Publications (in reverse chronological order as of March 2017)

80. Nuclear mechano-genomics, Caroline Uhler & G.V.Shivashankar, Nature Reviews Molecular Cell Biology, (invited review 2017 – under submission)

79. Chromosome intermingling as mechanical hotspots for genome regulation, Caroline Uhler & G.V.Shivashankar, Trends in Cell Biology (invited review 2017 – under submission)

78. Geometric confinement of cells induce nuclear reprogramming, Bibhas Roy, Prasuna Rao and G.V.Shivashankar (2017 – under review)

77. Cell-geometric-constraints differentially regulate TNFα-mediated gene expression programs, Aninda Mitra, Saradha.V. Pathy, Prasuna Rao and G.V.Shivashankar Proceedings of the National Academy of Sciences-USA – (final revision, 2017)

76. Cell geometry orients and repositions chromosomes to regulate genomic programs, Yejun Wang, Mallika Nagarajan, Caroline Uhler and G.V.Shivashankar Molecular Biology of the Cell, (final revision, 2017)

75. Nuclear positioning and its translation dynamics is regulated by cell geometry, K. Radhakrishna, Saradha V. Pathy and G.V. Shivashankar Biophysical Journal (2017 – in press)

74. Superresolution imaging of nanoscale chromosome contacts, Yejun Wang, Prasuna Ratna and G.V. Shivashankar Nature Sci Rep. (2017-in press)

73. Geometric control and modeling of genome reprogramming, Caroline Uhler and G.V. Shivashankar. BioArchitecture. 2016 Jul 19:1-9.

72. Nuclear plasticity and telomere dynamics is modulated by extra-cellular matrix constraints, Ekta Makhija, Jokhun Kamal and G.V.Shivashankar, Proceedings of the National Academy of Sciences-USA (2016) 113(1):E32-40.

71. Matrix Mechanics Controls FHL2 Movement to the Nucleus to Activate p21/CDKN1A Expression, Naotaka Nakazawa, Aneesh R. Sathe, G. V. Shivashankar and Mike Sheetz Proceedings of the National Academy of Sciences-USA (2016 - in press)

70. Nuclear transport of paxillin depends on focal adhesion dynamics and FAT Domains, Aneesh Sathe, G.V.Shivashankar and Mike Sheetz, Journal of Cell Science (2016 – in press)

69. Nuclear transport of paxillin depends on focal adhesion dynamics and FAT Domains, Aneesh Sathe, G.V.Shivashankar and Mike Sheetz, Journal of Cell Science (2016 – in press)

68. Chromosome intermingling - the physical basis of chromosome organization in differentiated cells, Shovamayee Maharana, K.Venkatesan Iyer, Nikhil Jain, Mallika Nagarajan, Yejun Wang and G.V.Shivashankar Nucleic Acids Research, (2016) doi: 10.1093/nar/gkw131

67. Regulation of nuclear morphology by actomyosin components and cell geometry. Ramdas NM, Qingsen Li, Shivashankar GV Proc IEEE Eng Med Biol Soc. 2015:342-5.

66. 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 4(11):1569-75.

65. Actin cytoskeleton differentially alters the dynamics of lamin A/C, HP1α and H2B core histone proteins to remodel chromatin condensation state in living cells, Kee Chua Toh, Nisha Ramdas and G.V.Shivashankar Integrative Biology, 2015 (10):1309-17.

64. Mechanical stimulation induces formin-dependent assembly of a perinuclear actin rim, Xiaowei Shao, Li Qingsen, Alexandar Mogilner, Alexandar Bershadsky and G.V.Shivashankar, Proceedings of the National Academy of Sciences-USA (2015) 112(20):E2595-601 3

63. Cytoskeletal control of nuclear morphology and chromatin organization, Nisha M Ramdas and G.V.Shivashankar, Journal of Molecular Biology (2015) 427(3):695-706

62. Micropillar displacements by cell traction forces are mechanically correlated with nuclear dynamics, Li Qingsen, Ekta Makhija, F.M. Hameed and G.V.Shivashankar, Biochemical and Biophysical Research Communications, (2015) 461(2):372-7

61. The regulation of gene expression during onset of differentiation by nuclear mechanical heterogeneity, Shefali Talwar, Nikhil Jain & G.V.Shivashankar Biomaterials. (2014) 35, 2411-19

60. The regulation of dynamic mechanical coupling between actin cytoskeleton and nucleus by matrix geometry Li Qingsen, Abhishek Kumar, Ekta Makhija & G.V.Shivashankar Biomaterials. (2014) 35, 961-69.

59. Super-resolution microscopy reveals decondensed chromatin structure at transcription sites, Yejun Wang, Shovamayee Maharana, Michelle Wang & G.V.Shivashankar Nature Sci Rep. (2014) Mar 26;4:4477

58. Acto-myosin contractility rotates the cell nucleus Abhishek Kumar, Ananyo Maitra, Madhuresh Sumit, Sriram Ramaswamy & G.V. Shivashankar Nature Sci Rep. 2014 Jan 21;4:3781

57. ATR mediates a mechanical checkpoint at the nuclear envelope in response to membrane stress. Amit Kumar, Michele Mazzanti, Martin Mistrik, Galina Beznusenko, Alexandre Mironov, Massimiliano Garre, Dario Parazzoli, G.V. Shivashankar, Giorgio Scita, Jiri Bartek and Marco Fioni (2014) Cell, 158, 633-646

56. Yap-Taz as mechanosensors and mechanotransducers in regulating organ size and tumor growth Low BC, Pan CQ, G.V.Shivashankar, Bershadsky A, Sudol M, Sheetz M. (2014) FEBS Lett. 19;588(16):2663-2670

55. Multivariate biophysical markers predictive of mesenchymal stromal cell multipotency, Wong Cheng Lee, Hui Shi, Zhiyong Poon, Lin Myint Nyan, Tanwi Kaushik, G V. Shivashankar, Jerry K Y Chan, Chwee Teck Lim, Jongyoon Han & Krystyn J. Van Vliet, Proceedings of the National Academy of Sciences-USA (2014) Oct 21;111(42):E4409-18

54. Probing Chromatin Structure and Dynamics Using Fluorescence Anisotropy Imaging, Ekta Makhija, K. Venkatesan Iyer, Shefali Talwar & G.V.Shivashankar CRC Handbook, Imaging Biological Mechanics (2014)

53. The C-terminal domain (CTD) in linker histones antagonizes anti-apoptotic proteins to modulate apoptotic outcomes at the mitochondrion. M.Garg, N.Ramdas, M.Vijayalakshmi, G.V.Shivashankar, A.Sarin Cell Death & Disease (2014) 5:e1058.

52. The linker histone H1.2 is an intermediate in the apoptotic response to cytokine deprivation to T-cell effectors Garg M, Perumalsamy LR, G.V.Shivashankar, Sarin A. Int J Cell Biol. (2014): 674753

51. Model for deformation of cell nucleus by cortical actin layer Gur Fabrikanth, Soumya Gupta, G.V.Shivashankar & Misha Kozlov Biophysical Journal (2013) 105:1316-23.

50. Cell geometric constraints induce modular gene-expression patterns via redistribution of HDAC3 regulated by actomyosin contractility Nikhil Jain, K.Venkatesan Iyer, Abhishek Kumar & G.V.Shivashankar Proceedings of the National Academy of Sciences (2013) 110: 11349-54

49. Correlated spatio-temporal fluctuations in chromatin compaction states characterize stem cells, Shefali Talwar, Abhishek Kumar, Madan Rao, Gautam Menon & G.V.Shivashankar Biophysical Journal (2013) 104:553-64

48. Dynamic organization of transcription factories is dependent on functional nuclear architecture Shovamayee Maharana, Divya Sharma, Shi Xianke & G.V. Shivashankar Biophysical Journal (2012) 103:851-859

47. Mechanical activation of cells reveals distinct timescales in chromatin remodeling and MKL nuclear transport Venkatesan Iyer, Stephanie Pulford, Alex Mogilner & G.V.Shivashankar Biophysical Journal (2012) 103:1416-1428

46. Mechanical force alters morphogenetic movements and segmental gene expression patterns during Drosophila embryogenesis Abhishek Kumar & G.V. Shivashankar PLoS One. 2012;7(3):e33089

45. Developmental heterogeneity in DNA packaging patterns influences T-cell activation and transmigration Soumya Gupta, Shefali Talwar, R.Indulaxmi, Lakshmi R. Perumalsamy, Apurva Sarin & G.V.Shivashankar PLoS One. 2012;7(9):e43718

44. Modeling and experimental methods to probe the link between global transcription and spatial organization of chromosomes K.Venkatesan Iyer, Shovamayee Maharana, Soumya Gupta, Albert Libchaber, Tsvi Tlusty & G.V. Shivashankar PLoS One. 2012;7(10):e46628. (Faculty of 1000 publication)

43. Dynamics of passive and active particles in the cell nucleus Feroz Meeran, Madan Rao & G.V.Shivashankar PLoS One. 2012;7(10):e45843.

42. Role of actin dependent nuclear deformation in regulating early gene expression, Soumya Gupta, Nimi Marcel, Apurva Sarin & G.V.Shivashankar PLoS-One. 2012;7(12):e53031

41. Mechanosignaling to cell nucleus and genome regulation G.V.Shivashankar, Annual Reviews of Biophysics, (2011), Vol.40, 361-378

40. Integrin adhesion drives the emergent polarisation of active cytoskeletal stresses to pattern cell delamination C Meghana, Nisha Ramdas, Feroz Hameed, Madan Rao, G.V. Shivashankar & Maithreyi Narasimha, Proceedings of the National Academy of SciencesUSA (2011), 108, 9107-9112

39. Dynamic organization of chromatin assembly & transcription factories in living cells Bidisha Sinha, Dipanjan Bhattacharya, Deepak Kumar Sinha, Shefali Talwar, Shovamayee Maharana, Soumya Gupta & G. V.Shivashankar, Methods Cell Biol. (2010) 98, 57-78 5

38. Prestressed Nuclear Organization in Living Cells, Aprotim Mazumder, Roopa T., Abhishek Kumar, K.Venkatesan Iyer, Nisha M Ramdas & G. V.Shivashankar, Methods Cell Biol. (2010) 98, 221-239

37. Emergence of prestressed eukaryotic nucleus during cellular differentiation and development Mazumder A, Shivashankar GV.J R Soc Interface. (2010) Suppl 3:S321-30.

36. Spatio-temporal plasticity in chromatin organization in mouse cell differentiation & during Drosophila embryogenesis Dipanjan Bhattacharya, Shefali Talwar, Aprotim Mazumder & G.V.Shivashankar, Biophysical Journal (2009) 96, 3832-3839

35. Probing structural stability of chromatin assembly sorted from living cells, FM Hameed, G.V.Soni, H.Krishnamurthy & G.V.Shivashankar, Biochem Biophys Res Commun. (2009) 385, 518-522

34. Probing the dynamic organization of transcription compartments and gene loci within the nucleus of living cells Deepak Kumar Sinha, Bidisha Banerjee, Shovamayee Maharana, & G.V.Shivashankar Biophysical Journal (2008) 95, 5432-5438

33. Dynamics of chromatin decondensation reveals the structural integrity of a mechanically prestressed cell nucleus T.Roopa, Aakash Basu, Aprotim Mazumder, L.Mahadevan & G.V.Shivashankar Biophysical Journal (2008) 95, 3028-3035

32. Gold-nanoparticle-assisted laser ablation of chromatin assembly reveals unusual aspects of nuclear architecture within living cells Aprotim Mazumder & G.V.Shivashankar Biophysical Journal (2007) 93, 2209-2216

31. Thermal fluctuations in histone during denaturation K.S.Nagapriya, A.K.Raychaudhuri & G.V.Shivashankar J Nanosci Nanotechnol (2007) 7, 2125-2128

30. Simulations of SIN Mutations and Histone Variants in Human Nucleosomes Reveal Altered Protein-DNA and Core Histone Interactions M.Vijayalaxmi, G.V.Shivashankar & R.Sowdhamini J Biomol Struct Dyn (2007) 25, 207-218

29. Trichostatin-A induces differential changes in histone protein dynamics and expression in HeLa cells Jyothsna Rao, Dipanjan Bhattacharya, Bidisha Banerjee, Apurva Sarin & G.V.Shivashankar Biochem Biophys Res Commun (2007) 363, 263-268

28. Mechanical unfolding of DNA-histone complex reveals distinct levels in its nanoscale organization. G.V.Soni, Feroz Meeran & G.V.Shivashankar Applied Physics Letters – (2007), 90, 163904

27. Direct measurement of chromatin fluidity using optical trap modulation force spectroscopy, T.Roopa & G.V.Shivashankar Biophysical Journal – (2006) 91, 4632-4637

26. Core and linker histones diffuse via distinct mechanisms within living cells Dipanjan Bhattacharya, Aprotim Mazumder, M.Anne & G.V.Shivashankar Biophysical Journal (2006), 91, 2326-2336

25. Chromatin assembly exhibits spatio-temporal heterogeneity within the cell nucleus Bidisha Banerjee, Dipanjan Bhattacharya & G.V.Shivashankar Biophysical Journal (2006), 91, 2297-2303 (Cover page)

24. Probing mRNA conformational heterogeneity using single-molecule fluorescence anisotropy Deepak Sinha, S.Sastry & G.V.Shivashankar Applied Physics Letters (2006) 88, 3901-3903

23. Origins & implications of long-tailed distributions in gene expression, Sandeep Krishna, Bidisha Banerjee, T.V.Ramakrishnan & G.V.Shivashankar Proceedings of the National Academy of Sciences-USA (2005), 102, 4771-4776

22. Kinetic measurement of ribosome motor stalling force Deepak Sinha, U.S.Bhalla & G.V.Shivashankar, Applied Physics Letters (2004), 85, 4789-4791

21. Probing collective dynamics of active particles using modulation force spectroscopy, G.V.Soni, G.Ananthakrishna & G.V.Shivashankar, Applied Physics Letters (2004), 85, 2414-2416

20. Dynamics of Membrane Nanotubulation and DNA Self-Assembly, T.Roopa, N.Kumar, S.Bhattacharya & G.V.Shivashankar, Biophysical Journal (2004), 87, 974-979

19. Development of single molecule tracking fluorescence microscope combined with force spectroscopy for gene expression analysis. Deepak Sinha, Dipanjan Bhattacharya, Bidisha Banerjee, Feroz Meeran & G.V.Shivashankar, Current Science, 2004, 87:239-244.

18. Tracking operator state fluctuations in gene expression in single cells. Bidisha Banerjee, S.Balasubramanian, G.Ananthakrishna, T.V.Ramakrishnan & G.V.Shivashankar Biophysical Journal (2004), 86, 3052-3059

17. Nanomechanics of membrane tubulation and DNA assembly T.Roopa & G.V.Shivashankar Applied Physics Letters (2003), 82, 1631-1633

16. Single particle tracking of correlated bacterial dynamicsG.V.Soni, B.M.Jaffar Ali, Y.Hatwalne & G.V.Shivashankar Biophysical Journal (2003), 84, 2634-2637

15. Development of an optical tweezer combined with micromanipulation for DNA & Protein nanobioscience, G.V.Soni, Feroz Meeran, T.Roopa & G.V.Shivashankar, Current Science (2002), 83, 1464-1470

14. Mesoscopic Biology G.V.Shivashankar, Pramana-Indian Journal of Physics, (2002) 58: 439-442

See full CV.