Publications List

• Mar D, Babenko IM, Zhang R, Noble WS, Denisenko O, Vaisar T, Bomsztyk K. A High-Throughput PIXUL-Matrix-Based Toolbox to Profile Frozen and Formalin-Fixed Paraffin-Embedded Tissues Multiomes. Lab Invest. 2024 Jan;104(1):100282. doi: 10.1016/j.labinv.2023.100282. Epub 2023 Nov 3. PMID: 37924947.
• Schactler SA, Scheuerman SJ, Lius A, Altemeier WA, An D, Matula TJ, Mikula M, Kulecka M, Denisenko O, Mar D, Bomsztyk K. CryoGrid-PIXUL-RNA: high throughput RNA isolation platform for tissue transcript analysis. BMC Genomics. 2023 Aug 8;24(1):446. doi: 10.1186/s12864-023-09527-7. PMID: 37553584; PMCID: PMC10408117.
• Levy S, Somasundaram L, Raj IX, Ic-Mex D, Phal A, Schmidt S, Ng WI, Mar D, Decarreau J, Moss N, Alghadeer A, Honkanen H, Sarthy J, Vitanza N, Hawkins RD, Mathieu J, Wang Y, Baker D, Bomsztyk K, and Ruohola-Baker H. dCas9 fusion to computer-designed PRC2 inhibitor reveals functional TATA box in distal promoter region. Cell Rep 38: 110457, 2022.
• Kint S, Van Criekinge W, Vandekerckhove L, De Vos WH, Bomsztyk K, Krause DS, and Denisenko O. Single cell epigenetic visualization assay. Nucleic Acids Res 49: e43, 2021
• Kopczynski M, Rumienczyk I, Kulecka M, Statkiewicz M, Pysniak K, Sandowska-Markiewicz Z, Wojcik-Trechcinska U, Goryca K, Pyziak K, Majewska E, Masiejczyk M, Wojcik-Jaszczynska K, Rzymski T,Bomsztyk K, Ostrowski J, and Mikula M. Selective Extracellular Signal-Regulated Kinase 1/2 (ERK1/2) Inhibition by the SCH772984 Compound Attenuates In Vitro and In Vivo Inflammatory Responses and Prolongs Survival in Murine Sepsis Models. Int J Mol Sci 22: 2021.
• Rumienczyk I, Kulecka M, Ostrowski J, Mar D, Bomsztyk K, Standage SW, and Mikula M. Multi-Organ Transcriptome Dynamics in a Mouse Model of Cecal Ligation and Puncture-Induced Polymicrobial Sepsis. J Inflamm Res 14: 2377-2388, 2021.
• Bomsztyk K, Wang Y. Genome-bound enzymes as epigenetic drug targets in cancer. Epigenomics. 2019 Oct;11(13):1463-1467. doi: 10.2217/epi-2019-0197. Epub 2019 Sep 19. PMID: 31536377.
• Kanter JE, Shao B, Kramer F, Barnhart S, Shimizu-Albergine M, Vaisar T, Graham MJ, Crooke RM, Manuel CR, Haeusler RA, Mar D, Bomsztyk K, Hokanson JE, Kinney GL, Snell-Bergeon JK, Heinecke JW, Bornfeldt KE. Increased apolipoprotein C3 drives cardiovascular risk in type 1 diabetes. J Clin Invest. 2019 Jul 11;129(10):4165-4179. doi: 10.1172/JCI127308. PMID: 31295146; PMCID: PMC6763229.
• Bomsztyk K, Mar D, Wang Y, Denisenko O, Ware C, Frazar CD, Blattler A, Maxwell AD, MacConaghy BE, Matula TJ. PIXUL-ChIP: integrated high-throughput sample preparation and analytical platform for epigenetic studies. Nucleic Acids Res. 2019 Jul 9;47(12):e69. doi: 10.1093/nar/gkz222. PMID: 30927002; PMCID: PMC6614803.
• Sharifian R, Okamura DM, Denisenko O, Zager RA, Johnson A, Gharib SA, Bomsztyk K. Distinct patterns of transcriptional and epigenetic alterations characterize acute and chronic kidney injury. Sci Rep. 2018 Dec 14;8(1):17870. doi: 10.1038/s41598-018-35943-x. PMID: 30552397; PMCID: PMC6294783.
• Haynes P, Bomsztyk K, Miller DG. Sporadic DUX4 expression in FSHD myocytes is associated with incomplete repression by the PRC2 complex and gain of H3K9 acetylation on the contracted D4Z4 allele. Epigenetics Chromatin. 2018 Aug 20;11(1):47. doi: 10.1186/s13072-018-0215-z. PMID: 30122154; PMCID: PMC6100714.
• Bomsztyk K, Denisenko O, Wang Y. DNA methylation yields epigenetic clues into the diabetic nephropathy of Pima Indians. Kidney Int. 2018 Jun;93(6):1272-1275. doi: 10.1016/j.kint.2018.02.015. PMID: 29792271.
• Denisenko O, Mar D, Trawczynski M, Bomsztyk K. Chromatin changes trigger laminin genes dysregulation in aging kidneys. Aging (Albany NY). 2018 May 29;10(5):1133-1145. doi: 10.18632/aging.101453. PMID: 29846172; PMCID: PMC5990391.
• Kotha SS, Hayes BJ, Phong KT, Redd MA, Bomsztyk K, Ramakrishnan A, Torok-Storb B, Zheng Y. Engineering a multicellular vascular niche to model hematopoietic cell trafficking. Stem Cell Res Ther. 2018 Mar 23;9(1):77. doi: 10.1186/s13287-018-0808-2. PMID: 29566751; PMCID: PMC5865379.
• Denisenko O, Lucas ES, Sun C, Watkins AJ, Mar D, Bomsztyk K, Fleming TP. Regulation of ribosomal RNA expression across the lifespan is fine-tuned by maternal diet before implantation. Biochim Biophys Acta. 2016 Jul;1859(7):906-13. doi: 10.1016/j.bbagrm.2016.04.001. Epub 2016 Apr 7. PMID: 27060415; PMCID: PMC4914606.
• Gharib SA, Mar D, Bomsztyk K, Denisenko O, Dhanireddy S, Liles WC, Altemeier WA. SYSTEM-WIDE MAPPING OF ACTIVATED CIRCUITRY IN EXPERIMENTAL SYSTEMIC INFLAMMATORY RESPONSE SYNDROME. Shock. 2016 Feb;45(2):148-56. doi: 10.1097/SHK.0000000000000507. Erratum in: Shock. 2016 Apr;45(4):469. Erratum in: Shock. 2016 Feb 12;: PMID: 26536201; PMCID: PMC4715796.
• Mikula M, Rubel T, Karczmarski J, Statkiewicz M, Bomsztyk K, Ostrowski J. Beads-free protein immunoprecipitation for a mass spectrometry-based interactome and posttranslational modifications analysis. Proteome Sci. 2015 Sep 2;13:23. doi: 10.1186/s12953-015-0079-0. PMID: 26336360; PMCID: PMC4557753.
• Mar D, Gharib SA, Zager RA, Johnson A, Denisenko O, Bomsztyk K. Heterogeneity of epigenetic changes at ischemia/reperfusion- and endotoxin-induced acute kidney injury genes. Kidney Int. 2015 Oct;88(4):734-44. doi: 10.1038/ki.2015.164. Epub 2015 Jun 10. PMID: 26061546; PMCID: PMC4589440.
• 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. M2 Macrophage Polarization Mediates Anti-inflammatory Effects of Endothelial Nitric Oxide Signaling. Diabetes. 2015 Aug;64(8):2836-46. doi: 10.2337/db14-1668. Epub 2015 Apr 6. PMID: 25845662; PMCID: PMC4512216.
• Mikula M, Bomsztyk K, Goryca K, Chojnowski K, Ostrowski J. Heterogeneous nuclear ribonucleoprotein (HnRNP) K genome-wide binding survey reveals its role in regulating 3′-end RNA processing and transcription termination at the early growth response 1 (EGR1) gene through XRN2 exonuclease. J Biol Chem. 2013 Aug 23;288(34):24788-98. doi: 10.1074/jbc.M113.496679. Epub 2013 Jul 15. PMID: 23857582; PMCID: PMC3750174.
• Bomsztyk K, Denisenko O. Epigenetic alterations in acute kidney injury. Semin Nephrol. 2013 Jul;33(4):327-40. doi: 10.1016/j.semnephrol.2013.05.005. PMID: 24011575; PMCID: PMC3768006.
• Mikula M, Bomsztyk K.Direct recruitment of ERK cascade components to inducible genes is regulated by heterogeneous nuclear ribonucleoprotein (hnRNP) K. J Biol Chem. 2011 Mar 18;286(11):9763-75. doi: 10.1074/jbc.M110.213330. Epub 2011 Jan 13. PMID: 21233203; PMCID: PMC3058954.

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