Charles Bayly-Jones
@charlesbj.bsky.social
Investigating protein nanomachines and their dynamics.
Laboratory head at Monash University 🇦🇺.
ARC DECRA Fellow.
Structural biologist. Author of WIGGLE. He/Him. 🏳️🌈
Laboratory head at Monash University 🇦🇺.
ARC DECRA Fellow.
Structural biologist. Author of WIGGLE. He/Him. 🏳️🌈
Pinned
Earlier this year, I was incredibly honoured to receive the Premier’s Award for Health and Medical Research in the Basic Science category.
This recognition is a huge testament to the amazing work of our entire team. 🙌💥🎉
Photography and video: @vicgovau.bsky.social
www.youtube.com/watch?v=9_Ht...
This recognition is a huge testament to the amazing work of our entire team. 🙌💥🎉
Photography and video: @vicgovau.bsky.social
www.youtube.com/watch?v=9_Ht...
I’ve officially started my lab at Monash University! 🎉
We’re diving into #cellgrowth and #lysosome biology, through the lens of molecular #structure and mechanism.
I’m thrilled to say that PhD student scholarships are available—so please share widely and get in touch if you’re interested. 🤩
We’re diving into #cellgrowth and #lysosome biology, through the lens of molecular #structure and mechanism.
I’m thrilled to say that PhD student scholarships are available—so please share widely and get in touch if you’re interested. 🤩
February 18, 2026 at 8:35 AM
I’ve officially started my lab at Monash University! 🎉
We’re diving into #cellgrowth and #lysosome biology, through the lens of molecular #structure and mechanism.
I’m thrilled to say that PhD student scholarships are available—so please share widely and get in touch if you’re interested. 🤩
We’re diving into #cellgrowth and #lysosome biology, through the lens of molecular #structure and mechanism.
I’m thrilled to say that PhD student scholarships are available—so please share widely and get in touch if you’re interested. 🤩
Tried it. Its awesome. Shame the code isn't available. Webserver only, how long will it last??
Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta www.biorxiv.org/content/10.64898/2026.02.13.705846v1 #cryoem
February 17, 2026 at 10:06 PM
Tried it. Its awesome. Shame the code isn't available. Webserver only, how long will it last??
Reposted by Charles Bayly-Jones
I've heard this position articulated by a lot of people, but I think this is hard to make precise. Much of this tracks a problem we already know in science: standards of authorship are not stable and there are many difficult edge cases.
Consider these cases...
Consider these cases...
Seeing ppl debate how to deal with paper submissions that are partly written by “AI”. Why are we having that conversation?
I would refuse to review or edit any paper that was not 100% written by its authors (i.e., the people who have authorial responsibility for the creation of a papers content).
I would refuse to review or edit any paper that was not 100% written by its authors (i.e., the people who have authorial responsibility for the creation of a papers content).
February 16, 2026 at 8:58 PM
I've heard this position articulated by a lot of people, but I think this is hard to make precise. Much of this tracks a problem we already know in science: standards of authorship are not stable and there are many difficult edge cases.
Consider these cases...
Consider these cases...
Reposted by Charles Bayly-Jones
Physically Grounded Generative Modeling of All-Atom Biomolecular Dynamics www.biorxiv.org/content/10.64898/2026.02.15.705956v1 #cryoem
February 16, 2026 at 8:10 AM
Physically Grounded Generative Modeling of All-Atom Biomolecular Dynamics www.biorxiv.org/content/10.64898/2026.02.15.705956v1 #cryoem
Reposted by Charles Bayly-Jones
Metadynamics meets diffusion-based structure prediction: the same trick that drives enhance sampling of MD trajectories can be adapted and applied as steering terms during generation to sample diverse conformations. Seems obvious in hindsight!
February 15, 2026 at 3:27 AM
Metadynamics meets diffusion-based structure prediction: the same trick that drives enhance sampling of MD trajectories can be adapted and applied as steering terms during generation to sample diverse conformations. Seems obvious in hindsight!
Reposted by Charles Bayly-Jones
How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller?
Excited to share our latest work in @science.org on a new small polymerase.
1/n
Excited to share our latest work in @science.org on a new small polymerase.
1/n
A small polymerase ribozyme that can synthesize itself and its complementary strand
The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...
www.science.org
February 13, 2026 at 11:42 AM
How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller?
Excited to share our latest work in @science.org on a new small polymerase.
1/n
Excited to share our latest work in @science.org on a new small polymerase.
1/n
Reposted by Charles Bayly-Jones
New online: Structure and function of the yeast amino acid-sensing SEAC–EGOC supercomplex
Structure and function of the yeast amino acid-sensing SEAC–EGOC supercomplex
Nature Structural & Molecular Biology, Published online: 12 February 2026; doi:10.1038/s41594-026-01746-2Tafur et al. determined the cryo-electron microscopy structure of the SEA complex (GATOR) bound to its substrate, the EGO complex (Ragulator–Rag), and showed that its GAP activity is essential for both rapid inactivation and reactivation of TORC1.
dlvr.it
February 13, 2026 at 8:53 AM
New online: Structure and function of the yeast amino acid-sensing SEAC–EGOC supercomplex
Reposted by Charles Bayly-Jones
New preprint from the Robertson Lab! We used AF ensemble generation for rigidity filtering with generative design to make cryoEM fiducials, enabling rapid inactive states of four drug targets and a beta2 extracellular fiducial to study GPCR activation!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
January 27, 2026 at 2:33 PM
New preprint from the Robertson Lab! We used AF ensemble generation for rigidity filtering with generative design to make cryoEM fiducials, enabling rapid inactive states of four drug targets and a beta2 extracellular fiducial to study GPCR activation!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Charles Bayly-Jones
Nature research paper: Construction of complex and diverse DNA sequences using DNA three-way junctions
go.nature.com/4qu2ExZ
go.nature.com/4qu2ExZ
Construction of complex and diverse DNA sequences using DNA three-way junctions - Nature
Sidewinder enables high-fidelity DNA assembly by separating the information that guides assembly from the final assembled sequence.
go.nature.com
January 21, 2026 at 6:08 PM
Nature research paper: Construction of complex and diverse DNA sequences using DNA three-way junctions
go.nature.com/4qu2ExZ
go.nature.com/4qu2ExZ
Not just biomedicine! Chemistry, physics, computer science, climate? Both ARC and NHMRC massively under funded. Success rates abysmal.
Skeptical of claim re budget increase by 250%? Aus R&D expenditure (%GDP) is stagnant, significantly below OECD average.
Inflation. Rising costs. USA exit. ?!?
Skeptical of claim re budget increase by 250%? Aus R&D expenditure (%GDP) is stagnant, significantly below OECD average.
Inflation. Rising costs. USA exit. ?!?
In the words of a world-renowned cardiologist, Australia’s young medical researchers are “left to flounder with total job insecurity and family pressures. It’s the best recipe we have for raiding our future, in terms of a medical research workforce and the benefits of medical research”
‘We’re losing careers’: Leading cardiologist warns Australian medical research is in crisis
The head of the Heart Research Institute is telling young scientists medical research is a “terrible career path”. There’s a $5 billion answer in the government’s budget.
www.theage.com.au
January 17, 2026 at 12:31 AM
Not just biomedicine! Chemistry, physics, computer science, climate? Both ARC and NHMRC massively under funded. Success rates abysmal.
Skeptical of claim re budget increase by 250%? Aus R&D expenditure (%GDP) is stagnant, significantly below OECD average.
Inflation. Rising costs. USA exit. ?!?
Skeptical of claim re budget increase by 250%? Aus R&D expenditure (%GDP) is stagnant, significantly below OECD average.
Inflation. Rising costs. USA exit. ?!?
First steps toward magnetic-elution affinity chromatographies, easily pattern surfaces, microfluidics, also probably cheaper than mag beads for robotic pipelines. Keen to see the data!
Great news! @mariaingaramo.bsky.social 's company (Nonfiction Labs) made a remote-controlled antibody.
Its binding turns on and off with a magnet.
This is a HUGE step towards our dream of magnetically controlled drugs. Imagine a cancer drug that ONLY attacks the tumor, not the rest of your body.
Its binding turns on and off with a magnet.
This is a HUGE step towards our dream of magnetically controlled drugs. Imagine a cancer drug that ONLY attacks the tumor, not the rest of your body.
January 13, 2026 at 9:59 PM
First steps toward magnetic-elution affinity chromatographies, easily pattern surfaces, microfluidics, also probably cheaper than mag beads for robotic pipelines. Keen to see the data!
Reposted by Charles Bayly-Jones
The latest research from our team is out in Cell @cp-cell.bsky.social! We used #cryo-EM, #imaging, #BRET, and #biosensors targeted to the lysosome to understand how the KICSTOR-GATOR1 complex turns off #mTORC1 in response to low levels of amino acids.
January 13, 2026 at 1:56 AM
The latest research from our team is out in Cell @cp-cell.bsky.social! We used #cryo-EM, #imaging, #BRET, and #biosensors targeted to the lysosome to understand how the KICSTOR-GATOR1 complex turns off #mTORC1 in response to low levels of amino acids.
Reposted by Charles Bayly-Jones
Excited to share our latest research, out today in Cell (@cellpress.bsky.social)
Using cryo-EM and cell-based studies, we reveal how large nutrient sensing protein complexes form at the lysosomal membrane to turn off mTORC1 and halt anabolic signalling.
Read the paper here: doi.org/10.1016/j.ce...
Using cryo-EM and cell-based studies, we reveal how large nutrient sensing protein complexes form at the lysosomal membrane to turn off mTORC1 and halt anabolic signalling.
Read the paper here: doi.org/10.1016/j.ce...
January 9, 2026 at 7:11 AM
Excited to share our latest research, out today in Cell (@cellpress.bsky.social)
Using cryo-EM and cell-based studies, we reveal how large nutrient sensing protein complexes form at the lysosomal membrane to turn off mTORC1 and halt anabolic signalling.
Read the paper here: doi.org/10.1016/j.ce...
Using cryo-EM and cell-based studies, we reveal how large nutrient sensing protein complexes form at the lysosomal membrane to turn off mTORC1 and halt anabolic signalling.
Read the paper here: doi.org/10.1016/j.ce...
Reposted by Charles Bayly-Jones
The government can’t claim that medical research is a priority while failing to treat it as one. Nine in 10 leading researchers in Australia are missing out on government support for world‑class proposals, leaving exceptional talent uncertain about their future.
Most researchers miss out on innovation grants while medical fund sits on $25b
Nine in 10 Australian researchers had their “ideas grant” applications rejected last year, even as Australia’s medical investment fund sits on $5 billion more than it was designed to hold.
www.theage.com.au
January 3, 2026 at 11:32 PM
The government can’t claim that medical research is a priority while failing to treat it as one. Nine in 10 leading researchers in Australia are missing out on government support for world‑class proposals, leaving exceptional talent uncertain about their future.
Reposted by Charles Bayly-Jones
Now online! Structure of the lysosomal KICSTOR-GATOR1-SAMTOR nutrient-sensing supercomplex
Structure of the lysosomal KICSTOR-GATOR1-SAMTOR nutrient-sensing supercomplex
This study reveals how KICSTOR and GATOR1 assemble into a crescent-shaped lysosomal complex that regulates mTORC1 during amino acid starvation and how SAMTOR binds KICSTOR in an S-adenosylmethionine-incompatible conformation to couple methionine sensing to mTORC1 regulation.
dlvr.it
January 8, 2026 at 3:59 PM
Now online! Structure of the lysosomal KICSTOR-GATOR1-SAMTOR nutrient-sensing supercomplex
January 8, 2026 at 7:49 PM
Thrilled to share our latest work @luptoncj.bsky.social @drellisdon.bsky.social @drmlhalls.bsky.social.
Structure of the lysosomal KICSTOR-GATOR1-SAMTOR nutrient-sensing supercomplex.
🧪🔬#cryoEM
Now online @cellpress.bsky.social.
doi.org/10.1016/j.ce...
Structure of the lysosomal KICSTOR-GATOR1-SAMTOR nutrient-sensing supercomplex.
🧪🔬#cryoEM
Now online @cellpress.bsky.social.
doi.org/10.1016/j.ce...
January 8, 2026 at 7:39 PM
Thrilled to share our latest work @luptoncj.bsky.social @drellisdon.bsky.social @drmlhalls.bsky.social.
Structure of the lysosomal KICSTOR-GATOR1-SAMTOR nutrient-sensing supercomplex.
🧪🔬#cryoEM
Now online @cellpress.bsky.social.
doi.org/10.1016/j.ce...
Structure of the lysosomal KICSTOR-GATOR1-SAMTOR nutrient-sensing supercomplex.
🧪🔬#cryoEM
Now online @cellpress.bsky.social.
doi.org/10.1016/j.ce...
Crowd sourcing request!! I'm trialling some dev software and I'm looking for nice public tomograms to use as case studies. Downloading all tomos and looking for good examples is tedious. Can anyone recommend specific tomos from EMPIAR/CZI that have multiple STA targets?
#teamtomo #cryoEM
#teamtomo #cryoEM
December 28, 2025 at 1:38 AM
Reposted by Charles Bayly-Jones
CryoEM folks, If you want to handle huge STAR file efficiently in Python, please try starfile-rs!
github.com/hanjinliu/star…
Reading a motion data of a particle from a 15 MB file is just like this ↓🤩
github.com/hanjinliu/star…
Reading a motion data of a particle from a 15 MB file is just like this ↓🤩
December 23, 2025 at 2:52 PM
CryoEM folks, If you want to handle huge STAR file efficiently in Python, please try starfile-rs!
github.com/hanjinliu/star…
Reading a motion data of a particle from a 15 MB file is just like this ↓🤩
github.com/hanjinliu/star…
Reading a motion data of a particle from a 15 MB file is just like this ↓🤩
Interesting discussion. Pros/cons of PDFs vs digital objects.
As our standards increase, the burden of evidence will so too. These monster figs are a consequence. Why are we still held to prehistoric paper press page limits? Why not have as many ext. data figs as necessary? A PDF can be 100 pgs.
As our standards increase, the burden of evidence will so too. These monster figs are a consequence. Why are we still held to prehistoric paper press page limits? Why not have as many ext. data figs as necessary? A PDF can be 100 pgs.
The obsession with a print-era portable format (PDF) is the only reason we have figures like this. Makes no sense on the Web. 1/2
Wow this is a seriously serious supplementary figure from @cellpress.bsky.social today. Panels A through UU.
I get that Cell likes to minimize the number of supplementary figures. But is this really what is happening here?
www.cell.com/cell/fulltex...
I get that Cell likes to minimize the number of supplementary figures. But is this really what is happening here?
www.cell.com/cell/fulltex...
December 18, 2025 at 6:24 AM
Interesting discussion. Pros/cons of PDFs vs digital objects.
As our standards increase, the burden of evidence will so too. These monster figs are a consequence. Why are we still held to prehistoric paper press page limits? Why not have as many ext. data figs as necessary? A PDF can be 100 pgs.
As our standards increase, the burden of evidence will so too. These monster figs are a consequence. Why are we still held to prehistoric paper press page limits? Why not have as many ext. data figs as necessary? A PDF can be 100 pgs.
Reposted by Charles Bayly-Jones
IsoNet2 determines cellular structures at submolecular resolution without averaging www.biorxiv.org/content/10.64898/2025.12.09.693325v1 #cryoem
December 12, 2025 at 11:42 AM
IsoNet2 determines cellular structures at submolecular resolution without averaging www.biorxiv.org/content/10.64898/2025.12.09.693325v1 #cryoem
Reposted by Charles Bayly-Jones
🧶🧬 We present LMi4Boltz:
www.biorxiv.org/content/10.1...
Boltz-2 is an excellent open source alternative to AlphaFold3. However, high VRAM use restricts modeling large complexes. Using careful memory management, we increase the Boltz-2 size limit by >60% while maintaining execution speed.
www.biorxiv.org/content/10.1...
Boltz-2 is an excellent open source alternative to AlphaFold3. However, high VRAM use restricts modeling large complexes. Using careful memory management, we increase the Boltz-2 size limit by >60% while maintaining execution speed.
October 31, 2025 at 8:54 PM
🧶🧬 We present LMi4Boltz:
www.biorxiv.org/content/10.1...
Boltz-2 is an excellent open source alternative to AlphaFold3. However, high VRAM use restricts modeling large complexes. Using careful memory management, we increase the Boltz-2 size limit by >60% while maintaining execution speed.
www.biorxiv.org/content/10.1...
Boltz-2 is an excellent open source alternative to AlphaFold3. However, high VRAM use restricts modeling large complexes. Using careful memory management, we increase the Boltz-2 size limit by >60% while maintaining execution speed.
Reposted by Charles Bayly-Jones
Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧
Icecream: High-Fidelity Equivariant Cryo-Electron Tomography
Cryo-electron tomography (cryo-ET) visualizes 3D cellular architecture in near-native states. Recent deep-learning methods (CryoCARE, IsoNet, DeepDeWedge, CryoLithe) improve denoising and artifact cor...
www.biorxiv.org
October 23, 2025 at 11:13 AM
Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧
Reposted by Charles Bayly-Jones
End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio
🌐 evedesign.bio
October 22, 2025 at 2:30 PM
End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio
🌐 evedesign.bio
Reposted by Charles Bayly-Jones
I guess… situations like this are where I really miss seeing the peer review file. Just baffling that this made the cut at Structure
October 15, 2025 at 1:02 PM
I guess… situations like this are where I really miss seeing the peer review file. Just baffling that this made the cut at Structure