Very happy to see this story out in the wild!

Elzo de Wit lab @ NKI@dewitlab.bsky.social · last mo.

(1/10) The majority of human genetic variation is located in non-coding regions. The great challenge of the post-genomic era is to assign function to these variants. We reasoned that combining haplotyping with allele-specific multiomics can help pinpoint the functional ones: rdcu.be/fgr5W. A thread:

New paper in Genes & Dev: we dissected how Sox2 — a key pluripotency TF — is regulated by a distal enhancer cluster (SCR) 100 kb away. The results challenge simple models of cohesin-mediated loop extrusion of gene regulation. genesdev.cshlp.org/content/earl... 🧵

💼 Hiring a Staff Technician at my Chromatin Systems Biology lab (UMC Utrecht). A wet lab role with real ownership: co-develop research lines, contribute to publications, build something from the ground up. Permanent position, pending tenure. Details & apply:

Vacature — Staff Technician - Wetlab

We are looking for a motivated and experienced Staff Technician to take ownership of the day-to-day operations of our wet lab. You ensure that operations run smoothly and are responsible for executing...

werkenbijumcutrecht.nl

@amandaanderssonr.bsky.social, @antonelladost.bsky.social, @robinhweide.bsky.social and @sorayang.bsky.social started their own labs in early 2026. Read about their time at the Hubrecht Institute, their new research groups and their transition into independence here: www.hubrecht.eu/postdocs-sta...

We are hiring! Looking for curious and motivated new colleagues to join my lab at the Karolinska Institute @ki.se. If you are interested in studying cell identity and pancreas biology using human organoids, (spatial)omics genome and bioengineering please reach out! #hiring #sciencejob #STEMJobs

🌱 As of Jan 1, I started as Assistant Professor at UMC Utrecht – Center for Molecular Medicine. Very grateful to @dewitlab.bsky.social and @jopkind.bsky.social and to the many other people who supported me along the way. I’ll be launching the lab soon, focusing on Chromatin Systems Biology.

Thrilled to share Marta Moreno Gonzalez’s paper, where we benchmarked whether existing imputation approaches can be repurposed for single-cell hPTM datasets. This is also a special milestone for me, as it’s my first last-author paper. @hubrechtinstitute.bsky.social @umcutrecht.bsky.social

Marta Moreno Gonzalez@martamorgonz.bsky.social · 7mo ago

1/ 🧬 Very excited to share our work on dissecting imputation strategies for single-cell histone modification data! academic.oup.com/nargab/artic... A huge thank you to @robinhweide.bsky.social, @jopkind.bsky.social and Jeroen de Ridder for their collaboration in this project!

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...

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...

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.

posit.co

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

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!

brailleinstitute.org

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 - @uweohler.bsky.social @prauten.bsky.social @mdc-bimsb.bsky.social @mdc-berlin.bsky.social @humboldtuni.bsky.social go.nature.com/4fcQzZr

Shortcomings of silhouette in single-cell integration benchmarking - Nature Biotechnology

Silhouette score is unsuitable as a metric for single-cell data integration.

go.nature.com

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

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?

go.nature.com

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/

🚨 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...

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...

biorxiv.org

🚨 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...

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...

doi.org

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/

ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants

Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...

biorxiv.org

Anshul Kundaje@anshulkundaje.bsky.social · 2y ago

Aiming to release our long awaited ChromBPNet preprint by early next week as well. I'm recovering from back to back infections for the past 6 weeks. But we're almost there. We have some solid variant prediction benchmarks in there against large supervised models and lots more. Stay tuned.

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 👇🏾

Itai Yanai@itaiyanai.bsky.social · 2y ago

The goal is not to have a zero risk project; those are generally not worth working on. People with a good relationship with risk are definitely not avoiding it. They are super honest about it and they basically make it their goal to slowly chip away at it. nightscience.buzzsprout.com/1744020/epis...

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.

Itai Yanai@itaiyanai.bsky.social · 2y ago

70% of scientists say they experience the imposter syndrome. I still experience it too sometimes, and what helps is talking with a science buddy with whom it’s ok to say stupid things, which may actually turn out to be good ideas.

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

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...

docs.bsky.app

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