Jakub Bartoszewicz
@jmbartoszewicz.bsky.social
Researcher @hpi.bsky.social. AI for viral/microbial bioinformatics, bio/molecular design, biosecurity 🧬 Previously MIT CSAIL, Robert Koch Institute
Pinned
I'm setting up my lab at @hpi.bsky.social, on the edge of vibrant Berlin! PhD/postdoc positions in AI for safe synthetic biology & infectious diseases (AMR), in collab with @melanianowicka.bsky.social.
Apply by Feb 24: email firstname.lastname@hpi.de with “[Open-25]” in the subject. DM for details!
Apply by Feb 24: email firstname.lastname@hpi.de with “[Open-25]” in the subject. DM for details!
Having a blast at #ismbeccb2025! Let's catch up if you're into AI for SynBio, bioLMs, phages, microbes, biosecurity. We're also always looking for PhD students/postdocs! Case in point: multiple 3yr postdoc positions. Work with us or other PIs at HPI near Berlin 🇪🇺!
lnkd.in/eD-ueQmV
lnkd.in/eASJEZAW
lnkd.in/eD-ueQmV
lnkd.in/eASJEZAW
July 23, 2025 at 1:52 PM
Having a blast at #ismbeccb2025! Let's catch up if you're into AI for SynBio, bioLMs, phages, microbes, biosecurity. We're also always looking for PhD students/postdocs! Case in point: multiple 3yr postdoc positions. Work with us or other PIs at HPI near Berlin 🇪🇺!
lnkd.in/eD-ueQmV
lnkd.in/eASJEZAW
lnkd.in/eD-ueQmV
lnkd.in/eASJEZAW
Reposted by Jakub Bartoszewicz
🧬 Passionate about #SyntheticBiology and eager to make an impact? There's still time to get involved and join us!✨
⏳Application deadline extended until March 14th!
👇 Open positions & application info:
⏳Application deadline extended until March 14th!
👇 Open positions & application info:
🚀 Join the #EUSynBioS Steering Committee!
🧬 Passionate about #SyntheticBiology? Based in #Europe? Help grow our community!
We are opening new positions, check them out & apply here 👉 linkedin.com/feed/update/...
#SynBio #ScienceCommunication #Policy
🧬 Passionate about #SyntheticBiology? Based in #Europe? Help grow our community!
We are opening new positions, check them out & apply here 👉 linkedin.com/feed/update/...
#SynBio #ScienceCommunication #Policy
European Synthetic Biology Society (EUSynBioS) on LinkedIn: #syntheticbiology #europe #synbio #europe #outreach #communication…
🧬 Are you passionate about #SyntheticBiology, based in #Europe and willing to help our growing community? ⭐️ 𝗝𝗼𝗶𝗻 𝘁𝗵𝗲 𝗘𝗨𝗦𝘆𝗻𝗕𝗶𝗼𝗦…
linkedin.com
March 10, 2025 at 11:46 AM
🧬 Passionate about #SyntheticBiology and eager to make an impact? There's still time to get involved and join us!✨
⏳Application deadline extended until March 14th!
👇 Open positions & application info:
⏳Application deadline extended until March 14th!
👇 Open positions & application info:
Reposted by Jakub Bartoszewicz
New paper (and #ICLR2025 Oral :)):
ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids arxiv.org/abs/2503.05025
Condition on your 3D layout (of ellipsoids) to generate proteins like this or to get better designability/diversity/novelty tradeoffs.
1/6
ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids arxiv.org/abs/2503.05025
Condition on your 3D layout (of ellipsoids) to generate proteins like this or to get better designability/diversity/novelty tradeoffs.
1/6
March 10, 2025 at 7:51 PM
New paper (and #ICLR2025 Oral :)):
ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids arxiv.org/abs/2503.05025
Condition on your 3D layout (of ellipsoids) to generate proteins like this or to get better designability/diversity/novelty tradeoffs.
1/6
ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids arxiv.org/abs/2503.05025
Condition on your 3D layout (of ellipsoids) to generate proteins like this or to get better designability/diversity/novelty tradeoffs.
1/6
Reposted by Jakub Bartoszewicz
Can generative AI write functional genomes? We don't know, because what's missing in this field is a thorough program of experimental testing.
thisgenomiclife.substack.com/p/can-genera...
thisgenomiclife.substack.com/p/can-genera...
Can generative AI write genomes on demand?
A reality check for generative DNA models
thisgenomiclife.substack.com
March 4, 2025 at 11:04 PM
Can generative AI write functional genomes? We don't know, because what's missing in this field is a thorough program of experimental testing.
thisgenomiclife.substack.com/p/can-genera...
thisgenomiclife.substack.com/p/can-genera...
Want to push the frontier on AI for safe synthetic biology and infectious disease? Just extended the deadline for PhD/Postdoc positions: apply by March 3rd!
I'm setting up my lab at @hpi.bsky.social, on the edge of vibrant Berlin! PhD/postdoc positions in AI for safe synthetic biology & infectious diseases (AMR), in collab with @melanianowicka.bsky.social.
Apply by Feb 24: email firstname.lastname@hpi.de with “[Open-25]” in the subject. DM for details!
Apply by Feb 24: email firstname.lastname@hpi.de with “[Open-25]” in the subject. DM for details!
February 26, 2025 at 11:58 AM
Want to push the frontier on AI for safe synthetic biology and infectious disease? Just extended the deadline for PhD/Postdoc positions: apply by March 3rd!
Reposted by Jakub Bartoszewicz
Check out our latest #phagetherapy review in Nature Reviews Methods Primers.
rdcu.be/d9H92
Happy to share a conceptual schematic for a “phrinter (phage printer)” 😊
Many thanks to all co-authors, editors and reviewers!
rdcu.be/d9H92
Happy to share a conceptual schematic for a “phrinter (phage printer)” 😊
Many thanks to all co-authors, editors and reviewers!
February 17, 2025 at 3:01 PM
Check out our latest #phagetherapy review in Nature Reviews Methods Primers.
rdcu.be/d9H92
Happy to share a conceptual schematic for a “phrinter (phage printer)” 😊
Many thanks to all co-authors, editors and reviewers!
rdcu.be/d9H92
Happy to share a conceptual schematic for a “phrinter (phage printer)” 😊
Many thanks to all co-authors, editors and reviewers!
Reposted by Jakub Bartoszewicz
[SAVE THE DATE] MLCB 2025 is happening Sept 10-11 at the NY Genome Center in NYC!
Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections!
Submission deadline: June 1
More details: mlcb.github.io
Help spread the word—please RT! #MLCB2025
Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections!
Submission deadline: June 1
More details: mlcb.github.io
Help spread the word—please RT! #MLCB2025
February 5, 2025 at 2:50 AM
[SAVE THE DATE] MLCB 2025 is happening Sept 10-11 at the NY Genome Center in NYC!
Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections!
Submission deadline: June 1
More details: mlcb.github.io
Help spread the word—please RT! #MLCB2025
Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections!
Submission deadline: June 1
More details: mlcb.github.io
Help spread the word—please RT! #MLCB2025
I'm setting up my lab at @hpi.bsky.social, on the edge of vibrant Berlin! PhD/postdoc positions in AI for safe synthetic biology & infectious diseases (AMR), in collab with @melanianowicka.bsky.social.
Apply by Feb 24: email firstname.lastname@hpi.de with “[Open-25]” in the subject. DM for details!
Apply by Feb 24: email firstname.lastname@hpi.de with “[Open-25]” in the subject. DM for details!
February 11, 2025 at 10:13 AM
I'm setting up my lab at @hpi.bsky.social, on the edge of vibrant Berlin! PhD/postdoc positions in AI for safe synthetic biology & infectious diseases (AMR), in collab with @melanianowicka.bsky.social.
Apply by Feb 24: email firstname.lastname@hpi.de with “[Open-25]” in the subject. DM for details!
Apply by Feb 24: email firstname.lastname@hpi.de with “[Open-25]” in the subject. DM for details!
Reposted by Jakub Bartoszewicz
A protein language model trained to predict subcellular localization for human proteins can generate de novo sequences with the desired localization and identify pathological mutations.
@itamarchinn.bsky.social @pgmikhael.bsky.social
www.science.org/doi/10.1126/...
@itamarchinn.bsky.social @pgmikhael.bsky.social
www.science.org/doi/10.1126/...
February 10, 2025 at 10:28 PM
A protein language model trained to predict subcellular localization for human proteins can generate de novo sequences with the desired localization and identify pathological mutations.
@itamarchinn.bsky.social @pgmikhael.bsky.social
www.science.org/doi/10.1126/...
@itamarchinn.bsky.social @pgmikhael.bsky.social
www.science.org/doi/10.1126/...
Reposted by Jakub Bartoszewicz
It's long seemed that molecular biology is a natural home for ML interpretability research, given the maturity of human-constructed models of biological mechanisms—permitting direct comparison with their ML-derived counterparts—unlike vision and NLP. Our first foray below👇.
Can we learn protein biology from a language model?
In new work led by @liambai.bsky.social and me, we explore how sparse autoencoders can help us understand biology—going from mechanistic interpretability to mechanistic biology.
In new work led by @liambai.bsky.social and me, we explore how sparse autoencoders can help us understand biology—going from mechanistic interpretability to mechanistic biology.
February 10, 2025 at 4:15 PM
It's long seemed that molecular biology is a natural home for ML interpretability research, given the maturity of human-constructed models of biological mechanisms—permitting direct comparison with their ML-derived counterparts—unlike vision and NLP. Our first foray below👇.
Reposted by Jakub Bartoszewicz
This might be the best paper on applying sparse autoencoders to protein language models. The authors identify how neural networks trained on amino acid sequences "discover" different features, some specific to individual protein families, other for substructures
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
February 10, 2025 at 12:15 PM
This might be the best paper on applying sparse autoencoders to protein language models. The authors identify how neural networks trained on amino acid sequences "discover" different features, some specific to individual protein families, other for substructures
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jakub Bartoszewicz
Can LLM agents discover novel protein functions? Introducing Gaia Agent 🌎 🤖: an AI biologist capable of reasoning across genomic contexts to predict functions of proteins! Gaia Agent is now integrated with Gaia Search at gaia.tatta.bio
December 17, 2024 at 1:38 PM
Can LLM agents discover novel protein functions? Introducing Gaia Agent 🌎 🤖: an AI biologist capable of reasoning across genomic contexts to predict functions of proteins! Gaia Agent is now integrated with Gaia Search at gaia.tatta.bio
Reposted by Jakub Bartoszewicz
In which esteemed colleague Jeremy Berg discusses how his contributions to racemic protein synthesis, inspired by Pauling, demonstrated that D-proteins are immunologically invisible #mirrorbiology
Pauling’s chapter ends “In ‘Through the Looking Glass' Alice said 'Perhaps looking-glass milk isn’t good to drink…Nobody knew that proteins are built of the left-handed amino acids; but Alice was justified in raising the question. The answer is that looking -glass milk is not good to drink.'
25/n
25/n
December 13, 2024 at 2:42 PM
In which esteemed colleague Jeremy Berg discusses how his contributions to racemic protein synthesis, inspired by Pauling, demonstrated that D-proteins are immunologically invisible #mirrorbiology
Reposted by Jakub Bartoszewicz
Sharing here a new commentary in Science Policy Forum that provides new analysis on risks related to the potential future creation of mirror bacteria — synthetic organisms in which all molecules have reversed chirality (i.e. are ‘mirrored’). 1/x
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Confronting risks of mirror life
Broad discussion is needed to chart a path forward.
www.science.org
December 12, 2024 at 7:30 PM
Sharing here a new commentary in Science Policy Forum that provides new analysis on risks related to the potential future creation of mirror bacteria — synthetic organisms in which all molecules have reversed chirality (i.e. are ‘mirrored’). 1/x
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Jakub Bartoszewicz
Can we bypass the resource bottleneck of pretraining genomic Foundation Models? Our work L2G repurposes language LLMs for genomics via cross-modal transfer, matching fine-tuned genomic FMs. Kudos to Wenduo & fantastic collab w/ @atalwalkar.bsky.social. L2G, language to genome; L2G, life’s too good!
L2G: Repurposing Language Models for Genomics Tasks https://www.biorxiv.org/content/10.1101/2024.12.09.627422v1
December 11, 2024 at 1:41 PM
Can we bypass the resource bottleneck of pretraining genomic Foundation Models? Our work L2G repurposes language LLMs for genomics via cross-modal transfer, matching fine-tuned genomic FMs. Kudos to Wenduo & fantastic collab w/ @atalwalkar.bsky.social. L2G, language to genome; L2G, life’s too good!
Reposted by Jakub Bartoszewicz
Check out this systematic benchmark of genome-wide, annotation agnostic DNALMs & strong baseline ab-initio models for biologically meaningful tasks in regulatory genomics 1/
(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA
Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn gen...
arxiv.org
December 11, 2024 at 2:54 AM
Check out this systematic benchmark of genome-wide, annotation agnostic DNALMs & strong baseline ab-initio models for biologically meaningful tasks in regulatory genomics 1/