iiinova — where your digital self keeps evolving

Reposted by Noura Maziak

Chema Martin @chemamd.bsky.social · 19/05/2026

🚨 We discovered a new mode of Hox gene regulation in annelids! 🪱 A distal enhancer acts as a "global control region", lifting Hox genes from Polycomb repression. This is reminiscent of Hox gene control in vertebrates, but the two modes likely evolved convergently. www.biorxiv.org/content/10.6...

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Reposted by Noura Maziak

Nicola Rennie @nrennie.bsky.social · 29/04/2026

📊 Five #ggplot2 functions I wish I'd known about earlier 📊 I've written a short blog (with examples) of some of the lesser-known {ggplot2} functions and arguments that make it easier to create better charts! Link: nrennie.rbind.io/blog/five-gg... #RStats #DataViz

nrennie.rbind.io

Five ggplot2 functions I wish I’d known about earlier – Nicola Rennie

There are a few small tweaks you can make to your ggplot2 code to improve your charts. However, they’re not often mentioned. So here’s a few functions and arguments I wish I’d known about earlier.

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Reposted by Noura Maziak

Tobias Warnecke @tobiaswarnecke.bsky.social · 08/04/2026

I wrote an essay. It’s about gain-of-function mutations. And penguins. Also ion channels, chihuahuas, the film Alien, recycled cardboard, and the Apollonian mind. Oh, and muffins. Thanks to the editors of #GENETICS @genetics-gsa.bsky.social for letting me take some stylistic liberties. 1/2

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Reposted by Noura Maziak

Mariko Bennett @nachoriko.bsky.social · 24/03/2026

I defended my PhD 10 years ago today. That was the least remarkable thing that happened that day. Sharing something I wrote about it last year. Since then "the horrors persist but so do we." And with dignity.

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Noura Maziak @nmaziak.bsky.social · 15/03/2026

A nice thing happened.. We got the cover of Nature Genetics! 😊🎉 The spheres trace nuclear stages through early embryogenesis, with color bursts capturing the diverse events that shape genome architecture. Art done by my friend and very talented artist @christophewirtz.bsky.social 🎨

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Noura Maziak @nmaziak.bsky.social · 10/03/2026

12/n This is just the beginning! We're excited to apply this and capture genome architecture dynamics across new systems. Watch this space! 👀🧬

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Noura Maziak @nmaziak.bsky.social · 10/03/2026

11/n We also used the protocol partnering with Ulrike Kutay's lab to ask: what happens when you perturb nuclear heterochromatin tethering? The result? Stunning linked changes between architecture and landscape in HCT116 cells at compartment switches. www.nature.com/articles/s41...

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Noura Maziak @nmaziak.bsky.social · 10/03/2026

10/n We also used @protocolsio.bsky.social, which was super helpful. Protocols below — I’ll keep adding more for other cell types and tweaks. Feel free to ask questions there 🙂 Fixation: doi.org/10.17504/pro... Pico-C: doi.org/10.17504/pro...

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Noura Maziak @nmaziak.bsky.social · 10/03/2026

9/n I am also very thankful for the support through the years from my lab & mentor @vaquerizaslab.bsky.social @vaquerizasjm.bsky.social

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Noura Maziak @nmaziak.bsky.social · 10/03/2026

8/n This was overall a mammoth effort from everyone, and I am very thankful for everyone that helped along the way, this includes @shelbyflies.bsky.social who also took the time to try to do some funky mutants for me.

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Noura Maziak @nmaziak.bsky.social · 10/03/2026

7/n To test this further we collaborated with @harrisonflylab.bsky.social to simultaneously deplete pioneer factors Zelda and GAF in embryos. This led to beautiful context-specific perturbations in architecture, further highlighting a modular regulatory logic behind genome establishment.

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Noura Maziak @nmaziak.bsky.social · 10/03/2026

6/n We asked if this was encoded in the sequence. Collaborating with @Jian Zhou and @ycz23.bsky.social, they built a deep learning model on our high-resolution data. The models predicted that different motifs make distinct, independent contributions to genome architecture.

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Noura Maziak @nmaziak.bsky.social · 10/03/2026

5/n We first blocked transcriptional elongation, now with a better granular view, we found that the effects were site-specific: some early loops stuck around, while insulation at active promoters mildly weakened, suggesting different regulatory dependencies.

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Noura Maziak @nmaziak.bsky.social · 10/03/2026

4/n Using cluster analysis (and ChromHMM), we found that the genome is shaped by a diverse landscape with strong context-dependent enrichments. So we set out to test this.

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Noura Maziak @nmaziak.bsky.social · 10/03/2026

3/n To our surprise, while much of the architecture emerges at NC14 with ZGA, we also found many stage-specific looping events that occur despite the very short time between interphases (~1.5 hours between NC9-NC14).

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Noura Maziak @nmaziak.bsky.social · 10/03/2026

2/n Pico-C let us take advantage of a beautiful system where we can stage distinct nuclear cycles (NCs) at interphase despite dramatic embryo-wide mitotic waves. This gave us unprecedented temporal and architectural resolution from NC 9–14.

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Noura Maziak @nmaziak.bsky.social · 10/03/2026

Excited to share my PhD work! The question: How is genome organization established? Here, we developed a low-input Micro-C method, Pico-C, and used it to map chromatin architecture across early stages of fly development. Here’s a quick Blue-torial 🙂 (1/n) www.nature.com/articles/s41...

nature.com

Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila - Nature Genetics

Pico-C, a low-input Micro-C approach, reveals that dynamic three-dimensional genome folding precedes zygotic genome activation in Drosophila.

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Reposted by Noura Maziak

Damir Baranasic @da-bar.bsky.social · 24/02/2026

Congratulations to @nmaziak.bsky.social, @vaquerizasjm.bsky.social et al: Pico-C (low-input Micro-C) shows 3D genome architecture reorganises before major zygotic genome activation in Drosophila, with early loop formation and stronger insulation. @natgenet.nature.com: www.nature.com/articles/s41...

nature.com

Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila - Nature Genetics

Pico-C, a low-input Micro-C approach, reveals that dynamic three-dimensional genome folding precedes zygotic genome activation in Drosophila.

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Noura Maziak @nmaziak.bsky.social · 24/02/2026

Thanks a ton Tobias, and always for the support!

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Reposted by Noura Maziak

Daniel Ibrahim @danielibrahim.bsky.social · 27/05/2025

How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭 Check out our paper - fresh off the press!!! We find widespread functional conservation of enhancers in absence of sequence homology Including: a bioinformatic tool to map sequence-diverged enhancers! rdcu.be/enVDN github.com/tobiaszehnde...

rdcu.be

Conservation of regulatory elements with highly diverged sequences across large evolutionary distances

Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...

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Noura Maziak @nmaziak.bsky.social · 21/01/2025

Bipartisanship at the face of fascism. Still. My god, you guys are just fantastic at everything but working.

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Noura Maziak @nmaziak.bsky.social · 08/12/2024

I never expected my first post here to be anything but science, yet today we celebrate the fall of a regime that’s brought decades of pain. The joy of this moment is worth sharing a thousand times over.

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