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Items tagged with: computationalbiology

Emma Rusch

10 months ago

Emma Rusch
10 months ago

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

Figure 3 of the review depicting the original and proposed extended rules of loop extrusion in cartoon diagrams. Figure caption:
Rules of loop extrusion. (a-e) The original rules of cohesin loop extrusion. (f-m) Subsequent rule extensions: (a) Cohesin extrude loops bi-directionally. (b) Upon collision of cohesins, extrusion is stalled on the collided sides. (c) Cohesin stochastically dissociates from chromatin. (d) Cohesin can stochastically reload after having been unloaded. (e) Cohesin is stopped upon collision with a bound CTCF oriented against the direction of extrusion. (f) Cohesin may extrude loops unidirectionally, switching the direction of extrusion periodically. (g) Cohesins may bypass each other upon collision. Left: Formation of overlapping loops (also called ‘Z-loops’) upon one cohesin side bypassing the colliding side of another cohesin. Right: Formation of nested loops upon one cohesin bypassing both the sides of another colliding cohesin. (h) Stalling of cohesin upon collision with randomly positioned MCMs. (i) Stalling and/or pushing of cohesin upon collision with moving RNAP. (j) Cohesins may get stalled and rapidly unloaded at TTSs. (k) Cohesins may get unloaded upon collision with other cohesins. (l) Cohesins may be loaded at a higher rate at specific sites, for example, enhancers. (m) Cohesin is protected from unloading upon stabilization at CTCFs.

#review #computationalbiology #cohesin #loopextrusion #3dgenome @golobor

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Francis Ouellette

1 year ago

Francis Ouellette
1 year ago

From @PLOS #ComputationalBiology | An overview of #bioinformatics courses delivered at the academic level in #Italy: Reflections and recommendations from BITS | #Education | Bioinformatics Italian Society (BITS) | https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010846

An overview of bioinformatics courses delivered at the academic level in Italy: Reflections and recommendations from BITS

In Italian universities, bioinformatics courses are increasingly being incorporated into different study paths.

^{journals.plos.org}

#Education #bioinformatics #italy #computationalbiology @PLOS :verified:

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