CSBJNov 17

🧬 Ever wondered how the genome actually looks when it folds inside the nucleus — and how fast we can simulate it?

🔗 Multiscale molecular modeling of chromatin with MultiMM: From nucleosomes to the whole genome. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.09.025

📚 CSBJ: https://www.csbj.org/

#ChromatinModeling #3DGenome #ComputationalBiology #Genomics #MolecularModeling #GenomeArchitecture #ChromatinStructure #HiC #ATACSeq #Biophysics #StructuralBiology

dpanne1Oct 30
🧬 Registration’s open for the 6th Annual Conference on Nuclear Topology & 3D Chromatin Architecture in Cancer – streaming live on Nov 25, 2025.
Hear from an amazing lineup: Maeshima, Panne, Yost, Snuderl, Schmitt, Zhong, Ramani, Javierre Martínez, Hansen & Ren.
💻 Join us online (free!):
https://nyulangone.zoom.us/webinar/register/WN_oqlWTAQ-RCeuZTRv14UcqA#/registration
#3Dgenome #CancerResearch #Chromatin #Science
CSBJMar 22, 2025

🧬 This review delves into the advancements in 3D genome architecture mapping, revealing how spatial genome organization influences gene expression, cellular function, and disease mechanisms.

🔗 Mapping the 3D genome architecture. Computational and Structural Biotech Journal, DOI: https://doi.org/10.1016/j.csbj.2024.12.018

📚 CSBJ: https://www.csbj.org/

#Genomics #3DGenome #HiC #Epigenomics #DNA #SingleCell

James Hawley, PhDJul 17, 2024

A paper I'm an author on has finally been published! Congrats to all the authors, especially the 3 co-leads.

https://www.nature.com/articles/s41588-024-01826-3

How structural variants affect the 3D chromatin structure in metastatic castration-resistant prostate cancer and facilitate a bunch of biologically interesting interactions in the nucleus is really interesting, especially how that affects gene expression and disease progression.

Please take a look!

#prostateCancer #bioinformatics #compBio #genomics #3Dgenome

Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer - Nature Genetics

A multiomic approach profiles the three-dimensional, epigenetic and mutational landscapes of 80 metastatic prostate cancer biopsies. Hi-C experiments identify an extrachromosomal circular DNA at the AR locus associated with therapy resistance.

Nature
Emma RuschJun 27, 2023
Super happy to share my first co-authored publication, a review on loop extrusion modeling by cohesins! @golobor, Flavia Corsi and I review recent discoveries made by the modeling of loop extrusion, the "rules" behind these models and propose future enhancements to models based on recent insights on the mechanism and regulation of cohesin-driven loop extrusion. Give it a read: https://authors.elsevier.com/c/1hIIR,LqAZXo9S #review #computationalBiology #3Dgenome #loopExtrusion #cohesin
CavalliLabMar 14, 2023
#TAD progress: Defining the separation landscape of topological domains for decoding consensus domain organization of #3Dgenome
https://genome.cshlp.org/cgi/content/long/gr.277187.122v1
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An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

CavalliLabFeb 21, 2023
A new variation of the #HiC method to study #3Dgenome interactions specifically for open #chromatin. "HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization" https://www.cell.com/molecular-cell/fulltext/S1097-2765(22)00098-3?
CavalliLabFeb 16, 2023
Using #3Dgenome interaction
data from #neuron cells differentiated from iPSCs to infer associations that might be linked with #Autism in what the authors define as "3D GWAS". Read: Interaction-integrated linear mixed model reveals 3D-genetic basis underlying Autism https://www.sciencedirect.com/science/article/pii/S0888754323000198
CavalliLabFeb 1, 2023
Anchoring #3Dgenome & #chromatin contacts to #cellnucleus landmarks: Mapping #nucleolus-associated chromatin interactions using nucleolus #HiC reveals pattern of #heterochromatin interactions.
@NatureComms https://doi.org/10.1038/s41467-023-36021-1
Gene RegulationJan 8, 2023

1st weekly digest of #GeneRegulation papers:

🧬#TranscriptionFactor atlas of differentiation https://www.sciencedirect.com/science/article/pii/S0092867422014702

🧬 #TFbinding directed heterochromatin (#ZFP462) https://www.nature.com/articles/s41556-022-01051-2

🧬#3Dgenome organisation of nuclear speckles & splicing https://www.biorxiv.org/content/10.1101/2023.01.04.522632v1

🧬 Nuclear partitioning by charge blocks (#MED1, #PolII) https://www.sciencedirect.com/science/article/pii/S0092867422015264

🧬 Transient loss of #Polycomb induces an #epigenetic cancer fate https://www.biorxiv.org/content/10.1101/2023.01.04.522799v1

🧬 RGT: a toolbox for NGS analysis https://www.biorxiv.org/content/10.1101/2022.12.31.522372v1