G. V. Shivashankar
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View article: Acute chromatin decompaction stiffens the nucleus as revealed by nanopillar-induced nuclear deformation in cells
Acute chromatin decompaction stiffens the nucleus as revealed by nanopillar-induced nuclear deformation in cells Open
Chromatin architecture is critical in determining nuclear mechanics. Most studies focus on the mechanical rigidity conferred by chromatin condensation from densely packed heterochromatin, but less is known on how transient chromatin decomp…
View article: Yielding behaviour of active particles in bulk and in confinement
Yielding behaviour of active particles in bulk and in confinement Open
Collective behaviour in dense assemblies of self-propelled active particles occurs in a wide range of biological phenomena, including the dynamical transitions of cellular and subcellular biological assemblies such as the cytoskeleton and …
View article: Compressive Forces Induce Epigenetic Activation of Aged Human Dermal Fibroblasts Through <scp>ERK</scp> Signaling Pathway
Compressive Forces Induce Epigenetic Activation of Aged Human Dermal Fibroblasts Through <span>ERK</span> Signaling Pathway Open
Age‐related changes in human dermal fibroblasts (HDFs) contribute to impaired wound healing and skin aging. While these changes result in altered mechanotransduction, the epigenetic basis of rejuvenating aging cells remains a significant c…
View article: Acute chromatin decompaction stiffens the nucleus as revealed by nanopillar-induced nuclear deformation in cells
Acute chromatin decompaction stiffens the nucleus as revealed by nanopillar-induced nuclear deformation in cells Open
Chromatin architecture is critical in determining nuclear mechanics. Most studies focus on the mechanical rigidity conferred by chromatin compaction from densely packed heterochromatin, but less is known on how transient changes in chromat…
View article: Regulation of p65 nuclear localization and chromatin states by compressive force
Regulation of p65 nuclear localization and chromatin states by compressive force Open
The tumor microenvironment (TME) is a dynamic ecosystem, that evolves with the developing tumor to support its growth and metastasis. A key aspect of TME evolution is the recruitment of stromal fibroblasts, carried out via the release of v…
View article: Remodeling of cytoskeleton, chromatin, and gene expression during mechanical rejuvenation of aged human dermal fibroblasts
Remodeling of cytoskeleton, chromatin, and gene expression during mechanical rejuvenation of aged human dermal fibroblasts Open
Aging is associated with a progressive decline in cellular function. To reset the aged cellular phenotype, various reprogramming approaches, including mechanical routes, have been explored. However, the epigenetic mechanisms underlying cel…
View article: Compressive forces induce epigenetic activation of aged human dermal fibroblasts through ERK signaling pathway
Compressive forces induce epigenetic activation of aged human dermal fibroblasts through ERK signaling pathway Open
Age-related changes in human dermal fibroblasts (HDFs) contribute to impaired wound healing and skin aging. While these changes result in altered mechanotransduction, the epigenetic basis of rejuvenating aging cells remains a significant c…
View article: Partially Shared Multi-Modal Embedding Learns Holistic Representation of Cell State
Partially Shared Multi-Modal Embedding Learns Holistic Representation of Cell State Open
Experimental technologies for jointly measuring different data modalities at the single-cell level offer different windows into cell state. To obtain a holistic understanding of cell state, computational methods are needed that carefully i…
View article: Imaging and AI based chromatin biomarkers for diagnosis and therapy evaluation from liquid biopsies
Imaging and AI based chromatin biomarkers for diagnosis and therapy evaluation from liquid biopsies Open
Multiple genomic and proteomic studies have suggested that peripheral blood mononuclear cells (PBMCs) respond to tumor secretomes and thus could provide possible avenues for tumor prognosis and treatment evaluation. We hypothesized that th…
View article: Adhesome Receptor Clustering is Accompanied by the Co- localization of the Associated Genes in the Cell Nucleus
Adhesome Receptor Clustering is Accompanied by the Co- localization of the Associated Genes in the Cell Nucleus Open
Proteins on the cell membrane cluster to respond to extracellular signals; for example, adhesion proteins cluster to enhance extracellular matrix sensing; or T-cell receptors cluster to enhance antigen sensing. Importantly, the maturation …
View article: Transcriptional changes are tightly coupled to chromatin reorganization during cellular aging
Transcriptional changes are tightly coupled to chromatin reorganization during cellular aging Open
Human life expectancy is constantly increasing and aging has become a major risk factor for many diseases, although the underlying gene regulatory mechanisms are still unclear. Using transcriptomic and chromosomal conformation capture (Hi‐…
View article: Yielding behaviour of active particles in bulk and in confinement
Yielding behaviour of active particles in bulk and in confinement Open
The investigation of collective behaviour in dense assemblies of self-propelled active particles has been motivated by a wide range of biological phenomena. Of particular interest are dynamical transitions of cellular and sub-cellular biol…
View article: Implanting mechanically reprogrammed fibroblasts for aged tissue regeneration and wound healing
Implanting mechanically reprogrammed fibroblasts for aged tissue regeneration and wound healing Open
Cell‐based therapies are essential for tissue regeneration and wound healing during aging. Autologous transplantation of aging cells is ineffective due to their increased senescence and reduced tissue remodeling capabilities. Alternatively…
View article: Detecting radio- and chemoresistant cells in 3D cancer co-cultures using chromatin biomarkers
Detecting radio- and chemoresistant cells in 3D cancer co-cultures using chromatin biomarkers Open
The heterogenous treatment response of tumor cells limits the effectiveness of cancer therapy. While this heterogeneity has been linked to cell-to-cell variability within the complex tumor microenvironment, a quantitative biomarker that id…
View article: Deleterious Mechanical Deformation Selects Mechanoresilient Cancer Cells with Enhanced Proliferation and Chemoresistance
Deleterious Mechanical Deformation Selects Mechanoresilient Cancer Cells with Enhanced Proliferation and Chemoresistance Open
Cancer cells in secondary tumors are found to form metastases more efficiently as compared to their primary tumor counterparts. This is partially due to the unfavorable microenvironments encountered by metastasizing cancer cells that resul…
View article: Chromatin remodeling due to transient-link-and-pass activity enhances subnuclear dynamics
Chromatin remodeling due to transient-link-and-pass activity enhances subnuclear dynamics Open
Spatiotemporal coordination of chromatin and subnuclear compartments is crucial for cells. Numerous enzymes act inside nucleus\textemdash some of those transiently link and pass two chromatin segments. Here we study how such an active pert…
View article: Supplementary Information from TGFβ Promotes Genomic Instability after Loss of RUNX3
Supplementary Information from TGFβ Promotes Genomic Instability after Loss of RUNX3 Open
Supplementary Methods, Legends for Supplementary Figures,Legend for Table 1 and References
View article: Supplementary Information from TGFβ Promotes Genomic Instability after Loss of RUNX3
Supplementary Information from TGFβ Promotes Genomic Instability after Loss of RUNX3 Open
Supplementary Methods, Legends for Supplementary Figures,Legend for Table 1 and References
View article: Supplementary Figures 1-8 from TGFβ Promotes Genomic Instability after Loss of RUNX3
Supplementary Figures 1-8 from TGFβ Promotes Genomic Instability after Loss of RUNX3 Open
This file contains Supplementary Figures 1-8. Fig.S1 shows Characterization of TGF-β-dependent EMT. Fig.S2 shows an analysis of endogenous DNA damage accumulation in the presence of TGF-β. Fig.S3 shows the Upregulation of NOX4 and downregu…
View article: Supplementary Figures 1-8 from TGFβ Promotes Genomic Instability after Loss of RUNX3
Supplementary Figures 1-8 from TGFβ Promotes Genomic Instability after Loss of RUNX3 Open
This file contains Supplementary Figures 1-8. Fig.S1 shows Characterization of TGF-β-dependent EMT. Fig.S2 shows an analysis of endogenous DNA damage accumulation in the presence of TGF-β. Fig.S3 shows the Upregulation of NOX4 and downregu…
View article: Data from TGFβ Promotes Genomic Instability after Loss of RUNX3
Data from TGFβ Promotes Genomic Instability after Loss of RUNX3 Open
Studies of genomic instability have historically focused on intrinsic mechanisms rather than extrinsic mechanisms based in the tumor microenvironment (TME). TGFβ is the most abundantly secreted cytokine in the TME, where it imparts various…
View article: Data from TGFβ Promotes Genomic Instability after Loss of RUNX3
Data from TGFβ Promotes Genomic Instability after Loss of RUNX3 Open
Studies of genomic instability have historically focused on intrinsic mechanisms rather than extrinsic mechanisms based in the tumor microenvironment (TME). TGFβ is the most abundantly secreted cytokine in the TME, where it imparts various…
View article: Supplementary Table.1 from TGFβ Promotes Genomic Instability after Loss of RUNX3
Supplementary Table.1 from TGFβ Promotes Genomic Instability after Loss of RUNX3 Open
Supplementary Table 1 shows the differential expression analysis of RNA sequencing data. A list of genes that are differentially expressed upon TGF-beta treatment as well as upon RUNX3-Knockdown are shown.
View article: Supplementary Table.1 from TGFβ Promotes Genomic Instability after Loss of RUNX3
Supplementary Table.1 from TGFβ Promotes Genomic Instability after Loss of RUNX3 Open
Supplementary Table 1 shows the differential expression analysis of RNA sequencing data. A list of genes that are differentially expressed upon TGF-beta treatment as well as upon RUNX3-Knockdown are shown.
View article: How enzymatic activity is involved in chromatin organization
How enzymatic activity is involved in chromatin organization Open
Spatial organization of chromatin plays a critical role in genome regulation. Previously, various types of affinity mediators and enzymes have been attributed to regulate spatial organization of chromatin from a thermodynamics perspective.…
View article: Author response: How enzymatic activity is involved in chromatin organization
Author response: How enzymatic activity is involved in chromatin organization Open
Article Figures and data Abstract Editor's evaluation Introduction Results Discussion Methods Data availability References Decision letter Author response Article and author information Metrics Abstract Spatial organization of chromatin pl…