naturepoker
@binomicalabs.org
Binomica Labs independent researcher by day, warehouse worker by night
Small thoughtful science
#phylogenetics #archaea #evolution #bioinformatics
@[email protected]
http://naturepoker.wordpress.com
https://orcid.org/0000-0002-6977-5440
Small thoughtful science
#phylogenetics #archaea #evolution #bioinformatics
@[email protected]
http://naturepoker.wordpress.com
https://orcid.org/0000-0002-6977-5440
Pinned
naturepoker
@binomicalabs.org
· Dec 31
Welcoming 2026 – independent research retrospective
2025 is gone, bringing with it another opportunity to share some highlights from a warehouse worker’s swing at studying our living history a sheaf of genome graphs and shelves full of protein…
naturepoker.wordpress.com
Happy 2026 everyone! Here's a Binomica labs retrospective post. An amateur independent researcher's perspective on genome sequencing, academic conferences and approaching research themes undertaken through 2025 🧪
naturepoker.wordpress.com/2025/12/31/w...
naturepoker.wordpress.com/2025/12/31/w...
Of all the potato derived snacks I've tried over the years, this one stands out as the best. Delicious, inexpensive, strangely filling and can serve as garnish/crunchy thing for soups and other foods if I feel like it.
January 30, 2026 at 9:59 PM
Of all the potato derived snacks I've tried over the years, this one stands out as the best. Delicious, inexpensive, strangely filling and can serve as garnish/crunchy thing for soups and other foods if I feel like it.
Reposted by naturepoker
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
www.science.org
January 30, 2026 at 6:11 AM
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Reposted by naturepoker
This is Callie. She is trained to accurately detect bowel cancer in order to provide rapid diagnoses through non-invasive testing. Some might call it lab work, but Callie is actually a sprocker spaniel. 14/10 incredible job, Callie (IG: medicaldetectiondogs)
January 29, 2026 at 11:40 PM
This is Callie. She is trained to accurately detect bowel cancer in order to provide rapid diagnoses through non-invasive testing. Some might call it lab work, but Callie is actually a sprocker spaniel. 14/10 incredible job, Callie (IG: medicaldetectiondogs)
Reposted by naturepoker
Pioneering work by the @kacarlab.bsky.social Ancestral state reconstruction, expression of ancient nitrogenases, measuring their isotope fractionation, reinterpretations of geobiological record. Super cool :)
The study shows that nitrogenase enzymes have maintained stable isotope signatures over billions of years, revealing how ancient #microbes shaped Earth’s #nitrogen cycle and offering a new experimental framework for probing early life.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Resurrected nitrogenases recapitulate canonical N-isotope biosignatures over two billion years - Nature Communications
The study shows that nitrogenase enzymes have maintained stable isotope signatures over billions of years, revealing how ancient microbes shaped Earth’s nitrogen cycle and offering a new experimental ...
www.nature.com
January 29, 2026 at 2:16 PM
Pioneering work by the @kacarlab.bsky.social Ancestral state reconstruction, expression of ancient nitrogenases, measuring their isotope fractionation, reinterpretations of geobiological record. Super cool :)
Continuing the 10 year streak of finishing all my taxes in January. Woot.
Still think all the form/lookup requirements in the US can be a bit silly when they have all the info already.
Still think all the form/lookup requirements in the US can be a bit silly when they have all the info already.
January 30, 2026 at 12:05 AM
Continuing the 10 year streak of finishing all my taxes in January. Woot.
Still think all the form/lookup requirements in the US can be a bit silly when they have all the info already.
Still think all the form/lookup requirements in the US can be a bit silly when they have all the info already.
Reposted by naturepoker
Calling all OrthoFinder users!
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
www.biorxiv.org
January 29, 2026 at 12:07 PM
Calling all OrthoFinder users!
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
🖥️🧬
Announcing a new tool for "denoising" long-read amplicon sequences: savont.
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads
Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont
github.com
January 28, 2026 at 7:52 PM
🖥️🧬
Reposted by naturepoker
Excited to announce our latest publication in reporting evidence for three (3!) new whole genome duplications (WGDs) in yeasts. Scientists have often wondered why WGD is so rare in fungi, it turns out we may just not have been looking hard enough! 🧪 🍄 🧬
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Discovery of additional ancient genome duplications in yeasts
Whole-genome duplication (WGD) has had profound macroevolutionary impacts on diverse lineages,1,2 preceding adaptive radiations in vertebrates,3,4,5 t…
www.sciencedirect.com
January 28, 2026 at 5:49 PM
Excited to announce our latest publication in reporting evidence for three (3!) new whole genome duplications (WGDs) in yeasts. Scientists have often wondered why WGD is so rare in fungi, it turns out we may just not have been looking hard enough! 🧪 🍄 🧬
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by naturepoker
We are looking for new editors for Microbiology, the flagship journal of @microbiologysociety.org
Deadline for applications is 16 Feb 2026
microbiologysociety.org/who-we-are/j...
Deadline for applications is 16 Feb 2026
microbiologysociety.org/who-we-are/j...
Jobs
View the current job vacancies at the Microbiology Society.
microbiologysociety.org
January 28, 2026 at 8:44 AM
We are looking for new editors for Microbiology, the flagship journal of @microbiologysociety.org
Deadline for applications is 16 Feb 2026
microbiologysociety.org/who-we-are/j...
Deadline for applications is 16 Feb 2026
microbiologysociety.org/who-we-are/j...
For USA based folks. Senate vote on ICE funding will likely be this Thursday.
Just going to leave this here - when contacting them please do identify with your name, city and zip so they know they're getting contacted by their own constituents.
www.senate.gov/senators/sen...
Just going to leave this here - when contacting them please do identify with your name, city and zip so they know they're getting contacted by their own constituents.
www.senate.gov/senators/sen...
U.S. Senate: Contacting U.S. Senators
www.senate.gov
January 28, 2026 at 6:23 PM
For USA based folks. Senate vote on ICE funding will likely be this Thursday.
Just going to leave this here - when contacting them please do identify with your name, city and zip so they know they're getting contacted by their own constituents.
www.senate.gov/senators/sen...
Just going to leave this here - when contacting them please do identify with your name, city and zip so they know they're getting contacted by their own constituents.
www.senate.gov/senators/sen...
Reposted by naturepoker
The internet's memory isn’t a cloud—it’s heat, power, and hard drives 🔥💾
Inside the Internet Archive’s trillion-page fight against digital forgetting, from PetaBox servers to legal battles over memory itself ⚙️📚
➡️ hackernoon.com/the-long-now...
#InternetArchive #DigitalPreservation #WebHistory
Inside the Internet Archive’s trillion-page fight against digital forgetting, from PetaBox servers to legal battles over memory itself ⚙️📚
➡️ hackernoon.com/the-long-now...
#InternetArchive #DigitalPreservation #WebHistory
January 28, 2026 at 12:00 AM
The internet's memory isn’t a cloud—it’s heat, power, and hard drives 🔥💾
Inside the Internet Archive’s trillion-page fight against digital forgetting, from PetaBox servers to legal battles over memory itself ⚙️📚
➡️ hackernoon.com/the-long-now...
#InternetArchive #DigitalPreservation #WebHistory
Inside the Internet Archive’s trillion-page fight against digital forgetting, from PetaBox servers to legal battles over memory itself ⚙️📚
➡️ hackernoon.com/the-long-now...
#InternetArchive #DigitalPreservation #WebHistory
Really regretting not picking up more apples during my last grocery. They were the best combination of sweet and apple-sour.
January 27, 2026 at 8:38 PM
Really regretting not picking up more apples during my last grocery. They were the best combination of sweet and apple-sour.
Very cool! 🦠🧫
New paper out in @pnas.org, and it made the cover! 👁️
We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.
‼️Check Paula’s 🧵 and the paper👇
𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...
We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.
‼️Check Paula’s 🧵 and the paper👇
𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...
January 27, 2026 at 8:37 PM
Very cool! 🦠🧫
Reposted by naturepoker
Congrats “RHAPSODY, REIMAGINED” by Andrea Hale 🎶 First Place winner of the Internet Archive’s 2026 Public Domain Film Remix Contest 🥇
A fabulously fun, rhythm-driven triumph of archival remix.
Full film ➡️ archive.org/details/rhap...
🧵 1/2
#PublicDomain #PublicDomainDay
A fabulously fun, rhythm-driven triumph of archival remix.
Full film ➡️ archive.org/details/rhap...
🧵 1/2
#PublicDomain #PublicDomainDay
January 27, 2026 at 8:36 PM
Congrats “RHAPSODY, REIMAGINED” by Andrea Hale 🎶 First Place winner of the Internet Archive’s 2026 Public Domain Film Remix Contest 🥇
A fabulously fun, rhythm-driven triumph of archival remix.
Full film ➡️ archive.org/details/rhap...
🧵 1/2
#PublicDomain #PublicDomainDay
A fabulously fun, rhythm-driven triumph of archival remix.
Full film ➡️ archive.org/details/rhap...
🧵 1/2
#PublicDomain #PublicDomainDay
Reposted by naturepoker
We just released #anvio v9, "eunice" 🎉
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
January 20, 2026 at 11:48 AM
We just released #anvio v9, "eunice" 🎉
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
Reposted by naturepoker
A new paper from the lab on virus-like particles called eCISs www.nature.com/articles/s41...
How bacteria evolved thousands of precision nanoinjectors?
Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
How bacteria evolved thousands of precision nanoinjectors?
Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
A comprehensive catalogue of receptor-binding domains in extracellular contractile injection systems - Nature Communications
Extracellular contractile injection systems (eCISs) are bacteriophage tail-derived toxin delivery complexes that are present in many prokaryotes. Here, the authors present an analysis of eCIS tail fib...
www.nature.com
January 26, 2026 at 1:26 PM
A new paper from the lab on virus-like particles called eCISs www.nature.com/articles/s41...
How bacteria evolved thousands of precision nanoinjectors?
Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
How bacteria evolved thousands of precision nanoinjectors?
Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
Article about that web browser Cursor wrote with LLM that made the rounds a while ago.
Apparently the thing barely compiles and would have cost several millions of dollars in frontier model tokens, so wasn't in any ballpark of cheap either.
www.theregister.com/2026/01/26/c...
Apparently the thing barely compiles and would have cost several millions of dollars in frontier model tokens, so wasn't in any ballpark of cheap either.
www.theregister.com/2026/01/26/c...
Cursor is better at marketing than coding
Opinion: Autonomous agents may generate millions of lines of code, but shipping software is another matter
www.theregister.com
January 26, 2026 at 7:26 PM
Article about that web browser Cursor wrote with LLM that made the rounds a while ago.
Apparently the thing barely compiles and would have cost several millions of dollars in frontier model tokens, so wasn't in any ballpark of cheap either.
www.theregister.com/2026/01/26/c...
Apparently the thing barely compiles and would have cost several millions of dollars in frontier model tokens, so wasn't in any ballpark of cheap either.
www.theregister.com/2026/01/26/c...
Curious thing about LLMs in particular, is that usually its solutions look more novel the less you know about the question at hand.
www.propublica.org/article/trum...
www.propublica.org/article/trum...
Government by AI? Trump Administration Plans to Write Regulations Using Artificial Intelligence
The Transportation Department, which oversees the safety of airplanes, cars and pipelines, plans to use Google Gemini to draft new regulations. “We don’t need the perfect rule,” said DOT’s top lawyer....
www.propublica.org
January 26, 2026 at 4:54 PM
Curious thing about LLMs in particular, is that usually its solutions look more novel the less you know about the question at hand.
www.propublica.org/article/trum...
www.propublica.org/article/trum...
Bioinformatics orphanage - repository of bioinformatics packages that are no longer maintained upstream but still have users, or is a dependency for other more frequently used packages.
I think this is a fun idea, and potentially an important one for the future...💻🧬
github.com/bioinformati...
I think this is a fun idea, and potentially an important one for the future...💻🧬
github.com/bioinformati...
Bioinformatics Orphanage
A place for bioinformatics software that has been abandoned - Bioinformatics Orphanage
github.com
January 26, 2026 at 4:41 PM
Bioinformatics orphanage - repository of bioinformatics packages that are no longer maintained upstream but still have users, or is a dependency for other more frequently used packages.
I think this is a fun idea, and potentially an important one for the future...💻🧬
github.com/bioinformati...
I think this is a fun idea, and potentially an important one for the future...💻🧬
github.com/bioinformati...
Done with morning shift - no more working outdoors until Wednesday!
Also picked up some bread and something called vegemite. Reminded me of marmite which I first encountered as a kid mistaking it for marmalade, and left me thinking that the world is indeed a big place.
Also picked up some bread and something called vegemite. Reminded me of marmite which I first encountered as a kid mistaking it for marmalade, and left me thinking that the world is indeed a big place.
January 26, 2026 at 3:41 PM
Done with morning shift - no more working outdoors until Wednesday!
Also picked up some bread and something called vegemite. Reminded me of marmite which I first encountered as a kid mistaking it for marmalade, and left me thinking that the world is indeed a big place.
Also picked up some bread and something called vegemite. Reminded me of marmite which I first encountered as a kid mistaking it for marmalade, and left me thinking that the world is indeed a big place.
Happiness is finding the perfect Philips bit for a very stubborn screw. If you're having issues with seized & stripping screws on a #Thinkpad P1 gen machines, the slightly larger looking bit at size 0 is the way to go. Also, new hardware donation at Binomica labs woot
January 25, 2026 at 10:51 PM
Happiness is finding the perfect Philips bit for a very stubborn screw. If you're having issues with seized & stripping screws on a #Thinkpad P1 gen machines, the slightly larger looking bit at size 0 is the way to go. Also, new hardware donation at Binomica labs woot
Reposted by naturepoker
A relative of the sea elephant (Pterotracheoidea) is slowly gaining popularity in Japan🫧 ͛.*
It drifts through the ocean, but despite its jellyfish like look, it’s actually a type of sea snail 🐚✨️
It drifts through the ocean, but despite its jellyfish like look, it’s actually a type of sea snail 🐚✨️
January 25, 2026 at 11:16 AM
A relative of the sea elephant (Pterotracheoidea) is slowly gaining popularity in Japan🫧 ͛.*
It drifts through the ocean, but despite its jellyfish like look, it’s actually a type of sea snail 🐚✨️
It drifts through the ocean, but despite its jellyfish like look, it’s actually a type of sea snail 🐚✨️
On to the final working shift of the day. Snow's starting a little earlier. Hoping we'll get some good amount this time, to be honest.
January 25, 2026 at 11:33 AM
On to the final working shift of the day. Snow's starting a little earlier. Hoping we'll get some good amount this time, to be honest.
Reposted by naturepoker
Interested in virome sequencing on @nanoporetech.com instruments? Check out our latest paper where we publish Twist-ONT, a modified protocol for the Twist Comprehensive Viral Research Panel (by @twistbioscience.com) so that it can be used with ONT.
www.sciencedirect.com/science/arti...
🧵1/7
🧪
www.sciencedirect.com/science/arti...
🧵1/7
🧪
Twist-ONT: Combining nanopore sequencing with the twist comprehensive viral research panel
The Twist Comprehensive Viral Research Panel (Twist CVRP) is a probe-based hybridization capture enrichment method for whole-genome sequencing, design…
www.sciencedirect.com
January 20, 2026 at 2:32 PM
Interested in virome sequencing on @nanoporetech.com instruments? Check out our latest paper where we publish Twist-ONT, a modified protocol for the Twist Comprehensive Viral Research Panel (by @twistbioscience.com) so that it can be used with ONT.
www.sciencedirect.com/science/arti...
🧵1/7
🧪
www.sciencedirect.com/science/arti...
🧵1/7
🧪