Daniel Mark Czajkowsky

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.

Specific Pupylation as IDEntity Reporter (SPIDER) for the identification of Protein-Biomolecule interactions

The paper introduces SPIDER, a method using pupylation and streptavidin-biotin to identify protein-biomolecule interactions, demonstrating its application in various biological contexts.

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.

Cell Lysate Microarray for Mapping the Network of Genetic Regulators for Histone Marks

The paper develops a cell lysate microarray (CLICK) to identify upstream regulators of histone marks using yeast knockout and temperature-sensitive mutant strains, revealing new regulators and enzymes involved in histone acylation.

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.