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  1. proslijedio/la je Tweet
    21. sij

    Regarding my question on how much time to spend networking, the senior colleague answered, "The friendly reviewers you suggested may show no more leniency towards your manuscript than complete strangers, so be nice in general but focus on the science".

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  2. proslijedio/la je Tweet
    13. sij

    On the existence and functionality of topologically associating domains [review by Jonathan Beagan & Jennifer Phillips-Cremins]

    The structural features of topologically associating domains. a–d, Heat-map representations (top) and schematized globular interactions (bottom) of TADs (a,b) and nested subTADs (c,d). e, Cartoon representation of different classes of contact domains parsed by their structural features and degree of nesting. f, Identification of contact-domain classes from e in cortical neuron Hi-C data, binned at 10-kb
    g, Cohesin translocation extrudes DNA in an ATP-dependent manner into long-range looping interactions that form the topological basis for TAD and subTAD loop domains.
h–k, Contact frequency heat maps of high-resolution Hi-C data, performed on embryonic stem cells (ESC, h,j) and neural progenitor cells
(NPC; i,k). h,i, Green arrows denote the corners of a subset of the nested chromatin domains
    a–c, Schematics of three emerging mechanisms through which loop domains can influence transcription: direct, strong contact of enhancers and promoters via persistent loops (red arcs) at the corners of domains (a), transient, weak contact of enhancers and promoters via transient loop extrusion (blue arcs) across the loop domain (b), and developmental miswiring of enhancers to non-target promoters outside of the TAD...
    f, Depiction of a model of long-range transcriptional regulation in
which an enhancer’s regulatory contribution trends with its activity signature and Hi-C contact frequency with the target gene. i, Cartoon of unencumbered development observed after perturbation of a TAD boundary opposing the Shh gene
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  3. proslijedio/la je Tweet
    8. lis 2019.

    For my friends who were busy with their proposal deadlines last week, you were not alone :)

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  4. 23. kol 2019.

    Rigorous Hi-C bias corrrection (HiCorr) can significantly improve the sensitivity and robustness of Hi-C loop calling at sub-TAD level, especially enhancer-promoter interactions.

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  5. proslijedio/la je Tweet
    27. ožu 2019.

    My university is piloting a new system for faculty annual reports. Regardless of intent, the implementation communicates that quantity matters, not quality. Filling out these items yearly creates the wrong culture and mindset about how to succeed in research.

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  6. 25. ožu 2019.
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  7. 13. ožu 2019.

    Single-Cell Heterogeneity Analysis and CRISPR Screen Identify Key β-Cell-Specific Disease Genes

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  8. proslijedio/la je Tweet
    8. pro 2018.

    Thank you to everyone who replied. Let me ask: Are there examples of funtional insight or prediction we wouldn't have without considering TADs other than the TADs themselves? Think super enhancers / enhancers (though I'm asking a question here, not making a statement... yet).

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  9. proslijedio/la je Tweet
    10. sij 2018.

    Easy Hi-C: A simple efficient protocol for 3D genome mapping in small cell populations

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  10. 2. srp 2014.

    Enhancer loops appear stable during development and are associated with paused polymerase

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