Convergent Research
@convergentresearch.bsky.social
A mission control for frontier technology.
To learn more about FROs, visit convergentresearch.org.
To learn more about FROs, visit convergentresearch.org.
Congratulations to @cworthy.org on their announcement today!
Learn more about this wonderful FRO here: www.youtube.com/watch?v=DA-e...
Learn more about this wonderful FRO here: www.youtube.com/watch?v=DA-e...
November 24, 2025 at 7:23 PM
Congratulations to @cworthy.org on their announcement today!
Learn more about this wonderful FRO here: www.youtube.com/watch?v=DA-e...
Learn more about this wonderful FRO here: www.youtube.com/watch?v=DA-e...
Reposted by Convergent Research
[C]Worthy has secured multi-year support from ORCA and the Patrick J. McGovern Foundation to scale open, trusted science tools for ocean-based carbon removal.
We can’t scale what we can’t measure—this funding accelerates our MRV models + datasets.
Full announcement: www.cworthy.org/media/cworth...
We can’t scale what we can’t measure—this funding accelerates our MRV models + datasets.
Full announcement: www.cworthy.org/media/cworth...
[C]Worthy Secures Multi-Year Support From ORCA and the Patrick J. McGovern Foundation to Scale Open-Source Marine Carbon-Removal Tools — [C]Worthy
New multi‑year awards affirm the need for infrastructure built through [C]Worthy’s approach of marrying open-source science and practical tools for industry use.
www.cworthy.org
November 24, 2025 at 4:26 PM
[C]Worthy has secured multi-year support from ORCA and the Patrick J. McGovern Foundation to scale open, trusted science tools for ocean-based carbon removal.
We can’t scale what we can’t measure—this funding accelerates our MRV models + datasets.
Full announcement: www.cworthy.org/media/cworth...
We can’t scale what we can’t measure—this funding accelerates our MRV models + datasets.
Full announcement: www.cworthy.org/media/cworth...
Reposted by Convergent Research
One experiment to highlight is with Cupriavidus necator. We used a bayesian optimizer in optuna to select electroporation conditions, a robot to run the experiments, and then the optimizer selected the next cycle of experiments. Landed on a protocol a bit better than the literature best in 3 cycles!
November 22, 2025 at 12:23 AM
One experiment to highlight is with Cupriavidus necator. We used a bayesian optimizer in optuna to select electroporation conditions, a robot to run the experiments, and then the optimizer selected the next cycle of experiments. Landed on a protocol a bit better than the literature best in 3 cycles!
Reposted by Convergent Research
Have a look if you are interested in how the team at @cultivarium.bsky.social is finding electroporation protocols for new microbes: both screening lots of conditions on a custom built electroporator concurrently, and cyclical iteration using bayesian optimization
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Active learning guides automated discovery of DNA delivery via electroporation for non-model microbes
Delivery of recombinant DNA is foundational for understanding and engineering a target organism. Electroporation can be applied to any cell type, yet identification of a working protocol for new organ...
www.biorxiv.org
November 22, 2025 at 12:23 AM
Have a look if you are interested in how the team at @cultivarium.bsky.social is finding electroporation protocols for new microbes: both screening lots of conditions on a custom built electroporator concurrently, and cyclical iteration using bayesian optimization
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Convergent Research
As we continue EvE's mission, we're excited to see our work impact the drug development, ML, and AI communities. More to come!
November 18, 2025 at 7:48 PM
As we continue EvE's mission, we're excited to see our work impact the drug development, ML, and AI communities. More to come!
Reposted by Convergent Research
👥 Leadership news: @ehouskee.bsky.social steps into the CEO role, leading us into our next phase, while founding CEO William Busa continues as EvE's Chief Scientific Officer.
November 18, 2025 at 7:48 PM
👥 Leadership news: @ehouskee.bsky.social steps into the CEO role, leading us into our next phase, while founding CEO William Busa continues as EvE's Chief Scientific Officer.
Reposted by Convergent Research
🤖 @futurehousesf.bsky.social used our data in the development of the ether0 chemistry reasoning model, showing the value of experimental group truth data for scientific AI models.
November 18, 2025 at 7:48 PM
🤖 @futurehousesf.bsky.social used our data in the development of the ether0 chemistry reasoning model, showing the value of experimental group truth data for scientific AI models.
Reposted by Convergent Research
💻 Our pharmome mapping data is now accessible to ML developers on @hf.co, making our purpose-built drug-target interaction data easily accessible for model development.
huggingface.co/blog/hugging...
huggingface.co/blog/hugging...
The Pharmome Map: a comprehensive public dataset for drug-target interaction modeling
A Blog post by Hugging Science on Hugging Face
huggingface.co
November 18, 2025 at 7:48 PM
💻 Our pharmome mapping data is now accessible to ML developers on @hf.co, making our purpose-built drug-target interaction data easily accessible for model development.
huggingface.co/blog/hugging...
huggingface.co/blog/hugging...
Reposted by Convergent Research
🤝 We're partnering with DrugBank to integrate our drug-target interaction data into their drug intelligence platform, bringing it directly to the drug development community with rich context and annotation. go.drugbank.com/evebio
Eve Bio and DrugBank
EvE Bio is now integrated into DrugBank, creating the largest public resource of drug–protein interactions and making off-target biology searchable, connected, and actionable for the first time.
go.drugbank.com
November 18, 2025 at 7:48 PM
🤝 We're partnering with DrugBank to integrate our drug-target interaction data into their drug intelligence platform, bringing it directly to the drug development community with rich context and annotation. go.drugbank.com/evebio
Reposted by Convergent Research
We're excited to share several new developments. Our pharmome mapping dataset is now more accessible and integrated than ever, and the use cases we imagined are coming to life! 🧪
evebio.org/pharmome-dat...
Here's what's new: 🧵
evebio.org/pharmome-dat...
Here's what's new: 🧵
Putting Pharmome Data in Researchers' Hands : EvE Bio
We've been busy at EvE Bio these last two years establishing the largest available pharmome mapping dataset. Now it’s making its way into the world to drive real discoveries.
evebio.org
November 18, 2025 at 7:48 PM
We're excited to share several new developments. Our pharmome mapping dataset is now more accessible and integrated than ever, and the use cases we imagined are coming to life! 🧪
evebio.org/pharmome-dat...
Here's what's new: 🧵
evebio.org/pharmome-dat...
Here's what's new: 🧵
Announced today: @evebio.bsky.social's pharmome-mapping dataset - the largest public map of how compounds do or don’t touch druggable targets - is now live on DrugBank's knowledgebase and available programmatically + interactively on Hugging Face, @hf.co.
Learn more: evebio.org/pharmome-dat...
Learn more: evebio.org/pharmome-dat...
Putting Pharmome Data in Researchers' Hands : EvE Bio
We've been busy at EvE Bio these last two years establishing the largest available pharmome mapping dataset. Now it’s making its way into the world to drive real discoveries.
evebio.org
November 18, 2025 at 3:44 PM
Announced today: @evebio.bsky.social's pharmome-mapping dataset - the largest public map of how compounds do or don’t touch druggable targets - is now live on DrugBank's knowledgebase and available programmatically + interactively on Hugging Face, @hf.co.
Learn more: evebio.org/pharmome-dat...
Learn more: evebio.org/pharmome-dat...
Reposted by Convergent Research
No one is immune to aging but what exactly happens to our immune system as it ages? @thibaultcolombani.bsky.social takes a molecular dive into the immune system and talks about understanding age-induced immune altercations through single-cell proteomics.
www.youtube.com/watch?v=WUU1...
www.youtube.com/watch?v=WUU1...
November 13, 2025 at 7:02 PM
No one is immune to aging but what exactly happens to our immune system as it ages? @thibaultcolombani.bsky.social takes a molecular dive into the immune system and talks about understanding age-induced immune altercations through single-cell proteomics.
www.youtube.com/watch?v=WUU1...
www.youtube.com/watch?v=WUU1...
Reposted by Convergent Research
Some video protocols by collaborator Felipe-Andrés Piedra:
prism.cultivarium.org/protocols/20...
prism.cultivarium.org/protocols/20...
prism.cultivarium.org/protocols/20...
prism.cultivarium.org/protocols/20...
prism.cultivarium.org/protocols/20...
prism.cultivarium.org/protocols/20...
prism.cultivarium.org
November 12, 2025 at 7:05 PM
Some video protocols by collaborator Felipe-Andrés Piedra:
prism.cultivarium.org/protocols/20...
prism.cultivarium.org/protocols/20...
prism.cultivarium.org/protocols/20...
prism.cultivarium.org/protocols/20...
prism.cultivarium.org/protocols/20...
prism.cultivarium.org/protocols/20...
Reposted by Convergent Research
Code+sequences: github.com/cultivarium/...
Plasmids (also on GitHub):
www.addgene.org/199102/
www.addgene.org/89477/
Genome (also on GitHub):
... stuck in submission at NCBI... for now.
If you're interested in using the mutant library yourself, reach out!
Plasmids (also on GitHub):
www.addgene.org/199102/
www.addgene.org/89477/
Genome (also on GitHub):
... stuck in submission at NCBI... for now.
If you're interested in using the mutant library yourself, reach out!
GitHub - cultivarium/Piscinibacter_sakaiensis_RB_TnSeq: Supporting code for "High-throughput genetics in a microbe that degrades and metabolizes plastic"
Supporting code for "High-throughput genetics in a microbe that degrades and metabolizes plastic" - cultivarium/Piscinibacter_sakaiensis_RB_TnSeq
github.com
November 12, 2025 at 7:05 PM
Code+sequences: github.com/cultivarium/...
Plasmids (also on GitHub):
www.addgene.org/199102/
www.addgene.org/89477/
Genome (also on GitHub):
... stuck in submission at NCBI... for now.
If you're interested in using the mutant library yourself, reach out!
Plasmids (also on GitHub):
www.addgene.org/199102/
www.addgene.org/89477/
Genome (also on GitHub):
... stuck in submission at NCBI... for now.
If you're interested in using the mutant library yourself, reach out!
Reposted by Convergent Research
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
November 12, 2025 at 7:05 PM
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
Reposted by Convergent Research
#Proteomics Tutorial drop!
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
Fantastic Proteins and Where to Find Them - PTI - Parallel Squared Technology Institute
Here, we will offer a tutorial for how to build instrument-specific spectral library predictions for PSMtag modified peptides using DIA-NN 2.3.0. This will allow users to do more accurate proteome-wid...
www.parallelsq.org
November 4, 2025 at 4:47 PM
#Proteomics Tutorial drop!
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
Reposted by Convergent Research
Whether you want to industrialize biology or biologize industry, we could use new financing structures. I propose BiBs (Bioindustrial Bucks). www.genengnews.com/industry-ne...
Bring on the BioIndustrial Bucks: Growing America’s Bioeconomy
Synthetic biology is ready for the next developmental milestone and America’s leadership depends on getting the financing right.
www.genengnews.com
November 4, 2025 at 10:00 AM
Whether you want to industrialize biology or biologize industry, we could use new financing structures. I propose BiBs (Bioindustrial Bucks). www.genengnews.com/industry-ne...
Reposted by Convergent Research
Register for free (www.cultivarium.org/portal) to access their fantastic work and engage with their growing community. Let's diversify our biological models for deeper understanding! (2/2)
Portal — Cultivarium
www.cultivarium.org
April 25, 2025 at 9:17 AM
Register for free (www.cultivarium.org/portal) to access their fantastic work and engage with their growing community. Let's diversify our biological models for deeper understanding! (2/2)
Reposted by Convergent Research
Thanks for contributing your expertise!!
I got to editing a few clips to show how I make plant tissue culture leaf disks from leaves obtained in open air. Uploaded for your consideration to the PRISM collection. Enjoyyyyy.
prism.cultivarium.org/protocols/20...
prism.cultivarium.org/protocols/20...
prism.cultivarium.org
October 18, 2025 at 11:55 AM
Thanks for contributing your expertise!!
Reposted by Convergent Research
A bit dense, but the important message is dead simple:
We got to cite the E = mc² paper!
Kidding :)
The important part is that combinations of isotopes unlock 100-1000x gains in protein measurement speed.
Here's how: www.biorxiv.org/content/10.1...
#TeamMassSpec #Proteomics 🧪
We got to cite the E = mc² paper!
Kidding :)
The important part is that combinations of isotopes unlock 100-1000x gains in protein measurement speed.
Here's how: www.biorxiv.org/content/10.1...
#TeamMassSpec #Proteomics 🧪
How to design 1000-plex mass tags using the differential mass defect
Multiplexing samples in mass spectrometry-based proteomics has long been accomplished by isotopologues of small molecules. These chemically-identical "mass tags" conjugate to peptides to encode sample...
www.biorxiv.org
October 24, 2025 at 2:08 PM
A bit dense, but the important message is dead simple:
We got to cite the E = mc² paper!
Kidding :)
The important part is that combinations of isotopes unlock 100-1000x gains in protein measurement speed.
Here's how: www.biorxiv.org/content/10.1...
#TeamMassSpec #Proteomics 🧪
We got to cite the E = mc² paper!
Kidding :)
The important part is that combinations of isotopes unlock 100-1000x gains in protein measurement speed.
Here's how: www.biorxiv.org/content/10.1...
#TeamMassSpec #Proteomics 🧪
Reposted by Convergent Research
Our new preprint outlining how to make 1000-plex mass tags!
A bit dense, but the important message is dead simple:
We got to cite the E = mc² paper!
Kidding :)
The important part is that combinations of isotopes unlock 100-1000x gains in protein measurement speed.
Here's how: www.biorxiv.org/content/10.1...
#TeamMassSpec #Proteomics 🧪
We got to cite the E = mc² paper!
Kidding :)
The important part is that combinations of isotopes unlock 100-1000x gains in protein measurement speed.
Here's how: www.biorxiv.org/content/10.1...
#TeamMassSpec #Proteomics 🧪
How to design 1000-plex mass tags using the differential mass defect
Multiplexing samples in mass spectrometry-based proteomics has long been accomplished by isotopologues of small molecules. These chemically-identical "mass tags" conjugate to peptides to encode sample...
www.biorxiv.org
October 24, 2025 at 2:41 PM
Our new preprint outlining how to make 1000-plex mass tags!
Reposted by Convergent Research
My commute to PTI.
November 3, 2025 at 2:36 PM
My commute to PTI.
Reposted by Convergent Research
It feels like unblocking a bottleneck. Thanks to @convergentresearch.bsky.social for supporting @parallelsq.bsky.social in this mission of unblocking research bottlenecks with non-profit focussed research organizations:
/n
www.nature.com/articles/d41...
/n
www.nature.com/articles/d41...
Unblock research bottlenecks with non-profit start-ups
‘Focused research organizations’ can take on mid-scale projects that don’t get tackled by academia, venture capitalists or government labs.
www.nature.com
November 1, 2025 at 4:59 PM
It feels like unblocking a bottleneck. Thanks to @convergentresearch.bsky.social for supporting @parallelsq.bsky.social in this mission of unblocking research bottlenecks with non-profit focussed research organizations:
/n
www.nature.com/articles/d41...
/n
www.nature.com/articles/d41...
Reposted by Convergent Research
Now, we are starting to use this approach for an experiment that I have wanted to do for a long time... but it was impractical:
- Simply not feasible with linearly scaling approaches and the resources we have.
timePlex makes it feasible, and I cannot stop thinking about it.
- Simply not feasible with linearly scaling approaches and the resources we have.
timePlex makes it feasible, and I cannot stop thinking about it.
November 1, 2025 at 4:59 PM
Now, we are starting to use this approach for an experiment that I have wanted to do for a long time... but it was impractical:
- Simply not feasible with linearly scaling approaches and the resources we have.
timePlex makes it feasible, and I cannot stop thinking about it.
- Simply not feasible with linearly scaling approaches and the resources we have.
timePlex makes it feasible, and I cannot stop thinking about it.
Reposted by Convergent Research
Combining this time domain multiplexing with mass domain multiplexing (plexDIA), we demonstrated combinatorial scaling of throughput. You can read about it www.biorxiv.org/content/10.1... and hear Jason describe it at the Parallel Squared Technology Institute Research Fest: youtu.be/2rLBk4IaZpk?...
Increasing Mass spectrometry throughput using time encoded sample multiplexing | Jason Derks
YouTube video by Parallel Squared Technology Institute
youtu.be
November 1, 2025 at 4:59 PM
Combining this time domain multiplexing with mass domain multiplexing (plexDIA), we demonstrated combinatorial scaling of throughput. You can read about it www.biorxiv.org/content/10.1... and hear Jason describe it at the Parallel Squared Technology Institute Research Fest: youtu.be/2rLBk4IaZpk?...