James Lingford
@jameslingford.bsky.social
PhD student in structural biology with @greening.bsky.social and @knottrna.bsky.social at Monash Uni. (he/him)
Interested in hydrogenases, evolution, protein design.
💻 https://www.jameslingford.com/
Interested in hydrogenases, evolution, protein design.
💻 https://www.jameslingford.com/
Our work is published today: ‘Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor’. This was a huge effort lead by @katyappler.bsky.social. Extremely grateful to have been a part of this amazing project! 😊🦠🧬
Links: www.nature.com/articles/s41...
www.nature.com/articles/s41...
Links: www.nature.com/articles/s41...
www.nature.com/articles/s41...
February 19, 2026 at 12:02 AM
Our work is published today: ‘Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor’. This was a huge effort lead by @katyappler.bsky.social. Extremely grateful to have been a part of this amazing project! 😊🦠🧬
Links: www.nature.com/articles/s41...
www.nature.com/articles/s41...
Links: www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by James Lingford
Finally out in @nature.com: a new piece of the puzzle of how complex life evolved. Lead by @archaeal.bsky.social & @katyappler.bsky.social. Great collab with @greening.bsky.social and @kassipan.bsky.social. More pieces to follow soon! www.nature.com/articles/s41...
February 18, 2026 at 5:59 PM
Finally out in @nature.com: a new piece of the puzzle of how complex life evolved. Lead by @archaeal.bsky.social & @katyappler.bsky.social. Great collab with @greening.bsky.social and @kassipan.bsky.social. More pieces to follow soon! www.nature.com/articles/s41...
Reposted by James Lingford
One of the biggest questions in biology is how complex cells evolved about 2 billion years ago. Here's my new story on how scientists are solving the mystery of eukaryotes like us. Gift link: nyti.ms/4qMbo22
February 18, 2026 at 7:17 PM
One of the biggest questions in biology is how complex cells evolved about 2 billion years ago. Here's my new story on how scientists are solving the mystery of eukaryotes like us. Gift link: nyti.ms/4qMbo22
Reposted by James Lingford
At long last! Check out the link to our publication in @nature.com to learn more. doi.org/10.1038/s415...
12/12
12/12
Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor - Nature
Sequencing of marine sediments finds 136 newly identified Heimdallarchaeia and several novel lineages, and indicates that Heimdallarchaeia evolved distinct metabolic capabilities from other Asgar...
doi.org
February 18, 2026 at 4:12 PM
At long last! Check out the link to our publication in @nature.com to learn more. doi.org/10.1038/s415...
12/12
12/12
Reposted by James Lingford
New paper from my team detailing a greatly expanded genomic database of Asgard archaea revealing of high energy metabolism those related to eukaryotes! Led by @katyappler.bsky.social lots of help from @jameslingford.bsky.social @valdeanda.bsky.social @kassipan.bsky.social doi.org/10.1038/s415...
February 18, 2026 at 4:00 PM
New paper from my team detailing a greatly expanded genomic database of Asgard archaea revealing of high energy metabolism those related to eukaryotes! Led by @katyappler.bsky.social lots of help from @jameslingford.bsky.social @valdeanda.bsky.social @kassipan.bsky.social doi.org/10.1038/s415...
Keep hearing hype around vibe coding and how its going to replace all coding very soon. So I look into pro-vibe coding communities on reddit. They all say you have to hold the hand of the AI at every step of the way and have very long but specific prompts, otherwise the AI makes a mess... 1/2
February 18, 2026 at 12:09 PM
Keep hearing hype around vibe coding and how its going to replace all coding very soon. So I look into pro-vibe coding communities on reddit. They all say you have to hold the hand of the AI at every step of the way and have very long but specific prompts, otherwise the AI makes a mess... 1/2
Reposted by James Lingford
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. 🤩
Reposted by James Lingford
Passioned by #bioenergetics? Do not miss our new article on the evolutionary history of oxidoreductases with G. Borrel and @sgribaldo.bsky.social @archaeal.bsky.social @valdeanda.bsky.social @pasteur.fr @cnrs.fr @cnrsbiologie.bsky.social @natecoevo.nature.com (www.nature.com/articles/s41...).
Evolution and diversity of oxidoreductases involved in redox balance and energy conservation - Nature Ecology & Evolution
HORBEC are protein complexes involved in the regulation of redox balance and energy conservation. The authors develop a bioinformatic tool for HORBEC annotation in bacterial and archaeal genomes and r...
www.nature.com
February 3, 2026 at 10:52 AM
Passioned by #bioenergetics? Do not miss our new article on the evolutionary history of oxidoreductases with G. Borrel and @sgribaldo.bsky.social @archaeal.bsky.social @valdeanda.bsky.social @pasteur.fr @cnrs.fr @cnrsbiologie.bsky.social @natecoevo.nature.com (www.nature.com/articles/s41...).
'The perpetual motion machine of AI-generated data and the distraction of ChatGPT as a "scientist"' (2024) www.nature.com/articles/s41...
An important read providing some sanity against the current AI hype slop that I've been inundated with these past couple of weeks
An important read providing some sanity against the current AI hype slop that I've been inundated with these past couple of weeks
February 13, 2026 at 1:54 AM
'The perpetual motion machine of AI-generated data and the distraction of ChatGPT as a "scientist"' (2024) www.nature.com/articles/s41...
An important read providing some sanity against the current AI hype slop that I've been inundated with these past couple of weeks
An important read providing some sanity against the current AI hype slop that I've been inundated with these past couple of weeks
Goodbye Lorne Proteins 2026. An inspiring few days seeing the best of protein science. @lorneproteins.bsky.social
February 11, 2026 at 11:48 PM
Goodbye Lorne Proteins 2026. An inspiring few days seeing the best of protein science. @lorneproteins.bsky.social
Reposted by James Lingford
The Elsevier investigation mentioned was initiated after a STAT news piece on the problem, co-authored with Cathryn, @dsamorod.bsky.social, @stairwaytokevin.bsky.social, @jedidiahcarlson.com, @jameslingford.bsky.social and @jowiph.bsky.social
www.statnews.com/2024/06/20/r...
www.statnews.com/2024/06/20/r...
Journals that published Richard Lynn's racist 'research' articles should retract them
Richard Lynn's work has been repeatedly condemned for using flawed methodology and deceptively collated data to support racism. It's past time to retract the studies.
www.statnews.com
November 26, 2025 at 3:33 PM
The Elsevier investigation mentioned was initiated after a STAT news piece on the problem, co-authored with Cathryn, @dsamorod.bsky.social, @stairwaytokevin.bsky.social, @jedidiahcarlson.com, @jameslingford.bsky.social and @jowiph.bsky.social
www.statnews.com/2024/06/20/r...
www.statnews.com/2024/06/20/r...
Super cool talk from @kmichie.bsky.social. Lots of examples of how AlphaFold3 does weird stuff
October 27, 2025 at 2:14 AM
Super cool talk from @kmichie.bsky.social. Lots of examples of how AlphaFold3 does weird stuff
Reposted by James Lingford
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
October 26, 2025 at 10:40 PM
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
As much as I like making plots with matplotlib and seaborn, the way repositioning legends/colourbars works is super unintuitive and a massive timesink.
October 21, 2025 at 9:54 PM
As much as I like making plots with matplotlib and seaborn, the way repositioning legends/colourbars works is super unintuitive and a massive timesink.
Reposted by James Lingford
Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵
📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk
📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk
Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology
imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for
>4,400 viruses, allowing mapping of form and function across the human and animal
virosphere. Viro3D i...
doi.org
September 26, 2025 at 2:06 PM
Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵
📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk
📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk
RFdiffusion3 is here: www.biorxiv.org/content/10.1...
September 19, 2025 at 7:56 AM
RFdiffusion3 is here: www.biorxiv.org/content/10.1...
Switched from using pandas to @pola.rs and it has been a total life saver. Handling dataframes is way more intuitive with the method chaining syntax. Prettier terminal printing, better error messages, lightning fast, fewer headaches.
September 18, 2025 at 2:21 AM
Switched from using pandas to @pola.rs and it has been a total life saver. Handling dataframes is way more intuitive with the method chaining syntax. Prettier terminal printing, better error messages, lightning fast, fewer headaches.
Recent advances in the inference of deep viral
evolutionary history journals.asm.org/doi/10.1128/...
A review on structural phylogenetics utility and limitations
evolutionary history journals.asm.org/doi/10.1128/...
A review on structural phylogenetics utility and limitations
September 2, 2025 at 10:35 PM
Recent advances in the inference of deep viral
evolutionary history journals.asm.org/doi/10.1128/...
A review on structural phylogenetics utility and limitations
evolutionary history journals.asm.org/doi/10.1128/...
A review on structural phylogenetics utility and limitations
Fantastic review on methodological developments in protein structural phylogenetics
academic.oup.com/gbe/article/...
academic.oup.com/gbe/article/...
Protein Structural Phylogenetics
Abstract. Protein structural phylogenetics is an interdisciplinary branch of molecular evolution that (i) uses 3D structural data to trace evolutionary his
academic.oup.com
September 1, 2025 at 11:15 PM
Fantastic review on methodological developments in protein structural phylogenetics
academic.oup.com/gbe/article/...
academic.oup.com/gbe/article/...
Large protein databases reveal structural complementarity and functional locality
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Large protein databases reveal structural complementarity and functional locality - Nature Communications
Researchers mapped the protein structure landscape, revealing structural complementarity across databases and functional clustering in specific regions. Their web tool helps explore this space, unlock...
www.nature.com
August 27, 2025 at 7:49 AM
Large protein databases reveal structural complementarity and functional locality
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by James Lingford
RFdiffusion2 is now live!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
August 22, 2025 at 12:51 AM
RFdiffusion2 is now live!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
This is a remarkable paper on protein evolution from the Lehner lab. What makes it especially cool is that all the code to reproduce all the analysis/plots is included in Jupyter notebooks up on Github
www.science.org/doi/10.1126/...
github.com/lehner-lab/c...
www.science.org/doi/10.1126/...
github.com/lehner-lab/c...
GitHub - lehner-lab/combinatorialcores: Source code for analyses and figure reproduction in "Genetics, energetics, and allostery in proteins with randomized cores and surfaces", Escobedo et. al Scienc...
Source code for analyses and figure reproduction in "Genetics, energetics, and allostery in proteins with randomized cores and surfaces", Escobedo et. al Science 2025 - lehner-lab/combina...
github.com
August 21, 2025 at 12:52 AM
This is a remarkable paper on protein evolution from the Lehner lab. What makes it especially cool is that all the code to reproduce all the analysis/plots is included in Jupyter notebooks up on Github
www.science.org/doi/10.1126/...
github.com/lehner-lab/c...
www.science.org/doi/10.1126/...
github.com/lehner-lab/c...
Just to piggyback on this critique of LLMs for coding with some of my own critiques:
• it's a bad idea to install a tool on your machine that has vast read+write permissions
• code that works but is really outputting false info is a real danger and hard to catch. LLMs make that danger worse
• it's a bad idea to install a tool on your machine that has vast read+write permissions
• code that works but is really outputting false info is a real danger and hard to catch. LLMs make that danger worse
Not sure how many scientists here have tried Claude Code or similar command line coding assistants. I had a complicated family property tax problem that was best solved by a brute force Monte Carlo simulation approach, so I spent a few days coding up and analyzing a model with Claude Code.
August 13, 2025 at 11:38 PM
Just to piggyback on this critique of LLMs for coding with some of my own critiques:
• it's a bad idea to install a tool on your machine that has vast read+write permissions
• code that works but is really outputting false info is a real danger and hard to catch. LLMs make that danger worse
• it's a bad idea to install a tool on your machine that has vast read+write permissions
• code that works but is really outputting false info is a real danger and hard to catch. LLMs make that danger worse
Does sequence clustering confound AlphaFold2?
www.sciencedirect.com/science/arti... From @hkws.bsky.social
www.sciencedirect.com/science/arti... From @hkws.bsky.social
Does sequence clustering confound AlphaFold2?
Predicting multiple conformational states of proteins represents a significant open challenge in structural biology. Increasingly many methods have be…
www.sciencedirect.com
August 11, 2025 at 2:11 AM
Does sequence clustering confound AlphaFold2?
www.sciencedirect.com/science/arti... From @hkws.bsky.social
www.sciencedirect.com/science/arti... From @hkws.bsky.social
Reposted by James Lingford
MMseqs2 v18 is out
- SIMD FW/BW alignment (preprint soon!)
- Sub. Mat. λ calculator by Eric Dawson
- Faster ARM SW by Alexander Nesterovskiy
- MSA-Pairformer’s proximity-based pairing for multimer prediction (www.biorxiv.org/content/10.1...; avail. in ColabFold API)
💾 github.com/soedinglab/M... & 🐍
- SIMD FW/BW alignment (preprint soon!)
- Sub. Mat. λ calculator by Eric Dawson
- Faster ARM SW by Alexander Nesterovskiy
- MSA-Pairformer’s proximity-based pairing for multimer prediction (www.biorxiv.org/content/10.1...; avail. in ColabFold API)
💾 github.com/soedinglab/M... & 🐍
August 5, 2025 at 8:25 AM
MMseqs2 v18 is out
- SIMD FW/BW alignment (preprint soon!)
- Sub. Mat. λ calculator by Eric Dawson
- Faster ARM SW by Alexander Nesterovskiy
- MSA-Pairformer’s proximity-based pairing for multimer prediction (www.biorxiv.org/content/10.1...; avail. in ColabFold API)
💾 github.com/soedinglab/M... & 🐍
- SIMD FW/BW alignment (preprint soon!)
- Sub. Mat. λ calculator by Eric Dawson
- Faster ARM SW by Alexander Nesterovskiy
- MSA-Pairformer’s proximity-based pairing for multimer prediction (www.biorxiv.org/content/10.1...; avail. in ColabFold API)
💾 github.com/soedinglab/M... & 🐍