Jie Xiao

The paper develops a polymer simulation framework to distinguish specific-folding interactions from polymer compaction in E. coli, revealing SFIs shape chromosome organization and gene expression.

This study identifies REP elements as dual regulators of 3'UTR function in E. coli, controlling transcription termination and mRNA stability in a context-dependent manner.

This study defines the substrate binding and activation mechanism of FtsW using simulations, mutagenesis, and assays, revealing conserved residues and structural constraints involved in lipid II binding and catalysis.

This study shows that chromosomal topological domains in E. coli repress transcription, reduce orientation effects, and modulate gene coupling through supercoiling changes.

This paper develops a computational model to quantify how DNA supercoiling and topoisomerases regulate bacterial transcription, showing distinct roles for topoisomerase I and gyrase in gene expression.

This paper identifies SddA, a periplasmic deacetylase that modulates daughter cell separation in E. coli by modifying denuded peptidoglycan strands, and links its function to amidase activation.

This paper shows FtsZ treadmilling acts as a template and conveyor to organize cell wall synthesis during bacterial division, with roles changing over time.

This study shows that the CRY2/CIB1 system can be used to precisely control protein localization in E. coli, enabling manipulation of cellular functions like cytokinesis.

This study investigates how positive and negative supercoiling influence 3D genome organization in E. coli using Hi-C and ChIP-seq data, finding positive supercoiling enhances spatial contacts more than negative supercoiling.

This paper improves gene regulatory network reconstruction by combining a new algorithm with a k-nearest neighbor mutual information estimator, achieving better precision-recall performance on synthetic datasets.

The paper shows that histone H4 is asymmetrically inherited in Drosophila male germline stem cells during asymmetric division, while H2A and H2B are symmetrically inherited.

This study identifies a phage-encoded cationic antimicrobial peptide, Gp28, that disrupts bacterial outer membranes during lysis, functioning similarly to human antimicrobial peptides like LL-37.

This study shows that RNA polymerase forms distinct spatial clusters in E. coli independent of rRNA transcription, with cluster organization influenced by nucleoid structure.

The paper improves 3D superresolution imaging by using weighted likelihood estimation to enhance z-axis localization precision, especially when PSFs deviate from standard models.

The bacterial tubulin FtsZ uses GTP hydrolysis to power treadmilling, driving processive synthesis of the septal cell wall.