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Soft inclusion in a confined fluctuating active gel.

Singh Vishen A, Rupprecht JF, Shivashankar GV, Prost J, Rao M.

Phys Rev E. 2018 Mar;97(3-1):032602. doi: 10.1103/PhysRevE.97.032602.


Laterally confined growth of cells induces nuclear reprogramming in the absence of exogenous biochemical factors.

Roy B, Venkatachalapathy S, Ratna P, Wang Y, Jokhun DS, Nagarajan M, Shivashankar GV.

Proc Natl Acad Sci U S A. 2018 May 22;115(21):E4741-E4750. doi: 10.1073/pnas.1714770115. Epub 2018 May 7.


Nuclear Mechanopathology and Cancer Diagnosis.

Uhler C, Shivashankar GV.

Trends Cancer. 2018 Apr;4(4):320-331. doi: 10.1016/j.trecan.2018.02.009. Epub 2018 Mar 16. Review.


Mechanical Strain Alters Cellular and Nuclear Dynamics at Early Stages of Oligodendrocyte Differentiation.

Makhija E, Jagielska A, Zhu L, Bost AC, Ong W, Chew SY, Shivashankar GV, Van Vliet KJ.

Front Cell Neurosci. 2018 Mar 6;12:59. doi: 10.3389/fncel.2018.00059. eCollection 2018.


Maximal Fluctuations of Confined Actomyosin Gels: Dynamics of the Cell Nucleus.

Rupprecht JF, Singh Vishen A, Shivashankar GV, Rao M, Prost J.

Phys Rev Lett. 2018 Mar 2;120(9):098001. doi: 10.1103/PhysRevLett.120.098001.


Machine Learning for Nuclear Mechano-Morphometric Biomarkers in Cancer Diagnosis.

Radhakrishnan A, Damodaran K, Soylemezoglu AC, Uhler C, Shivashankar GV.

Sci Rep. 2017 Dec 20;7(1):17946. doi: 10.1038/s41598-017-17858-1.


DNA damage causes rapid accumulation of phosphoinositides for ATR signaling.

Wang YH, Hariharan A, Bastianello G, Toyama Y, Shivashankar GV, Foiani M, Sheetz MP.

Nat Commun. 2017 Dec 14;8(1):2118. doi: 10.1038/s41467-017-01805-9.


Network analysis identifies chromosome intermingling regions as regulatory hotspots for transcription.

Belyaeva A, Venkatachalapathy S, Nagarajan M, Shivashankar GV, Uhler C.

Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):13714-13719. doi: 10.1073/pnas.1708028115. Epub 2017 Dec 11.


Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks.

Michelini F, Pitchiaya S, Vitelli V, Sharma S, Gioia U, Pessina F, Cabrini M, Wang Y, Capozzo I, Iannelli F, Matti V, Francia S, Shivashankar GV, Walter NG, d'Adda di Fagagna F.

Nat Cell Biol. 2017 Dec;19(12):1400-1411. doi: 10.1038/ncb3643. Epub 2017 Nov 27.


TGFβ Promotes Genomic Instability after Loss of RUNX3.

Krishnan V, Chong YL, Tan TZ, Kulkarni M, Bin Rahmat MB, Tay LS, Sankar H, Jokhun DS, Ganesan A, Chuang LSH, Voon DC, Shivashankar GV, Thiery JP, Ito Y.

Cancer Res. 2018 Jan 1;78(1):88-102. doi: 10.1158/0008-5472.CAN-17-1178. Epub 2017 Oct 26.


Regulation of genome organization and gene expression by nuclear mechanotransduction.

Uhler C, Shivashankar GV.

Nat Rev Mol Cell Biol. 2017 Dec;18(12):717-727. doi: 10.1038/nrm.2017.101. Epub 2017 Oct 18. Review.


Chromosome Intermingling: Mechanical Hotspots for Genome Regulation.

Uhler C, Shivashankar GV.

Trends Cell Biol. 2017 Nov;27(11):810-819. doi: 10.1016/j.tcb.2017.06.005. Epub 2017 Jul 17. Review.


Orientation and repositioning of chromosomes correlate with cell geometry-dependent gene expression.

Wang Y, Nagarajan M, Uhler C, Shivashankar GV.

Mol Biol Cell. 2017 Jul 7;28(14):1997-2009. doi: 10.1091/mbc.E16-12-0825. Epub 2017 Jun 14.


Coupling between chromosome intermingling and gene regulation during cellular differentiation.

Wang Y, Jain N, Nagarajan M, Maharana S, Iyer KV, Talwar S, Shivashankar GV.

Methods. 2017 Jul 1;123:66-75. doi: 10.1016/j.ymeth.2017.05.022. Epub 2017 May 26. Review.


Nuclear Positioning and Its Translational Dynamics Are Regulated by Cell Geometry.

Radhakrishnan AV, Jokhun DS, Venkatachalapathy S, Shivashankar GV.

Biophys J. 2017 May 9;112(9):1920-1928. doi: 10.1016/j.bpj.2017.03.025.


Mechanical Strain Promotes Oligodendrocyte Differentiation by Global Changes of Gene Expression.

Jagielska A, Lowe AL, Makhija E, Wroblewska L, Guck J, Franklin RJM, Shivashankar GV, Van Vliet KJ.

Front Cell Neurosci. 2017 Apr 20;11:93. doi: 10.3389/fncel.2017.00093. eCollection 2017.


Cell geometry dictates TNFα-induced genome response.

Mitra A, Venkatachalapathy S, Ratna P, Wang Y, Jokhun DS, Shivashankar GV.

Proc Natl Acad Sci U S A. 2017 May 16;114(20):E3882-E3891. doi: 10.1073/pnas.1618007114. Epub 2017 May 1.


Letter from the editors.

Gunning P, Shivashankar GV.

Bioarchitecture. 2016 Nov;6(6):105. doi: 10.1080/19490992.2016.1291050. No abstract available.


Dynamic interaction between actin and nesprin2 maintain the cell nucleus in a prestressed state.

Kumar A, Shivashankar GV.

Methods Appl Fluoresc. 2016 Nov 11;4(4):044008. doi: 10.1088/2050-6120/4/4/044008.


Superresolution imaging of nanoscale chromosome contacts.

Wang Y, Ratna P, Shivashankar GV.

Sci Rep. 2017 Feb 10;7:42422. doi: 10.1038/srep42422.


How cells respond to environmental cues - insights from bio-functionalized substrates.

Ruprecht V, Monzo P, Ravasio A, Yue Z, Makhija E, Strale PO, Gauthier N, Shivashankar GV, Studer V, Albiges-Rizo C, Viasnoff V.

J Cell Sci. 2017 Jan 1;130(1):51-61. doi: 10.1242/jcs.196162. Epub 2016 Nov 17. Review.


Matrix mechanics controls FHL2 movement to the nucleus to activate p21 expression.

Nakazawa N, Sathe AR, Shivashankar GV, Sheetz MP.

Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):E6813-E6822. Epub 2016 Oct 14.


Geometric control and modeling of genome reprogramming.

Uhler C, Shivashankar GV.

Bioarchitecture. 2016 Jul 3;6(4):76-84. doi: 10.1080/19490992.2016.1201620. Epub 2016 Jul 19.


Nuclear transport of paxillin depends on focal adhesion dynamics and FAT domains.

Sathe AR, Shivashankar GV, Sheetz MP.

J Cell Sci. 2016 May 15;129(10):1981-8. doi: 10.1242/jcs.172643. Epub 2016 Apr 11.


Chromosome intermingling-the physical basis of chromosome organization in differentiated cells.

Maharana S, Iyer KV, Jain N, Nagarajan M, Wang Y, Shivashankar GV.

Nucleic Acids Res. 2016 Jun 20;44(11):5148-60. doi: 10.1093/nar/gkw131. Epub 2016 Mar 2.


Regulation of nuclear morphology by actomyosin components and cell geometry.

Ramdas NM, Li Q, Shivashankar GV.

Conf Proc IEEE Eng Med Biol Soc. 2015;2015:342-5. doi: 10.1109/EMBC.2015.7318369.


Nuclear deformability and telomere dynamics are regulated by cell geometric constraints.

Makhija E, Jokhun DS, Shivashankar GV.

Proc Natl Acad Sci U S A. 2016 Jan 5;113(1):E32-40. doi: 10.1073/pnas.1513189113. Epub 2015 Dec 22.


Novel localization of formin mDia2: importin β-mediated delivery to and retention at the cytoplasmic side of the nuclear envelope.

Shao X, Kawauchi K, Shivashankar GV, Bershadsky AD.

Biol Open. 2015 Oct 30;4(11):1569-75. doi: 10.1242/bio.013649.



Shivashankar GV, Sheetz M, Matsudaira P.

Integr Biol (Camb). 2015 Oct;7(10):1091-2. doi: 10.1039/c5ib90040a. Epub 2015 Sep 25. No abstract available.


Actin cytoskeleton differentially alters the dynamics of lamin A, HP1α and H2B core histone proteins to remodel chromatin condensation state in living cells.

Toh KC, Ramdas NM, Shivashankar GV.

Integr Biol (Camb). 2015 Oct;7(10):1309-17. doi: 10.1039/c5ib00027k. Epub 2015 Sep 11.


Mechanical stimulation induces formin-dependent assembly of a perinuclear actin rim.

Shao X, Li Q, Mogilner A, Bershadsky AD, Shivashankar GV.

Proc Natl Acad Sci U S A. 2015 May 19;112(20):E2595-601. doi: 10.1073/pnas.1504837112. Epub 2015 May 4.


Micropillar displacements by cell traction forces are mechanically correlated with nuclear dynamics.

Li Q, Makhija E, Hameed FM, Shivashankar GV.

Biochem Biophys Res Commun. 2015 May 29;461(2):372-7. doi: 10.1016/j.bbrc.2015.04.041. Epub 2015 Apr 22.


Multivariate biophysical markers predictive of mesenchymal stromal cell multipotency.

Lee WC, Shi H, Poon Z, Nyan LM, Kaushik T, Shivashankar GV, Chan JK, Lim CT, Han J, Van Vliet KJ.

Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):E4409-18. doi: 10.1073/pnas.1402306111. Epub 2014 Oct 8.


Cytoskeletal control of nuclear morphology and chromatin organization.

Ramdas NM, Shivashankar GV.

J Mol Biol. 2015 Feb 13;427(3):695-706. doi: 10.1016/j.jmb.2014.09.008. Epub 2014 Oct 2.


ATR mediates a checkpoint at the nuclear envelope in response to mechanical stress.

Kumar A, Mazzanti M, Mistrik M, Kosar M, Beznoussenko GV, Mironov AA, Garrè M, Parazzoli D, Shivashankar GV, Scita G, Bartek J, Foiani M.

Cell. 2014 Jul 31;158(3):633-46. doi: 10.1016/j.cell.2014.05.046.


YAP/TAZ as mechanosensors and mechanotransducers in regulating organ size and tumor growth.

Low BC, Pan CQ, Shivashankar GV, Bershadsky A, Sudol M, Sheetz M.

FEBS Lett. 2014 Aug 19;588(16):2663-70. doi: 10.1016/j.febslet.2014.04.012. Epub 2014 Apr 18. Review.


The linker histone h1.2 is an intermediate in the apoptotic response to cytokine deprivation in T-effectors.

Garg M, Perumalsamy LR, Shivashankar GV, Sarin A.

Int J Cell Biol. 2014;2014:674753. doi: 10.1155/2014/674753. Epub 2014 Feb 13.


Super-resolution microscopy reveals decondensed chromatin structure at transcription sites.

Wang Y, Maharana S, Wang MD, Shivashankar GV.

Sci Rep. 2014 Mar 26;4:4477. doi: 10.1038/srep04477.


The C-terminal domain (CTD) in linker histones antagonizes anti-apoptotic proteins to modulate apoptotic outcomes at the mitochondrion.

Garg M, Ramdas N, Vijayalakshmi M, Shivashankar GV, Sarin A.

Cell Death Dis. 2014 Feb 13;5:e1058. doi: 10.1038/cddis.2014.20.


Actomyosin contractility rotates the cell nucleus.

Kumar A, Maitra A, Sumit M, Ramaswamy S, Shivashankar GV.

Sci Rep. 2014 Jan 21;4:3781. doi: 10.1038/srep03781.


The regulation of gene expression during onset of differentiation by nuclear mechanical heterogeneity.

Talwar S, Jain N, Shivashankar GV.

Biomaterials. 2014 Mar;35(8):2411-9. doi: 10.1016/j.biomaterials.2013.12.010. Epub 2013 Dec 30.


The regulation of dynamic mechanical coupling between actin cytoskeleton and nucleus by matrix geometry.

Li Q, Kumar A, Makhija E, Shivashankar GV.

Biomaterials. 2014 Jan;35(3):961-9. doi: 10.1016/j.biomaterials.2013.10.037. Epub 2013 Oct 31.


Model of T-cell nuclear deformation by the cortical actin layer.

Fabrikant G, Gupta S, Shivashankar GV, Kozlov MM.

Biophys J. 2013 Sep 17;105(6):1316-23. doi: 10.1016/j.bpj.2013.07.024.


Cell geometric constraints induce modular gene-expression patterns via redistribution of HDAC3 regulated by actomyosin contractility.

Jain N, Iyer KV, Kumar A, Shivashankar GV.

Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11349-54. doi: 10.1073/pnas.1300801110. Epub 2013 Jun 24.


Correlated spatio-temporal fluctuations in chromatin compaction states characterize stem cells.

Talwar S, Kumar A, Rao M, Menon GI, Shivashankar GV.

Biophys J. 2013 Feb 5;104(3):553-64. doi: 10.1016/j.bpj.2012.12.033.


Role of actin dependent nuclear deformation in regulating early gene expression.

Gupta S, Marcel N, Sarin A, Shivashankar GV.

PLoS One. 2012;7(12):e53031. doi: 10.1371/journal.pone.0053031. Epub 2012 Dec 28.


Dynamics of passive and active particles in the cell nucleus.

Hameed FM, Rao M, Shivashankar GV.

PLoS One. 2012;7(10):e45843. doi: 10.1371/journal.pone.0045843. Epub 2012 Oct 15.


Mechanical activation of cells induces chromatin remodeling preceding MKL nuclear transport.

Iyer KV, Pulford S, Mogilner A, Shivashankar GV.

Biophys J. 2012 Oct 3;103(7):1416-28. doi: 10.1016/j.bpj.2012.08.041. Epub 2012 Oct 2.


Modeling and experimental methods to probe the link between global transcription and spatial organization of chromosomes.

Iyer KV, Maharana S, Gupta S, Libchaber A, Tlusty T, Shivashankar GV.

PLoS One. 2012;7(10):e46628. doi: 10.1371/journal.pone.0046628. Epub 2012 Oct 1.


Dynamic organization of transcription compartments is dependent on functional nuclear architecture.

Maharana S, Sharma D, Shi X, Shivashankar GV.

Biophys J. 2012 Sep 5;103(5):851-9.

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