Krishna Mohan Parsi

Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation

The paper temporally maps nuclear reorganization during human stem cell differentiation and identifies three temporally ordered transitions in nuclear structure and function.

Haplotype-resolved genome architecture mapping uncovers pervasive structural heterogeneity between human homologous chromosomes

The paper introduces CoPhasing, a method to phase chromatin contacts with haplotype specificity, revealing structural differences between homologous chromosomes.

Identification of genome safe harbor loci for human gene therapy based on evolutionary biology and comparative genomics

The paper identifies genome safe harbor loci for gene therapy using evolutionary biology and comparative genomics, finding nine loci with sustained transgene expression in human hematopoietic stem cells.

Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations

The paper uses polymer physics models to simulate and analyze the 3D structure of the LTN1 gene region, comparing results with Hi-C data to predict structural features for microscopy experiments.

Discovery and characterization of LNCSOX17 as an essential regulator in human endoderm formation

The paper identifies and characterizes LNCSOX17, a lncRNA essential for human endoderm formation, showing its role in regulating transcriptome and differentiation.

Systematic evaluation of chromosome conformation capture assays

This study evaluates 3C-based assays to understand how experimental parameters affect chromatin interaction detection and quantification, leading to the development of Hi-C 3.0.

Ultrastructural details of mammalian chromosome architecture

This study improves chromosome architecture mapping by using Micro-C to achieve nucleosome-resolution insights in human cells, revealing new looping interactions and structural patterns.

AGO1 in association with NEAT1 lncRNA contributes to nuclear and 3D chromatin architecture in human cells

This study shows AGO1 and NEAT1 lncRNA maintain 3D chromatin architecture by regulating TADs and A/B compartments in human cells.