENTAL SYSTEMIC INFLAMMATORY RESPONSE SYNDROME.

Gharib SA, Mar D, Bomsztyk K, Denisenko O, Dhanireddy S, Liles WC, Altemeier WA.

Shock. 2016 Feb;45(2):148-56. doi: 10.1097/SHK.0000000000000507. Erratum in: Shock. 2016 Feb 12;:. Shock. 2016 Apr;45(4):469.

7.

Quadruplex formation by both G-rich and C-rich DNA strands of the C9orf72 (GGGGCC)8•(GGCCCC)8 repeat: effect of CpG methylation.

Zamiri B, Mirceta M, Bomsztyk K, Macgregor RB Jr, Pearson CE.

Nucleic Acids Res. 2015 Nov 16;43(20):10055-64. doi: 10.1093/nar/gkv1008. Epub 2015 Oct 1.

8.

Beads-free protein immunoprecipitation for a mass spectrometry-based interactome and posttranslational modifications analysis.

Mikula M, Rubel T, Karczmarski J, Statkiewicz M, Bomsztyk K, Ostrowski J.

Proteome Sci. 2015 Sep 2;13:23. doi: 10.1186/s12953-015-0079-0. eCollection 2015.

9.

Temporal Dissection of Rate Limiting Transcriptional Events Using Pol II ChIP and RNA Analysis of Adrenergic Stress Gene Activation.

Morris DP, Lei B, Longo LD, Bomsztyk K, Schwinn DA, Michelotti GA.

PLoS One. 2015 Aug 5;10(8):e0134442. doi: 10.1371/journal.pone.0134442. eCollection 2015. Erratum in: PLoS One. 2015;10(10):e0140710.

10.

Heterogeneity of epigenetic changes at ischemia/reperfusion- and endotoxin-induced acute kidney injury genes.

Mar D, Gharib SA, Zager RA, Johnson A, Denisenko O, Bomsztyk K.

Kidney Int. 2015 Oct;88(4):734-44. doi: 10.1038/ki.2015.164. Epub 2015 Jun 10.

11.

Experimental acute lung injury induces multi-organ epigenetic modifications in key angiogenic genes implicated in sepsis-associated endothelial dysfunction.

Bomsztyk K, Mar D, An D, Sharifian R, Mikula M, Gharib SA, Altemeier WA, Liles WC, Denisenko O.

Crit Care. 2015 May 11;19:225. doi: 10.1186/s13054-015-0943-4.

12.

M2 Macrophage Polarization Mediates Anti-inflammatory Effects of Endothelial Nitric Oxide Signaling.

Lee WJ, Tateya S, Cheng AM, Rizzo-DeLeon N, Wang NF, Handa P, Wilson CL, Clowes AW, Sweet IR, Bomsztyk K, Schwartz MW, Kim F.

Diabetes. 2015 Aug;64(8):2836-46. doi: 10.2337/db14-1668. Epub 2015 Apr 6.

13.

Losartan reverses permissive epigenetic changes in renal glomeruli of diabetic db/db mice.

Reddy MA, Sumanth P, Lanting L, Yuan H, Wang M, Mar D, Alpers CE, Bomsztyk K, Natarajan R.

Kidney Int. 2014 Feb;85(2):362-73. doi: 10.1038/ki.2013.387. Epub 2013 Oct 2.

14.

Epigenetic alterations in acute kidney injury.

Bomsztyk K, Denisenko O.

Semin Nephrol. 2013 Jul;33(4):327-40. doi: 10.1016/j.semnephrol.2013.05.005. Review.

15.

Synchronous recruitment of epigenetic modifiers to endotoxin synergistically activated Tnf-α gene in acute kidney injury.

Bomsztyk K, Flanagin S, Mar D, Mikula M, Johnson A, Zager R, Denisenko O.

PLoS One. 2013 Jul 30;8(7):e70322. doi: 10.1371/journal.pone.0070322. Print 2013.

16.

Activation of Wnt/β-catenin signaling increases apoptosis in melanoma cells treated with trail.

Zimmerman ZF, Kulikauskas RM, Bomsztyk K, Moon RT, Chien AJ.

PLoS One. 2013 Jul 15;8(7):e69593. doi: 10.1371/journal.pone.0069593. Print 2013.

17.
18.

Epigenetic changes in renal genes dysregulated in mouse and rat models of type 1 diabetes.

Komers R, Mar D, Denisenko O, Xu B, Oyama TT, Bomsztyk K.

Lab Invest. 2013 May;93(5):543-52. doi: 10.1038/labinvest.2013.47. Epub 2013 Mar 18.

19.

Acyl-CoA synthetase 1 is induced by Gram-negative bacteria and lipopolysaccharide and is required for phospholipid turnover in stimulated macrophages.

Rubinow KB, Wall VZ, Nelson J, Mar D, Bomsztyk K, Askari B, Lai MA, Smith KD, Han MS, Vivekanandan-Giri A, Pennathur S, Albert CJ, Ford DA, Davis RJ, Bornfeldt KE.

J Biol Chem. 2013 Apr 5;288(14):9957-70. doi: 10.1074/jbc.M113.458372. Epub 2013 Feb 20.

20.

Chromatin structure of two genomic sites for targeted transgene integration in induced pluripotent stem cells and hematopoietic stem cells.

van Rensburg R, Beyer I, Yao XY, Wang H, Denisenko O, Li ZY, Russell DW, Miller DG, Gregory P, Holmes M, Bomsztyk K, Lieber A.

Gene Ther. 2013 Feb;20(2):201-14. doi: 10.1038/gt.2012.25. Epub 2012 Mar 22.

21.

Microplate-based platform for combined chromatin and DNA methylation immunoprecipitation assays.

Yu J, Feng Q, Ruan Y, Komers R, Kiviat N, Bomsztyk K.

BMC Mol Biol. 2011 Nov 18;12:49. doi: 10.1186/1471-2199-12-49.

22.

Allele-specific transcriptional elongation regulates monoallelic expression of the IGF2BP1 gene.

Thomas BJ, Rubio ED, Krumm N, Broin PO, Bomsztyk K, Welcsh P, Greally JM, Golden AA, Krumm A.

Epigenetics Chromatin. 2011 Aug 3;4:14. doi: 10.1186/1756-8935-4-14.

23.

Maternal malnutrition and placental insufficiency induce global downregulation of gene expression in fetal kidneys.

Denisenko O, Lin B, Louey S, Thornburg K, Bomsztyk K, Bagby S.

J Dev Orig Health Dis. 2011 Apr;2(2):124-33. doi: 10.1017/S2040174410000632.

24.

Direct recruitment of ERK cascade components to inducible genes is regulated by heterogeneous nuclear ribonucleoprotein (hnRNP) K.

Mikula M, Bomsztyk K.

J Biol Chem. 2011 Mar 18;286(11):9763-75. doi: 10.1074/jbc.M110.213330. Epub 2011 Jan 13.

25.

Profiling RNA polymerase II using the fast chromatin immunoprecipitation method.

Nelson J, Denisenko O, Bomsztyk K.

Methods Mol Biol. 2011;703:219-34. doi: 10.1007/978-1-59745-248-9_15.

PMID:
21125493
26.

Direct recruitment of insulin receptor and ERK signaling cascade to insulin-inducible gene loci.

Nelson JD, LeBoeuf RC, Bomsztyk K.

Diabetes. 2011 Jan;60(1):127-37. doi: 10.2337/db09-1806. Epub 2010 Oct 7.

27.

Poly(ADP-ribose) polymerase-1 (PARP-1) contributes to the barrier function of a vertebrate chromatin insulator.

Aker M, Bomsztyk K, Emery DW.

J Biol Chem. 2010 Nov 26;285(48):37589-97. doi: 10.1074/jbc.M110.174532. Epub 2010 Sep 27.

28.

Halogenated imidazole derivatives block RNA polymerase II elongation along mitogen inducible genes.

Mikula M, Hanusek K, Paziewska A, Dzwonek A, Rubel T, Bomsztyk K, Ostrowski J.

BMC Mol Biol. 2010 Jan 15;11:4. doi: 10.1186/1471-2199-11-4.

29.

The fast chromatin immunoprecipitation method.

Nelson J, Denisenko O, Bomsztyk K.

Methods Mol Biol. 2009;567:45-57. doi: 10.1007/978-1-60327-414-2_3. Review.

PMID:
19588084
30.

BRG1 increases transcription of proinflammatory genes in renal ischemia.

Naito M, Zager RA, Bomsztyk K.

J Am Soc Nephrol. 2009 Aug;20(8):1787-96. doi: 10.1681/ASN.2009010118. Epub 2009 Jun 25.

31.

High ambient glucose augments angiotensin II-induced proinflammatory gene mRNA expression in human mesangial cells: effects of valsartan and simvastatin.

Naito M, Shenoy A, Aoyama I, Koopmeiners JS, Komers R, Schnaper HW, Bomsztyk K.

Am J Nephrol. 2009;30(2):99-111. doi: 10.1159/000203619. Epub 2009 Feb 19.

32.

Renal ischemia-induced cholesterol loading: transcription factor recruitment and chromatin remodeling along the HMG CoA reductase gene.

Naito M, Bomsztyk K, Zager RA.

Am J Pathol. 2009 Jan;174(1):54-62. doi: 10.2353/ajpath.2009.080602. Epub 2008 Dec 18.

33.

Growth and development alter susceptibility to acute renal injury.

Zager RA, Johnson AC, Naito M, Lund SR, Kim N, Bomsztyk K.

Kidney Int. 2008 Sep;74(5):674-8. doi: 10.1038/ki.2008.251. Epub 2008 Jun 18.

34.

Endotoxin mediates recruitment of RNA polymerase II to target genes in acute renal failure.

Naito M, Bomsztyk K, Zager RA.

J Am Soc Nephrol. 2008 Jul;19(7):1321-30. doi: 10.1681/ASN.2007121368. Epub 2008 Apr 16.

35.

Microplate-based chromatin immunoprecipitation method, Matrix ChIP: a platform to study signaling of complex genomic events.

Flanagin S, Nelson JD, Castner DG, Denisenko O, Bomsztyk K.

Nucleic Acids Res. 2008 Feb;36(3):e17. doi: 10.1093/nar/gkn001. Epub 2008 Jan 18.

36.

Transcription of laminin gamma1 chain gene in rat mesangial cells: constitutive and inducible RNA polymerase II recruitment and chromatin states.

Nelson JD, Flanagin S, Kawata Y, Denisenko O, Bomsztyk K.

Am J Physiol Renal Physiol. 2008 Mar;294(3):F525-33. doi: 10.1152/ajprenal.00299.2007. Epub 2008 Jan 9.

37.

Role of chromatin structure in integration of helper-dependent adenoviral vectors containing the beta-globin locus control region.

Sova P, Wang H, Bomsztyk K, Stamatoyannopoulos G, Lieber A.

Hum Gene Ther. 2008 Feb;19(2):153-66. doi: 10.1089/hum.2007.091.

PMID:
18177253
38.

Epistatic interaction between the K-homology domain protein HEK2 and SIR1 at HMR and telomeres in yeast.

Denisenko O, Bomsztyk K.

J Mol Biol. 2008 Jan 25;375(4):1178-87. Epub 2007 Nov 12.

39.

Maleate nephrotoxicity: mechanisms of injury and correlates with ischemic/hypoxic tubular cell death.

Zager RA, Johnson AC, Naito M, Bomsztyk K.

Am J Physiol Renal Physiol. 2008 Jan;294(1):F187-97. Epub 2007 Oct 17.

40.

Quantitative model for binary measurements of protein-protein interactions.

Shi YY, Miller GA, Denisenko O, Qian H, Bomsztyk K.

J Comput Biol. 2007 Sep;14(7):1011-23.

PMID:
17803377
41.

Clustering coefficients of protein-protein interaction networks.

Miller GA, Shi YY, Qian H, Bomsztyk K.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 May;75(5 Pt 1):051910. Epub 2007 May 16.

PMID:
17677101
42.

Heterogeneous nuclear ribonucleoprotein K contributes to angiotensin II stimulation of vascular endothelial growth factor mRNA translation.

Feliers D, Lee MJ, Ghosh-Choudhury G, Bomsztyk K, Kasinath BS.

Am J Physiol Renal Physiol. 2007 Aug;293(2):F607-15. Epub 2007 Jun 20.

43.

Protocol for the fast chromatin immunoprecipitation (ChIP) method.

Nelson JD, Denisenko O, Bomsztyk K.

Nat Protoc. 2006;1(1):179-85.

PMID:
17406230
44.

Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences.

Shi YY, Miller GA, Qian H, Bomsztyk K.

Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11527-32. Epub 2006 Jul 21.

45.

RACK1 binds to Smad3 to modulate transforming growth factor-beta1-stimulated alpha2(I) collagen transcription in renal tubular epithelial cells.

Okano K, Schnaper HW, Bomsztyk K, Hayashida T.

J Biol Chem. 2006 Sep 8;281(36):26196-204. Epub 2006 Jul 18.

46.

Heterogeneous nuclear ribonucleoprotein K modulates angiotensinogen gene expression in kidney cells.

Wei CC, Zhang SL, Chen YW, Guo DF, Ingelfinger JR, Bomsztyk K, Chan JS.

J Biol Chem. 2006 Sep 1;281(35):25344-55. Epub 2006 Jul 12.

47.

Landscape of the hnRNP K protein-protein interactome.

Mikula M, Dzwonek A, Karczmarski J, Rubel T, Dadlez M, Wyrwicz LS, Bomsztyk K, Ostrowski J.

Proteomics. 2006 Apr;6(8):2395-406.

PMID:
16518874
48.

Casein kinases phosphorylate multiple residues spanning the entire hnRNP K length.

Mikula M, Karczmarski J, Dzwonek A, Rubel T, Hennig E, Dadlez M, Bujnicki JM, Bomsztyk K, Ostrowski J.

Biochim Biophys Acta. 2006 Feb;1764(2):299-306. Epub 2006 Jan 6.

PMID:
16448870
49.

Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.

Klimek-Tomczak K, Mikula M, Dzwonek A, Paziewska A, Karczmarski J, Hennig E, Bujnicki JM, Bragoszewski P, Denisenko O, Bomsztyk K, Ostrowski J.

Br J Cancer. 2006 Feb 27;94(4):586-92.

50.

Fast chromatin immunoprecipitation assay.

Nelson JD, Denisenko O, Sova P, Bomsztyk K.

Nucleic Acids Res. 2006 Jan 5;34(1):e2.

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