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Items: 1 to 50 of 104

1.

Chromosome territories and the global regulation of the genome.

Fritz AJ, Sehgal N, Pliss A, Xu J, Berezney R.

Genes Chromosomes Cancer. 2019 Jul;58(7):407-426. doi: 10.1002/gcc.22732. Epub 2019 Mar 18. Review.

PMID:
30664301
2.

Large-scale probabilistic 3D organization of human chromosome territories.

Sehgal N, Fritz AJ, Vecerova J, Ding H, Chen Z, Stojkovic B, Bhattacharya S, Xu J, Berezney R.

Hum Mol Genet. 2016 Feb 1;25(3):419-36. doi: 10.1093/hmg/ddv479. Epub 2015 Nov 24.

3.

Reorganization of the interchromosomal network during keratinocyte differentiation.

Sehgal N, Seifert B, Ding H, Chen Z, Stojkovic B, Bhattacharya S, Xu J, Berezney R.

Chromosoma. 2016 Jun;125(3):389-403. doi: 10.1007/s00412-015-0546-5. Epub 2015 Oct 21.

PMID:
26490167
4.

Fluctuations and synchrony of RNA synthesis in nucleoli.

Pliss A, Kuzmin AN, Kachynski AV, Baev A, Berezney R, Prasad PN.

Integr Biol (Camb). 2015 Jun;7(6):681-92. doi: 10.1039/c5ib00008d.

PMID:
25985251
5.

MATR3 disruption in human and mouse associated with bicuspid aortic valve, aortic coarctation and patent ductus arteriosus.

Quintero-Rivera F, Xi QJ, Keppler-Noreuil KM, Lee JH, Higgins AW, Anchan RM, Roberts AE, Seong IS, Fan X, Lage K, Lu LY, Tao J, Hu X, Berezney R, Gelb BD, Kamp A, Moskowitz IP, Lacro RV, Lu W, Morton CC, Gusella JF, Maas RL.

Hum Mol Genet. 2015 Apr 15;24(8):2375-89. doi: 10.1093/hmg/ddv004. Epub 2015 Jan 7.

6.

Cell type specific alterations in interchromosomal networks across the cell cycle.

Fritz AJ, Stojkovic B, Ding H, Xu J, Bhattacharya S, Berezney R.

PLoS Comput Biol. 2014 Oct 2;10(10):e1003857. doi: 10.1371/journal.pcbi.1003857. eCollection 2014 Oct. Erratum in: PLoS Comput Biol. 2014 Dec;10(12):e1004064.

7.

Gene density and chromosome territory shape.

Sehgal N, Fritz AJ, Morris K, Torres I, Chen Z, Xu J, Berezney R.

Chromosoma. 2014 Oct;123(5):499-513. doi: 10.1007/s00412-014-0480-y. Epub 2014 Aug 9.

8.

Non-Random Patterns in the Distribution of NOR-Bearing Chromosome Territories in Human Fibroblasts: A Network Model of Interactions.

Pliss A, Fritz AJ, Stojkovic B, Ding H, Mukherjee L, Bhattacharya S, Xu J, Berezney R.

J Cell Physiol. 2015 Feb;230(2):427-39. doi: 10.1002/jcp.24726.

9.

Wide-scale alterations in interchromosomal organization in breast cancer cells: defining a network of interacting chromosomes.

Fritz AJ, Stojkovic B, Ding H, Xu J, Bhattacharya S, Gaile D, Berezney R.

Hum Mol Genet. 2014 Oct 1;23(19):5133-46. doi: 10.1093/hmg/ddu237. Epub 2014 May 15.

10.

Assembly of the SLIP1-SLBP complex on histone mRNA requires heterodimerization and sequential binding of SLBP followed by SLIP1.

Bansal N, Zhang M, Bhaskar A, Itotia P, Lee E, Shlyakhtenko LS, Lam TT, Fritz A, Berezney R, Lyubchenko YL, Stafford WF, Thapar R.

Biochemistry. 2013 Jan 22;52(3):520-36. doi: 10.1021/bi301074r. Epub 2013 Jan 11.

11.

Alterations in replication timing of cancer-related genes in malignant human breast cancer cells.

Fritz A, Sinha S, Marella N, Berezney R.

J Cell Biochem. 2013 May;114(5):1074-83. doi: 10.1002/jcb.24447.

12.

A dominant negative Cx43 mutant differentially affects tumorigenic and invasive properties in human metastatic melanoma cells.

Zucker SN, Bancroft TA, Place DE, Des Soye B, Bagati A, Berezney R.

J Cell Physiol. 2013 Apr;228(4):853-9. doi: 10.1002/jcp.24235.

PMID:
23042412
13.

The prolyl isomerase Pin1 targets stem-loop binding protein (SLBP) to dissociate the SLBP-histone mRNA complex linking histone mRNA decay with SLBP ubiquitination.

Krishnan N, Lam TT, Fritz A, Rempinski D, O'Loughlin K, Minderman H, Berezney R, Marzluff WF, Thapar R.

Mol Cell Biol. 2012 Nov;32(21):4306-22. doi: 10.1128/MCB.00382-12. Epub 2012 Aug 20.

14.

Preferential induction of apoptotic cell death in melanoma cells as compared with normal keratinocytes using a non-thermal plasma torch.

Zucker SN, Zirnheld J, Bagati A, DiSanto TM, Des Soye B, Wawrzyniak JA, Etemadi K, Nikiforov M, Berezney R.

Cancer Biol Ther. 2012 Nov;13(13):1299-306. doi: 10.4161/cbt.21787. Epub 2012 Aug 16.

15.

Chromatin dynamics in living cells: identification of oscillatory motion.

Pliss A, Malyavantham KS, Bhattacharya S, Berezney R.

J Cell Physiol. 2013 Mar;228(3):609-16. doi: 10.1002/jcp.24169.

PMID:
22886456
16.

Computing maximum association graph in microscopic nucleus images.

Stojkovic B, Zhu Y, Xu J, Fritz A, Zeitz MJ, Vecerova J, Berezney R.

Med Image Comput Comput Assist Interv. 2010;13(Pt 2):530-7.

PMID:
20879356
17.

The architecture of functional neighborhoods within the mammalian cell nucleus.

Malyavantham KS, Bhattacharya S, Berezney R.

Adv Enzyme Regul. 2010;50(1):126-34. doi: 10.1016/j.advenzreg.2009.10.003. Epub 2009 Dec 3. Review. No abstract available.

18.

Chromosomal rearrangements during human epidermal keratinocyte differentiation.

Marella NV, Seifert B, Nagarajan P, Sinha S, Berezney R.

J Cell Physiol. 2009 Oct;221(1):139-46. doi: 10.1002/jcp.21855.

PMID:
19626667
19.

Cytogenetic and cDNA microarray expression analysis of MCF10 human breast cancer progression cell lines.

Marella NV, Malyavantham KS, Wang J, Matsui S, Liang P, Berezney R.

Cancer Res. 2009 Jul 15;69(14):5946-53. doi: 10.1158/0008-5472.CAN-09-0420. Epub 2009 Jul 7. Erratum in: Cancer Res. 2009 Oct 1;69(19):7894.

20.

Matrin 3: chromosomal distribution and protein interactions.

Zeitz MJ, Malyavantham KS, Seifert B, Berezney R.

J Cell Biochem. 2009 Sep 1;108(1):125-33. doi: 10.1002/jcb.22234.

PMID:
19562669
21.

A probabilistic model for the arrangement of a subset of human chromosome territories in WI38 human fibroblasts.

Zeitz MJ, Mukherjee L, Bhattacharya S, Xu J, Berezney R.

J Cell Physiol. 2009 Oct;221(1):120-9. doi: 10.1002/jcp.21842.

PMID:
19507193
22.

Cell type specific chromosome territory organization in the interphase nucleus of normal and cancer cells.

Marella NV, Bhattacharya S, Mukherjee L, Xu J, Berezney R.

J Cell Physiol. 2009 Oct;221(1):130-8. doi: 10.1002/jcp.21836.

PMID:
19496171
23.

Chromatin dynamics is correlated with replication timing.

Pliss A, Malyavantham K, Bhattacharya S, Zeitz M, Berezney R.

Chromosoma. 2009 Aug;118(4):459-70. doi: 10.1007/s00412-009-0208-6. Epub 2009 Mar 19.

24.

Organization of the amplified type I interferon gene cluster and associated chromosome regions in the interphase nucleus of human osteosarcoma cells.

Zeitz MJ, Marella NV, Malyavantham KS, Goetze S, Bode J, Raska I, Berezney R.

Chromosome Res. 2009;17(3):305-19. doi: 10.1007/s10577-009-9023-4. Epub 2009 Mar 13.

25.

Ladder-like amplification of the type I interferon gene cluster in the human osteosarcoma cell line MG63.

Marella NV, Zeitz MJ, Malyavantham KS, Pliss A, Matsui S, Goetze S, Bode J, Raska I, Berezney R.

Chromosome Res. 2008;16(8):1177-92. doi: 10.1007/s10577-008-1267-x. Epub 2008 Nov 15.

26.

Identifying functional neighborhoods within the cell nucleus: proximity analysis of early S-phase replicating chromatin domains to sites of transcription, RNA polymerase II, HP1gamma, matrin 3 and SAF-A.

Malyavantham KS, Bhattacharya S, Barbeitos M, Mukherjee L, Xu J, Fackelmayer FO, Berezney R.

J Cell Biochem. 2008 Oct 1;105(2):391-403. doi: 10.1002/jcb.21834.

27.

Spatio-temporal dynamics of replication and transcription sites in the mammalian cell nucleus.

Malyavantham KS, Bhattacharya S, Alonso WD, Acharya R, Berezney R.

Chromosoma. 2008 Dec;117(6):553-67. doi: 10.1007/s00412-008-0172-6. Epub 2008 Jul 4.

28.

Comparison of intensity based similarity measures for matching genomic structures in microscopic images of living cells.

Bhattacharya S, Acharya R, Pliss A, Malyavantham KS, Berezney R.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:3057-61.

PMID:
17946542
29.

On mobility analysis of functional sites from time lapse microscopic image sequences of living cell nucleus.

Mukherjee L, Singh V, Xu J, Malyavantham KS, Berezney R.

Med Image Comput Comput Assist Interv. 2006;9(Pt 2):577-85.

PMID:
17354819
30.

Automated matching of genomic structures in microscopic images of living cells using an information theoretic approach.

Bhattacharya S, Acharya R, Pliss A, Malyavantham KS, Berezney R.

Conf Proc IEEE Eng Med Biol Soc. 2005;6:6425-8.

PMID:
17281739
31.

Fractal analysis of replication site images of the human cell nucleus.

Bhattacharya S, Malyavantham KS, Acharya R, Berezney R.

Conf Proc IEEE Eng Med Biol Soc. 2004;2:1443-6.

PMID:
17271966
32.

Motion tracking and intensity surface recovery in microscopic nuclear images.

Mukherjee L, Lin M, Xu J, Berezney R.

Med Image Comput Comput Assist Interv. 2005;8(Pt 1):876-84.

PMID:
16685929
33.

Spatio-temporal dynamics of genomic organization and function in the mammalian cell nucleus.

Berezney R, Malyavantham KS, Pliss A, Bhattacharya S, Acharya R.

Adv Enzyme Regul. 2005;45:17-26. Epub 2005 Sep 1. No abstract available.

PMID:
16139341
34.

Activation of NMDA receptors induces protein kinase A-mediated phosphorylation and degradation of matrin 3. Blocking these effects prevents NMDA-induced neuronal death.

Giordano G, Sánchez-Pérez AM, Montoliu C, Berezney R, Malyavantham K, Costa LG, Calvete JJ, Felipo V.

J Neurochem. 2005 Aug;94(3):808-18. Epub 2005 Jul 5.

35.

Replication-coupled modulation of early replicating chromatin domains detected by anti-actin antibody.

Fidlerová H, Masata M, Malínský J, Fialová M, Cvacková Z, Louzecká A, Koberna K, Berezney R, Raska I.

J Cell Biochem. 2005 Apr 1;94(5):899-916.

PMID:
15714458
36.

Spatio-temporal dynamics at rDNA foci: global switching between DNA replication and transcription.

Pliss A, Koberna K, Vecerová J, Malínský J, Masata M, Fialová M, Raska I, Berezney R.

J Cell Biochem. 2005 Feb 15;94(3):554-65.

PMID:
15543556
37.

Electron microscopy of DNA replication in 3-D: evidence for similar-sized replication foci throughout S-phase.

Koberna K, Ligasová A, Malínský J, Pliss A, Siegel AJ, Cvacková Z, Fidlerová H, Masata M, Fialová M, Raska I, Berezney R.

J Cell Biochem. 2005 Jan 1;94(1):126-38.

PMID:
15523671
38.

Nuclear matrix bound fibroblast growth factor receptor is associated with splicing factor rich and transcriptionally active nuclear speckles.

Somanathan S, Stachowiak EK, Siegel AJ, Stachowiak MK, Berezney R.

J Cell Biochem. 2003 Nov 1;90(4):856-69.

PMID:
14587039
39.

Integrative nuclear FGFR1 signaling (INFS) as a part of a universal "feed-forward-and-gate" signaling module that controls cell growth and differentiation.

Stachowiak MK, Fang X, Myers JM, Dunham SM, Berezney R, Maher PA, Stachowiak EK.

J Cell Biochem. 2003 Nov 1;90(4):662-91. Review.

PMID:
14587025
40.

Diacylglycerol kinase-theta is localized in the speckle domains of the nucleus.

Tabellini G, Bortul R, Santi S, Riccio M, Baldini G, Cappellini A, Billi AM, Berezney R, Ruggeri A, Cocco L, Martelli AM.

Exp Cell Res. 2003 Jul 1;287(1):143-54.

PMID:
12799190
41.
42.

Regulating the mammalian genome: the role of nuclear architecture.

Berezney R.

Adv Enzyme Regul. 2002;42:39-52. Review. No abstract available.

PMID:
12123705
43.

Integrative nuclear FGFR1 signaling (INFS) pathway mediates activation of the tyrosine hydroxylase gene by angiotensin II, depolarization and protein kinase C.

Peng H, Myers J, Fang X, Stachowiak EK, Maher PA, Martins GG, Popescu G, Berezney R, Stachowiak MK.

J Neurochem. 2002 May;81(3):506-24.

44.

Targeting of PCNA to sites of DNA replication in the mammalian cell nucleus.

Somanathan S, Suchyna TM, Siegel AJ, Berezney R.

J Cell Biochem. 2001;81(1):56-67.

PMID:
11180397
45.

25 years of contributions to characterizing gene expression and replication within the three-dimensional context of nuclear architecture.

Stein GS, Berezney R.

Crit Rev Eukaryot Gene Expr. 2000;10(1):v-vi. No abstract available.

PMID:
10813388
46.

Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci.

Berezney R, Dubey DD, Huberman JA.

Chromosoma. 2000 Mar;108(8):471-84. Review.

PMID:
10794569
47.

25 years of contributions to characterizing gene expression and replication within the three-dimensional context of nuclear architecture.

Stein ES, Berezney R.

Crit Rev Eukaryot Gene Expr. 1999;9(3-4):v-vi. No abstract available.

PMID:
10651233
48.
50.

The new paradigm: integrating genomic function and nuclear architecture.

Berezney R, Wei X.

J Cell Biochem Suppl. 1998;30-31:238-42. Review.

PMID:
9893276

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