Francis O'Reilly
@fjoreilly.bsky.social
Structural Systems Biology at NCI/NIH. Views are my own. #TeamMassSpec
Reposted by Francis O'Reilly
We are excited to share our preprint describing DirectContacts2! Here we develop a machine learning model to discriminate between direct and indirect protein interactions. We use our model to construct a highly accurate wiring diagram of the human cell.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
DirectContacts2: A network of direct physical protein interactions derived from high-throughput mass spectrometry experiments
Cellular function is driven by the activity proteins in stable complexes. Protein complex assembly depends on the direct physical association of component proteins. Advances in macromolecular structur...
www.biorxiv.org
July 29, 2025 at 8:58 PM
We are excited to share our preprint describing DirectContacts2! Here we develop a machine learning model to discriminate between direct and indirect protein interactions. We use our model to construct a highly accurate wiring diagram of the human cell.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
‼️ Exciting new preprint from a close collaboration with Kylie Walters' group. Our study maps the binding sites of key regulators of the proteasome in situ.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Structures of dynamic interactors at native proteasomes by PhIX-MS and cryoelectron microscopy
Proteasome function depends on a network of transient interactions that remain structurally and functionally unresolved. We developed PhIX-MS (Photo-induced In situ Crosslinking-Mass Spectrometry), a ...
www.biorxiv.org
August 5, 2025 at 4:21 PM
‼️ Exciting new preprint from a close collaboration with Kylie Walters' group. Our study maps the binding sites of key regulators of the proteasome in situ.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Francis O'Reilly
New preprint: In situ Architecture of #Plasmodesmata.
Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.
🔗 doi.org/10.1101/2025...
🧪🧵1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM
Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.
🔗 doi.org/10.1101/2025...
🧪🧵1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM
July 26, 2025 at 3:38 PM
New preprint: In situ Architecture of #Plasmodesmata.
Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.
🔗 doi.org/10.1101/2025...
🧪🧵1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM
Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.
🔗 doi.org/10.1101/2025...
🧪🧵1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM
A great lineup of speakers!
Time to get signed up for the Symposium on Structural Proteomics! This time at @humantechnopole.bsky.social in Milan 6th-8th October Full speaker lineup announced. Thanks to @thermofishersci.bsky.social @brukercorporation.bsky.social, Affipro and MSVision for support
Info
ssp2025.squarespace.com
Info
ssp2025.squarespace.com
July 22, 2025 at 3:31 PM
A great lineup of speakers!
Time to get signed up for the next Symposium on Structural Proteomics! This time in beautiful Milan 6th-8th October.
ssp2025.squarespace.com
ssp2025.squarespace.com
July 21, 2025 at 2:05 PM
Time to get signed up for the next Symposium on Structural Proteomics! This time in beautiful Milan 6th-8th October.
ssp2025.squarespace.com
ssp2025.squarespace.com
Reposted by Francis O'Reilly
Beautiful work from my friend @kiranrpatil.bsky.social . Gut bacteria can accumulate Forever chemicals and help us get rid of them! Happy we could contribute! www.nature.com/articles/s41...
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances - Nature Microbiology
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances (PFAS), commonly known as forever chemicals, in intracellular aggregates. Colonization of gnotobiotic mice with bioaccumulating bac...
www.nature.com
July 1, 2025 at 11:25 AM
Beautiful work from my friend @kiranrpatil.bsky.social . Gut bacteria can accumulate Forever chemicals and help us get rid of them! Happy we could contribute! www.nature.com/articles/s41...
Reposted by Francis O'Reilly
We have a 3-year funded postdoc position to work on structures of #amyloid filaments. If you are an expert in protein biochemistry, structural biology or #cryoEM / #cryoET, this could be for you! Feel free to email me with any questions. Come join us! 🤩
www.nature.com/naturecareer...
www.nature.com/naturecareer...
Postdoctoral Scientist - Structural Studies - Dr Sjors Scheres - LMB 2640 - Cambridgeshire job with MRC Laboratory of Molecular Biology (LMB) | 12840844
Postdoctoral Scientist Starting Salary: £41,344 Fixed term: 3 years MRC Laboratory of Molecular Biology, Cambridge, UK We are looking for a postdoc...
www.nature.com
June 25, 2025 at 2:01 PM
We have a 3-year funded postdoc position to work on structures of #amyloid filaments. If you are an expert in protein biochemistry, structural biology or #cryoEM / #cryoET, this could be for you! Feel free to email me with any questions. Come join us! 🤩
www.nature.com/naturecareer...
www.nature.com/naturecareer...
Reposted by Francis O'Reilly
Biblically accurate nitrogen
Fear not! For I bring you glad tidings of great hypervalency
June 2, 2025 at 3:10 AM
Biblically accurate nitrogen
Reposted by Francis O'Reilly
🎉 Congratulations to Wolfgang Baumeister @maxplanck.de, awarded the 2025 #ShawPrize in Life Science & Medicine for pioneering work in cryo-ET!
Learn more 👉 europa.eu/!JBXDBG
#FrontierResearch #ERCSyG #CryoET #StructuralBiology #shawprize2025
Learn more 👉 europa.eu/!JBXDBG
#FrontierResearch #ERCSyG #CryoET #StructuralBiology #shawprize2025
ERC grantee wins the Shaw Prize in Life Science and Medicine
2025 Shaw Prize honours ERC-funded research in molecular imaging
europa.eu
May 28, 2025 at 7:49 AM
🎉 Congratulations to Wolfgang Baumeister @maxplanck.de, awarded the 2025 #ShawPrize in Life Science & Medicine for pioneering work in cryo-ET!
Learn more 👉 europa.eu/!JBXDBG
#FrontierResearch #ERCSyG #CryoET #StructuralBiology #shawprize2025
Learn more 👉 europa.eu/!JBXDBG
#FrontierResearch #ERCSyG #CryoET #StructuralBiology #shawprize2025
Reposted by Francis O'Reilly
We've updated our AFESM website to now include biome filtering, allowing exploration of protein structures adapted to specific environments.
🌐 afesm.foldseek.com
Read more about the work in the skeetorial
🦋 bsky.app/profile/mart...
or our preprint
📄 www.biorxiv.org/content/10.1...
🌐 afesm.foldseek.com
Read more about the work in the skeetorial
🦋 bsky.app/profile/mart...
or our preprint
📄 www.biorxiv.org/content/10.1...
May 15, 2025 at 2:03 PM
We've updated our AFESM website to now include biome filtering, allowing exploration of protein structures adapted to specific environments.
🌐 afesm.foldseek.com
Read more about the work in the skeetorial
🦋 bsky.app/profile/mart...
or our preprint
📄 www.biorxiv.org/content/10.1...
🌐 afesm.foldseek.com
Read more about the work in the skeetorial
🦋 bsky.app/profile/mart...
or our preprint
📄 www.biorxiv.org/content/10.1...
Reposted by Francis O'Reilly
We are looking for a postdoctoral fellow to join us to explore telomerase regulation by histones. Please get in touch if this may interest you.
Excellent opportunity available for a motivated #postdoc to join @kellythd-nguyen.bsky.social’s group investigating the roles of histones in regulating telomerase using a multi-disciplinary approach.
More details: www.nature.com/naturecareer...
Apply by 04 MAY
#PostdocJobs #ScienceJobs
More details: www.nature.com/naturecareer...
Apply by 04 MAY
#PostdocJobs #ScienceJobs
April 16, 2025 at 5:25 PM
We are looking for a postdoctoral fellow to join us to explore telomerase regulation by histones. Please get in touch if this may interest you.
Reposted by Francis O'Reilly
I’m excited to share my first paper in the Farnung lab, in which we report four cryo-EM structures of the human DNA replication machinery engaging with and progressing into a nucleosome.
🔬 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
April 6, 2025 at 10:43 AM
I’m excited to share my first paper in the Farnung lab, in which we report four cryo-EM structures of the human DNA replication machinery engaging with and progressing into a nucleosome.
Reposted by Francis O'Reilly
One of our satellite-tagged Cuckoos has hitched a ride on a cruise ship and is now in the UK, the earliest one of our superstar Cuckoos has ever reached us! 😮🛥️🧵
April 1, 2025 at 7:00 AM
One of our satellite-tagged Cuckoos has hitched a ride on a cruise ship and is now in the UK, the earliest one of our superstar Cuckoos has ever reached us! 😮🛥️🧵
Reposted by Francis O'Reilly
The latest discovery from the lab and great colleagues at McMaster and U Illinois, Chicago. Lariocidin, a new lasso peptide antibiotic that inhibits the ribosome. rdcu.be/efdha
A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome
Nature - A new lasso peptide antibiotic exhibits broad-spectrum activity against Gram-negative and Gram-positive bacteria by interfering with bacterial protein synthesis, is unaffected by common...
rdcu.be
March 26, 2025 at 7:28 PM
The latest discovery from the lab and great colleagues at McMaster and U Illinois, Chicago. Lariocidin, a new lasso peptide antibiotic that inhibits the ribosome. rdcu.be/efdha
Reposted by Francis O'Reilly
In a new Science study, cryo–electron tomography captures the in-cell architecture of the mitochondrial respiratory chain, illuminating how the coordinated action of molecular machines drives life’s fundamental energy conversion.
Learn more in this week's issue: scim.ag/3FA3Ygq
Learn more in this week's issue: scim.ag/3FA3Ygq
March 20, 2025 at 6:05 PM
In a new Science study, cryo–electron tomography captures the in-cell architecture of the mitochondrial respiratory chain, illuminating how the coordinated action of molecular machines drives life’s fundamental energy conversion.
Learn more in this week's issue: scim.ag/3FA3Ygq
Learn more in this week's issue: scim.ag/3FA3Ygq
Reposted by Francis O'Reilly
“You see, that was funny because no one could imagine one banana costing $10.”
March 12, 2025 at 2:48 PM
“You see, that was funny because no one could imagine one banana costing $10.”
Happy retirement to Francis Collins, a scientific and administrative hero. He was always a strong advocate for the importance of biological research and the results are obvious and impressive.
March 1, 2025 at 7:25 PM
Happy retirement to Francis Collins, a scientific and administrative hero. He was always a strong advocate for the importance of biological research and the results are obvious and impressive.
Reposted by Francis O'Reilly
Out of the lab, into the wild: when @pauligroup.bsky.social's Andi Pauli puts on her @ox.ac.uk blue, you know it's business time! Austria's national broadcast ORF interviewed her on how #Vienna has become such an amazing place for life science research.
February 7, 2025 at 1:59 PM
Out of the lab, into the wild: when @pauligroup.bsky.social's Andi Pauli puts on her @ox.ac.uk blue, you know it's business time! Austria's national broadcast ORF interviewed her on how #Vienna has become such an amazing place for life science research.
Reposted by Francis O'Reilly
Foldseek-Multimer—now published in @naturemethods.bsky.social—our fast multimer search tool, enables complex comparisons against the full PDB in seconds. It comes with BFMD, a collection of 300K+ predictions gathered from community projects.
📄 nature.com/articles/s41...
🌐 search.foldseek.com
📄 nature.com/articles/s41...
🌐 search.foldseek.com
February 6, 2025 at 8:25 AM
Foldseek-Multimer—now published in @naturemethods.bsky.social—our fast multimer search tool, enables complex comparisons against the full PDB in seconds. It comes with BFMD, a collection of 300K+ predictions gathered from community projects.
📄 nature.com/articles/s41...
🌐 search.foldseek.com
📄 nature.com/articles/s41...
🌐 search.foldseek.com
Reposted by Francis O'Reilly
Ever wondered how Pol II speed is controlled during productive elongation?
Our study reveals that the helicase RECQL5 triggers transcription braking, while the transcription-coupled DNA repair complex restores the elongation rate. #cryoEM #transcription
www.biorxiv.org/content/10.1...
Our study reveals that the helicase RECQL5 triggers transcription braking, while the transcription-coupled DNA repair complex restores the elongation rate. #cryoEM #transcription
www.biorxiv.org/content/10.1...
February 3, 2025 at 12:23 PM
Ever wondered how Pol II speed is controlled during productive elongation?
Our study reveals that the helicase RECQL5 triggers transcription braking, while the transcription-coupled DNA repair complex restores the elongation rate. #cryoEM #transcription
www.biorxiv.org/content/10.1...
Our study reveals that the helicase RECQL5 triggers transcription braking, while the transcription-coupled DNA repair complex restores the elongation rate. #cryoEM #transcription
www.biorxiv.org/content/10.1...
Reposted by Francis O'Reilly
To everyone in a similar scenario: the tactic my doctor's office has taught me is to ask, in writing, for:
1) the name, board specialty, and license number of the doctor making the determination the treatment was not medically necessary;
1) the name, board specialty, and license number of the doctor making the determination the treatment was not medically necessary;
March 26, 2024 at 2:16 AM
To everyone in a similar scenario: the tactic my doctor's office has taught me is to ask, in writing, for:
1) the name, board specialty, and license number of the doctor making the determination the treatment was not medically necessary;
1) the name, board specialty, and license number of the doctor making the determination the treatment was not medically necessary;
Reposted by Francis O'Reilly
We are very excited to share our recent preprint on the nuclear import mechanism of the proteasome, driven by the multivalent adaptor AKIRIN2! www.biorxiv.org/content/10.1... 🧵 1/6
A multivalent adaptor mechanism drives the nuclear import of proteasomes
Nuclear protein homeostasis, including the turnover of transcription factors, critically depends on nuclear proteasomes. After each cell division, proteasomes need to be re-imported into the newly for...
www.biorxiv.org
December 5, 2024 at 8:11 PM
We are very excited to share our recent preprint on the nuclear import mechanism of the proteasome, driven by the multivalent adaptor AKIRIN2! www.biorxiv.org/content/10.1... 🧵 1/6
Reposted by Francis O'Reilly
First paper of our lab today @natureportfolio.bsky.social by Nussi!
We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!
@embl.org #RNAbiology #RNASky
t.co/a24Xxcxdo0
We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!
@embl.org #RNAbiology #RNASky
t.co/a24Xxcxdo0
December 4, 2024 at 8:53 PM
First paper of our lab today @natureportfolio.bsky.social by Nussi!
We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!
@embl.org #RNAbiology #RNASky
t.co/a24Xxcxdo0
We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!
@embl.org #RNAbiology #RNASky
t.co/a24Xxcxdo0