Reposted by Brad Chapman
AI model Helixer predicts eukaryotic genes ab initio, directly from a plain text FASTA file.
No RNA-seq.
No protein homology.
No repeats, hints, or curated evidence.
Raw genome → accurate gene models.
Deep learning + HMM, published in @natmethods.nature.com
www.nature.com/articles/s41...
No RNA-seq.
No protein homology.
No repeats, hints, or curated evidence.
Raw genome → accurate gene models.
Deep learning + HMM, published in @natmethods.nature.com
www.nature.com/articles/s41...
Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods
By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and invertebrat...
www.nature.com
November 26, 2025 at 6:00 AM
AI model Helixer predicts eukaryotic genes ab initio, directly from a plain text FASTA file.
No RNA-seq.
No protein homology.
No repeats, hints, or curated evidence.
Raw genome → accurate gene models.
Deep learning + HMM, published in @natmethods.nature.com
www.nature.com/articles/s41...
No RNA-seq.
No protein homology.
No repeats, hints, or curated evidence.
Raw genome → accurate gene models.
Deep learning + HMM, published in @natmethods.nature.com
www.nature.com/articles/s41...
Reposted by Brad Chapman
Newest preprint from our lab: a new family of promising synthetic CO2 fixation cycles that may outcompete the Calvin cycle and that Vittorio Rainaldi realized to a great extent in E. coli! Up to 11 heterologous enzymes in a cascade supporting CO2 fixation & growth! www.biorxiv.org/content/10.1...
Modular in vivo engineering of the reductive methylaspartate cycles for synthetic CO2 fixation
Biological carbon fixation is currently limited to seven naturally occurring pathways. Synthetic carbon fixation pathways have the potential to surpass aerobic natural pathways in efficiency, but none...
www.biorxiv.org
November 25, 2025 at 5:54 PM
Newest preprint from our lab: a new family of promising synthetic CO2 fixation cycles that may outcompete the Calvin cycle and that Vittorio Rainaldi realized to a great extent in E. coli! Up to 11 heterologous enzymes in a cascade supporting CO2 fixation & growth! www.biorxiv.org/content/10.1...
Reposted by Brad Chapman
popEVE is out in Nature Genetics! 🎉
We built a proteome-wide model that combines cross-species and human population variation to rank missense variants by disease severity and help diagnose rare genetic disorders.
rdcu.be/eRu7K
We built a proteome-wide model that combines cross-species and human population variation to rank missense variants by disease severity and help diagnose rare genetic disorders.
rdcu.be/eRu7K
Proteome-wide model for human disease genetics
Nature Genetics - popEVE is a proteome-wide deep generative model to identify and predict pathogenicity of missense mutations causing genetic disorders.
rdcu.be
November 24, 2025 at 1:35 PM
popEVE is out in Nature Genetics! 🎉
We built a proteome-wide model that combines cross-species and human population variation to rank missense variants by disease severity and help diagnose rare genetic disorders.
rdcu.be/eRu7K
We built a proteome-wide model that combines cross-species and human population variation to rank missense variants by disease severity and help diagnose rare genetic disorders.
rdcu.be/eRu7K
Reposted by Brad Chapman
Delighted to report that our group's passion project over the last 6+ years to make DNA cloning more accessible, efficient, and scalable using a software-assisted workflow called CloneCoordinate is now out in ACS Synbio!
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
CloneCoordinate: Open-Source Software for Collaborative DNA Construction
Custom DNA constructs have never been more common or important in the life sciences. Many researchers therefore devote substantial time and effort to molecular cloning, aided by abundant computer-aide...
pubs.acs.org
November 21, 2025 at 7:40 PM
Delighted to report that our group's passion project over the last 6+ years to make DNA cloning more accessible, efficient, and scalable using a software-assisted workflow called CloneCoordinate is now out in ACS Synbio!
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
Reposted by Brad Chapman
The last five months with Claude Code have completely changed how we work.
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
Agentic Coding For Scientists
A four-part series on using coding agents like Claude Code for scientific programming, covering fundamentals, workflows, best practices, and the human side of AI-assisted development.
matsen.group
November 13, 2025 at 5:08 PM
The last five months with Claude Code have completely changed how we work.
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
Reposted by Brad Chapman
Claude scientific skills 🧬🖥️🧪
github.com/K-Dense-AI/c...
🧬 Bioinformatics & Genomics
🧪 Cheminformatics & Drug Discovery
🔬 Proteomics & Mass Spectrometry
🤖 Machine Learning & AI
🔮 Materials Science & Chemistry
📊 Data Analysis & Visualization
github.com/K-Dense-AI/c...
🧬 Bioinformatics & Genomics
🧪 Cheminformatics & Drug Discovery
🔬 Proteomics & Mass Spectrometry
🤖 Machine Learning & AI
🔮 Materials Science & Chemistry
📊 Data Analysis & Visualization
November 12, 2025 at 10:14 AM
Claude scientific skills 🧬🖥️🧪
github.com/K-Dense-AI/c...
🧬 Bioinformatics & Genomics
🧪 Cheminformatics & Drug Discovery
🔬 Proteomics & Mass Spectrometry
🤖 Machine Learning & AI
🔮 Materials Science & Chemistry
📊 Data Analysis & Visualization
github.com/K-Dense-AI/c...
🧬 Bioinformatics & Genomics
🧪 Cheminformatics & Drug Discovery
🔬 Proteomics & Mass Spectrometry
🤖 Machine Learning & AI
🔮 Materials Science & Chemistry
📊 Data Analysis & Visualization
Reposted by Brad Chapman
We're thrilled to announce SeqHub, an AI-enabled platform for biological sequence analysis. SeqHub brings together sequence search, genome annotation, and data sharing in one place.
October 28, 2025 at 1:47 PM
We're thrilled to announce SeqHub, an AI-enabled platform for biological sequence analysis. SeqHub brings together sequence search, genome annotation, and data sharing in one place.
Reposted by Brad Chapman
A functional map of CDK-drug interactions at single amino acid resolution https://www.biorxiv.org/content/10.1101/2025.11.02.685764v1
November 4, 2025 at 2:49 AM
A functional map of CDK-drug interactions at single amino acid resolution https://www.biorxiv.org/content/10.1101/2025.11.02.685764v1
Reposted by Brad Chapman
Very excited to finally share my PhD paper, about advancing #chloroplast #synbio through high-throughput plastome engineering of #Chlamydomonas.
Huge thanks to the whole team!
www.nature.com/articles/s41...
Huge thanks to the whole team!
www.nature.com/articles/s41...
November 3, 2025 at 4:26 PM
Very excited to finally share my PhD paper, about advancing #chloroplast #synbio through high-throughput plastome engineering of #Chlamydomonas.
Huge thanks to the whole team!
www.nature.com/articles/s41...
Huge thanks to the whole team!
www.nature.com/articles/s41...
Reposted by Brad Chapman
How can we study target engagement and selectivity of covalent inhibitors? Which electrophilic probes are best suited to study a certain amino acid?
Our study on "Profiling the proteome-wide selectivity of diverse electrophiles" is published in Nature Chemistry.(1/7)
www.nature.com/articles/s41...
Our study on "Profiling the proteome-wide selectivity of diverse electrophiles" is published in Nature Chemistry.(1/7)
www.nature.com/articles/s41...
Profiling the proteome-wide selectivity of diverse electrophiles - Nature Chemistry
Covalent inhibitors are powerful entities in drug discovery. Now the amino acid selectivity and reactivity of a diverse electrophile library have been assessed proteome-wide using an unbiased workflow...
www.nature.com
October 30, 2025 at 10:27 AM
How can we study target engagement and selectivity of covalent inhibitors? Which electrophilic probes are best suited to study a certain amino acid?
Our study on "Profiling the proteome-wide selectivity of diverse electrophiles" is published in Nature Chemistry.(1/7)
www.nature.com/articles/s41...
Our study on "Profiling the proteome-wide selectivity of diverse electrophiles" is published in Nature Chemistry.(1/7)
www.nature.com/articles/s41...
Reposted by Brad Chapman
🔥🔥🔥 Friday Evening, Paper Out, Feierabend 🔥🔥🔥
When evolution and enzyme engineering team up, they can convince microbes to assimilate sustainable carbon substrates preparing them for a life in a circular bioeconomy.
doi.org/10.1016/j.ym...
When evolution and enzyme engineering team up, they can convince microbes to assimilate sustainable carbon substrates preparing them for a life in a circular bioeconomy.
doi.org/10.1016/j.ym...
Redirecting
doi.org
October 24, 2025 at 5:00 PM
🔥🔥🔥 Friday Evening, Paper Out, Feierabend 🔥🔥🔥
When evolution and enzyme engineering team up, they can convince microbes to assimilate sustainable carbon substrates preparing them for a life in a circular bioeconomy.
doi.org/10.1016/j.ym...
When evolution and enzyme engineering team up, they can convince microbes to assimilate sustainable carbon substrates preparing them for a life in a circular bioeconomy.
doi.org/10.1016/j.ym...
Reposted by Brad Chapman
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 Brad Chapman
Our latest work on the nitrogenase-like methylthio-alkane reductase, which specifically reduces reduces carbon-sulfide bonds is now out @natcatal.nature.com: doi.org/10.1038/s419.... We find for the first time large #nitrogenase metalloclusters (P- and L-cluster) outside nitrogenases.
October 23, 2025 at 10:09 AM
Our latest work on the nitrogenase-like methylthio-alkane reductase, which specifically reduces reduces carbon-sulfide bonds is now out @natcatal.nature.com: doi.org/10.1038/s419.... We find for the first time large #nitrogenase metalloclusters (P- and L-cluster) outside nitrogenases.
Reposted by Brad Chapman
🚀 Thrilled to share our new Nature Communications article:
“A blueprint for designing the next-generation of synthetic C1 microbes”
We propose a framework to unlock sustainable, carbon-efficient biomanufacturing using non-canonical hosts.
🔗 www.nature.com/articles/s41... A short 🧵1/4
“A blueprint for designing the next-generation of synthetic C1 microbes”
We propose a framework to unlock sustainable, carbon-efficient biomanufacturing using non-canonical hosts.
🔗 www.nature.com/articles/s41... A short 🧵1/4
A blueprint for designing the next-generation of synthetic C1 microbes - Nature Communications
Synthetic one-carbon assimilation could contribute to a more sustainable and circular carbon economy, but much work in this field has focused on model microorganisms. Here the authors provide their perspective on the potential value of non-model microbes, and how that potential could be realised.
www.nature.com
October 8, 2025 at 9:10 AM
🚀 Thrilled to share our new Nature Communications article:
“A blueprint for designing the next-generation of synthetic C1 microbes”
We propose a framework to unlock sustainable, carbon-efficient biomanufacturing using non-canonical hosts.
🔗 www.nature.com/articles/s41... A short 🧵1/4
“A blueprint for designing the next-generation of synthetic C1 microbes”
We propose a framework to unlock sustainable, carbon-efficient biomanufacturing using non-canonical hosts.
🔗 www.nature.com/articles/s41... A short 🧵1/4
Reposted by Brad Chapman
🚨 New paper alert!
Sex and smoking bias in the selection of somatic mutations in human bladder
www.nature.com/articles/s41...
by @raquelbmi.bsky.social, @ferriol.bsky.social et al (in collaboration with Rosana Risques lab in @uwmedicine.bsky.social)
Sex and smoking bias in the selection of somatic mutations in human bladder
www.nature.com/articles/s41...
by @raquelbmi.bsky.social, @ferriol.bsky.social et al (in collaboration with Rosana Risques lab in @uwmedicine.bsky.social)
Sex and smoking bias in the selection of somatic mutations in human bladder - Nature
Sex bias and association with smoking history identified in the landscape of driver mutations and clonal expansions in normal human bladder tissue may explain the higher bladder cancer risk in men and smokers.
www.nature.com
October 8, 2025 at 4:44 PM
🚨 New paper alert!
Sex and smoking bias in the selection of somatic mutations in human bladder
www.nature.com/articles/s41...
by @raquelbmi.bsky.social, @ferriol.bsky.social et al (in collaboration with Rosana Risques lab in @uwmedicine.bsky.social)
Sex and smoking bias in the selection of somatic mutations in human bladder
www.nature.com/articles/s41...
by @raquelbmi.bsky.social, @ferriol.bsky.social et al (in collaboration with Rosana Risques lab in @uwmedicine.bsky.social)
Reposted by Brad Chapman
Out First Release in @science.org this week:
The development of a directed evolution strategy with proof of concept in plant immune protein engineering.
www.science.org/doi/10.1126/...
The development of a directed evolution strategy with proof of concept in plant immune protein engineering.
www.science.org/doi/10.1126/...
Engineered geminivirus replicons enable rapid in planta directed evolution
Directed evolution can rapidly generate genetic variants with new and enhanced properties, yet efficient platforms for performing such evolution directly in plant cells have been lacking. We developed...
www.science.org
October 7, 2025 at 9:54 AM
Out First Release in @science.org this week:
The development of a directed evolution strategy with proof of concept in plant immune protein engineering.
www.science.org/doi/10.1126/...
The development of a directed evolution strategy with proof of concept in plant immune protein engineering.
www.science.org/doi/10.1126/...
Reposted by Brad Chapman
I'm excited to share our pre-print about a new variant benchmarking tool we've been working on for the past few months!
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
October 6, 2025 at 8:07 PM
I'm excited to share our pre-print about a new variant benchmarking tool we've been working on for the past few months!
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
Reposted by Brad Chapman
A blueprint for designing the next-generation of #synthetic C1 #microbes @natureportfolio.nature.com / We outline how to engineer non-canonical hosts, apply modeling & C1-inducible promoters & integrate sustainability metrics for carbon-efficient #biomanufacturing
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A blueprint for designing the next-generation of synthetic C1 microbes - Nature Communications
Synthetic one-carbon assimilation could contribute to a more sustainable and circular carbon economy, but much work in this field has focused on model microorganisms. Here the authors provide their perspective on the potential value of non-model microbes, and how that potential could be realised.
www.nature.com
October 3, 2025 at 1:34 PM
A blueprint for designing the next-generation of #synthetic C1 #microbes @natureportfolio.nature.com / We outline how to engineer non-canonical hosts, apply modeling & C1-inducible promoters & integrate sustainability metrics for carbon-efficient #biomanufacturing
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Brad Chapman
Interested in using microbes to degrade plastics?
We made the discovery that two breakdown products of PET, MHET and BHET, are readily taken up by E. coli cells
Our latest preprint exploits this surprise to realize improvements in cell-based upcycling
www.biorxiv.org/content/10.1...
We made the discovery that two breakdown products of PET, MHET and BHET, are readily taken up by E. coli cells
Our latest preprint exploits this surprise to realize improvements in cell-based upcycling
www.biorxiv.org/content/10.1...
Robust cellular transformations of PET deconstruction products by import of glycol esters
Efforts to transform polyethylene terephthalate (PET) deconstruction products using live cells have been limited by terephthalic acid (TPA) uptake. Here, we used an intracellular carboxylate reduction...
www.biorxiv.org
October 3, 2025 at 12:26 PM
Interested in using microbes to degrade plastics?
We made the discovery that two breakdown products of PET, MHET and BHET, are readily taken up by E. coli cells
Our latest preprint exploits this surprise to realize improvements in cell-based upcycling
www.biorxiv.org/content/10.1...
We made the discovery that two breakdown products of PET, MHET and BHET, are readily taken up by E. coli cells
Our latest preprint exploits this surprise to realize improvements in cell-based upcycling
www.biorxiv.org/content/10.1...
Reposted by Brad Chapman
Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin
September 30, 2025 at 2:19 AM
Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin
Reposted by Brad Chapman
I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5)
doi.org/10.1101/2025.09.24.678028 #proteindesign
doi.org/10.1101/2025.09.24.678028 #proteindesign
September 28, 2025 at 9:16 PM
I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5)
doi.org/10.1101/2025.09.24.678028 #proteindesign
doi.org/10.1101/2025.09.24.678028 #proteindesign
Reposted by Brad Chapman
And new paper out: Pleias 1.0: the First Family of Language Models Trained on Fully Open Data
How we train an open everything model on a new pretraining environment with releasable data (Common Corpus) with an open source framework (Nanotron from HuggingFace).
www.sciencedirect.com/science/arti...
How we train an open everything model on a new pretraining environment with releasable data (Common Corpus) with an open source framework (Nanotron from HuggingFace).
www.sciencedirect.com/science/arti...
September 27, 2025 at 11:44 AM
And new paper out: Pleias 1.0: the First Family of Language Models Trained on Fully Open Data
How we train an open everything model on a new pretraining environment with releasable data (Common Corpus) with an open source framework (Nanotron from HuggingFace).
www.sciencedirect.com/science/arti...
How we train an open everything model on a new pretraining environment with releasable data (Common Corpus) with an open source framework (Nanotron from HuggingFace).
www.sciencedirect.com/science/arti...
Reposted by Brad Chapman
You can read more in our post at www.jurabio.com/blog/leavs; preprint forthcoming.
@jura.bsky.social @eliweinstein.bsky.social @mgollub.bsky.social @highvariance.bsky.social
@jura.bsky.social @eliweinstein.bsky.social @mgollub.bsky.social @highvariance.bsky.social
LeaVS: Accelerating learning for biological AI — JURA Bio, Inc.
A fundamental lesson of modern AI is that scale is essential: training bigger models on bigger datasets unlocks new capabilities. A fundamental lesson of AI engineering is that scaling up isn't trivia...
www.jurabio.com
September 22, 2025 at 12:15 PM
You can read more in our post at www.jurabio.com/blog/leavs; preprint forthcoming.
@jura.bsky.social @eliweinstein.bsky.social @mgollub.bsky.social @highvariance.bsky.social
@jura.bsky.social @eliweinstein.bsky.social @mgollub.bsky.social @highvariance.bsky.social
Reposted by Brad Chapman
MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com
📄 www.nature.com/articles/s41...
💿 mmseqs.com
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
www.nature.com
September 21, 2025 at 8:06 AM
MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com
📄 www.nature.com/articles/s41...
💿 mmseqs.com
Reposted by Brad Chapman
Introducing a new metabolic cycle - the McG cycle - into Arabidopsis to convert 3PG to acetyl coA. This then feeds into endogenous lipid synthesis increasing plant lipids, seed yield and biomass. Out this week in @science.org!
www.science.org/doi/10.1126/...
#PlantScience
www.science.org/doi/10.1126/...
#PlantScience
Dual-cycle CO2 fixation enhances growth and lipid synthesis in Arabidopsis thaliana
Carbon fixation through the Calvin-Benson-Bassham (CBB) cycle accounts for the majority of carbon dioxide (CO2) uptake from the atmosphere. The CBB cycle generates C3 carbohydrates but is inefficient ...
www.science.org
September 12, 2025 at 8:54 AM
Introducing a new metabolic cycle - the McG cycle - into Arabidopsis to convert 3PG to acetyl coA. This then feeds into endogenous lipid synthesis increasing plant lipids, seed yield and biomass. Out this week in @science.org!
www.science.org/doi/10.1126/...
#PlantScience
www.science.org/doi/10.1126/...
#PlantScience