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
· 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.
Perfect calm and silence before the snow weather in the city right now
December 23, 2025 at 9:51 AM
Perfect calm and silence before the snow weather in the city right now
Reposted by naturepoker
When we say "no, everything hasn't been digitized," I need you to understand that we really mean is that virtually nothing has been digitized. This is because the realm of primary sources that historians use is incomprehensibly large.
Seems like it's worth posting this one again.
Why Do Historians Still Have To Go To Archives?
Why do historians go to archives? Hasn’t everything already been digitized?
contingentmagazine.org
December 22, 2025 at 1:40 AM
When we say "no, everything hasn't been digitized," I need you to understand that we really mean is that virtually nothing has been digitized. This is because the realm of primary sources that historians use is incomprehensibly large.
Reposted by naturepoker
The final form of my 2nd postdoc paper with the Bassler Lab! Turns out our favorite quorum-sensing phage isn’t a one-off, but rather a member of a globally dispersed family of phages that sense a universal autoinducer.
#phagesky #microsky
journals.asm.org/doi/10.1128/...
#phagesky #microsky
journals.asm.org/doi/10.1128/...
A family of linear plasmid phages that detect a quorum-sensing autoinducer exists in multiple bacterial species | mBio
The discovery of quorum-sensing responsive linear plasmid phages has transformed understanding
of phage-bacterial interactions by demonstrating inter-domain chemical communication.
To date, however, e...
journals.asm.org
December 21, 2025 at 4:19 PM
The final form of my 2nd postdoc paper with the Bassler Lab! Turns out our favorite quorum-sensing phage isn’t a one-off, but rather a member of a globally dispersed family of phages that sense a universal autoinducer.
#phagesky #microsky
journals.asm.org/doi/10.1128/...
#phagesky #microsky
journals.asm.org/doi/10.1128/...
NGL, this gave me a chortle
May I recommend a subscription to @theonion.com print edition as a holiday gift, because their ads continue to rule
December 22, 2025 at 3:23 AM
NGL, this gave me a chortle
Reposted by naturepoker
Closing out my year with a journal editor shocker 🧵
Checking new manuscripts today I reviewed a paper attributing 2 papers to me I did not write. A daft thing for an author to do of course. But intrigued I web searched up one of the titles and that's when it got real weird...
Checking new manuscripts today I reviewed a paper attributing 2 papers to me I did not write. A daft thing for an author to do of course. But intrigued I web searched up one of the titles and that's when it got real weird...
December 19, 2025 at 5:20 PM
Closing out my year with a journal editor shocker 🧵
Checking new manuscripts today I reviewed a paper attributing 2 papers to me I did not write. A daft thing for an author to do of course. But intrigued I web searched up one of the titles and that's when it got real weird...
Checking new manuscripts today I reviewed a paper attributing 2 papers to me I did not write. A daft thing for an author to do of course. But intrigued I web searched up one of the titles and that's when it got real weird...
"Fake citations have turned into a nightmare for research librarians, who by some estimates are wasting up to 15 percent of their work hours responding to requests for nonexistent records that ChatGPT or Google Gemini alluded to."
www.rollingstone.com/culture/cult...
www.rollingstone.com/culture/cult...
AI Is Inventing Academic Papers That Don't Exist -- And They're Being Cited in Real Journals
Academic articles from authors using large language model are creating an ecosystem of fake research that threatens human knowledge itself.
www.rollingstone.com
December 20, 2025 at 3:35 PM
"Fake citations have turned into a nightmare for research librarians, who by some estimates are wasting up to 15 percent of their work hours responding to requests for nonexistent records that ChatGPT or Google Gemini alluded to."
www.rollingstone.com/culture/cult...
www.rollingstone.com/culture/cult...
Fortran is still going strong, I see.
Just published in JOSS: 'FSML – A Modern Fortran Statistics and Machine Learning Library' https://doi.org/10.21105/joss.09058
December 20, 2025 at 3:30 PM
Fortran is still going strong, I see.
Reposted by naturepoker
"..based on a common wavefront design that can be adapted to support a variety of dynamic programming algorithms: local, global, and semi-global alignment of genomic and protein sequences with a variety of commonly used scoring schemes" from
@martinsteinegger.bsky.social andco
@martinsteinegger.bsky.social andco
Accelign: a GPU-based Library for Accelerating Pairwise Sequence Alignment https://www.biorxiv.org/content/10.64898/2025.12.17.694868v1
December 20, 2025 at 11:05 AM
"..based on a common wavefront design that can be adapted to support a variety of dynamic programming algorithms: local, global, and semi-global alignment of genomic and protein sequences with a variety of commonly used scoring schemes" from
@martinsteinegger.bsky.social andco
@martinsteinegger.bsky.social andco
Reposted by naturepoker
Jules Verne and Marcel Proust have long since left the building, but Le Zimmer is still open at Place du Châtelet, No. 1, on the border between the 1st and 4th Arrondissements.
Your table is waiting.
Your table is waiting.
This historic 100-year-old Parisian brasserie, frequented by Jules Verne and Marcel Proust, is still open… and its history is incredible!
Discover this magnificent century-old historic brasserie in Paris: the Zimmer. A mythical place where gastronomy and Art Nouveau intermingle.
parissecret.com
December 19, 2025 at 8:18 PM
Jules Verne and Marcel Proust have long since left the building, but Le Zimmer is still open at Place du Châtelet, No. 1, on the border between the 1st and 4th Arrondissements.
Your table is waiting.
Your table is waiting.
Got out of back to back night shift-morning side job. One benefit of the netherworld style scheduling is I can down a can of beer and pizza rolls at 10:30 in the morning and still be a considered a normal, functioning member of the society.
December 20, 2025 at 3:26 PM
Got out of back to back night shift-morning side job. One benefit of the netherworld style scheduling is I can down a can of beer and pizza rolls at 10:30 in the morning and still be a considered a normal, functioning member of the society.
Screening multiple databases for a side project - globdb.org stands out as particularly impressive in both coverage and quality control.
When they say they deduplicated the data, they really mean it - here's how a quick sourmash-UPGMA cluster stacks up, all the way to about 140k samples
When they say they deduplicated the data, they really mean it - here's how a quick sourmash-UPGMA cluster stacks up, all the way to about 140k samples
December 20, 2025 at 2:55 AM
Screening multiple databases for a side project - globdb.org stands out as particularly impressive in both coverage and quality control.
When they say they deduplicated the data, they really mean it - here's how a quick sourmash-UPGMA cluster stacks up, all the way to about 140k samples
When they say they deduplicated the data, they really mean it - here's how a quick sourmash-UPGMA cluster stacks up, all the way to about 140k samples
Reposted by naturepoker
rapidgzip can! github.com/mxmlnkn/rapi...
GitHub - mxmlnkn/rapidgzip: Gzip Decompression and Random Access for Modern Multi-Core Machines
Gzip Decompression and Random Access for Modern Multi-Core Machines - mxmlnkn/rapidgzip
github.com
December 19, 2025 at 6:46 PM
rapidgzip can! github.com/mxmlnkn/rapi...
Oh, pigz can't decompress in parallel - makes sense when I think about it. Bummer.
December 19, 2025 at 6:44 PM
Oh, pigz can't decompress in parallel - makes sense when I think about it. Bummer.
You know what, I think I earned some ice cream today.
December 18, 2025 at 11:55 PM
You know what, I think I earned some ice cream today.
Reposted by naturepoker
if tumblr dies I need this video to make it's seasonal rotation here instead just in case, Happy holidays 🎄
December 18, 2025 at 2:05 AM
if tumblr dies I need this video to make it's seasonal rotation here instead just in case, Happy holidays 🎄
Going through Archaeal data on NCBI and other curated sources. Wow, some of the assemblies out there are really bad, even non-MAGs. I have mixed feelings about labs uploading assemblies without QC...
December 18, 2025 at 11:49 PM
Going through Archaeal data on NCBI and other curated sources. Wow, some of the assemblies out there are really bad, even non-MAGs. I have mixed feelings about labs uploading assemblies without QC...
Reposted by naturepoker
So question for single-cell peeps. It seems that ParseBio is even more locked-down than 10x! Is it the case that if I'm not a "registered" ParseBio customer, I can't even access their splitpipe software? Is there any archived version of splitpipe available?
December 17, 2025 at 6:46 PM
So question for single-cell peeps. It seems that ParseBio is even more locked-down than 10x! Is it the case that if I'm not a "registered" ParseBio customer, I can't even access their splitpipe software? Is there any archived version of splitpipe available?
Reposted by naturepoker
find it remarkable that folks upload the unpublished, confidential work of others to those sites.
December 16, 2025 at 3:46 PM
find it remarkable that folks upload the unpublished, confidential work of others to those sites.
Reposted by naturepoker
Announcing bamdam: a new open source tool for studying ancient DNA 🧬 It shrinks massive metagenomic files by 10x and helps distinguish ancient sequences from contamination. Tested on the oldest DNA yet uncovered (2M years) link.springer.com/article/10.1... @bdesan.bsky.social @russcd.bsky.social
Bamdam: a post-mapping authentication toolkit for ancient metagenomics - Genome Biology
Ancient metagenomic studies using capture or shotgun sequencing often perform pairwise alignment of individual reads against large reference databases followed by lowest common ancestor assignment for...
link.springer.com
December 16, 2025 at 9:04 PM
Announcing bamdam: a new open source tool for studying ancient DNA 🧬 It shrinks massive metagenomic files by 10x and helps distinguish ancient sequences from contamination. Tested on the oldest DNA yet uncovered (2M years) link.springer.com/article/10.1... @bdesan.bsky.social @russcd.bsky.social
Sweet - confirmed heading to DC for the summer ASM 2026 with more independent research goodness.
December 16, 2025 at 5:14 PM
Sweet - confirmed heading to DC for the summer ASM 2026 with more independent research goodness.
Reposted by naturepoker
DOE's Office of Science is making a big push into AI, and that includes our work at the @jgi.doe.gov . We want to hear your thoughts (+ and -) on AI-enabled biological data. Consider joining one of our interviews or focus groups by filling out this form!
🧪🧬🦠🖥️ #secmet
jointgeno.me/PortalStorie...
🧪🧬🦠🖥️ #secmet
jointgeno.me/PortalStorie...
Tell Us Your JGI Portal Stories
The JGI Portal teams (IMG, Mycocosm, Phycocosm, Phytozome, and SMC) would love to sit with you (over Zoom) to hear your stories relating to your usage of the portals, your unsupported use cases, and p...
jointgeno.me
December 15, 2025 at 5:16 PM
DOE's Office of Science is making a big push into AI, and that includes our work at the @jgi.doe.gov . We want to hear your thoughts (+ and -) on AI-enabled biological data. Consider joining one of our interviews or focus groups by filling out this form!
🧪🧬🦠🖥️ #secmet
jointgeno.me/PortalStorie...
🧪🧬🦠🖥️ #secmet
jointgeno.me/PortalStorie...
Reposted by naturepoker
🫤
December 15, 2025 at 8:21 PM
🫤
Reposted by naturepoker
Preprint Alert!
With @tmthrz.bsky.social and @rayanchikhi.bsky.social we aim to tackle practical unitigs compression!
A thread:
With @tmthrz.bsky.social and @rayanchikhi.bsky.social we aim to tackle practical unitigs compression!
A thread:
Inverted colored de Bruijn Graph for practical kmer sets storage https://www.biorxiv.org/content/10.64898/2025.12.08.692073v1
December 15, 2025 at 3:19 PM
Preprint Alert!
With @tmthrz.bsky.social and @rayanchikhi.bsky.social we aim to tackle practical unitigs compression!
A thread:
With @tmthrz.bsky.social and @rayanchikhi.bsky.social we aim to tackle practical unitigs compression!
A thread:
Reposted by naturepoker
This is rad. 🧪
Take a journey through time down a new NSF COLDEX ice core borehole just completed by the team in #Antarctica!
If you’re at #AGU25 stop by the COLDEX booth in the Exhibit Hall to talk to COLDEX team members from across the 15-institution center funded by NSF! @agu.org Follow us on IG @ coldex_stc
If you’re at #AGU25 stop by the COLDEX booth in the Exhibit Hall to talk to COLDEX team members from across the 15-institution center funded by NSF! @agu.org Follow us on IG @ coldex_stc
December 15, 2025 at 2:37 AM
This is rad. 🧪
