Sign in

Matt Durrant

@mgdurrant.bsky.social
554 followers 158 following 27 posts

Mobile genetic element whisperer. Computational Biologist @arcinstitute.org. Genetics PhD @stanfordmedicine.bsky.social. I post about programmable recombinases and genome design.

PostsRepliesMedia
Matt Durrant @mgdurrant.bsky.social · 19/01/2025
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.
020
Matt Durrant @mgdurrant.bsky.social · 12/01/2025
My wife woke up angry because Ariana Grande stole me from her in a dream.
020
Matt Durrant @mgdurrant.bsky.social · 12/01/2025
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.
010
Matt Durrant @mgdurrant.bsky.social · 19/12/2024
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.
020
Reposted by Matt Durrant
Aude Bernheim @audeber.bsky.social · 16/12/2024
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-...
academic.oup.com
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
011050
Reposted by Matt Durrant
Dmitri Petrov @petrovadmitri.bsky.social · 11/12/2024
This whole story is amazing, intuitive in retrospect, and likely exceptionally important medically. Do read the paper and the whole thread!
1132
Matt Durrant @mgdurrant.bsky.social · 04/12/2024
Isn’t the solution to ChatGPT doing everyone’s homework to just have more exams and to weight them more heavily?
000
Reposted by Matt Durrant
Hani Goodarzi @genophoria.bsky.social · 03/12/2024
Come join us at @arcinstitute.org !
0146
Matt Durrant @mgdurrant.bsky.social · 02/12/2024
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.
010
Matt Durrant @mgdurrant.bsky.social · 02/12/2024
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.
010
Matt Durrant @mgdurrant.bsky.social · 27/11/2024
Where can I get my hands on a woolly mammoth genome? Was expecting more than mitochondria on NCBI.
132
Reposted by Matt Durrant
Diego del Alamo @delalamo.xyz · 25/11/2024
Yet more evidence that transfer learning of sequence-only PLMs does not benefit from scale beyond 650M params 🧵
Fig. 3. Impact of ESM Model size on transfer learning. LassoCV regression results using ESM mean embeddings for 35 DMS datasets. The x-axis represents different ESM model sizes: ESM1v 650M (orange) and ESM2 8M, 35M, 150M, 650M, 3B, and 15B (blues). The y-axis displays R^2 for each task.
77820
Reposted by Matt Durrant
Sebastian S. Cocioba @atinygreencell.bsky.social · 25/11/2024
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. 🦠💪
1331335
Matt Durrant @mgdurrant.bsky.social · 25/11/2024
That’s the last of my faculty applications! Now we wait🤞
110
Matt Durrant @mgdurrant.bsky.social · 24/11/2024
Could really use the bookmark button….
100
Matt Durrant @mgdurrant.bsky.social · 24/11/2024
Really is impressive to see the growth here!
020
Reposted by Matt Durrant
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 23/11/2024
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-...
6339126
Reposted by Matt Durrant
Michael Baym @baym.lol · 23/11/2024
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!
48335
Reposted by Matt Durrant
Eric Topol @erictopol.bsky.social · 14/11/2024
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/...
320740
Reposted by Matt Durrant
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 14/11/2024
Evo: A genomic language model of prokaryote genomes generates functional cas9 proteins and transposons. @brianhiestand.bsky.social www.science.org/doi/10.1126/...
Evo, a 7-billion-parameter genomic foundation model, learns biological complexity from individual nucleotides to whole genomes.
Pretraining a genomic foundation model across prokaryotic life.Fine-tuning on CRISPR-Cas sequences enables generative design of protein-RNA complexes.Fig. 4. Fine-tuning on IS200/IS605 sequences enables generative design of transposable biological systems.
05927
Reposted by Matt Durrant
Hani Goodarzi @genophoria.bsky.social · 14/11/2024
Really cool model from Brian Hie and Patrick Hsu! www.science.org/doi/10.1126/...
0188
Matt Durrant @mgdurrant.bsky.social · 14/11/2024
The Great Kettlebell Swing Forward
000
Matt Durrant @mgdurrant.bsky.social · 14/11/2024
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
bit.ly
Contents | Science 386, 6723
052
Reposted by Matt Durrant
Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 09/10/2023
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...
hectorzenil.medium.com
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…
084
Matt Durrant @mgdurrant.bsky.social · 06/10/2023
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.
000
Matt Durrant @mgdurrant.bsky.social · 04/10/2023
Does anyone know where I could find some measure of brain drain per year for each country?
000
Reposted by Matt Durrant
Jonathan Pritchard @jkpritch.bsky.social · 01/10/2023
I'm delighted to release the first half of my new textbook in human genetics: web.stanford.edu/group/pritch... "An Owner's Guide to the Human Genome: an introduction to human population genetics, variation and disease"
web.stanford.edu
An Owner's Guide to the Human Genome
An Owner's Guide to the Human Genome
8296175
Matt Durrant @mgdurrant.bsky.social · 02/10/2023
Photo taken out of our car window driving down big cottonwood canyon yesterday! #Utah
000
Matt Durrant @mgdurrant.bsky.social · 28/09/2023
Such a cool paper! Congratulations to the authors. It’s a very exciting time to be studying mobile genetic elements, in terms of both fundamental biology and translational potential. www.nature.com/articles/s41...
nature.com
Transposon-encoded nucleases use guide RNAs to promote their selfish spread - Nature
TnpB and IscB nucleases use transposon-encoded guide RNAs to target genomic sequences for cleavage, thereby favouring copying and spreading of transposable elements.
033
Matt Durrant @mgdurrant.bsky.social · 28/09/2023
Such a cool paper! Great job @shsternberg and team. It’s a very exciting time to be studying mobile genetic elements, in terms of both fundamental biology and translational potential. www.nature.com/articles/s41...
nature.com
Transposon-encoded nucleases use guide RNAs to promote their selfish spread - Nature
TnpB and IscB nucleases use transposon-encoded guide RNAs to target genomic sequences for cleavage, thereby favouring copying and spreading of transposable elements.
000
Matt Durrant @mgdurrant.bsky.social · 26/09/2023
In your experience, how long does it typically take for an editor to finally send out a paper for review?
000
Matt Durrant @mgdurrant.bsky.social · 25/09/2023
So are AI-generated proteins not patentable? www.wired.com/story/ai-art...
wired.com
Why This Award-Winning Piece of AI Art Can’t Be Copyrighted
Matthew Allen’s AI art won first prize at the Colorado State Fair. But the US government has ruled it can’t be copyrighted because it’s too much “machine” and not enough “human.”
000
Matt Durrant @mgdurrant.bsky.social · 23/09/2023
Unpopular opinion: Oppenheimer wasn't a very good movie.
010
Matt Durrant @mgdurrant.bsky.social · 22/09/2023
www.chemistryworld.com/news/pioneer...
chemistryworld.com
Pioneers in synthetic biology and next-generation DNA sequencing ...
Data science divinations and community chatter pick favourites for chemistry's top prize
000
Reposted by Matt Durrant
Jonathan Pritchard @jkpritch.bsky.social · 11/09/2023
In terms of impact it clearly should...but my guess is that it won't, partly because it's hard to choose who should get it and also perhaps a bias against technology. And the Nobel's view of science via brilliant jumps is so outdated that it's often forced to choose smaller discrete contributions
011
Matt Durrant @mgdurrant.bsky.social · 10/09/2023
Will next-generation sequencing receive a Nobel prize, and if it does who will it be awarded to?
140