🧪✨ Introducing BenchAid🧪! Our new molecular biology AI agent is live at benchaid.farnunglab.com. Over the last months, we built BenchAid🧪 to streamline many of our bench workflows to help move our lab faster. Try it out!

Happy to share part of my postdoctoral work at the @lucas.farnunglab.com lab. Great collaboration with @voslab.org and @andersshansen.bsky.social. “Structural basis for CTCF-mediated chromatin organization” www.biorxiv.org/content/10.6...

If you like our story here, consider applying to our labs for your post-doc! We have exciting projects ranging from transcription and DNA replication to genome organization and chromatin remodeling (and even lab automation and agentic molecular biology AI, more on this soon)!

This was a serendipitous finding with so many involved (👀 @voslab.org and @andersshansen.bsky.social). Especially proud of Farnung Lab contributors @mosorio91.bsky.social (on the job market) and PhD candidate Alex Stone. Biochemistry, structural biology, and cell-based assays (Micro-C!!!).

🚨Preprint alert🚨 How does chromatin “architecture” form at CTCF sites? Our new preprint with @voslab.org and @andersshansen.bsky.social shows CTCF dimerization promotes nucleosome oligomerization on chromatin. tinyurl.com/CTCF-nucleos...

If you are looking for more history and inspiration from Freeman Hrabowski, his TED talk is very powerful. Well worth the 15 minutes. www.ted.com/talks/freema...

🧪🧬New preprint We present cryo-EM structures of reconstituted CTCF–nucleosome complexes, showing CTCF dimerization drives nucleosome oligomerization into defined higher-order assemblies. Disrupting CTCF–CTCF interfaces in mESCs reduces looping and impairs differentiation. tinyurl.com/CTCF-nucleos...

Exciting work from @lucas.farnunglab.com & @voslab.org report structures of CTCF-nucleosome complexes, revealing that CTCF dimers promote oligomerization of nucleosomes into defined higher-order assemblies involving specific histone-histone and CTCF-CTCF interactions. www.biorxiv.org/content/10.6...

Here is the official announcement. Now more than ever, acknowledging the contributions of immigrants is so important. Thank you @vilcekfoundation.bsky.social, and congrats to my fellow awardees. Can't wait to meet you all.

🧬📄 Preprint update (v2): We added new biochemical experiments that clarify how IWS1 associates with the transcription elongation complex and further define competition between IWS1 and RECQL5. 🧪⚙️ www.biorxiv.org/content/10.1... Structural model is already available in the PDB (9MLC).

Join us today at 11 am EST. I will present our lab's latest research and introduce our lab AI agent Benchmate🧪.

Presenting our research tomorrow @aicc-ireland.bsky.social Please join via Zoom!

Science update from my postdoc Peiyuan Chai - his work “glycoRNA complexed with heparan sulfate regulates VEGF-A signaling” is now published @nature.com uncovering a new layer or glycoRNA-regulation of growth factor mediated control physiological processes rdcu.be/e1bBX

The Vlaming lab continues to grow! It's an exciting time in the Vlaming lab: we've just had our 2nd PhD student join, and the 3rd is joining in February. Now, we're looking to recruit a postdoc!

After a short break in our webinars we are delighted to be back up & running this month! First up, on Jan 30th we will be joined by @lucas.farnunglab.com from @harvardmed.bsky.social 🔬 Shortly after, on Feb 13th we will be hosting @heardlab.bsky.social from @crick.ac.uk 🧬 Registration details 👇

Lucas Farnung will use "visual biochemistry" at atomic resolution to see exactly how errors in DNA replication drive cancer. This high-def view will reveal brand-new targets for drug development. 🔬 @harvardmed.bsky.social @lucas.farnunglab.com

📢 Announcing The Mark Foundation 2026 Emerging Leader Award winners! 📢 We are committing $3.75 million to 5 visionary early-career scientists poised to lead the next generation of oncology breakthroughs. We can't wait to see their impact! themarkfoundation.org/2026/01/2026...

This is also a good occasion to highlight that we are looking for post-doctoral researchers that are interested in understanding the fundamental mechanisms of transcription, DNA replication, and chromatin.

Honored to receive The Mark Foundation for Cancer Research 2026 Emerging Leader Award. Grateful to my lab and all who support the Farnung Lab—thank you!

Benchmate🧪 and its LabBook are making good UI progress.

Benchmate🧪 has its own custom-written ELN now.

Benchmate gonna benchmate...

We are thrilled to share our latest work uncovering the mechanistic basis of target-directed microRNA degradation (TDMD). This work was driven by @jakobfarnung.bsky.social and @elenaslo.bsky.social in a fantastic collaboration with Brenda Schulman's lab. tinyurl.com/E3TDMD (1/5)

Here it is! A new chapter in RNA biology and degradation mechanisms. My brother @jakobfarnung.bsky.social and @elenaslo.bsky.social show that an E3 not only induces the degradation of proteins but also of RNA. Congrats!

When RNA Degradation 🤝 meets 🤝 Protein Degradation! tinyurl.com/E3TDMD In a collaboration of @bartellab.bsky.social and Schulman lab, we show that, in target-directed microRNA degradation (TDMD), 2-RNA-factors recruit an E3 ligase and induce the degradation of not only a protein but also RNA (1/5).

"Benchmate, generate LICv1 primers for Midnolin." Benchmate🧪: ✅

Hey, I'm Benchmate🧪. I am a molecular biology agent living in Lucas' terminal. That plasmid cloned 3 years ago? Found it. Purified protein in the -80? I know the concentration and can write the next protocol. Need primers for that gene? Give me 30 seconds.

Happy Holidays from the Farnung lab!

$15k stipend to support 9 weeks of full time summer research! For rising juniors/seniors who are able to travel to and obtain housing at the location of the lab they are placed in! I did an HHMI summer experience in 2013 and it changed everything for me! Apply…or tell someone to apply! 🧪🧠

"My advice to other undergraduates: Just go for it!" — Lalitha Ravipati, alum, Summer Undergraduate Research Program Rising junior or senior who's interested in working alongside some of the nation's top scientists this summer? Apply now: bit.ly/CechFellows 🧪

The Richard and Susan Smith Family Foundation, which supports our work, has produced a short film about our research:

A great way to dive into cutting-edge biological research and learn from leading scientists. Apply to join the Farnung lab or other HHMI labs this summer!

What's going on with ConSurf? consurf.tau.ac.il

Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp

Very well done story on 60 Minutes about the harms of grant terminations and freezes at Harvard with Joan Brugge, Don Engbar, David Liu, and a very compelling young cancer patient, now cured with Liu's technology. Transcript and video here www.cbsnews.com/news/researc...

How did @biorxivpreprint make it this far without a #StructuralBiology "subject area"? 🤔 I will choose "biophysics" as the closest one, but this feels inexact for this paper...

@ckadoch.bsky.social and I are excited to welcome you to Geneva for the 2026 Keystone Symposium on Epigenetics and Gene Regulation in Health and Disease — short talk and poster slots are still open. Don’t miss the deadlines. Video: youtu.be/sLfyuQuH8F0

Happy to share our latest publication, in which we show that the arrangement of nucleosomes around CTCF sites contributes to higher-order organisation of chromatin into TADs: www.embopress.org/doi/full/10....

I love AlphaFold—but please include PAE (Predicted Aligned Error) plots for every “interaction.” Pretty PDBs ≠ proof. If the PAE doesn’t show an interface, it ain’t one. Show the plots. Structural biology's reputation is on the line.

🧬 Meet ORF Verifier (orfverifier.farnunglab.com) 🧬 Validating ORFs from plasmid sequences—such as those from @plasmidsaurus.bsky.social —can be tedious and error-prone. Manual inspection and alignments in tools like SnapGene take time and attention. ORF Verifier automates sequence verification.

We have added new functionality to include a plot of protein disorder using IUPred scores generated by iupred2a.elte.hu. Generate IUPred scores for your POI and upload the JSON file to generate this plot.

Leider wahr. #DenkIchAnDeutschland gersemann.substack.com/p/2-how-germ...

Della Syau successfully defended her PhD thesis today. Congrats, Dr. Syau. Strike #3!

We have added additional functionalities including a collapsible protein pane and zoom scrolling. domaindesigner.farnunglab.com

Historically, viruses were thought to primarily use host cell's translational machinery. New work from @harvardcellbio.bsky.social faculty Amy Lee reveals that a giant DNA virus encodes its own IF4F initiation complex, suggesting an unexpected evolutionary innovation. www.biorxiv.org/content/10.1...

New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com

🌟 Our customers never stop innovating. This NFC-to-Quartzy workflow is a perfect example of why we built an API — so labs can create the exact tools they need to make science run smoother. Check out how they did it.

🚀 Ordering lab supplies just got way easier in our lab. We built a workflow (github.com/farnunglab/N...) where tapping an NFC tag on a reagent bottle automatically triggers an order request in Quartzy. No more scribbling notes or hunting for a computer. Here’s how 👇

Find up to date links to the Farnung lab's cloning, experiment designer, and buffer preparation software tools here: www.farnunglab.com/tools

This one is a bit of a departure from the usual and definitely a work in progress! We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below. Read on for details... 1/x