Robin H. van der weide

differential contribution of H3K9 methyltransferases to boundaries at satellites

A new and fascinating story from @bencarty.bsky.social and the group, with crucial help from the teams of @naltemose.bsky.social, Simona Giunta, and @dfachinetti.bsky.social. Many thanks to all for a fantastic collaboration.
www.nature.com/articles/s41...

When plotting, LLMs see what they expect to see - Posit Data science agents need to accurately read plots even when the content contradicts their expectations. Our testing shows today's LLMs still struggle here.

Introducing bluffbench, a new tool to evaluate how well LLMs actually see data plots.

When we trick LLMs with secret #RStats transformations, they can miss the visual contradiction.

bluffbench helps us measure this "blind spot" in AI coding agents. Learn more: posit.co/blog/introdu...

Atkinson Hyperlegible Font - Braille Institute Read easier with Atkinson Hyperlegible Font, crafted for low-vision readers. Download for free and enjoy clear letters and numbers on your computer!

periodic reminder of the existence of Atkinson Hyperlegible, a free font available from the Braille Institute designed to improve readability for people with low vision

I use it in talks because it's pretty and also because, as an audience member, I am perpetually squinting at people's slides

I need a reference manager that's amazing for both organizing and reading on a laptop & tablet. 📑

It's a showdown: Paperpile vs. ReadCube Papers. What's your go-to and why?

#Academia #Paperpile #ReadCube

Shortcomings of silhouette in single-cell integration benchmarking - Nature Biotechnology Silhouette score is unsuitable as a metric for single-cell data integration.

Shortcomings of silhouette in single-cell integration benchmarking - @uweohler.bsky.social @prauten.bsky.social @mdc-bimsb.bsky.social @mdc-berlin.bsky.social @humboldtuni.bsky.social go.nature.com/4fcQzZr

Should I tell anyone that I suspect misconduct in a paper I’m reviewing? A cancer researcher is suspicious about a paper they’ve been asked to review. What steps should they take?

Agony aunt 🖋️ A cancer researcher is suspicious about a paper they’ve been asked to review. What steps should they take?

go.nature.com/3UhImt0

We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab.
www.biorxiv.org/content/10.1...
1/

Reconfiguration of genome-lamina interactions marks the commissioning of limb cell-fates Diverse forms of heterochromatin block inappropriate transcription and safeguard differentiation and cell identity. Yet, how and when heterochromatin is reconfigured to facilitate changes in cell-fate...

🚨 Preprint 🚨
Ever wondered how cells prepare their genomes to enable new cell-fates? In this team up with the Kind lab, we show that genes are repositioned in the nucleus to get ready for future activation and tissue formation. Read 🧵👇 to find out how and when this happens!

doi.org/10.1101/2025...

Congrats!

Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomics Antibodies (Ab) are essential for detecting specific epitopes in microscopy and genomics, but can produce artifacts leading to erroneous interpretations. Here, we characterize a novel artifact, Ab-tra...

🚨 Preprint alert 🚨
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...

Our ChromBPNet preprint out!

www.biorxiv.org/content/10.1...

Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

1/🚀 Excited to share RegVelo, our new cell model combining RNA velocity with gene regulatory network (GRN) dynamics to model cellular changes and predict in silico perturbations. Here's how it works and why it matters! 🧵👇
biorxiv.org/content/10.1101/2024.12.11.627935v1

Very excited to see our work on genome-wide mapping DNA repair in single cells out @naturecomms.bsky.social
Amazing work by Kim de Luca & Pim Rullens. Wonderful collaboration with the Legube lab, @mariekeoudelaar.bsky.social & @jjachowicz.bsky.social . rdcu.be/d0ZAM

1. You have limited time to make scientific contributions. Do the big things
2.Go back and forth between day and night science
3. Give adequate attention to the thinking and analysis aspects of research
4. Do your go-no-go experiments early on to avoid wasting time
5. Face risk early

And more 👇🏾

I used to have imposter syndrome. I don't any more. At some point I came to terms with the fact that I'm really an imposter. I'm totally ok with it & simply decided to do my best with the opportunities that presented themselves to me, until my luck runs out. It's surprisingly effective.

Action Intent Links | Bluesky Authors, websites, and apps can use action intent links to implement "Share on Bluesky" buttons, or similar in-app actions. Logged-in users will be directed to the corresponding action view in the Blu...

We strongly suggest that academic publishers and other platforms that host research rapidly implement a Share to Bluesky button for their articles. Here's how:

docs.bsky.app/docs/advance...

#AcademicSky #HigherEd #Altmetrics

Doing good science is 90% finding a science buddy to constantly talk to about the project.