naturepoker
@binomicalabs.org
Binomica Labs independent researcher by day, warehouse worker by night
Small thoughtful science
#phylogenetics #archaea #evolution #bioinformatics
@naturepoker@genomic.social
http://naturepoker.wordpress.com
https://orcid.org/0000-0002-6977-5440
Small thoughtful science
#phylogenetics #archaea #evolution #bioinformatics
@naturepoker@genomic.social
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...
Hmm Vegemite with powdered cheddar and a cheap bologna slice is pretty good too.
February 14, 2026 at 10:52 AM
Hmm Vegemite with powdered cheddar and a cheap bologna slice is pretty good too.
Ohhh something to keep an eye out for. When they say it's the definitive biography of Darwin they really mean it.
Historian of science Janet Browne, author of the definitive biography of Charles Darwin (Voyaging, 1995; The Power of Place, 2002) will publish an abridged and updated one-volume version this June with @princetonupress.bsky.social: bit.ly/4mS7R0Q
#DarwinDay #HPS #histsci
#DarwinDay #HPS #histsci
February 12, 2026 at 10:06 PM
Ohhh something to keep an eye out for. When they say it's the definitive biography of Darwin they really mean it.
Reposted by naturepoker
Happy Darwin Day!
Obviously the emblem of this day should be his favorite organisms, barnacles! Darwin was one of the first to recognize they are crustaceans, and made many contributions to their anatomy and development
🧪 #evosky
Obviously the emblem of this day should be his favorite organisms, barnacles! Darwin was one of the first to recognize they are crustaceans, and made many contributions to their anatomy and development
🧪 #evosky
Oh no I'm almost failing #Crustmas on day 2! Did you know that barnacles are crustaceans? They hold on by their antennae, secrete cement and their plates, and feed using their legs!
🧪🦑
🧪🦑
February 12, 2024 at 12:47 PM
Happy Darwin Day!
Obviously the emblem of this day should be his favorite organisms, barnacles! Darwin was one of the first to recognize they are crustaceans, and made many contributions to their anatomy and development
🧪 #evosky
Obviously the emblem of this day should be his favorite organisms, barnacles! Darwin was one of the first to recognize they are crustaceans, and made many contributions to their anatomy and development
🧪 #evosky
Reposted by naturepoker
If you’d like to hear me chat about Emmy Noether, the #history of #physics, the #energy problem, and my book¹:
gateway.on24.com/wcc/eh/42775...
(Free registration required to see the video, sorry.)
[1] amzn.to/3Y1wfCG
gateway.on24.com/wcc/eh/42775...
(Free registration required to see the video, sorry.)
[1] amzn.to/3Y1wfCG
Einstein's Tutor with Dr. Lee Phillips
Einstein's Tutor with Dr. Lee Phillips
gateway.on24.com
February 12, 2026 at 9:57 PM
If you’d like to hear me chat about Emmy Noether, the #history of #physics, the #energy problem, and my book¹:
gateway.on24.com/wcc/eh/42775...
(Free registration required to see the video, sorry.)
[1] amzn.to/3Y1wfCG
gateway.on24.com/wcc/eh/42775...
(Free registration required to see the video, sorry.)
[1] amzn.to/3Y1wfCG
Some #julialang for fun. I took David Lynch's #PS2 ad, grayscaled it & wrote some simple functions to introduce bunch of dumb processing noises. Post-scaled down with ffmpeg in shell.
Never processed video stream programmatically before - this was completely painless.
#retrogaming #playstation
Never processed video stream programmatically before - this was completely painless.
#retrogaming #playstation
February 12, 2026 at 9:42 PM
Some #julialang for fun. I took David Lynch's #PS2 ad, grayscaled it & wrote some simple functions to introduce bunch of dumb processing noises. Post-scaled down with ffmpeg in shell.
Never processed video stream programmatically before - this was completely painless.
#retrogaming #playstation
Never processed video stream programmatically before - this was completely painless.
#retrogaming #playstation
Reposted by naturepoker
You did not get your #MSCA and you are upset, because you really wanted to work on somatic cell evolution on the way to malignancy with single cell data and 🧬machine learning 💻?
Then get in touch!
There are other ways to fund a postdoc ;-)
Then get in touch!
There are other ways to fund a postdoc ;-)
February 11, 2026 at 11:05 AM
You did not get your #MSCA and you are upset, because you really wanted to work on somatic cell evolution on the way to malignancy with single cell data and 🧬machine learning 💻?
Then get in touch!
There are other ways to fund a postdoc ;-)
Then get in touch!
There are other ways to fund a postdoc ;-)
Reposted by naturepoker
Apusomonad rhodopsins: A new family of ultraviolet to blue light–absorbing rhodopsin channels www.pnas.org/doi/full/10....
Apusomonad rhodopsins: A new family of ultraviolet to blue light–absorbing rhodopsin channels | PNAS
Apusomonads are sediment-dwelling bacterivorous protists that are sister to all Opisthokonta.
They have been found to show a negative phototactic r...
www.pnas.org
February 11, 2026 at 9:33 AM
Apusomonad rhodopsins: A new family of ultraviolet to blue light–absorbing rhodopsin channels www.pnas.org/doi/full/10....
Reposted by naturepoker
How small can you go?
“Convergent extreme reductive evolution in ancient planthopper symbioses”
#MicroSky
“Convergent extreme reductive evolution in ancient planthopper symbioses”
#MicroSky
Our new paper in @natcomms.nature.com is now online-early!
We describe independent evolution of bacterial genomes of only ~50–52 kb — the smallest known outside cellular organelles — revealing striking convergence toward minimal gene sets.
🔗 doi.org/10.1038/s414...
We describe independent evolution of bacterial genomes of only ~50–52 kb — the smallest known outside cellular organelles — revealing striking convergence toward minimal gene sets.
🔗 doi.org/10.1038/s414...
February 11, 2026 at 12:13 PM
How small can you go?
“Convergent extreme reductive evolution in ancient planthopper symbioses”
#MicroSky
“Convergent extreme reductive evolution in ancient planthopper symbioses”
#MicroSky
Fact. These 'studies' coming out all the time with contradictory claims is a perennial topic of discussion among warehouse and welder types I work with. And rare academic responses to the confusion can sound pretty evasive/arrogant on top of it.
One of the biggest contributors to scientific scepticism among laypeople, IME, is these idiotic nutritional epi studies that come out with conflicting results every year and are uncritically picked up by credulous journos looking for clickbait. Get in the 🗑️.
#episky #statsky
#episky #statsky
You know that coffee & dementia study that's going around?
It's hogwash.
For starters, it's not pre-registered (that I could find), which means it may have been the product of a fishing expedition looking for dementia associations.
But even if it's not ...
www.nytimes.com/2026/02/09/h...
It's hogwash.
For starters, it's not pre-registered (that I could find), which means it may have been the product of a fishing expedition looking for dementia associations.
But even if it's not ...
www.nytimes.com/2026/02/09/h...
February 11, 2026 at 1:07 PM
Fact. These 'studies' coming out all the time with contradictory claims is a perennial topic of discussion among warehouse and welder types I work with. And rare academic responses to the confusion can sound pretty evasive/arrogant on top of it.
Today's breakfast is canned kimchi and coke zero on frozen solid block of dunkin donuts coffee... And I have to say, this is pretty good O_O
February 11, 2026 at 8:15 AM
Today's breakfast is canned kimchi and coke zero on frozen solid block of dunkin donuts coffee... And I have to say, this is pretty good O_O
성균관 암흑 학생회 ㅋㅋ
February 11, 2026 at 8:14 AM
성균관 암흑 학생회 ㅋㅋ
Reposted by naturepoker
Now out & nicely formatted in @isme-microbes.bsky.social
A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.
A few highlights... 🧵 (1/n)
doi.org/10.1093/isme...
A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.
A few highlights... 🧵 (1/n)
doi.org/10.1093/isme...
Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny
Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring
doi.org
February 9, 2026 at 8:31 PM
Now out & nicely formatted in @isme-microbes.bsky.social
A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.
A few highlights... 🧵 (1/n)
doi.org/10.1093/isme...
A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.
A few highlights... 🧵 (1/n)
doi.org/10.1093/isme...
Reposted by naturepoker
We have a cover!
Click here for preordering the book: mitpress.mit.edu/978026204909...
Click here for preordering the book: mitpress.mit.edu/978026204909...
November 20, 2024 at 5:05 AM
We have a cover!
Click here for preordering the book: mitpress.mit.edu/978026204909...
Click here for preordering the book: mitpress.mit.edu/978026204909...
Reposted by naturepoker
The State Dept is reviewing the online presence of all applicants for F,M,J,H1B visas. I warn clients all the time about the risks of international travel. Visa processing today is a minefield & it's key to weigh risks before going. This is one example of what we are seeing.
Spoke with a PI whose postdoc is trapped abroad because of social media vetting. It appears the postdoc missed disclosing one account and it's unclear if they can come back… ever.
This is the country we live in now.
This is the country we live in now.
February 7, 2026 at 2:51 PM
The State Dept is reviewing the online presence of all applicants for F,M,J,H1B visas. I warn clients all the time about the risks of international travel. Visa processing today is a minefield & it's key to weigh risks before going. This is one example of what we are seeing.
Emergency pickup for new data arriving my lab. Novel protein folding data takes up quite a bit of space - especially if there's 800k of them!
February 7, 2026 at 5:06 PM
Emergency pickup for new data arriving my lab. Novel protein folding data takes up quite a bit of space - especially if there's 800k of them!
Man subway be priced like luxury eating these days. C'mon.
February 7, 2026 at 3:00 PM
Man subway be priced like luxury eating these days. C'mon.
Not too happy to get all these extreme cold warning messages when I have early morning shifts throughout the weekend and early week next week.
February 7, 2026 at 8:20 AM
Not too happy to get all these extreme cold warning messages when I have early morning shifts throughout the weekend and early week next week.
Reposted by naturepoker
Comparative genomics of Borrelia lusitaniae
Complete genome sequences of three isolates. Each has very few plasmids. A most unusual feature is that their important cp26 plasmids are partially degraded dimers, carrying multiple, distinct ospC genes.
academic.oup.com/g3journal/ad...
#MicroSky
Complete genome sequences of three isolates. Each has very few plasmids. A most unusual feature is that their important cp26 plasmids are partially degraded dimers, carrying multiple, distinct ospC genes.
academic.oup.com/g3journal/ad...
#MicroSky
Comparative genomics of Borrelia lusitaniae
Abstract. Human Lyme disease is a frequent tick-borne human disease that is caused by several species in the Borrelia burgdorferi sensu lato (BBSL) clade o
academic.oup.com
February 5, 2026 at 5:03 PM
Just heard about Chomsky and Epstein.
Man, I really think living in any sort of siloed/sheltered culture for most of one's life will rot your brain. It's not an if, just when.
Man, I really think living in any sort of siloed/sheltered culture for most of one's life will rot your brain. It's not an if, just when.
February 5, 2026 at 1:10 PM
Just heard about Chomsky and Epstein.
Man, I really think living in any sort of siloed/sheltered culture for most of one's life will rot your brain. It's not an if, just when.
Man, I really think living in any sort of siloed/sheltered culture for most of one's life will rot your brain. It's not an if, just when.
Catching up on some personal #prophage work. Couple of tooling changes worth noting.
1> Genomad is noticeably faster at bulk processing compared to other comparable pipelines. If you haven't already you should really try it out
2> Latest Phold gpu performance feels a LOT faster and lighter
💻🧬🧫🦠
1> Genomad is noticeably faster at bulk processing compared to other comparable pipelines. If you haven't already you should really try it out
2> Latest Phold gpu performance feels a LOT faster and lighter
💻🧬🧫🦠
February 4, 2026 at 11:28 PM
Catching up on some personal #prophage work. Couple of tooling changes worth noting.
1> Genomad is noticeably faster at bulk processing compared to other comparable pipelines. If you haven't already you should really try it out
2> Latest Phold gpu performance feels a LOT faster and lighter
💻🧬🧫🦠
1> Genomad is noticeably faster at bulk processing compared to other comparable pipelines. If you haven't already you should really try it out
2> Latest Phold gpu performance feels a LOT faster and lighter
💻🧬🧫🦠
Reposted by naturepoker
My weekly update on NIH funding.
This is for all projects.
The breakdown for competing and non-competing awards will follow.
1/4
This is for all projects.
The breakdown for competing and non-competing awards will follow.
1/4
February 4, 2026 at 3:35 PM
My weekly update on NIH funding.
This is for all projects.
The breakdown for competing and non-competing awards will follow.
1/4
This is for all projects.
The breakdown for competing and non-competing awards will follow.
1/4
Reposted by naturepoker
@juliacon.org will host a minisymposia on "Bringing Julia to the Computational Humanities and Social Sciences" by @alextantos.bsky.social, Julia Müller and Axel Bohmann.
Find out more at pretalx.com/juliacon-202... and submit your proposal to juliacon.org/2026/cfp
#julialang #digitalhumanities
Find out more at pretalx.com/juliacon-202... and submit your proposal to juliacon.org/2026/cfp
#julialang #digitalhumanities
January 29, 2026 at 2:51 PM
@juliacon.org will host a minisymposia on "Bringing Julia to the Computational Humanities and Social Sciences" by @alextantos.bsky.social, Julia Müller and Axel Bohmann.
Find out more at pretalx.com/juliacon-202... and submit your proposal to juliacon.org/2026/cfp
#julialang #digitalhumanities
Find out more at pretalx.com/juliacon-202... and submit your proposal to juliacon.org/2026/cfp
#julialang #digitalhumanities
That Dunkin coffee and sausage wrap really hit the spot. Tonight's shift was BRUTAL.
February 4, 2026 at 1:18 PM
That Dunkin coffee and sausage wrap really hit the spot. Tonight's shift was BRUTAL.
Reposted by naturepoker
Preprint alert!
arxiv.org/abs/2602.03525
TLDR:
ZOR filters are STATIC filters with false positives.
-Almost memory optimal: <1% overhead over the theoretical lower bound (!!!)
-Fast queries: ~100 ns
-Construction cannot fail
A thread:
arxiv.org/abs/2602.03525
TLDR:
ZOR filters are STATIC filters with false positives.
-Almost memory optimal: <1% overhead over the theoretical lower bound (!!!)
-Fast queries: ~100 ns
-Construction cannot fail
A thread:
ZOR filters: fast and smaller than fuse filters
Probabilistic membership filters support fast approximate membership queries with a controlled false-positive probability $\varepsilon$ and are widely used across storage, analytics, networking, and b...
arxiv.org
February 4, 2026 at 12:28 PM
Preprint alert!
arxiv.org/abs/2602.03525
TLDR:
ZOR filters are STATIC filters with false positives.
-Almost memory optimal: <1% overhead over the theoretical lower bound (!!!)
-Fast queries: ~100 ns
-Construction cannot fail
A thread:
arxiv.org/abs/2602.03525
TLDR:
ZOR filters are STATIC filters with false positives.
-Almost memory optimal: <1% overhead over the theoretical lower bound (!!!)
-Fast queries: ~100 ns
-Construction cannot fail
A thread: