Profile avatar
binomicalabs.org
Binomica Labs independent researcher by day, warehouse worker by night Small thoughtful science #phylogenetics #archaea #sequencing #bioinformatics @[email protected] http://naturepoker.wordpress.com https://orcid.org/0000-0002-6977-5440
1,414 posts 2,823 followers 1,623 following
Prolific Poster

Useful #101s from the @ebpgenome.bsky.social for those involved in biodiverse reference genome creation Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation doi.org/10.1093/giga...

🧬🖥️ oarfish v0.9.0 is out! The big improvement in this version is future-oriented. v0.9.0 allows the user to pass in transcript sequences via the `--annotated` option, the `--novel` option, or both. The provenance will be separately tracked to that later 1/4

This is an interesting initiative. I wonder if independent researchers can contribute too. 🦠🧫 www.nature.com/articles/s41...

A short video with a Mesquite tip showing how to display chronograms from a BEAST divergence dating analysis. youtu.be/CvxX8GauqLo 🧪 #evolbio @waynemaddison.bsky.social

A parting gift to stay connected ❤️ 🧪 Starter Packs for #zebrafish Community: ZF Resources: go.bsky.app/JcC5df3 #WomenInScience V1: go.bsky.app/4BegEjv #WomenInScience V2: go.bsky.app/VoebYrt ZF PIs V1: go.bsky.app/2cHYybY ZF PIs V2: go.bsky.app/4zBuxAF ZF PIs V3: go.bsky.app/JvjuSZg

#MicroSky

Unexpected side effect of learning #julialang is I've gotten weirdly good at R 🤔 No such carry over effect to #python for me, strangely enough.

You say this is an onion article - I lived through school staff telling kids this in MS 141 in Bronx, back in early 2000's.

Holy cow humidity out in the city right now is brutal. All through the late night shift I was simultaneously drowning in humid air and staggering from not drinking enough water.

🚨Call for papers on Non-traditional model organisms for #BMCBiology🚨 Guest Editors: Eve Gazave @stemdevevo.bsky.social, @ijmonod.bsky.social Vladimír Hampl, @sciencecharles.bsky.social Jason Podrabsky, Portland State U Deanne Whitworth, U of Queensland www.biomedcentral.com/collections/...

A really useful resource

🚨 Our GW paper is out in Nature Methods!🥲 GW is a fast genomics browser (up to 100x faster!) github.com/kcleal/gw Also, just released a Python interface for GW github.com/kcleal/gwplot 📝 nature.com/articles/s4159… #Genomics #Bioinformatics

Oof. You can't even log in to USCIS site with #firefox anymore. Having a chrome installation in the background is increasingly becoming necessary to get work done. It's going back to IE era all over again :(

Happy #WorldMicrobiomeDay! 🦠 If you are a starter in this field, as I was until recently, here are some highly recommended articles from @natmicrobiol.nature.com that may help you understand, plan, and even improve your microbiome studies - A starter pack you might say! 😊🧵 #MicrobiomeSky #MicroSky

Preprint🚨 #microsky 🦠 “Cultivation of Methanonezhaarchaeia, the third class of methanogens within the phylum Thermoproteota”, authored by @kohtzarchaeota.bsky.social & Sylvia Nupp, expands the diversity of methanogens! 90% enriched, methylotrophic culture from a hot spring. A 🧵 tinyurl.com/yw8ku2bj

The Society has supported the microbiology community for 80 years. Now we invite you to get involved by submitting your research, helping to shape the future of science and innovation. Publish with us - microb.io/Publishing-f...

Jeez. The heatwave in NYC is brutal. It's actually a bit hard to breathe in the lab 🫠

Ethical scientific journals and where to find them....here is DAFNEE, a #database of non-profit journals in #Ecology and #Evolution #EvoBio, to choose an ethical place where to publish your next articles! (1/2) dafnee.isem-evolution.fr 🧪 #science

I gotta tell ya folks, I felt like such a city bumpkin taking all those photos of wide open fields in Kansas while oohing and ahhing.

#OpenScience lobbyists, skeptics and everything in between: consider coming to Munich in May 2026 (gorgeous time to visit..) to discuss the future of Open Research! FOR2026 is open for submissions: opensciencestudies.eu/for-2026-con... pls help spread the word 🙏 #philsci #sts #methods #policy 🧪

The ASM journey took me from NY to Chicago to LA overland, trailing tornadoes, downed power lines and ending with a burning engine at the entrance to the Mojave desert, where we hitched a ride on a bus and vaulted some fences to catch the last tram out of Union station. Took some good photos though!

You have no idea how happy I was to find this at some random bodega in Queens. It's like watching civilization progress one step at a time.

Whoa Mamdani actually won the #NYC primary. I never thought I'd live to see the day the machine politics in NYC loses out. Very excited

plz read will's entire bluetorial 🧵 and enjoy the time lapse images. next, snowflake yeast will move to NASA's JPL... #MicroSky #FungiFriends 🧪

Good to see the airport staff has a sense of humor

A process server delivered a letter regarding my "hostile" and "defamatory" attacks on #ColossalBio co-founder Ben Lamm, insinuating I'm a misogynist and a failed scientist. Nothing I've said is defamation, but you can read it a judge for yourself. I've redacted my home address 1/n

For ANME enthusiasts & for those who wonder how a methanogen turns into a methanotroph 👇New work by Orphanlab Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea www.science.org/doi/10.1126/... @caltech.edu @mblscience.bsky.social

As bone broke as I am right now, I'm sorely tempted. IMHO a great opportunity to pick up what will be a piece of scifi-cyberpunk cultural ephemera of our moment in time. Still kicking myself for giving up that Mondo2k collection from a friend of mine.

Why is it always the singularity/h+ offshoots that turn creepy/violent when things don't go their way? I've known my share of old, burnt out Mondo2k readers and Usenet ranters who used to argue with bruces or greatdismal - they're perfectly fine, maybe even great weirdos.

#ColossalBio shouldn't be blaming the less-than-glowing outcome of their weird (outdated?) PR strategy on researchers merely doing their jobs. Regardless of your personal take, this is a dangerous pattern of behavior 🧪

🖥️🧬

Nice! Looking into low biomass samples for next year's project too. 🦠🧫

I tried going through LA metro (LA's tram/subway equivalent) and their brand new LAX transit hub that opened up just this month, skipping the usual Union station bus ($12 something). E to Expo/Crenshaw and transfer to K, then free 10 min shuttle to LAX. $1.75 for an hour trip. Not bad!

Oh goodness one bottle of Snapple is 85% of daily recommended sugar for an adult. I don't want to spend all my daily sugar allotment on this crap.

Last day in LA. Glad I could take a quick detour at the natural History museum! @markowenmartin.bsky.social

New pre-print alert! 🚨🫁 COPD affects millions worldwide. While we know bacterial dysbiosis drives disease, the role of bacteriophages remains unexplored. We re-analysed 135 COPD metagenomes to characterise the lung virome for the first time 🫁 1/9 www.biorxiv.org/content/10.1...

Aw darn it, the MoCA closes on Mondays. I really wanted to check out the Rothko room before leaving LA 😔

I've got to hand it to LA, the weather is fantastic here. Sunny like May, Autumn-cool in the evenings. I don't know why anyone would ever stay inside.

A great thing about a gigantic conference like #ASMicrobe is the diversity of represented interests - which makes it far easier to figure out what niche my current focus generally falls under. For me, when in doubt checking out an EEB poster or session worked out perfectly.

Researchers want overhead-payment reforms—NOT drastic cuts that would devastate research. Their ask: Protect indirect-cost funding, safeguard labs, avoid drastic drops in medical, climate, and tech innovation. zurl.co/ffIm2 #StandUpForScience #HigherEd

More people should stop by EEB-SUNDAY-1139 - Mining the ATCC Genome Portal: Genomic Insights into Unsequenced Taxa and Rare Historical Strains in the American Type Culture Collection, and talk to Scott. Treasure trove of microbial info there, forgotten human records and cells alike #asmicrobe 🦠🧫

Absolutely delighted by the morning's talk- Geovirology: Bacteriophage influences on bacterial geochemical signatures by Cynthia Silveira, University of Miami That IV bag-glove box setup for studying PSB samples was amazing. Also, viral/bacterial geological records? Wow #asmicrobe

First podcast experience of my life done - that was fun! Much thank you to Karl for the and the podcast crew for being so considerate. #asmicrobe