Ranya Virk
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View article: Leveraging chromatin packing domains to target chemoevasion in vivo
Leveraging chromatin packing domains to target chemoevasion in vivo Open
Cancer cells exhibit a remarkable resilience to cytotoxic stress, often adapting through transcriptional changes linked to alterations in chromatin structure. In several types of cancer, these adaptations involve epigenetic modifications a…
View article: Leveraging chromatin packing domains to target chemoevasion<i>in vivo</i>
Leveraging chromatin packing domains to target chemoevasion<i>in vivo</i> Open
Cancer cells exhibit a remarkable resilience to cytotoxic stress, often adapting through transcriptional changes linked to alterations in chromatin structure. In several types of cancer, these adaptations involve epigenetic modifications a…
View article: The Impact of Charge Regulation and Ionic Intranuclear Environment on the Nucleosome Core Particle
The Impact of Charge Regulation and Ionic Intranuclear Environment on the Nucleosome Core Particle Open
We theoretically investigate how the intranuclear environment influences the charge of a nucleosome core particle (NCP) - the fundamental unit of chromatin consisting of DNA wrapped around a core of histone proteins. The molecular-based th…
View article: Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM)
Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM) Open
Chromatin organization over multiple length scales plays a critical role in the regulation of transcription. Deciphering the interplay of these processes requires high-resolution, three-dimensional, quantitative imaging of chromatin struct…
View article: A Call to Diversify the Lingua Franca of Academic STEM Communities
A Call to Diversify the Lingua Franca of Academic STEM Communities Open
The current bias in the STEM academy favors English-language research publications, creating a barrier between English-speaking and non-English speaking researchers that is detrimental to the continuity and evolution of STEM research. In t…
View article: Chromatin Reprogramming via Contact Guidance-Induced Nuclear Deformation Promotes Stem Cell Differentiation
Chromatin Reprogramming via Contact Guidance-Induced Nuclear Deformation Promotes Stem Cell Differentiation Open
Efficient manipulation of cell fate is important for regenerative engineering applications. Lineage-specific differentiation of stem cells is particularly challenging due to their inherent plasticity. Engineered topographies may alter cell…
View article: Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function
Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function Open
nano-ChIA combines multiple nanoimaging modalities to uncover 4D chromatin organization and its relationship to molecular function.
View article: Exposure of mammary cells to lipid activates gene expression changes associated with ER-negative breast cancer via chromatin remodeling
Exposure of mammary cells to lipid activates gene expression changes associated with ER-negative breast cancer via chromatin remodeling Open
Improved understanding of local breast biology that favors the development of estrogen receptor negative (ER-) breast cancer (BC) would foster better prevention strategies. We have previously shown that overexpression of specific lipid met…
View article: Characterizing chromatin packing scaling in whole nuclei using interferometric microscopy
Characterizing chromatin packing scaling in whole nuclei using interferometric microscopy Open
Chromatin is the macromolecular assembly containing the cell’s genetic information, and its architectural conformation facilitates accessibility to activation sites and thus gene expression. We have developed an analytical framework to qua…
View article: Nanoscale Chromatin Imaging and Analysis (nano-ChIA) platform bridges 4-D chromatin organization with molecular function
Nanoscale Chromatin Imaging and Analysis (nano-ChIA) platform bridges 4-D chromatin organization with molecular function Open
In eukaryotic cells, chromatin structure is linked to transcription processes through the regulation of genome organization. Extending across multiple length-scales - from the nucleosome to higher-order three-dimensional structures - chrom…
View article: Physical and data structure of 3D genome
Physical and data structure of 3D genome Open
New theoretical and experimental work suggests that 10-nm chromatin fiber is folded into tree-like domains in single cells.
View article: Disordered chromatin packing regulates phenotypic plasticity
Disordered chromatin packing regulates phenotypic plasticity Open
The CPMC model demonstrates the regulatory role of chromatin’s physical structure on transcription and phenotypic plasticity.
View article: Physical and data structure of 3D genome
Physical and data structure of 3D genome Open
With the textbook view of chromatin folding based on the 30nm fiber being challenged, it has been proposed that interphase DNA has an irregular 10nm nucleosome polymer structure whose folding philosophy is unknown. Nevertheless, experiment…