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

Martin Filipovski successfully defended his PhD thesis today! Congrats, Dr. Filipovski.

In our IWS1 story, we also visualize the histone reader LEDGF PWWP domain on a transcribed downstream nucleosome. Because the PWWP requires both DNA gyres for binding, it binds to the promoter-distal side of the nucleosome during transcription through the nucleosome.

New insights into transcriptional elongation by IWS1 from the @lucas.farnunglab.com lab. This work establishes IWS1 as a scaffold to organiz the elongation complex, illustrating how disordered regions regulate transcription elongationhttps://www.biorxiv.org/content/10.1101/2025.08.28.672863v1

🧬 Transcription elongation by RNA polymerase II relies on a web of elongation factors. Our new work shows how IWS1 acts as a modular scaffold to stabilize & stimulate elongation. Fantastic work by Della Syau! www.biorxiv.org/content/10.1...

Our collaborative paper with the Arndt lab is out today: doi.org/10.1093/nar/... (originally bioRxiv: www.biorxiv.org/content/10.1...). Here we asked the question of how CHD1 localizes to chromatin.

New work from the @sshaolab.bsky.social lab with Gu and Elledge labs reveals structure of TXNL1 bound to proteasome and mechanism of its ubiquitin-independent degradation www.nature.com/articles/s41...

RNA N-glycosylation enables immune evasion and homeostatic efferocytosis by chemically caging acp3U. Excited to report this work lead by Vinnie @vinnieviruses.bsky.social and in collaboration with @vijayrathinam.bsky.social in @nature.com www.nature.com/articles/s41...

Thoughts from our own Tom Rapoport on the role of basic science in curing disease. magazine.hms.harvard.edu/articles/rev...

Congratulations to our own @sophiero.bsky.social and team for achieving 3rd place 🥉 in the Merck Innovation Cup 2025. The entire lab is very proud of Sophie's achievement!

I am pleased to announce Reactor—the complex formation calculator for multi-component protein complex formation experiments. Developed by the Farnung Lab @harvardmed.bsky.social. reactor-farnunglab.pythonanywhere.com 1/n

Asking for a friend, what is the gold-standard™️ for generating a composite cryo-EM map atm?

🎥 Our @harvard.edu undergrad Yerosen Daba is runningthe Harvard College Instagram page today. Check out his story here: www.instagram.com/stories/harv... And learn what we do in the Farnung lab (and perhaps you get to meet the man, the myth, the legend aka Boltzmann too)! 📸⚡

Work from our own Corey Allard allardlab.hms.harvard.edu & Nick Bellono reveals a process by which foreign chloroplasts (derived from algae food sources) are incorporated into novel, host-derived organelles termed “kleptosomes". \https://www.sciencedirect.com/science/article/pii/S0092867425006373

New work from @xingulab.bsky.social @sshaolab.bsky.social & Elledge lab report structure of Midnolin-proteasome complex & its role in controlling myeloma via ubiquitin-independent degradation. www.cell.com/molecular-ce...

Beyond excited… www.hhmi.org/programs/fre...

Congratulations to our own Lucas Farnung @lucas.farnunglab.com who has been named as one of 30 Freeman Hrabowski Scholars for 2025 by the Howard Hughes Medical Institute (HHMI). So well deserved deserved !! www.hhmi.org/programs/fre...

First PhD candidate (congrats, Dr. James!) to graduate today and check out this beautiful nucleosome/ocean cake made by PhD candidate Della Syau:

Congratulations to 🎓 Dr. Allison James 🎉. Allison is the first PhD candidate to graduate from the Farnung Lab!

My message to Trump’s NIH Director? No one in America wants us to do LESS cancer research. No one is asking Trump to make it harder to cure Alzheimer's disease. Yet Trump is cutting all of this NOW and demanding an $18 BILLION cut to NIH next year. Not on my watch.

Schulman lab is ready for the GRK2243 Symposium: Understanding ubiquitination: from molecular mechanisms to disease in würzburg #wUeBI2025 @grk2243.bsky.social @jakobfarnung.bsky.social @samuelmaiwald.bsky.social @hannahbkmpr.bsky.social

Check out @jonmarkert.bsky.social's recent talk for the @fnucleosome.bsky.social series, covering his recent breakthrough paper (www.science.org/stoken/autho...) on co-transcriptional histone mark deposition of H3K36me3: www.youtube.com/watch?v=ByJr...

New work @harvard by Miguel Gonzalez-Lozano @harperlabhms.bsky.social & @ernstschmid.bsky.social in Johannes Walter lab charts structural interactome of endosomes. #XL-MS #Alphafold Funded by @asapresearch.parkinsonsroadmap.org & NIH. Science continues-despite attacks www.nature.com/articles/s41...

Excited to share our latest study on how K29/K48-branched #ubiquitin chains are forged by the #E3 ligase TRIP12, and how this suggests a consensus mechanism for chain formation by HECT E3s! @natsmb.nature.com 1/7 www.nature.com/articles/s41...

 🧬🎉Thrilled to share our new chromatin remodeling study! We reveal three states of human CHD1 and identify a novel "anchor element" that interacts with the acidic patch—conserved among remodelers. Our structures clarify mechanisms of remodeler recruitment! Link: authors.elsevier.com/a/1l2ik3vVUP...

Watching Sven elucidate this mechanism from an unbiased screen onwards has been one of my favorite experiences as a PI. In these challenging times for science at Harvard, it reminds me of the sheer joy of doing science and making discoveries.

CONGRATULATIONS!! to @harvardcellbio.bsky.social faculty member Tommy Kirchhausen for his election to the American Academy of Arts and Sciences. So well deserved! www.amacad.org/new-members-...

Cup? Platter? Stained glass? Our imaginations were inspired (even during uncertain times!) by these beautiful molecular complexes: the Erlin and prohibitin complexes implicated in quality control at the ER and mitochondria, respectively. Check them out here: www.biorxiv.org/content/10.1...