Zhifeng Shao

An invariant network architecture with broadly expressed regulators distinguishes cell-type from cell-state identity in situ

The paper constructs state-level regulatory networks in mouse liver hepatocytes, revealing an invariant sub-network of broadly expressed TFs that defines cell-type identity, distinct from state-specific variations.

ChromPolymerDB: A High-Resolution Database of Single-Cell 3D Chromatin Structures for Functional Genomics

ChromPolymerDB reconstructs single-cell 3D chromatin structures from bulk Hi-C data and provides a database for analyzing chromatin conformation across 50 human cell types.

Histo-LCM-Hi-C reveals the 3D chromatin conformation of spatially localized rare cells in tissues at high resolution

The paper introduces Histo-LCM-Hi-C to study 3D chromatin structure of rare tissue cells, showing distinct chromatin organization in liver Kupffer cells compared to whole liver and in vitro macrophages.

Perfringolysin O pore-forming complexes are predominantly integral multiples of six subunits

The paper investigates the structural composition of Perfringolysin O (PFO) complexes, finding that they are predominantly hexameric and built from hexameric sub-complexes.

Robust Acquisition of High Resolution Spatial Transcriptomes from Preserved Tissues with Immunofluorescence Based Laser Capture Microdissection

This paper introduces a method to obtain high-resolution spatial transcriptomes from preserved tissues using immunofluorescence-based laser capture microdissection, demonstrating its effectiveness in analyzing transcript isoforms in mouse small intestine cells.

High-Resolution Single-Cell 3D-Models of Chromatin Ensembles during Drosophila Embryogenesis

The paper introduces a computational method to reconstruct high-resolution 3D chromatin conformations from population Hi-C data, revealing chromatin structure dynamics during Drosophila embryogenesis.

CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single-cells

CHROMATIX reconstructs many-body chromatin interactions from Hi-C data and identifies functional features in transcriptionally active loci.

Sub-kb resolution Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells

The paper uses sub-kb resolution Hi-C in D. melanogaster to show TADs are conserved between insects and mammals, with similar insulator protein pairings and structural organization.