#3dgenome — Public Fediverse posts

🧬 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

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

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

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

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

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

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

#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

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?

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

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

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

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

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

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

I am presenting this poster at #neurips2022 at the #mlsb workshop. If you are here, you are probably already interested in #MachineLearning. If you are also interested in #PolymerPhysics and #chromosome #structures, come check it out. #3dgenome #deeplearning

Hello everyone! I am Atreya, a PhD candidate in UT Austin. I had been lurking here for some time, and finally decided to write about myself. My research is on #3dgenome and #condensin. I am also dabbling in #deeplearning for some time. Apart from research, I like talking about #darkskies #photography and #scicomm.

#introduction

Hi everyone! 👋 My name is Emma (she/her), I am a #computationalBiologist with a CS background and currently working on my #PhD. I am interested in all things #3DGenome organization, chromosome topology, #geneRegulation, enhancer-promoter interaction. I analyze data, develop analysis tools and develop models and polymer #simulations for my daily work.

Looking forward to getting to know some of you!

#introduction

Hi everyone! 👋 My name is Emma (she/her), a #computationalBiologist with a CS background and currently working on my #PhD. I am interested in all things #3DGenome organization, chromosome topology, #geneRegulation, enhancer-promoter interaction. I analyze data, develop analysis tools and develop models and polymer #simulations for my daily work.

Looking forward to getting to know some of you!