Matt Durrant
@mgdurrant.bsky.social
Mobile genetic element whisperer. Computational Biologist @arcinstitute.org. Genetics PhD @stanfordmedicine.bsky.social.
I post about programmable recombinases and genome design.
I post about programmable recombinases and genome design.
Me to son: You have way too many toys! Go pick one and we’ll donate it to charity.
*10 minutes later*
Me: woah woah woah slow down, too many memories with that one.
*10 minutes later*
Me: woah woah woah slow down, too many memories with that one.
January 19, 2025 at 3:58 PM
Me to son: You have way too many toys! Go pick one and we’ll donate it to charity.
*10 minutes later*
Me: woah woah woah slow down, too many memories with that one.
*10 minutes later*
Me: woah woah woah slow down, too many memories with that one.
My wife woke up angry because Ariana Grande stole me from her in a dream.
January 12, 2025 at 7:00 PM
My wife woke up angry because Ariana Grande stole me from her in a dream.
As kids, my mom used to regularly take me and my sister to public recycling dumpsters, have us climb in, and we’d dig around to find coupons in magazines and newspapers. We were not poor.
January 12, 2025 at 6:59 PM
As kids, my mom used to regularly take me and my sister to public recycling dumpsters, have us climb in, and we’d dig around to find coupons in magazines and newspapers. We were not poor.
My grandfather compiled a history of all of my ancestors on his side going back 5 generations, 62 people in total, some born in the mid 1700s. I can confirm that life is much better now than it was then.
December 19, 2024 at 3:36 PM
My grandfather compiled a history of all of my ancestors on his side going back 5 generations, 62 people in total, some born in the mid 1700s. I can confirm that life is much better now than it was then.
Reposted by Matt Durrant
Out in NAR, AntiDefenseFinder & our "systematic" analysis of inhibitors of antiphage systems wt Bondy-Denomy lab led by @ftesson.bsky.social and E. Huiting.
Not so "systematic" as very few known, fun stuff on MGE, antidefense islands and cool phages exaptations!
academic.oup.com/nar/advance-...
Not so "systematic" as very few known, fun stuff on MGE, antidefense islands and cool phages exaptations!
academic.oup.com/nar/advance-...
Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements
Abstract. The co-evolution of prokaryotes, phages and mobile genetic elements (MGEs) has driven the diversification of defense and anti-defense systems ali
academic.oup.com
December 16, 2024 at 8:53 AM
Out in NAR, AntiDefenseFinder & our "systematic" analysis of inhibitors of antiphage systems wt Bondy-Denomy lab led by @ftesson.bsky.social and E. Huiting.
Not so "systematic" as very few known, fun stuff on MGE, antidefense islands and cool phages exaptations!
academic.oup.com/nar/advance-...
Not so "systematic" as very few known, fun stuff on MGE, antidefense islands and cool phages exaptations!
academic.oup.com/nar/advance-...
Reposted by Matt Durrant
This whole story is amazing, intuitive in retrospect, and likely exceptionally important medically. Do read the paper and the whole thread!
Major distinguishing feature: it is *pre-emptive*. The host reaches outside, grabs bacteria (or bacterial fragments), brings them inside, & develops an immune response against them. In a very real sense, the host is *vaccinating itself* against the colonist. 41/55
December 11, 2024 at 7:20 PM
This whole story is amazing, intuitive in retrospect, and likely exceptionally important medically. Do read the paper and the whole thread!
Isn’t the solution to ChatGPT doing everyone’s homework to just have more exams and to weight them more heavily?
December 4, 2024 at 3:02 AM
Isn’t the solution to ChatGPT doing everyone’s homework to just have more exams and to weight them more heavily?
Reposted by Matt Durrant
Come join us at @arcinstitute.org !
Want to start your own lab out of grad school? Arc’s Science Fellows receive funding for a team of 2-4 people! Applications due Jan 15 from new-career scientists in Neurobiology or Immunology.
Join Arc co-founder Patrick Hsu for an info session Fri 12/6 10 am PST. Register here: shorturl.at/r1cgD
Join Arc co-founder Patrick Hsu for an info session Fri 12/6 10 am PST. Register here: shorturl.at/r1cgD
December 3, 2024 at 12:54 AM
Come join us at @arcinstitute.org !
If the government is going to start banning food dyes and vaccines I only ask that they ban such things in a time-staggered way throughout the country so we can get some nice natural experiment data.
December 2, 2024 at 3:57 AM
If the government is going to start banning food dyes and vaccines I only ask that they ban such things in a time-staggered way throughout the country so we can get some nice natural experiment data.
I hereby announce my candidacy for the presidency in 2028. If you vote for me, I will give you complete immunity for all crimes you commit between now and the end of my time in office.
December 2, 2024 at 3:43 AM
I hereby announce my candidacy for the presidency in 2028. If you vote for me, I will give you complete immunity for all crimes you commit between now and the end of my time in office.
Where can I get my hands on a woolly mammoth genome? Was expecting more than mitochondria on NCBI.
November 27, 2024 at 12:15 AM
Where can I get my hands on a woolly mammoth genome? Was expecting more than mitochondria on NCBI.
Reposted by Matt Durrant
Yet more evidence that transfer learning of sequence-only PLMs does not benefit from scale beyond 650M params 🧵
November 25, 2024 at 7:34 AM
Yet more evidence that transfer learning of sequence-only PLMs does not benefit from scale beyond 650M params 🧵
Reposted by Matt Durrant
Microbiology will always be one of the most satisfying fields of natural science. Nigh-infinite levels of biodiversity, perpetual room for novel findings, and an evergreen requirement for the advancement of human civilization. 10/10. Big fan. Would recommend.
🦠💪
🦠💪
November 25, 2024 at 1:12 PM
Microbiology will always be one of the most satisfying fields of natural science. Nigh-infinite levels of biodiversity, perpetual room for novel findings, and an evergreen requirement for the advancement of human civilization. 10/10. Big fan. Would recommend.
🦠💪
🦠💪
That’s the last of my faculty applications! Now we wait🤞
November 25, 2024 at 6:52 AM
That’s the last of my faculty applications! Now we wait🤞
Could really use the bookmark button….
November 24, 2024 at 4:15 AM
Could really use the bookmark button….
Really is impressive to see the growth here!
November 24, 2024 at 3:18 AM
Really is impressive to see the growth here!
Reposted by Matt Durrant
Our Big Fantastic Virus Database (BFVD) is now published NAR! It contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web.
🌐 bfvd.foldseek.com
💾 bfvd.steineggerlab.workers.dev
📄 academic.oup.com/nar/advance-...
🌐 bfvd.foldseek.com
💾 bfvd.steineggerlab.workers.dev
📄 academic.oup.com/nar/advance-...
November 23, 2024 at 9:12 PM
Our Big Fantastic Virus Database (BFVD) is now published NAR! It contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web.
🌐 bfvd.foldseek.com
💾 bfvd.steineggerlab.workers.dev
📄 academic.oup.com/nar/advance-...
🌐 bfvd.foldseek.com
💾 bfvd.steineggerlab.workers.dev
📄 academic.oup.com/nar/advance-...
Reposted by Matt Durrant
We've long been able to find new phages and figure out what they interact with. But what about the other direction: if you have a gene, like an antibiotic resistance efflux pump, or a phage defense system, and you want to find phages that do or do not interact with it?
Now you can!
Now you can!
What if we dug into a sample a little more “wild” and a little less characterized? We combined our strains with a wastewater sample (thank you citizens of Boston for your ~contributions~), and again we found fluorescent hits! Each was isolated and characteristics confirmed on monoculture lawns. 5/
November 23, 2024 at 6:49 PM
We've long been able to find new phages and figure out what they interact with. But what about the other direction: if you have a gene, like an antibiotic resistance efflux pump, or a phage defense system, and you want to find phages that do or do not interact with it?
Now you can!
Now you can!
Reposted by Matt Durrant
New at Science
Evo, a large language of life (LLLM) genomic foundation model, predicting & generating tasks from molecular to genomic scale
science.org/doi/10.1126/...
Evo, a large language of life (LLLM) genomic foundation model, predicting & generating tasks from molecular to genomic scale
science.org/doi/10.1126/...
November 14, 2024 at 7:16 PM
New at Science
Evo, a large language of life (LLLM) genomic foundation model, predicting & generating tasks from molecular to genomic scale
science.org/doi/10.1126/...
Evo, a large language of life (LLLM) genomic foundation model, predicting & generating tasks from molecular to genomic scale
science.org/doi/10.1126/...
Reposted by Matt Durrant
Evo: A genomic language model of prokaryote genomes generates functional cas9 proteins and transposons.
@brianhiestand.bsky.social
www.science.org/doi/10.1126/...
@brianhiestand.bsky.social
www.science.org/doi/10.1126/...
November 14, 2024 at 8:53 PM
Evo: A genomic language model of prokaryote genomes generates functional cas9 proteins and transposons.
@brianhiestand.bsky.social
www.science.org/doi/10.1126/...
@brianhiestand.bsky.social
www.science.org/doi/10.1126/...
Reposted by Matt Durrant
Really cool model from Brian Hie and Patrick Hsu! www.science.org/doi/10.1126/...
November 14, 2024 at 7:35 PM
Really cool model from Brian Hie and Patrick Hsu! www.science.org/doi/10.1126/...
The Great Kettlebell Swing Forward
November 14, 2024 at 10:50 PM
The Great Kettlebell Swing Forward
Thrilled to see this published! Lots of progress since our preprint, including experimental validation of Evo-generated Cas9 and IS200/IS605 transposases. I am definitely a true believer when it comes to DNA language models, they have quickly become central to my discovery efforts. bit.ly/3OsmUPr
Contents | Science 386, 6723
bit.ly
November 14, 2024 at 9:07 PM
Thrilled to see this published! Lots of progress since our preprint, including experimental validation of Evo-generated Cas9 and IS200/IS605 transposases. I am definitely a true believer when it comes to DNA language models, they have quickly become central to my discovery efforts. bit.ly/3OsmUPr
Reposted by Matt Durrant
This post is long but informative (even if mostly written before the newest paper):
The 8 Fallacies of Assembly Theory
hectorzenil.medium.com/test-8f0be54...
The 8 Fallacies of Assembly Theory
hectorzenil.medium.com/test-8f0be54...
The 8 Fallacies of Assembly Theory
In response to the alleged misunderstandings evident in our exposure of the many serious issues undermining the foundations and methods of…
hectorzenil.medium.com
October 8, 2023 at 11:05 PM
This post is long but informative (even if mostly written before the newest paper):
The 8 Fallacies of Assembly Theory
hectorzenil.medium.com/test-8f0be54...
The 8 Fallacies of Assembly Theory
hectorzenil.medium.com/test-8f0be54...
What are some unwritten rules in academia that would be helpful for new folks to know?
One rule I learned the hard way was that you don't reach out to other PIs about collaborating without discussing it with your PI first.
One rule I learned the hard way was that you don't reach out to other PIs about collaborating without discussing it with your PI first.
October 6, 2023 at 6:35 PM
What are some unwritten rules in academia that would be helpful for new folks to know?
One rule I learned the hard way was that you don't reach out to other PIs about collaborating without discussing it with your PI first.
One rule I learned the hard way was that you don't reach out to other PIs about collaborating without discussing it with your PI first.