56 citations · 247 across the 11 of their papers we have counts for
11 papers
Loop Extrusion Reversal by Condensin Motor is Mediated by Catch Bonds
Atreya Dey, Guang Shi, Ryota Takaki +1
Structural Maintenance Complexes (SMC) are energy consuming motors that are important in folding the genome by loop extrusion (LE) in all stages of the cell cycle. Single molecule…
Epigenetic state encodes locus-specific chromatin mechanics
Guang Shi, D. Thirumalai
Chromatin is repeatedly deformed in vivo during transcription, nuclear remodeling, and confined migration - yet how mechanical response varies from locus to locus, and how it relat…
Static Three-Dimensional Structures Determine Fast Dynamics Between Distal Loci Pairs in Interphase Chromosomes
Guang Shi, Sucheol Shin, D. Thirumalai
Live-cell imaging experiments have shown that the distal dynamics between enhancers and promoters are unexpectedly rapid and incompatible with standard polymer models. The discorda…
Organization and Dynamics of Chromosomes
D. Thirumalai, Guang Shi, Sucheol Shin +1
How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advanc…
Theory of the center-of-mass diffusion and viscosity of microstructured and variable sequence copolymer liquids
Guang Shi, Kenneth S. Schweizer
Biomolecular condensates formed through the phase separation of proteins and nucleic acids are widely observed, offering a fundamental means of organizing intracellular materials i…
From Effective Interactions Extracted Using Hi-C Data to Chromosome Structures in Conventional and Inverted Nuclei
Sucheol Shin, Guang Shi, D. Thirumalai
Contact probabilities between loci, separated by arbitrary genomic distance, for a number of cell types have been reported using genome-wide chromosome conformation capture (Hi-C)…
Transcription-induced active forces suppress chromatin motion
Sucheol Shin, Guang Shi, Hyun Woo Cho +1
The organization of interphase chromosomes in a number of species is starting to emerge thanks to advances in a variety of experimental techniques. However, much less is known abou…
A maximum-entropy model to predict 3D structural ensembles of chromatins from pairwise distances: Applications to Interphase Chromosomes and Structural Variants
Guang Shi, D. Thirumalai
The principles that govern the organization of genomes, which are needed for a deeper understanding of how chromosomes are packaged and function in eukaryotic cells, could be decip…
From Hi-C Contact Map to Three-dimensional Organization of Interphase Human Chromosomes
Guang Shi, D. Thirumalai
The probability of two loci, separated by a certain genome length, being in contact can be inferred using the Chromosome Conformation Capture (3C) method and related Hi-C experimen…
Theory and Simulations of condensin mediated loop extrusion in DNA
Ryota Takaki, Atreya Dey, Guang Shi +1
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops…
Conformational Heterogeneity in Human Interphase Chromosome Organization Reconciles the FISH and Hi-C Paradox
Guang Shi, D. Thirumalai
Hi-C experiments are used to infer the contact probabilities between loci separated by varying genome lengths. Contact probability should decrease as the spatial distance between t…