Lucas Farnung
@lucas.farnunglab.com
Assistant Professor of Cell Biology at Harvard Medical School | HHMI Freeman Hrabowski Scholar | Nexus of chromatin, transcription, replication, and epigenetics. farnunglab.com
Pinned
Lucas Farnung
@lucas.farnunglab.com
· Apr 6
🔬 New from the Farnung Lab: We established a fully in vitro reconstituted chromatin replication system and report the first cryo-EM snapshots of the human replisome engaging nucleosomes. Brilliant work by @felixsteinruecke.bsky.social with support from @jonmarkert.bsky.social! tinyurl.com/replisome
The Richard and Susan Smith Family Foundation, which supports our work, has produced a short film about our research:
November 26, 2025 at 1:22 AM
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!
Calling all rising juniors & seniors: Interested in biological or biomedical research? Applications for our ’26 Summer Undergraduate Research Experience Program are now open! Nine weeks, hands-on research, & mentorship from some of the nation’s top scientists — learn more: bit.ly/CechFellows
Summer Undergraduate Research Experience | HHMI
The Cech Fellows Program is a paid, nine-week summer research experience empowering the next generation of scientific leaders.
bit.ly
November 21, 2025 at 6:24 PM
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
consurfdb.tau.ac.il
November 20, 2025 at 4:51 PM
What's going on with ConSurf? consurf.tau.ac.il
Reposted by Lucas Farnung
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
Proteome-wide in silico screening for human protein-protein interactions
Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...
biorxiv.org
November 12, 2025 at 9:26 PM
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
Reposted by Lucas Farnung
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...
Transcript and video here
www.cbsnews.com/news/researc...
Battle between Trump and universities hurting scientific research in need of federal funding
Federal research funding to universities has fueled breakthroughs for years. The White House is pressuring universities to align with the president's political agenda, or risk losing their funding.
www.cbsnews.com
November 10, 2025 at 1:03 AM
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...
Transcript and video here
www.cbsnews.com/news/researc...
Reposted by Lucas Farnung
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...
I will choose "biophysics" as the closest one, but this feels inexact for this paper...
November 9, 2025 at 5:53 PM
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...
I will choose "biophysics" as the closest one, but this feels inexact for this paper...
Reposted by Lucas Farnung
@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
Video: youtu.be/sLfyuQuH8F0
KSQA: Dr Karim-Jean Armache / Dr. Cigall Kadoch (Epigenetics and Gene Regulation)
YouTube video by KeystoneSymposia
youtu.be
November 3, 2025 at 2:43 PM
@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
Video: youtu.be/sLfyuQuH8F0
Reposted by Lucas Farnung
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....
October 27, 2025 at 11:49 AM
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.
October 24, 2025 at 5:44 PM
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.
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.
ORF Verifier
orfverifier.farnunglab.com
October 13, 2025 at 12:33 PM
🧬 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.
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.
October 13, 2025 at 12:23 PM
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.
Della Syau successfully defended her PhD thesis today. Congrats, Dr. Syau. Strike #3!
October 9, 2025 at 12:02 AM
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
New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com
October 4, 2025 at 7:19 PM
We have added additional functionalities including a collapsible protein pane and zoom scrolling. domaindesigner.farnunglab.com
Reposted by Lucas Farnung
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...
Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life
In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral transcripts. Here, we discover that giant DNA virus...
www.biorxiv.org
October 2, 2025 at 6:10 PM
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
September 29, 2025 at 3:01 PM
New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com
Reposted by Lucas Farnung
🌟 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.
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 👇
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 👇
September 26, 2025 at 3:52 PM
🌟 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.
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 👇
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 👇
September 26, 2025 at 1:15 PM
🚀 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 👇
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
Services 3 — Farnung Lab
www.farnunglab.com
September 25, 2025 at 12:55 PM
Find up to date links to the Farnung lab's cloning, experiment designer, and buffer preparation software tools here: www.farnunglab.com/tools
Reposted by Lucas Farnung
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
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
September 13, 2025 at 12:05 AM
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
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.
September 4, 2025 at 9:55 PM
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.
September 3, 2025 at 3:42 PM
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.
Reposted by Lucas Farnung
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
Structure and function of IWS1 in transcription elongation
Transcription elongation by RNA polymerase II is a tightly regulated process that requires coordinated interactions between elongation factors. IWS1 (Interacts with SPT6) has been implicated as a core...
www.biorxiv.org
August 29, 2025 at 4:32 PM
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...
August 29, 2025 at 10:14 AM
🧬 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...
Reposted by Lucas Farnung
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.
A direct interaction between the Chd1 CHCT domain and Rtf1 controls Chd1 distribution and nucleosome positioning on active genes
Abstract. The nucleosome remodeler Chd1 is required for the re-establishment of nucleosome positioning in the wake of transcription elongation by RNA Polym
doi.org
August 28, 2025 at 11:07 PM
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.