Understanding 3D genome organization by multidisciplinary methods

I Jerkovic, G Cavalli - Nature Reviews Molecular Cell Biology, 2021 - nature.com
Understanding how chromatin is folded in the nucleus is fundamental to understanding its
function. Although 3D genome organization has been historically difficult to study owing to a …

Machine learning meets omics: applications and perspectives

R Li, L Li, Y Xu, J Yang - Briefings in Bioinformatics, 2022 - academic.oup.com
The innovation of biotechnologies has allowed the accumulation of omics data at an
alarming rate, thus introducing the era of 'big data'. Extracting inherent valuable knowledge …

Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism

EM Pujadas Liwag, X Wei, N Acosta, LM Carter, J Yang… - Genome biology, 2024 - Springer
Background B-type lamins are critical nuclear envelope proteins that interact with the three-
dimensional genomic architecture. However, identifying the direct roles of B-lamins on …

[PDF][PDF] Nuclear genome organization in fungi: From gene folding to Rabl chromosomes

DE Torres, AT Reckard, AD Klocko… - FEMS Microbiology …, 2023 - academic.oup.com
Comparative genomics has recently provided unprecedented insights into the biology and
evolution of the fungal lineage. In the postgenomics era, a major research interest focuses …

Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data

Z Li, S Portillo-Ledesma, T Schlick - Current Opinion in Cell Biology, 2023 - Elsevier
Chromosome conformation capture technologies that provide frequency information for
contacts between genomic regions have been crucial for increasing our understanding of …

A new precision medicine initiative at the dawn of exascale computing

R Nussinov, H Jang, G Nir, CJ Tsai… - Signal Transduction and …, 2021 - nature.com
Which signaling pathway and protein to select to mitigate the patient's expected drug
resistance? The number of possibilities facing the physician is massive, and the drug …

Extracellular matrix cues regulate mechanosensing and mechanotransduction of cancer cells

CT Mierke - Cells, 2024 - mdpi.com
Extracellular biophysical properties have particular implications for a wide spectrum of
cellular behaviors and functions, including growth, motility, differentiation, apoptosis, gene …

Structures and functions of chromatin fibers

P Chen, W Li, G Li - Annual review of biophysics, 2021 - annualreviews.org
In eukaryotes, genomic DNA is packaged into chromatin in the nucleus. The accessibility of
DNA is dependent on the chromatin structure and dynamics, which essentially control DNA …

Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO

H Wang, J Yang, Y Zhang, J Qian, J Wang - Nature Communications, 2022 - nature.com
High-resolution reconstruction of spatial chromosome organizations from chromatin contact
maps is highly demanded, but is hindered by extensive pairwise constraints, substantial …

Federating structural models and data: outcomes from a workshop on archiving integrative structures

HM Berman, PD Adams, AA Bonvin, SK Burley… - Structure, 2019 - cell.com
Structures of biomolecular systems are increasingly computed by integrative modeling. In
this approach, a structural model is constructed by combining information from multiple …