Memory effects of transcription regulator− DNA interactions in bacteria

W Jung, TY Chen, AG Santiago, P Chen - Proceedings of the National …, 2024 - pnas.org
Memory effect refers to the phenomenon where past events influence a system's current and
future states or behaviors. In biology, memory effects often arise from intra-or intermolecular …

[HTML][HTML] Integrative modeling of JCVI-Syn3A nucleoids with a modular approach

DS Goodsell, L Autin - Current Research in Structural Biology, 2024 - Elsevier
A lattice-based method is presented for creating 3D models of entire bacterial nucleoids
integrating ultrastructural information cryoelectron tomography, genomic and proteomic …

Circuit Topology Analysis of Single-Cell HiC Data

B Scalvini, A Mashaghi - Bacterial Chromatin: Methods and Protocols, 2024 - Springer
The 3D fold structure of the genome is intricately linked to its function. As a result, descriptors
of 3D genome conformation are becoming increasingly important as markers for disease …

Replicating Chromosomes in Whole-Cell Models of Bacteria

BR Gilbert, Z Luthey-Schulten - Bacterial Chromatin: Methods and …, 2024 - Springer
Computational models of cells cannot be considered complete unless they include the most
fundamental process of life, the replication of genetic material. In a recent study, we …