Paul Saary
@biopaul.bsky.social
Reposted by Paul Saary
@sacrozhangt.bsky.social and I wrote a commentary on Jordi van Gestel and Carol Gross's latest paper, check it out!
www.pnas.org/doi/10.1073/...
Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)
www.pnas.org/doi/10.1073/...
Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)
November 13, 2025 at 2:54 PM
@sacrozhangt.bsky.social and I wrote a commentary on Jordi van Gestel and Carol Gross's latest paper, check it out!
www.pnas.org/doi/10.1073/...
Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)
www.pnas.org/doi/10.1073/...
Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)
Pretty amazing Postdoc opportunity
1 week left to apply for a postdoc position in beautiful Switzerland doing awesome mucosal immunology. See below for details! Please re-post to spread the word!
We have an opening for a postdoctoral researcher in my group at the Botnar Institute for Immune Engineering in Basel, Switzerland. The project is aimed at developing novel mucosal adjuvants for application in oral vaccines. Deadline to apply 16.11.25! Please re-post 🔬🧬
join.com/companies/im...
join.com/companies/im...
November 10, 2025 at 4:18 PM
Pretty amazing Postdoc opportunity
Reposted by Paul Saary
No, but taxing the rich could
October 29, 2025 at 6:09 AM
No, but taxing the rich could
Very cool thread about t2t assembly of human genome.
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
www.biorxiv.org
September 23, 2025 at 7:06 AM
Very cool thread about t2t assembly of human genome.
Reposted by Paul Saary
A frequent thought during seminars on ostensibly unrelated topics
September 18, 2025 at 8:44 PM
A frequent thought during seminars on ostensibly unrelated topics
Reposted by Paul Saary
Now out as preprint: versions 2.0 of both BiG-SCAPE and BiG-SLiCE have been released! With significant speed and accuracy increases, as well as new interactive functionalities. www.biorxiv.org/content/10.1...
BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters
Microbial metabolic gene clusters encode the biosynthesis or catabolism of metabolites that facilitate ecological specialization, mediate microbiome interactions and constitute a major source of medic...
www.biorxiv.org
September 1, 2025 at 10:35 PM
Now out as preprint: versions 2.0 of both BiG-SCAPE and BiG-SLiCE have been released! With significant speed and accuracy increases, as well as new interactive functionalities. www.biorxiv.org/content/10.1...
Reposted by Paul Saary
What’s the next PDB? Maybe it’s …the PDB.
We just launched @diffuseproject.bsky.social a structural biology initiative exploring protein motion & rethinking how we generate and use experimental data. Quick 🧵👇
www.diffuse.science
We just launched @diffuseproject.bsky.social a structural biology initiative exploring protein motion & rethinking how we generate and use experimental data. Quick 🧵👇
www.diffuse.science
The Diffuse Project
The Diffuse Project
www.diffuse.science
August 12, 2025 at 4:16 PM
What’s the next PDB? Maybe it’s …the PDB.
We just launched @diffuseproject.bsky.social a structural biology initiative exploring protein motion & rethinking how we generate and use experimental data. Quick 🧵👇
www.diffuse.science
We just launched @diffuseproject.bsky.social a structural biology initiative exploring protein motion & rethinking how we generate and use experimental data. Quick 🧵👇
www.diffuse.science
That sounds almost too good to be true. Excited to see some external validation
🧬Latent-X is our first frontier model for protein design.
For mini-binders, our AI model achieved picomolar binding affinities — the strongest reported vs prior methods in head-to-head lab validation.
Explore our best binders here: platform.latentlabs.com
More details on the breakthrough in this🧵
For mini-binders, our AI model achieved picomolar binding affinities — the strongest reported vs prior methods in head-to-head lab validation.
Explore our best binders here: platform.latentlabs.com
More details on the breakthrough in this🧵
July 25, 2025 at 2:53 PM
That sounds almost too good to be true. Excited to see some external validation
Reposted by Paul Saary
And just like that @katharinaweins.bsky.social and Elvira Isenring managed to make us look cooler than we'll ever be:
www.youtube.com/watch?v=8t8R...
www.youtube.com/watch?v=8t8R...
Bioimaging | UZH Research Spotlight
YouTube video by Universität Zürich
www.youtube.com
June 24, 2025 at 5:39 PM
And just like that @katharinaweins.bsky.social and Elvira Isenring managed to make us look cooler than we'll ever be:
www.youtube.com/watch?v=8t8R...
www.youtube.com/watch?v=8t8R...
Reposted by Paul Saary
Exclusive: Famed protein structure competition nears end as NIH grant money runs out | Science | AAAS www.science.org/content/arti... 🧪
Exclusive: Famed protein structure competition nears end as NIH grant money runs out
Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold
www.science.org
July 3, 2025 at 9:18 PM
Exclusive: Famed protein structure competition nears end as NIH grant money runs out | Science | AAAS www.science.org/content/arti... 🧪
Reposted by Paul Saary
Nice work by @avsecz.bsky.social and team - three things to highlight here for me :
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
June 25, 2025 at 3:14 PM
Nice work by @avsecz.bsky.social and team - three things to highlight here for me :
Reposted by Paul Saary
Powerful stuff from @juliosaezrod.bsky.social who found himself on the other end of the process - as a patient not a computational biology researcher - giving him insight into both research and patient perspectives. Huge credit to Julio for talking about his experiences here
June 20, 2025 at 8:06 AM
Powerful stuff from @juliosaezrod.bsky.social who found himself on the other end of the process - as a patient not a computational biology researcher - giving him insight into both research and patient perspectives. Huge credit to Julio for talking about his experiences here
Reposted by Paul Saary
Preprint alert! 🦌
Our new abundance index, REINDEER2, is out!
It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput.
Short thread!
www.biorxiv.org/content/10.1...
github.com/Yohan-Hernan...
Our new abundance index, REINDEER2, is out!
It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput.
Short thread!
www.biorxiv.org/content/10.1...
github.com/Yohan-Hernan...
www.biorxiv.org
June 19, 2025 at 9:13 AM
Preprint alert! 🦌
Our new abundance index, REINDEER2, is out!
It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput.
Short thread!
www.biorxiv.org/content/10.1...
github.com/Yohan-Hernan...
Our new abundance index, REINDEER2, is out!
It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput.
Short thread!
www.biorxiv.org/content/10.1...
github.com/Yohan-Hernan...
Reposted by Paul Saary
The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.
May 28, 2025 at 10:18 AM
The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.
No benefit to the US, I mean it only enables a large chunk of research in and around all pharma. But yeah, no real benefit there
NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.
May 29, 2025 at 8:31 AM
No benefit to the US, I mean it only enables a large chunk of research in and around all pharma. But yeah, no real benefit there
Reposted by Paul Saary
This is terrible news, HMMER & Infernal are at the heart of DBs like Pfam, Rfam & Dfam. And vital pipelines such as AlphaFold.
NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.
May 29, 2025 at 7:00 AM
This is terrible news, HMMER & Infernal are at the heart of DBs like Pfam, Rfam & Dfam. And vital pipelines such as AlphaFold.
Reposted by Paul Saary
We observed chimeric contigs where the assembly software reported a single contig that brought together sequences from two distinct taxa, sometimes three or more, and even sequences that belonged to distinct domains of life.
April 28, 2025 at 8:08 AM
We observed chimeric contigs where the assembly software reported a single contig that brought together sequences from two distinct taxa, sometimes three or more, and even sequences that belonged to distinct domains of life.