[HTML][HTML] Multiscale modeling of genome organization with maximum entropy optimization
ABSTRACT Three-dimensional (3D) organization of the human genome plays an essential
role in all DNA-templated processes, including gene transcription, gene regulation, and …
role in all DNA-templated processes, including gene transcription, gene regulation, and …
The role of coevolutionary signatures in protein interaction dynamics, complex inference, molecular recognition, and mutational landscapes
F Morcos, JN Onuchic - Current opinion in structural biology, 2019 - Elsevier
Highlights•Coevolution of molecular interfaces induces direct correlations between sites of
interacting sequences.•Global models that identify direct correlations in sequences of …
interacting sequences.•Global models that identify direct correlations in sequences of …
A scalable computational approach for simulating complexes of multiple chromosomes
Significant efforts have been recently made to obtain the three-dimensional (3D) structure of
the genome with the goal of understanding how structures may affect gene regulation and …
the genome with the goal of understanding how structures may affect gene regulation and …
Motorized chain models of the ideal chromosome
Z Cao, PG Wolynes - Proceedings of the National Academy of Sciences, 2024 - pnas.org
An array of motor proteins consumes chemical energy in setting up the architectures of
chromosomes. Here, we explore how the structure of ideal polymer chains is influenced by …
chromosomes. Here, we explore how the structure of ideal polymer chains is influenced by …
[HTML][HTML] 3D epigenomics and 3D epigenopathies
KH Lee, J Kim, JH Kim - BMB reports, 2024 - ncbi.nlm.nih.gov
Mammalian genomes are intricately compacted to form sophisticated 3-dimensional
structures within the tiny nucleus, so called 3D genome folding. Despite their shapes …
structures within the tiny nucleus, so called 3D genome folding. Despite their shapes …
Chromosome modeling on downsampled Hi-C maps enhances the compartmentalization signal
AB Oliveira Junior, CP Estrada, EL Aiden… - The Journal of …, 2021 - ACS Publications
The human genome is organized within a nucleus where chromosomes fold into an
ensemble of different conformations. Chromosome conformation capture techniques such as …
ensemble of different conformations. Chromosome conformation capture techniques such as …
Braiding topology and the energy landscape of chromosome organization proteins
D Krepel, A Davtyan, NP Schafer… - Proceedings of the …, 2020 - National Acad Sciences
Assemblies of structural maintenance of chromosomes (SMC) proteins and kleisin subunits
are essential to chromosome organization and segregation across all kingdoms of life. While …
are essential to chromosome organization and segregation across all kingdoms of life. While …
Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci
GB Brandani, C Gu, S Gopi, S Takada - PNAS nexus, 2024 - academic.oup.com
Chromatin, the complex assembly of DNA and associated proteins, plays a pivotal role in
orchestrating various genomic functions. To aid our understanding of the principles …
orchestrating various genomic functions. To aid our understanding of the principles …
[HTML][HTML] DNA looping by protamine follows a nonuniform spatial distribution
DNA looping plays an important role in cells in both regulating and protecting the genome.
Often, studies of looping focus on looping by prokaryotic transcription factors like lac …
Often, studies of looping focus on looping by prokaryotic transcription factors like lac …
Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies
DNA-binding response regulators (DBRRs) are a broad class of proteins that operate in
tandem with their partner kinase proteins to form two-component signal transduction …
tandem with their partner kinase proteins to form two-component signal transduction …