💾 mlst 2.25.0 has been released!
Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks @microbiologikat.bsky.social) and updated the databases.
#bioinformatiocs #microbiology #genomics
github.com/tseemann/mls...
Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks @microbiologikat.bsky.social) and updated the databases.
#bioinformatiocs #microbiology #genomics
github.com/tseemann/mls...
Releases · tseemann/mlst
:id: Scan contig files against PubMLST typing schemes - tseemann/mlst
github.com
December 22, 2025 at 9:15 PM
💾 mlst 2.25.0 has been released!
Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks @microbiologikat.bsky.social) and updated the databases.
#bioinformatiocs #microbiology #genomics
github.com/tseemann/mls...
Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks @microbiologikat.bsky.social) and updated the databases.
#bioinformatiocs #microbiology #genomics
github.com/tseemann/mls...
🚀 New proof-of-principle:
An interactive, searchable MLST hash database... all in your browser! 🔥
Live demo ➡️ lskatz.github.io/mlst-hash-te...
A natural extension of the hash database spec I developed last year: lskatz.github.io/mlst-hash-te...
🧵
An interactive, searchable MLST hash database... all in your browser! 🔥
Live demo ➡️ lskatz.github.io/mlst-hash-te...
A natural extension of the hash database spec I developed last year: lskatz.github.io/mlst-hash-te...
🧵
Home
Using the MLST hash template as an example genomic epi database
lskatz.github.io
April 28, 2025 at 12:41 PM
🚀 New proof-of-principle:
An interactive, searchable MLST hash database... all in your browser! 🔥
Live demo ➡️ lskatz.github.io/mlst-hash-te...
A natural extension of the hash database spec I developed last year: lskatz.github.io/mlst-hash-te...
🧵
An interactive, searchable MLST hash database... all in your browser! 🔥
Live demo ➡️ lskatz.github.io/mlst-hash-te...
A natural extension of the hash database spec I developed last year: lskatz.github.io/mlst-hash-te...
🧵
you have to try it, better than tinder and grindr
➡️ theblowers.com/@mensohot
➡️ theblowers.com/@mensohot
July 25, 2025 at 7:10 AM
Delighted that the final version of our Candida parapsilosis outbreak +MLST creation manuscript is out now in The Lancet Microbe.
doi.org/10.1016/j.la...
Thread of the main findings below!
doi.org/10.1016/j.la...
Thread of the main findings below!
Redirecting
doi.org
November 16, 2024 at 11:11 AM
Delighted that the final version of our Candida parapsilosis outbreak +MLST creation manuscript is out now in The Lancet Microbe.
doi.org/10.1016/j.la...
Thread of the main findings below!
doi.org/10.1016/j.la...
Thread of the main findings below!
Hoje é dia de levar o senhor medo de agulha pra fazer exame de sangue
September 6, 2025 at 1:03 PM
Hoje é dia de levar o senhor medo de agulha pra fazer exame de sangue
Ma'am there is nothing wrong with your butt, I do not wish to imply that, but also as a mom who sometimes wears jean shorts if you ever publish a picture of me from that angle I am going to call up some Etsy witches and ask them for their mlst powerful curses.
April 2, 2026 at 2:45 AM
Ma'am there is nothing wrong with your butt, I do not wish to imply that, but also as a mom who sometimes wears jean shorts if you ever publish a picture of me from that angle I am going to call up some Etsy witches and ask them for their mlst powerful curses.
I would dare say one of the mlst common missions is humanitarian relief. Tons of MEUs end up responding to natural disasters, because you have helos for lifting supplies and a thousand plus able bodies to help with everything from sandbags to feeding to provididing security
March 21, 2026 at 7:29 PM
I would dare say one of the mlst common missions is humanitarian relief. Tons of MEUs end up responding to natural disasters, because you have helos for lifting supplies and a thousand plus able bodies to help with everything from sandbags to feeding to provididing security
My conversation on the Machine Learning Street Talk podcast.
I spoke to Tim and Keith about semantics, philosophy of mind, Large Language Models, AI ethics, evolution, metaphysics, and the end of the world.
www.patreon.com/posts/elliot...
I spoke to Tim and Keith about semantics, philosophy of mind, Large Language Models, AI ethics, evolution, metaphysics, and the end of the world.
www.patreon.com/posts/elliot...
Elliot Murphy - Language, Knowledge, Semantics | Machine Learning Street Talk (MLST)
Get more from Machine Learning Street Talk (MLST) on Patreon
www.patreon.com
December 2, 2024 at 9:22 AM
My conversation on the Machine Learning Street Talk podcast.
I spoke to Tim and Keith about semantics, philosophy of mind, Large Language Models, AI ethics, evolution, metaphysics, and the end of the world.
www.patreon.com/posts/elliot...
I spoke to Tim and Keith about semantics, philosophy of mind, Large Language Models, AI ethics, evolution, metaphysics, and the end of the world.
www.patreon.com/posts/elliot...
I remember your big criticism of this era of music (in mlst genres) was it pretended the recession wasnt happening. It was all Obama positivity and Tech Optimism.
Too late to call to Startup Pop though.
Too late to call to Startup Pop though.
May 1, 2025 at 5:35 AM
I remember your big criticism of this era of music (in mlst genres) was it pretended the recession wasnt happening. It was all Obama positivity and Tech Optimism.
Too late to call to Startup Pop though.
Too late to call to Startup Pop though.
The Machine Learning Street Talk (MLST) podcast just dropped an episode with Nicholas Carlini on Spotify! open.spotify.com/episode/6hpi...
Nicholas Carlini (Google DeepMind)
Machine Learning Street Talk (MLST) · Episode
open.spotify.com
January 26, 2025 at 4:42 PM
The Machine Learning Street Talk (MLST) podcast just dropped an episode with Nicholas Carlini on Spotify! open.spotify.com/episode/6hpi...
Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
July 30, 2025 at 2:11 AM
Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Thanks for recommending MLST, Henrique :D
February 25, 2025 at 1:55 PM
Thanks for recommending MLST, Henrique :D
Let's Fucking Go 🇨🇳
January 14, 2025 at 12:29 AM
Let's Fucking Go 🇨🇳
I really like @yoshuabengio.bsky.social's humility in the recent Machine Learning Street Talk episode on AI safety, whether it's on probability of doom, different risk scenarios, AGI timeline, or other topics:
Yoshua Bengio - Designing out Agency for Safe AI
Machine Learning Street Talk (MLST) · Episode
open.spotify.com
January 17, 2025 at 1:19 PM
I really like @yoshuabengio.bsky.social's humility in the recent Machine Learning Street Talk episode on AI safety, whether it's on probability of doom, different risk scenarios, AGI timeline, or other topics:
It's a pleasure to work with @piermorgante.bsky.social on MLST!
Super excited to work on these wonderful titles [with awesome EiCs @kylecranmer.bsky.social and @pierregentine.bsky.social–Jimeng and Jay are sadly not on BlueSky yet] as your friendly neighborhood editor! #AskMeAnything about them or publishing with us #EditorsLife #MachineLearning
Have you ever wondered what it's like behind the scenes at the #MachineLearning series journals?
Discover the journey through the eyes of our commissioning editor @piermorgante.bsky.social !
👉Don't forget to check our #ML series: bit.ly/3Fi29oE
Discover the journey through the eyes of our commissioning editor @piermorgante.bsky.social !
👉Don't forget to check our #ML series: bit.ly/3Fi29oE
June 2, 2025 at 6:25 PM
It's a pleasure to work with @piermorgante.bsky.social on MLST!
We show how to estimate the impact of research ideas before they were even born -- just published in #MLST
[paper] iopscience.iop.org/article/10.1...
[GitHub]: github.com/artificial-s...
spearheaded by @xmgu.bsky.social
Important for future artificial muses, to generate impactful new ideas.
[paper] iopscience.iop.org/article/10.1...
[GitHub]: github.com/artificial-s...
spearheaded by @xmgu.bsky.social
Important for future artificial muses, to generate impactful new ideas.
May 10, 2025 at 12:08 PM
We show how to estimate the impact of research ideas before they were even born -- just published in #MLST
[paper] iopscience.iop.org/article/10.1...
[GitHub]: github.com/artificial-s...
spearheaded by @xmgu.bsky.social
Important for future artificial muses, to generate impactful new ideas.
[paper] iopscience.iop.org/article/10.1...
[GitHub]: github.com/artificial-s...
spearheaded by @xmgu.bsky.social
Important for future artificial muses, to generate impactful new ideas.
Frustrated by trying to publish in the large conferences? MLST is a great venue to share research at the intersection of AI/ML and the physical sciences.
🌟Discover the latest research that has got the scientific community talking🌟
Be one of the first to unlock MLST's brand new research hub - where we will share the latest and most cited articles published in the journal, all in one place.
🔓Unlock the research: https://ow.ly/7yM550XtYnq
Be one of the first to unlock MLST's brand new research hub - where we will share the latest and most cited articles published in the journal, all in one place.
🔓Unlock the research: https://ow.ly/7yM550XtYnq
December 5, 2025 at 1:08 PM
Frustrated by trying to publish in the large conferences? MLST is a great venue to share research at the intersection of AI/ML and the physical sciences.
New #compchem paper out in MLST. We study the transferability of both invariant and equivariant neural networks when training these either exclusively on total molecular energies or in combination with data from different atomic partitioning schemes:
iopscience.iop.org/article/10.1...
iopscience.iop.org/article/10.1...
Transferability of atom-based neural networks - IOPscienceSearch
Transferability of atom-based neural networks, Frederik Ø Kjeldal, Janus J Eriksen
iopscience.iop.org
December 7, 2024 at 8:49 AM
New #compchem paper out in MLST. We study the transferability of both invariant and equivariant neural networks when training these either exclusively on total molecular energies or in combination with data from different atomic partitioning schemes:
iopscience.iop.org/article/10.1...
iopscience.iop.org/article/10.1...
Kleborate v3 is also out now, it calls Kaptive v3 for rapid serotype prediction, plus speciation, MLST, AMR and virulence genotyping. (V3 is also now available via Pathogenwatch and Bactopia) - so get Kleborating! #KLEBS24
November 20, 2024 at 6:12 PM
Kleborate v3 is also out now, it calls Kaptive v3 for rapid serotype prediction, plus speciation, MLST, AMR and virulence genotyping. (V3 is also now available via Pathogenwatch and Bactopia) - so get Kleborating! #KLEBS24
An interesting thread by Tim Scarfe/MLST on AI filmmaking (who is for some reason still primarily posting on X).
x.com/MLStreetTalk...
x.com/MLStreetTalk...
December 1, 2025 at 2:43 PM
An interesting thread by Tim Scarfe/MLST on AI filmmaking (who is for some reason still primarily posting on X).
x.com/MLStreetTalk...
x.com/MLStreetTalk...
One of mlst beautiful gifts I have ever gotten by @riverrt.bsky.social qwq
I love it soo muchhh...
I have no idea why I havent posted it sooner, its magnificent and special for me 💖💖💖
Thank you so much hun 💖
I love it soo muchhh...
I have no idea why I havent posted it sooner, its magnificent and special for me 💖💖💖
Thank you so much hun 💖
January 22, 2026 at 9:27 AM
One of mlst beautiful gifts I have ever gotten by @riverrt.bsky.social qwq
I love it soo muchhh...
I have no idea why I havent posted it sooner, its magnificent and special for me 💖💖💖
Thank you so much hun 💖
I love it soo muchhh...
I have no idea why I havent posted it sooner, its magnificent and special for me 💖💖💖
Thank you so much hun 💖
We learnt how to assemble DNA fragments from a recently published N. meningitidis outbreak study www.cdc.gov/mmwr/volumes... using SKESA 🧬, practiced using BLAST for species identification and MLST for strain typing, and explored how serogroups are determined!
#idsky #microsky #rstats
#idsky #microsky #rstats
Learning About Assemblying DNA, BLAST, and Multiple Loci Sequence Testing (MLST) - A Note To Myself | Everyday Is A School Day
We learnt how to assemble DNA fragments from a recently published *N. meningitidis* outbreak study using SKESA 🧬, practiced using BLAST for species identification and MLST for strain typing, and explo...
www.kenkoonwong.com
September 15, 2025 at 11:06 PM
We learnt how to assemble DNA fragments from a recently published N. meningitidis outbreak study www.cdc.gov/mmwr/volumes... using SKESA 🧬, practiced using BLAST for species identification and MLST for strain typing, and explored how serogroups are determined!
#idsky #microsky #rstats
#idsky #microsky #rstats
For anyone who saw my MLST interview from December and wanted to make sense of Deepseek R1 from that prompt augmentation perspective, here is an R1 delta addendum you might enjoy: 👉 x.com/rao2z/status...
February 3, 2025 at 5:23 PM
For anyone who saw my MLST interview from December and wanted to make sense of Deepseek R1 from that prompt augmentation perspective, here is an R1 delta addendum you might enjoy: 👉 x.com/rao2z/status...
Ferm defensor del JOMO Joy of missing out, o MLST me la sua tot
December 20, 2024 at 12:01 PM
Ferm defensor del JOMO Joy of missing out, o MLST me la sua tot
🧬 New #GenEpiBioTrain course!
Bacterial Strain Taxonomy for Genomic Surveillance
📅 22–23.10, 09:00–12:00 (CEST)
Learn how bacterial pathogens are classified & named in genomic surveillance – from #MLST & #cgMLST to SNP-based & k-mer clustering.
Info: bit.ly/48qT5df
#ECDCTraining #IDsky #EpiSky
Bacterial Strain Taxonomy for Genomic Surveillance
📅 22–23.10, 09:00–12:00 (CEST)
Learn how bacterial pathogens are classified & named in genomic surveillance – from #MLST & #cgMLST to SNP-based & k-mer clustering.
Info: bit.ly/48qT5df
#ECDCTraining #IDsky #EpiSky
October 8, 2025 at 2:34 PM
🧬 New #GenEpiBioTrain course!
Bacterial Strain Taxonomy for Genomic Surveillance
📅 22–23.10, 09:00–12:00 (CEST)
Learn how bacterial pathogens are classified & named in genomic surveillance – from #MLST & #cgMLST to SNP-based & k-mer clustering.
Info: bit.ly/48qT5df
#ECDCTraining #IDsky #EpiSky
Bacterial Strain Taxonomy for Genomic Surveillance
📅 22–23.10, 09:00–12:00 (CEST)
Learn how bacterial pathogens are classified & named in genomic surveillance – from #MLST & #cgMLST to SNP-based & k-mer clustering.
Info: bit.ly/48qT5df
#ECDCTraining #IDsky #EpiSky