Liangqi Xie

Cohesin prevents local mixing of condensed euchromatic domains in living human cells

This study shows cohesin maintains condensed euchromatic domains in human cells by preventing local mixing, which is crucial for transcriptional insulation.

Chromatin is a long-range force generator that regulates plasma membrane tension and cell integrity independently of gene expression

The paper investigates how chromatin organization affects cell mechanics during NETosis, finding that chromatin decompaction increases plasma membrane tension and cell volume independently of gene expression.

Accurate and robust 3D genome feature discovery from multiplexed DNA FISH

ArcFISH identifies 3D genome features from multiplexed DNA FISH data by modeling axis-specific measurement errors, showing reliable detection of chromatin loops, TAD boundaries, and A/B compartments.

Alternating 2D and 3D Culture Reduces Cell Size and Extends the Lifespan of Placenta-Derived MSCs

This paper shows that alternating 2D and 3D culture reduces cell size and extends the lifespan of placenta-derived MSCs while preserving their immunomodulatory function.

Scalable Culture of Mammalian Cells in RGD Peptide-Modified Alginate Hydrogel Microtubes

This study develops AlgTubes, RGD peptide-modified alginate hydrogel microtubes, to enable scalable culture of myoblasts and adipocytes for cultured meat, achieving higher cell densities than traditional bioreactors.

Spatial organization of the 3D genome encodes gene co-expression programs in single cells

The paper investigates how 3D genome organization, specifically through Cohesin, influences gene co-expression in single cells and reveals its role in maintaining long-range chromatin interactions.

Assessing the impact of Brd2 depletion on chromatin compartmentalization

This study reanalyzes Brd2 depletion effects on chromatin compartments using Micro-C data and cooltools, showing persistent but reduced compartment strength changes.

SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data

SnapFISH identifies chromatin loops from multiplexed DNA FISH data with high sensitivity and accuracy in mouse embryonic stem cells.

Super-resolution Imaging Reveals 3D Structure and Organizing Mechanism of Accessible Chromatin

This study uses super-resolution imaging to reveal the 3D structure and organizing mechanism of accessible chromatin domains.

A stable mode of bookmarking by TBP recruits RNA Polymerase II to mitotic chromosomes

The paper shows TBP remains bound to promoters during mitosis, stabilizing RNA Polymerase II association and enabling transcriptional reactivation.

A Dynamic Mode of Mitotic Bookmarking by Transcription Factors

The paper shows that many transcription factors remain bound to mitotic chromosomes, challenging previous findings of their exclusion and revealing dynamic interactions that depend on DNA binding and nuclear import.