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
· Oct 21
Now that we have pinned posts:
I'm a self-taught biologist in #NYC studying the microbial tree of life with lots of long-read sequencing focus.
Most of my study is self-funded from warehouse and other odd jobs - I'm hoping to document paths to a working class, independent researcher for others.
I'm a self-taught biologist in #NYC studying the microbial tree of life with lots of long-read sequencing focus.
Most of my study is self-funded from warehouse and other odd jobs - I'm hoping to document paths to a working class, independent researcher for others.
I was going to write something about end of a long hard day, and realized its only 5pm and I have another half shift ahead🫠
November 29, 2025 at 10:17 PM
I was going to write something about end of a long hard day, and realized its only 5pm and I have another half shift ahead🫠
🦠🧫
Ribosome -less zombies in the ocean 🦠🧟
Globally occurring pelagiphage infections create ribosome-deprived cells - Nature Communications
SAR11 bacteria and their phages are abundant in the oceans. Here the authors quantify the number of phage-infected SAR11 cells using microscopy techniques and discover phage-infected cells without any...
www.nature.com
November 29, 2025 at 5:10 PM
🦠🧫
Reposted by naturepoker
If you missed my talk but still want some tips for writing good code for scientists, my slides are here:
daxkellie.quarto.pub/a-guide-to-w...
All the links and references are there too in case you want to see more! 😀🧪🌏
#ESA2025 #rstats #quartopub
daxkellie.quarto.pub/a-guide-to-w...
All the links and references are there too in case you want to see more! 😀🧪🌏
#ESA2025 #rstats #quartopub
November 26, 2025 at 6:12 AM
If you missed my talk but still want some tips for writing good code for scientists, my slides are here:
daxkellie.quarto.pub/a-guide-to-w...
All the links and references are there too in case you want to see more! 😀🧪🌏
#ESA2025 #rstats #quartopub
daxkellie.quarto.pub/a-guide-to-w...
All the links and references are there too in case you want to see more! 😀🧪🌏
#ESA2025 #rstats #quartopub
Reposted by naturepoker
Yippee! All five of my F2 #ResistanceProject ladies are now laying! I still need to perform #RrstrictionMapping to see who is homozygous or heterozygous for these sweet sweet immunity markers. #EgyptianFayoumi #BielefelderKennhuhn #Chickens #ChickensOfBSky
November 27, 2025 at 11:49 PM
Yippee! All five of my F2 #ResistanceProject ladies are now laying! I still need to perform #RrstrictionMapping to see who is homozygous or heterozygous for these sweet sweet immunity markers. #EgyptianFayoumi #BielefelderKennhuhn #Chickens #ChickensOfBSky
I try to bring a cheap film camera when I'm out for work, and occasionally they produce some interesting shots. Here's an early morning shot in #nyc taken with a plastic cam from 1970's. Negative developed with #caffenol and scanned with my phone.
#filmphotography
#filmphotography
November 27, 2025 at 11:12 PM
I try to bring a cheap film camera when I'm out for work, and occasionally they produce some interesting shots. Here's an early morning shot in #nyc taken with a plastic cam from 1970's. Negative developed with #caffenol and scanned with my phone.
#filmphotography
#filmphotography
It's sad and depressing that there's an incentive to spam preprint servers with nonsense like this, causing real damage.
In light of record submission rates and a large volume of AI-generated slop, SocArXiv recently implemented a policy requiring ORCIDs linked in the OSF profile of submitting authors, and narrowing our focus to social science subjects. Today we are taking two more steps:
/1
/1
November 27, 2025 at 7:51 PM
It's sad and depressing that there's an incentive to spam preprint servers with nonsense like this, causing real damage.
Exciting talk on sequencing the world by Mark Blaxter at @linneansociety.bsky.social today, I think the talk will be uploaded to youtube at some point. Lots of focus on Hi-C and genome organization
If you want to take a look at his presentation, it's available on tinyurl.com/ToL-LinnSoc2...
If you want to take a look at his presentation, it's available on tinyurl.com/ToL-LinnSoc2...
_ToL ToL_all_hands_Sept2025
September 2025
tinyurl.com
November 27, 2025 at 7:04 PM
Exciting talk on sequencing the world by Mark Blaxter at @linneansociety.bsky.social today, I think the talk will be uploaded to youtube at some point. Lots of focus on Hi-C and genome organization
If you want to take a look at his presentation, it's available on tinyurl.com/ToL-LinnSoc2...
If you want to take a look at his presentation, it's available on tinyurl.com/ToL-LinnSoc2...
Reposted by naturepoker
Sweet Potato Dish Stopped Being Healthy 5 Ingredients Ago
November 27, 2025 at 7:00 PM
Sweet Potato Dish Stopped Being Healthy 5 Ingredients Ago
Not buying unnecessary crap is a society killing hoarding behavior now?
If a phone still works fine, it’s not “device hoarding” to keep using it. It’s common sense.
November 27, 2025 at 7:00 PM
Not buying unnecessary crap is a society killing hoarding behavior now?
Most butterflies and moths have 31 chromosomes, but there's one with 229 chromosomes O_o
This level of variation is possible among macro scale organisms, physically indistinguishable from the rest of the taxon? The more I learn about the world...
This level of variation is possible among macro scale organisms, physically indistinguishable from the rest of the taxon? The more I learn about the world...
November 27, 2025 at 6:59 PM
Most butterflies and moths have 31 chromosomes, but there's one with 229 chromosomes O_o
This level of variation is possible among macro scale organisms, physically indistinguishable from the rest of the taxon? The more I learn about the world...
This level of variation is possible among macro scale organisms, physically indistinguishable from the rest of the taxon? The more I learn about the world...
Listening in on today's Linnean Society genomics talk. Parasites are 1/3 of known species, who knew? And apparently we're describing 2000 new species per year, while 150 go extinct per year.
November 27, 2025 at 6:22 PM
Listening in on today's Linnean Society genomics talk. Parasites are 1/3 of known species, who knew? And apparently we're describing 2000 new species per year, while 150 go extinct per year.
Reposted by naturepoker
#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software
✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨🔬 Built by a researcher — for researchers!
👉 Check it out at opencloning.org
✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨🔬 Built by a researcher — for researchers!
👉 Check it out at opencloning.org
November 24, 2025 at 4:57 PM
#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software
✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨🔬 Built by a researcher — for researchers!
👉 Check it out at opencloning.org
✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨🔬 Built by a researcher — for researchers!
👉 Check it out at opencloning.org
Oh boy. MDPI publication invitation mails are getting a bit desperate...
The more I learn about the landscape of these things though, the more I feel people should be publishing in nonprofit society journals.
The more I learn about the landscape of these things though, the more I feel people should be publishing in nonprofit society journals.
November 26, 2025 at 6:53 PM
Oh boy. MDPI publication invitation mails are getting a bit desperate...
The more I learn about the landscape of these things though, the more I feel people should be publishing in nonprofit society journals.
The more I learn about the landscape of these things though, the more I feel people should be publishing in nonprofit society journals.
I for one welcome the new laptop-benchmarked search tools. Stuff like this enables previously difficult or impossible study under independent research contexts. For example, my warehouse lab's grid's so terrible running all threads on the main workstation trips the circuit breaker.
🧬💻
🧬💻
This is AMAZING! And it's so fantastic to see Fulgor helping out in these large-scale search tasks cc @jermp.bsky.social @ale-campa.bsky.social !
Optimized k-mer search across millions of bacterial genomes on laptops https://www.biorxiv.org/content/10.1101/2025.11.23.690050v1
November 26, 2025 at 6:07 PM
I for one welcome the new laptop-benchmarked search tools. Stuff like this enables previously difficult or impossible study under independent research contexts. For example, my warehouse lab's grid's so terrible running all threads on the main workstation trips the circuit breaker.
🧬💻
🧬💻
Reposted by naturepoker
Family cookbooks, filled with handwritten notes, sometimes held together with rubber bands, tell the story of generations of homemakers. They are irreplaceable treasures.
🦃 Celebrate the cultural & family histories on their worn & stained pages ➡️ blog.archive.org/2024/09/30/v...
#Thanksgiving
🦃 Celebrate the cultural & family histories on their worn & stained pages ➡️ blog.archive.org/2024/09/30/v...
#Thanksgiving
November 26, 2025 at 6:02 PM
Family cookbooks, filled with handwritten notes, sometimes held together with rubber bands, tell the story of generations of homemakers. They are irreplaceable treasures.
🦃 Celebrate the cultural & family histories on their worn & stained pages ➡️ blog.archive.org/2024/09/30/v...
#Thanksgiving
🦃 Celebrate the cultural & family histories on their worn & stained pages ➡️ blog.archive.org/2024/09/30/v...
#Thanksgiving
I didn't know @[email protected] preprint server was a thing - operated by OSF for preprinting works submitted in BioHackathons.
Always happy to check out new #preprint servers - I feel like that's where the most exciting ideas are found these days.
#bioinformatics
biohackrxiv.org
Always happy to check out new #preprint servers - I feel like that's where the most exciting ideas are found these days.
#bioinformatics
biohackrxiv.org
OSF
biohackrxiv.org
November 26, 2025 at 6:03 PM
I didn't know @[email protected] preprint server was a thing - operated by OSF for preprinting works submitted in BioHackathons.
Always happy to check out new #preprint servers - I feel like that's where the most exciting ideas are found these days.
#bioinformatics
biohackrxiv.org
Always happy to check out new #preprint servers - I feel like that's where the most exciting ideas are found these days.
#bioinformatics
biohackrxiv.org
Reposted by naturepoker
Darwin had earlier made detailed observations of the emotional displays of his “little animalcule of a son,” William Erasmus, which he used in Expression.
D’s wife Emma worried that if she were “out of temper,” he would just be “forming theories about me.”
🧪🌱🐋 #HistSTM #Evobio #Psychsky
D’s wife Emma worried that if she were “out of temper,” he would just be “forming theories about me.”
🧪🌱🐋 #HistSTM #Evobio #Psychsky
November 26, 2025 at 4:54 PM
Reposted by naturepoker
Work from my amazing undergrad @leyan-wang.bsky.social is just preprinted! TL;DR: If you worry that ARG methods might fail on unphased data due to phasing errors, you may not need to.
Check it out & consider reposting to support a great young scientist!
Check it out & consider reposting to support a great young scientist!
We are excited to share our recent work on the surprising robustness of Ancestral Recombination Graph (ARG) inference tools to computational phasing errors, now available on BioRxiv: biorxiv.org/content/10.1....
This work is co-advised by @yundeng.bsky.social and Rasmus Nielsen.
1/7
This work is co-advised by @yundeng.bsky.social and Rasmus Nielsen.
1/7
Robustness of Ancestral Recombination Graph Inference Tools to Phasing Errors
Ancestral Recombination Graphs (ARGs) are fundamental population genetic structures that encode the genealogical history of a sample of haplotypes along the genome. They have recently received substan...
biorxiv.org
November 26, 2025 at 5:12 PM
Work from my amazing undergrad @leyan-wang.bsky.social is just preprinted! TL;DR: If you worry that ARG methods might fail on unphased data due to phasing errors, you may not need to.
Check it out & consider reposting to support a great young scientist!
Check it out & consider reposting to support a great young scientist!
Reposted by naturepoker
Less than two weeks left to submit your nominations for the Dobzhansky Prize! This award recognizes the accomplishments and future promise of an outstanding early-career evolutionary biologist. Submit your nomination by Dec. 1! shorturl.at/p70wY
November 18, 2025 at 10:16 PM
Less than two weeks left to submit your nominations for the Dobzhansky Prize! This award recognizes the accomplishments and future promise of an outstanding early-career evolutionary biologist. Submit your nomination by Dec. 1! shorturl.at/p70wY
Holy cow DDR5 ram prices shot up from $82 to $310/$190 to $700 in a three month period. GPU's are holding steady, but that's steady on a relative price peak too. Not a great time to put a lab rig together.
arstechnica.com/gadgets/2025...
arstechnica.com/gadgets/2025...
GPU prices are coming to earth just as RAM costs shoot into the stratosphere
Some RAM kits are over three times as expensive as they were three months ago.
arstechnica.com
November 26, 2025 at 3:38 PM
Holy cow DDR5 ram prices shot up from $82 to $310/$190 to $700 in a three month period. GPU's are holding steady, but that's steady on a relative price peak too. Not a great time to put a lab rig together.
arstechnica.com/gadgets/2025...
arstechnica.com/gadgets/2025...
Reposted by naturepoker
I like the term "intercellular biodiversity" (much more than the old trope of "parasitism") #MicroSky
According to the microbial ecologist Puri López-García, pictured here at a salt flat in the Chilean Andes, some 25% to 50% of all bacterial cells may be parasites of other cells.
A Cell So Minimal That It Challenges Definitions of Life | Quanta Magazine
The newly described microbe represents a world of parasitic, intercellular biodiversity only beginning to be revealed by genome sequencing.
www.quantamagazine.org
November 26, 2025 at 9:40 AM
I like the term "intercellular biodiversity" (much more than the old trope of "parasitism") #MicroSky
Reposted by naturepoker
WE ARE RECRUITING PHD STUDENTS!!!
We have three(!) funded PhD studentships advertising presently. If any of these are of interest, please reach out! Thread below with links to more information on each project.
#Drosophila #Evolution #Immunity #SelfishGene #Aphids
Thread with links below 🧵 1/4
We have three(!) funded PhD studentships advertising presently. If any of these are of interest, please reach out! Thread below with links to more information on each project.
#Drosophila #Evolution #Immunity #SelfishGene #Aphids
Thread with links below 🧵 1/4
November 15, 2025 at 3:35 PM
WE ARE RECRUITING PHD STUDENTS!!!
We have three(!) funded PhD studentships advertising presently. If any of these are of interest, please reach out! Thread below with links to more information on each project.
#Drosophila #Evolution #Immunity #SelfishGene #Aphids
Thread with links below 🧵 1/4
We have three(!) funded PhD studentships advertising presently. If any of these are of interest, please reach out! Thread below with links to more information on each project.
#Drosophila #Evolution #Immunity #SelfishGene #Aphids
Thread with links below 🧵 1/4
There's so much work to do but I just spent 15 minutes watching a video someone petting a fat chihuahua.
November 26, 2025 at 12:14 PM
There's so much work to do but I just spent 15 minutes watching a video someone petting a fat chihuahua.
I'm reviving an old tradition I had donating blood and volunteering for a couple of days every holiday season. Went in for the donation today, and holy cow they REALLY wanted that blood. I'm feeling a bit dizzy now.
November 25, 2025 at 5:27 PM
I'm reviving an old tradition I had donating blood and volunteering for a couple of days every holiday season. Went in for the donation today, and holy cow they REALLY wanted that blood. I'm feeling a bit dizzy now.
Reposted by naturepoker
I also also have a standalone article, here: https://sciencedirect.com/science/article/abs/pii/S0160932718300528
Full disclosure: analysis to a certain extent changed by the time of the dissertation.
🌱🐋🧪 #histSTM #evobio 🐡
Full disclosure: analysis to a certain extent changed by the time of the dissertation.
🌱🐋🧪 #histSTM #evobio 🐡
November 24, 2025 at 4:58 PM
I also also have a standalone article, here: https://sciencedirect.com/science/article/abs/pii/S0160932718300528
Full disclosure: analysis to a certain extent changed by the time of the dissertation.
🌱🐋🧪 #histSTM #evobio 🐡
Full disclosure: analysis to a certain extent changed by the time of the dissertation.
🌱🐋🧪 #histSTM #evobio 🐡