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Items: 29

1.

Tobacco-Related Alterations in Airway Gene Expression are Rapidly Reversed Within Weeks Following Smoking-Cessation.

Hijazi K, Malyszko B, Steiling K, Xiao X, Liu G, Alekseyev YO, Dumas YM, Hertsgaard L, Jensen J, Hatsukami D, Brooks DR, O'Connor G, Beane J, Lenburg ME, Spira A.

Sci Rep. 2019 May 6;9(1):6978. doi: 10.1038/s41598-019-43295-3.

2.

Effect of long-term corticosteroid treatment on microRNA and gene-expression profiles in COPD.

Faiz A, Steiling K, Roffel MP, Postma DS, Spira A, Lenburg ME, Borggrewe M, Eijgenraam TR, Jonker MR, Koppelman GH, Pouwels SD, Liu G, Alekseyev YO, Lam S, Hiemstra PS, Sterk PJ, Timens W, Brandsma CA, Heijink IH, van den Berge M.

Eur Respir J. 2019 Apr 25;53(4). pii: 1801202. doi: 10.1183/13993003.01202-2018. Print 2019 Apr.

PMID:
30846474
3.

Impact of acute exposure to cigarette smoke on airway gene expression.

Billatos E, Faiz A, Gesthalter Y, LeClerc A, Alekseyev YO, Xiao X, Liu G, Ten Hacken NHT, Heijink IH, Timens W, Brandsma CA, Postma DS, van den Berge M, Spira A, Lenburg ME.

Physiol Genomics. 2018 Sep 1;50(9):705-713. doi: 10.1152/physiolgenomics.00092.2017. Epub 2018 Jun 22.

4.

A Next-Generation Sequencing Primer-How Does It Work and What Can It Do?

Alekseyev YO, Fazeli R, Yang S, Basran R, Maher T, Miller NS, Remick D.

Acad Pathol. 2018 May 6;5:2374289518766521. doi: 10.1177/2374289518766521. eCollection 2018 Jan-Dec. Review.

5.

Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction.

Herbert ZT, Kershner JP, Butty VL, Thimmapuram J, Choudhari S, Alekseyev YO, Fan J, Podnar JW, Wilcox E, Gipson J, Gillaspy A, Jepsen K, BonDurant SS, Morris K, Berkeley M, LeClerc A, Simpson SD, Sommerville G, Grimmett L, Adams M, Levine SS.

BMC Genomics. 2018 Mar 15;19(1):199. doi: 10.1186/s12864-018-4585-1.

6.

TLR3 Signaling Promotes the Induction of Unique Human BDCA-3 Dendritic Cell Populations.

Colletti NJ, Liu H, Gower AC, Alekseyev YO, Arendt CW, Shaw MH.

Front Immunol. 2016 Mar 14;7:88. doi: 10.3389/fimmu.2016.00088. eCollection 2016.

7.

Negative regulation of Bmi-1 by AMPK and implication in cancer progression.

Huang D, He X, Zou J, Guo P, Jiang S, Lv N, Alekseyev Y, Luo L, Luo Z.

Oncotarget. 2016 Feb 2;7(5):6188-200. doi: 10.18632/oncotarget.6748.

8.

Tumor Cell-Derived Periostin Regulates Cytokines That Maintain Breast Cancer Stem Cells.

Lambert AW, Wong CK, Ozturk S, Papageorgis P, Raghunathan R, Alekseyev Y, Gower AC, Reinhard BM, Abdolmaleky HM, Thiagalingam S.

Mol Cancer Res. 2016 Jan;14(1):103-13. doi: 10.1158/1541-7786.MCR-15-0079. Epub 2015 Oct 27.

9.

Gene-expression profiling of buccal epithelium among non-smoking women exposed to household air pollution from smoky coal.

Wang TW, Vermeulen RC, Hu W, Liu G, Xiao X, Alekseyev Y, Xu J, Reiss B, Steiling K, Downward GS, Silverman DT, Wei F, Wu G, Li J, Lenburg ME, Rothman N, Spira A, Lan Q.

Carcinogenesis. 2015 Dec;36(12):1494-501. doi: 10.1093/carcin/bgv150. Epub 2015 Oct 14.

10.

Low-dose radiation affects cardiac physiology: gene networks and molecular signaling in cardiomyocytes.

Coleman MA, Sasi SP, Onufrak J, Natarajan M, Manickam K, Schwab J, Muralidharan S, Peterson LE, Alekseyev YO, Yan X, Goukassian DA.

Am J Physiol Heart Circ Physiol. 2015 Dec 1;309(11):H1947-63. doi: 10.1152/ajpheart.00050.2015. Epub 2015 Sep 25.

11.

Defining the nasal transcriptome in granulomatosis with polyangiitis (Wegener's).

Grayson PC, Steiling K, Platt M, Berman JS, Zhang X, Xiao J, Alekseyev YO, Liu G, Monach PA, Kaplan MJ, Spira A, Merkel PA.

Arthritis Rheumatol. 2015 May;67(8):2233-9. doi: 10.1002/art.39185.

12.

Evaluation of commercially available RNA amplification kits for RNA sequencing using very low input amounts of total RNA.

Shanker S, Paulson A, Edenberg HJ, Peak A, Perera A, Alekseyev YO, Beckloff N, Bivens NJ, Donnelly R, Gillaspy AF, Grove D, Gu W, Jafari N, Kerley-Hamilton JS, Lyons RH, Tepper C, Nicolet CM.

J Biomol Tech. 2015 Apr;26(1):4-18. doi: 10.7171/jbt.15-2601-001.

13.

Distinct gene signatures in aortic tissue from ApoE-/- mice exposed to pathogens or Western diet.

Kramer CD, Weinberg EO, Gower AC, He X, Mekasha S, Slocum C, Beaulieu LM, Wetzler L, Alekseyev Y, Gibson FC 3rd, Freedman JE, Ingalls RR, Genco CA.

BMC Genomics. 2014 Dec 24;15:1176. doi: 10.1186/1471-2164-15-1176.

14.

Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data.

Campbell JD, Liu G, Luo L, Xiao J, Gerrein J, Juan-Guardela B, Tedrow J, Alekseyev YO, Yang IV, Correll M, Geraci M, Quackenbush J, Sciurba F, Schwartz DA, Kaminski N, Johnson WE, Monti S, Spira A, Beane J, Lenburg ME.

RNA. 2015 Feb;21(2):164-71. doi: 10.1261/rna.046060.114. Epub 2014 Dec 17.

15.

Transcriptional responses of neonatal mouse lung to hyperoxia by Nrf2 status.

McGrath-Morrow SA, Lauer T, Collaco JM, Lopez A, Malhotra D, Alekseyev YO, Neptune E, Wise R, Biswal S.

Cytokine. 2014 Jan;65(1):4-9. doi: 10.1016/j.cyto.2013.09.021. Epub 2013 Oct 17.

16.

Airway gene expression in COPD is dynamic with inhaled corticosteroid treatment and reflects biological pathways associated with disease activity.

van den Berge M, Steiling K, Timens W, Hiemstra PS, Sterk PJ, Heijink IH, Liu G, Alekseyev YO, Lenburg ME, Spira A, Postma DS.

Thorax. 2014 Jan;69(1):14-23. doi: 10.1136/thoraxjnl-2012-202878. Epub 2013 Aug 7.

17.

A dynamic bronchial airway gene expression signature of chronic obstructive pulmonary disease and lung function impairment.

Steiling K, van den Berge M, Hijazi K, Florido R, Campbell J, Liu G, Xiao J, Zhang X, Duclos G, Drizik E, Si H, Perdomo C, Dumont C, Coxson HO, Alekseyev YO, Sin D, Pare P, Hogg JC, McWilliams A, Hiemstra PS, Sterk PJ, Timens W, Chang JT, Sebastiani P, O'Connor GT, Bild AH, Postma DS, Lam S, Spira A, Lenburg ME.

Am J Respir Crit Care Med. 2013 May 1;187(9):933-42. doi: 10.1164/rccm.201208-1449OC.

18.

A gene expression signature of emphysema-related lung destruction and its reversal by the tripeptide GHK.

Campbell JD, McDonough JE, Zeskind JE, Hackett TL, Pechkovsky DV, Brandsma CA, Suzuki M, Gosselink JV, Liu G, Alekseyev YO, Xiao J, Zhang X, Hayashi S, Cooper JD, Timens W, Postma DS, Knight DA, Lenburg ME, Hogg JC, Spira A.

Genome Med. 2012 Aug 31;4(8):67. doi: 10.1186/gm367. eCollection 2012.

19.

Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq.

Beane J, Vick J, Schembri F, Anderlind C, Gower A, Campbell J, Luo L, Zhang XH, Xiao J, Alekseyev YO, Wang S, Levy S, Massion PP, Lenburg M, Spira A.

Cancer Prev Res (Phila). 2011 Jun;4(6):803-17. doi: 10.1158/1940-6207.CAPR-11-0212.

20.

Protein kinase CK1alphaLS promotes vascular cell proliferation and intimal hyperplasia.

Panchenko MP, Siddiquee Z, Dombkowski DM, Alekseyev YO, Lenburg ME, Walker JD, Macgillivray TE, Preffer FI, Stone JR.

Am J Pathol. 2010 Sep;177(3):1562-72. doi: 10.2353/ajpath.2010.100327. Epub 2010 Aug 9.

21.

Smad signaling is required to maintain epigenetic silencing during breast cancer progression.

Papageorgis P, Lambert AW, Ozturk S, Gao F, Pan H, Manne U, Alekseyev YO, Thiagalingam A, Abdolmaleky HM, Lenburg M, Thiagalingam S.

Cancer Res. 2010 Feb 1;70(3):968-78. doi: 10.1158/0008-5472.CAN-09-1872. Epub 2010 Jan 19.

22.

Similarities and differences between smoking-related gene expression in nasal and bronchial epithelium.

Zhang X, Sebastiani P, Liu G, Schembri F, Zhang X, Dumas YM, Langer EM, Alekseyev Y, O'Connor GT, Brooks DR, Lenburg ME, Spira A.

Physiol Genomics. 2010 Mar 3;41(1):1-8. doi: 10.1152/physiolgenomics.00167.2009. Epub 2009 Dec 1.

23.

Inactivation of AMPK alters gene expression and promotes growth of prostate cancer cells.

Zhou J, Huang W, Tao R, Ibaragi S, Lan F, Ido Y, Wu X, Alekseyev YO, Lenburg ME, Hu GF, Luo Z.

Oncogene. 2009 May 7;28(18):1993-2002. doi: 10.1038/onc.2009.63. Epub 2009 Apr 6.

24.

DNA polymerase V allows bypass of toxic guanine oxidation products in vivo.

Neeley WL, Delaney S, Alekseyev YO, Jarosz DF, Delaney JC, Walker GC, Essigmann JM.

J Biol Chem. 2007 Apr 27;282(17):12741-8. Epub 2007 Feb 24.

25.

Aflatoxin B1 formamidopyrimidine adducts are preferentially repaired by the nucleotide excision repair pathway in vivo.

Alekseyev YO, Hamm ML, Essigmann JM.

Carcinogenesis. 2004 Jun;25(6):1045-51. Epub 2004 Jan 23.

PMID:
14742311
28.

Significance of nucleobase shape complementarity and hydrogen bonding in the formation and stability of the closed polymerase-DNA complex.

Dzantiev L, Alekseyev YO, Morales JC, Kool ET, Romano LJ.

Biochemistry. 2001 Mar 13;40(10):3215-21.

PMID:
11258938

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