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Higher order genomic organization and epigenetic control maintain cellular identity and prevent breast cancer.

Fritz AJ, Gillis NE, Gerrard DL, Rodriguez PD, Hong D, Rose JT, Ghule PN, Bolf EL, Gordon JA, Tye CE, Boyd JR, Tracy KM, Nickerson JA, van Wijnen AJ, Imbalzano AN, Heath JL, Frietze SE, Zaidi SK, Carr FE, Lian JB, Stein JL, Stein GS.

Genes Chromosomes Cancer. 2019 Jul;58(7):484-499. doi: 10.1002/gcc.22731. Epub 2019 Mar 15. Review.


BRG1 is a prognostic indicator and a potential therapeutic target for prostate cancer.

Muthuswami R, Bailey L, Rakesh R, Imbalzano AN, Nickerson JA, Hockensmith JW.

J Cell Physiol. 2019 Jan 22. doi: 10.1002/jcp.28161. [Epub ahead of print]


RUNX1-dependent mechanisms in biological control and dysregulation in cancer.

Hong D, Fritz AJ, Gordon JA, Tye CE, Boyd JR, Tracy KM, Frietze SE, Carr FE, Nickerson JA, Van Wijnen AJ, Imbalzano AN, Zaidi SK, Lian JB, Stein JL, Stein GS.

J Cell Physiol. 2019 Jun;234(6):8597-8609. doi: 10.1002/jcp.27841. Epub 2018 Dec 4. Review.


Mitotic Gene Bookmarking: An Epigenetic Program to Maintain Normal and Cancer Phenotypes.

Zaidi SK, Nickerson JA, Imbalzano AN, Lian JB, Stein JL, Stein GS.

Mol Cancer Res. 2018 Nov;16(11):1617-1624. doi: 10.1158/1541-7786.MCR-18-0415. Epub 2018 Jul 12. Review.


Epithelial-to-mesenchymal transition and cancer stem cells contribute to breast cancer heterogeneity.

Hong D, Fritz AJ, Zaidi SK, van Wijnen AJ, Nickerson JA, Imbalzano AN, Lian JB, Stein JL, Stein GS.

J Cell Physiol. 2018 Dec;233(12):9136-9144. doi: 10.1002/jcp.26847. Epub 2018 Jul 3. Review.


Nuclear organization mediates cancer-compromised genetic and epigenetic control.

Zaidi SK, Fritz AJ, Tracy KM, Gordon JA, Tye CE, Boyd J, Van Wijnen AJ, Nickerson JA, Imbalzano AN, Lian JB, Stein JL, Stein GS.

Adv Biol Regul. 2018 Aug;69:1-10. doi: 10.1016/j.jbior.2018.05.001. Epub 2018 May 9. Review.


Casein kinase 2-mediated phosphorylation of Brahma-related gene 1 controls myoblast proliferation and contributes to SWI/SNF complex composition.

Padilla-Benavides T, Nasipak BT, Paskavitz AL, Haokip DT, Schnabl JM, Nickerson JA, Imbalzano AN.

J Biol Chem. 2017 Nov 10;292(45):18592-18607. doi: 10.1074/jbc.M117.799676. Epub 2017 Sep 22.


The BRG1 ATPase of human SWI/SNF chromatin remodeling enzymes as a driver of cancer.

Wu Q, Lian JB, Stein JL, Stein GS, Nickerson JA, Imbalzano AN.

Epigenomics. 2017 Jun;9(6):919-931. doi: 10.2217/epi-2017-0034. Epub 2017 May 19. Review.


Mammalian SWI/SNF Enzymes and the Epigenetics of Tumor Cell Metabolic Reprogramming.

Nickerson JA, Wu Q, Imbalzano AN.

Front Oncol. 2017 Apr 4;7:49. doi: 10.3389/fonc.2017.00049. eCollection 2017. Review.


The mammalian LINC complex regulates genome transcriptional responses to substrate rigidity.

Alam SG, Zhang Q, Prasad N, Li Y, Chamala S, Kuchibhotla R, Kc B, Aggarwal V, Shrestha S, Jones AL, Levy SE, Roux KJ, Nickerson JA, Lele TP.

Sci Rep. 2016 Dec 1;6:38063. doi: 10.1038/srep38063.


The BRG1 chromatin remodeling enzyme links cancer cell metabolism and proliferation.

Wu Q, Madany P, Dobson JR, Schnabl JM, Sharma S, Smith TC, van Wijnen AJ, Stein JL, Lian JB, Stein GS, Muthuswami R, Imbalzano AN, Nickerson JA.

Oncotarget. 2016 Jun 21;7(25):38270-38281. doi: 10.18632/oncotarget.9505.


The Ultrastructural Signature of Human Embryonic Stem Cells.

Underwood JM, Becker KA, Stein GS, Nickerson JA.

J Cell Biochem. 2017 Apr;118(4):764-774. doi: 10.1002/jcb.25736. Epub 2016 Dec 29.


Identifying Nuclear Matrix-Attached DNA Across the Genome.

Dobson JR, Hong D, Barutcu AR, Wu H, Imbalzano AN, Lian JB, Stein JL, van Wijnen AJ, Nickerson JA, Stein GS.

J Cell Physiol. 2017 Jun;232(6):1295-1305. doi: 10.1002/jcp.25596. Epub 2017 Jan 5.


SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells.

Barutcu AR, Lajoie BR, Fritz AJ, McCord RP, Nickerson JA, van Wijnen AJ, Lian JB, Stein JL, Dekker J, Stein GS, Imbalzano AN.

Genome Res. 2016 Sep;26(9):1188-201. doi: 10.1101/gr.201624.115. Epub 2016 Jul 19.


Identification of a Chemical Probe for Family VIII Bromodomains through Optimization of a Fragment Hit.

Gerstenberger BS, Trzupek JD, Tallant C, Fedorov O, Filippakopoulos P, Brennan PE, Fedele V, Martin S, Picaud S, Rogers C, Parikh M, Taylor A, Samas B, O'Mahony A, Berg E, Pallares G, Torrey AD, Treiber DK, Samardjiev IJ, Nasipak BT, Padilla-Benavides T, Wu Q, Imbalzano AN, Nickerson JA, Bunnage ME, Müller S, Knapp S, Owen DR.

J Med Chem. 2016 May 26;59(10):4800-11. doi: 10.1021/acs.jmedchem.6b00012. Epub 2016 May 3.


Targeting the chromatin remodeling enzyme BRG1 increases the efficacy of chemotherapy drugs in breast cancer cells.

Wu Q, Sharma S, Cui H, LeBlanc SE, Zhang H, Muthuswami R, Nickerson JA, Imbalzano AN.

Oncotarget. 2016 May 10;7(19):27158-75. doi: 10.18632/oncotarget.8384.


Use of HCA in subproteome-immunization and screening of hybridoma supernatants to define distinct antibody binding patterns.

Szafran AT, Mancini MG, Nickerson JA, Edwards DP, Mancini MA.

Methods. 2016 Mar 1;96:75-84. doi: 10.1016/j.ymeth.2015.10.021. Epub 2015 Oct 30.


Coordinated Dynamics of RNA Splicing Speckles in the Nucleus.

Zhang Q, Kota KP, Alam SG, Nickerson JA, Dickinson RB, Lele TP.

J Cell Physiol. 2016 Jun;231(6):1269-75. doi: 10.1002/jcp.25224. Epub 2015 Nov 24.


Differential Toxicity of Nuclear RNA Foci versus Dipeptide Repeat Proteins in a Drosophila Model of C9ORF72 FTD/ALS.

Tran H, Almeida S, Moore J, Gendron TF, Chalasani U, Lu Y, Du X, Nickerson JA, Petrucelli L, Weng Z, Gao FB.

Neuron. 2015 Sep 23;87(6):1207-1214. doi: 10.1016/j.neuron.2015.09.015.


C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization.

Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS.

J Cell Physiol. 2016 Jan;231(1):31-5. doi: 10.1002/jcp.25062. Review.


Direct force probe reveals the mechanics of nuclear homeostasis in the mammalian cell.

Neelam S, Chancellor TJ, Li Y, Nickerson JA, Roux KJ, Dickinson RB, Lele TP.

Proc Natl Acad Sci U S A. 2015 May 5;112(18):5720-5. doi: 10.1073/pnas.1502111112. Epub 2015 Apr 21.


The SWI/SNF ATPases Are Required for Triple Negative Breast Cancer Cell Proliferation.

Wu Q, Madany P, Akech J, Dobson JR, Douthwright S, Browne G, Colby JL, Winter GE, Bradner JE, Pratap J, Sluder G, Bhargava R, Chiosea SI, van Wijnen AJ, Stein JL, Stein GS, Lian JB, Nickerson JA, Imbalzano AN.

J Cell Physiol. 2015 Nov;230(11):2683-94. doi: 10.1002/jcp.24991.


Subnuclear domain proteins in cancer cells support the functions of RUNX2 in the DNA damage response.

Yang S, Quaresma AJ, Nickerson JA, Green KM, Shaffer SA, Imbalzano AN, Martin-Buley LA, Lian JB, Stein JL, van Wijnen AJ, Stein GS.

J Cell Sci. 2015 Feb 15;128(4):728-40. doi: 10.1242/jcs.160051. Epub 2015 Jan 20.


BRG1, a SWI/SNF chromatin remodeling enzyme ATPase, is required for maintenance of nuclear shape and integrity.

Imbalzano AN, Imbalzano KM, Nickerson JA.

Commun Integr Biol. 2013 Sep 1;6(5):e25153. doi: 10.4161/cib.25153. Epub 2013 Jun 4.


Amyotrophic lateral sclerosis-linked FUS/TLS alters stress granule assembly and dynamics.

Baron DM, Kaushansky LJ, Ward CL, Sama RR, Chian RJ, Boggio KJ, Quaresma AJ, Nickerson JA, Bosco DA.

Mol Neurodegener. 2013 Aug 31;8:30. doi: 10.1186/1750-1326-8-30.


Modulation of Nuclear Shape by Substrate Rigidity.

Lovett DB, Shekhar N, Nickerson JA, Roux KJ, Lele TP.

Cell Mol Bioeng. 2013 Jun 1;6(2):230-238.


Oncogenic targeting of BRM drives malignancy through C/EBPβ-dependent induction of α5 integrin.

Damiano L, Stewart KM, Cohet N, Mouw JK, Lakins JN, Debnath J, Reisman D, Nickerson JA, Imbalzano AN, Weaver VM.

Oncogene. 2014 May 8;33(19):2441-53. doi: 10.1038/onc.2013.220. Epub 2013 Jun 17.


Regulation of mRNA export by the PI3 kinase/AKT signal transduction pathway.

Quaresma AJ, Sievert R, Nickerson JA.

Mol Biol Cell. 2013 Apr;24(8):1208-21. doi: 10.1091/mbc.E12-06-0450. Epub 2013 Feb 20.


Nuclear shape changes are induced by knockdown of the SWI/SNF ATPase BRG1 and are independent of cytoskeletal connections.

Imbalzano KM, Cohet N, Wu Q, Underwood JM, Imbalzano AN, Nickerson JA.

PLoS One. 2013;8(2):e55628. doi: 10.1371/journal.pone.0055628. Epub 2013 Feb 6.


Wnt3 function in the epiblast is required for the maintenance but not the initiation of gastrulation in mice.

Tortelote GG, Hernández-Hernández JM, Quaresma AJ, Nickerson JA, Imbalzano AN, Rivera-Pérez JA.

Dev Biol. 2013 Feb 1;374(1):164-73. doi: 10.1016/j.ydbio.2012.10.013. Epub 2012 Oct 16.


The human nucleolar protein FTSJ3 associates with NIP7 and functions in pre-rRNA processing.

Morello LG, Coltri PP, Quaresma AJ, Simabuco FM, Silva TC, Singh G, Nickerson JA, Oliveira CC, Moore MJ, Zanchin NI.

PLoS One. 2011;6(12):e29174. doi: 10.1371/journal.pone.0029174. Epub 2011 Dec 16.


An architectural genetic and epigenetic perspective.

Stein GS, Stein JL, van Wijnen AJ, Lian JB, Zaidi SK, Nickerson JA, Montecino MA, Young DW.

Integr Biol (Camb). 2011 Apr;3(4):297-303. doi: 10.1039/c0ib00103a. Epub 2010 Dec 24. Review.


Architectural genetic and epigenetic control of regulatory networks: compartmentalizing machinery for transcription and chromatin remodeling in nuclear microenvironments.

Stein GS, van Wijnen AJ, Imbalzano AN, Montecino M, Zaidi SK, Lian JB, Nickerson JA, Stein JL.

Crit Rev Eukaryot Gene Expr. 2010;20(2):149-55. Review.


Live cell imaging of the cancer-related transcription factor RUNX2 during mitotic progression.

Pockwinse SM, Kota KP, Quaresma AJ, Imbalzano AN, Lian JB, van Wijnen AJ, Stein JL, Stein GS, Nickerson JA.

J Cell Physiol. 2011 May;226(5):1383-9. doi: 10.1002/jcp.22465.


Subnuclear localization and intranuclear trafficking of transcription factors.

Zaidi SK, Medina RF, Pockwinse SM, Bakshi R, Kota KP, Ali SA, Young DW, Nickerson JA, Javed A, Montecino M, van Wijnen AJ, Lian JB, Stein JL, Stein GS.

Methods Mol Biol. 2010;647:77-93. doi: 10.1007/978-1-60761-738-9_4.


SWI/SNF chromatin remodeling enzyme ATPases promote cell proliferation in normal mammary epithelial cells.

Cohet N, Stewart KM, Mudhasani R, Asirvatham AJ, Mallappa C, Imbalzano KM, Weaver VM, Imbalzano AN, Nickerson JA.

J Cell Physiol. 2010 Jun;223(3):667-78. doi: 10.1002/jcp.22072.


Beta1 integrins mediate cell proliferation in three-dimensional cultures by regulating expression of the sonic hedgehog effector protein, GLI1.

Goel HL, Underwood JM, Nickerson JA, Hsieh CC, Languino LR.

J Cell Physiol. 2010 Jul;224(1):210-7. doi: 10.1002/jcp.22116.


Ectopic runx2 expression in mammary epithelial cells disrupts formation of normal acini structure: implications for breast cancer progression.

Pratap J, Imbalzano KM, Underwood JM, Cohet N, Gokul K, Akech J, van Wijnen AJ, Stein JL, Imbalzano AN, Nickerson JA, Lian JB, Stein GS.

Cancer Res. 2009 Sep 1;69(17):6807-14. doi: 10.1158/0008-5472.CAN-09-1471. Epub 2009 Aug 18.


Increasingly transformed MCF-10A cells have a progressively tumor-like phenotype in three-dimensional basement membrane culture.

Imbalzano KM, Tatarkova I, Imbalzano AN, Nickerson JA.

Cancer Cell Int. 2009 Mar 16;9:7. doi: 10.1186/1475-2867-9-7.


The biochemistry of RNA metabolism studied in situ.

Nickerson JA.

RNA Biol. 2009 Jan-Mar;6(1):25-30. Epub 2009 Jan 2. Review.


In situ nuclear organization of regulatory machinery.

Pockwinse SM, Zaidi SK, Medina RF, Bakshi R, Kota KP, Ali SA, Young DW, Nickerson JA, Javed A, Montecino M, van Wijnen AJ, Lian JB, Stein JL, Stein GS.

Methods Mol Biol. 2008;455:239-59. doi: 10.1007/978-1-59745-104-8_17.


Binding of ATP to UAP56 is necessary for mRNA export.

Kota KP, Wagner SR, Huerta E, Underwood JM, Nickerson JA.

J Cell Sci. 2008 May 1;121(Pt 9):1526-37. doi: 10.1242/jcs.021055. Epub 2008 Apr 14.


Mitotic occupancy and lineage-specific transcriptional control of rRNA genes by Runx2.

Young DW, Hassan MQ, Pratap J, Galindo M, Zaidi SK, Lee SH, Yang X, Xie R, Javed A, Underwood JM, Furcinitti P, Imbalzano AN, Penman S, Nickerson JA, Montecino MA, Lian JB, Stein JL, van Wijnen AJ, Stein GS.

Nature. 2007 Jan 25;445(7126):442-6.


Methods for measuring rates of protein binding to insoluble scaffolds in living cells: histone H1-chromatin interactions.

Lele T, Wagner SR, Nickerson JA, Ingber DE.

J Cell Biochem. 2006 Dec 1;99(5):1334-42.


An improved mathematical approach for determination of molecular kinetics in living cells with FRAP.

Lele T, Oh P, Nickerson JA, Ingber DE.

Mech Chem Biosyst. 2004 Sep;1(3):181-90.


The ultrastructure of MCF-10A acini.

Underwood JM, Imbalzano KM, Weaver VM, Fischer AH, Imbalzano AN, Nickerson JA.

J Cell Physiol. 2006 Jul;208(1):141-8.


Proteomic analysis of SRm160-containing complexes reveals a conserved association with cohesin.

McCracken S, Longman D, Marcon E, Moens P, Downey M, Nickerson JA, Jessberger R, Wilde A, Caceres JF, Emili A, Blencowe BJ.

J Biol Chem. 2005 Dec 23;280(51):42227-36. Epub 2005 Sep 13.


PTEN enters the nucleus by diffusion.

Liu F, Wagner S, Campbell RB, Nickerson JA, Schiffer CA, Ross AH.

J Cell Biochem. 2005 Oct 1;96(2):221-34. Erratum in: J Cell Biochem. 2016 Mar;117(3):806.


Pulse energy dependence of subcellular dissection by femtosecond laser pulses.

Heisterkamp A, Maxwell IZ, Mazur E, Underwood JM, Nickerson JA, Kumar S, Ingber DE.

Opt Express. 2005 May 16;13(10):3690-6.


Brg1, the ATPase subunit of the SWI/SNF chromatin remodeling complex, is required for myeloid differentiation to granulocytes.

Vradii D, Wagner S, Doan DN, Nickerson JA, Montecino M, Lian JB, Stein JL, van Wijnen AJ, Imbalzano AN, Stein GS.

J Cell Physiol. 2006 Jan;206(1):112-8.


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