Just a reminder that Large Language Models is just one type of AI. It is not synonymous with AI and indeed the key aspects which make LLMs work - big attention networks, very large embedding spaces - have many applications.

Oh hey… what’s all this now? THATS RIGHT! The ATCC Genome Portal now has whole exome and RNAseq data for 900+ cell lines and organoids models, with more data coming. Currently >4k datasets : all produced in house by my team under ISO using benchmarked and standardized methods. genomes.ATCC.org

Something wicked this way comes... 🧬🧬🧬 (to the ATCC Genome Portal on Monday, Dec 1st...) (wicked in a good, different, leap forward way... 😄)

In 2003, Dr. Nathan Myhrvold pointed out that GenBank was doubling in size every 18 months - much like Moore's Law. 22 years later - that trend is continuing. (www.ncbi.nlm.nih.gov/genbank/stat...) How much longer is that going to be sustainable? #bioinformatics #genomics

🧵 Several months ago I started a Friday afternoon journal club focused on Yarrowia lipolytica, metabolic engineering, and functional genomics.

Good read about terrible things www.thehastingscenter.org/what-researc...

Currently attending the annual Virginia Tech CEZAP Symposium on Emerging Infectious Diseases - and Dr. Vincent Racaniello (host of TWIV / MicrobeTV podcast) is the key note. Really love his career talk - I hope the students and postdoc here take his advice to heart.

The 400 richest Americans are now worth a record $6.6 trillion. The entire bottom 50% of America is worth just $4.2 trillion. Read that back. When 400 people control more wealth than half a country’s population, we have a very serious problem.

The following is REAL footage from Portland, 2025. Viewer discretion is advised.

Things editors read when reviewing the comments of reviewers for a microbial forensics paper... "to account for potential batch effects, please include acquisition date, transport conditions, storage conditions and duration for all cadavers included in the study" 👀

I feel like this photo of masked, armed men pepper spraying a pastor protecting his community is going to be a defining picture of this moment in America for a long, long time.

Our Q3 2025 Data Release! 500 new microbial genomes, incl. 474 bacteria, 17 viruses, 9 fungi. 429 unique species, 26 "unclassified" species, and 24 new type-strains. We now have 6,250 authenticated reference genomes on the AGP. Come by and check it out! more coming! #genomics genomes.atcc.org

"... the American Type Culture Collection (ATCC) Genome Portal (genomes.atcc.org) which is the only authenticated reference genome database for ATCC microbes, the largest general culture collection in the world..." 🎯 www.cell.com/iscience/ful... 😊 cc: @officialatcc.bsky.social

“It’s can only good happen.” LMAO

Latest paper from my group explores the differential response of five model cell lines used in leukemia research to to EF24, a synthetic cucurmin analog. journals.plos.org/plosone/arti... #genomics #RNAseq #biopharma #EF24 #naturalproducts #leukemia

Hey scRNAseq people… what’s this about not needing to do biological replicates? What now? I’m sorry - yes it’s expensive to do. Complain to 10X Genomics - not the RA Fisher and his legacy. 🙃 RA Fisher, Jacques Monod, Francois Jacob, and Barbara McClintock are watching. 🤣

What the F is this… I can’t create “a mouse in a business suit” who is accepting $10 from a protestor who is also holding a sign that says “Free Speech” The F’ing irony of this has me fuming…

This is epic! @officialatcc.bsky.social announced the winners of the 2025 Photo contest! They look amazing! Check the Alt text and follow the link for tons more. www.atcc.org/about-us/upc... I love this! Please reshare! #microscopy #biology #research #science #cellbiology #microbiology #biotech 🧪🧬

TTW you’re totally vibing to a Hendrix cover band’s long long jam session at a local brewery … and they finally end the jam - you’re the only one who yells out “All right!!!” …

paper submitted. 😀

In Germany, scientists have made a breakthrough in treating Parkinson’s by implanting a chip in the brain that sends precise signals to restore movement. A stunning leap in neuroscience—witness the power of innovation and the beauty of science in action. Powerfull content

This hits right on time… My wife and I had the great privilege of visiting the African-American Museum in DC, and let me just tell you if you have not been…It is a masterpiece—go.

Newsom: "He doesn't play by a different set of rules. He doesn't believe in the rules. As a consequence, we need to disabuse ourselves of the way things have been done. It's not enough to just hold hands, have a candlelight vigil, talk about way the world should be...we have got to meet fire w/fire"

🧪 🧬🖥️ Lots of buzz and hype about this - so I’m curious what you think :: What do you consider “AI ready” data in the life sciences? #bioinformatics #genomics #AI #AIready

I've written a primer on CBRN, an oft-misunderstood area of defence and security. I was a CBRN specialist at one point so have some experience of the topic - far too many hours spent in a respirator and full noddy suit! Let me know thoughts and feelings below.

Modern-Day Oracles or Bullshit Machines? Jevin West (@jevinwest.bsky.social) and I have spent the last eight months developing the course on large language models (LLMs) that we think every college freshman needs to take. thebullshitmachines.com

Yet another position open at @officialatcc.bsky.social ! Love #genomics / #bioinformatics? Work closely with me and my team in shaping the future of ATCC’s digital biology research and product development. Please repost! 🙏 Product Manager, Digital Biology careers-atcc.icims.com/jobs/4001/pr...

"Ghislaine Maxwell remains the only child-rapist in history to receive well-wishes from a president of the United States." Lawrence O'Donnell

Since we passed the Affordable Care Act, Republicans have tried over and over to repeal it. And over and over, they’ve failed — in part because millions of people now depend on the ACA for quality, affordable health care.

"The U.S. has no standards for biological data so that it's curated, labeled and ready to be fed into AI models, which has resulted in a mix of high- and low-quality data across the U.S. government and in the private sector." www.axios.com/pro/tech-pol...

There and back again... A few months ago I wrote an essay on moving from academia to biotech. Today I published a follow-up: moving from biotech to academia. doi.org/10.59350/004...

#NSCEB is having real world impacts on future US GOV funding priorities. Amid all the negative things happening with funding being cut across so many agencies for life sciences research - a bright spot is potentially new opportunities in biotech and biodiversity funding www.axios.com/pro/tech-pol...

The @officialatcc.bsky.social blog has been running this series called "100 for 100" highlighting strains we've accessioned for the last 100 years. Today included one I wrote on Yarrowia lipolytica. If you're curious about the "origin story" of this super kewl yeast: www.atcc.org/blogs/2025/t...

912 applications for one position … WTH!?!?!?! 🤦🏻‍♂️

FYI - session proposals for @asm.org ASMicrobe 2026 are due today! I just submitted one 😊 on industrial microbiology and upcycling waste into energy or something useful. Fingers crossed! 🤞 🏭🦠 ➕ 🗑️💩 🟰 (💊|⛽|⚡|🧪|🍰)

New #bioinformatics Scientist opening at @officialatcc.bsky.social ! Love #genomics? Want to help build a digital biology future? We're sequencing our entire collection 😱 Our focus? Authenticated Reference Data. Digital Standards. Reproducibility. Join us! careers-atcc.icims.com/jobs/4000/sc...

New #bioinformatics Scientist opening at @officialatcc.bsky.social ! Love #genomics? Want to help build a digital biology future? We're sequencing our entire collection 😱 Our focus? Authenticated Reference Data. Digital Standards. Reproducibility. Join us! careers-atcc.icims.com/jobs/4000/sc...

Yikes … we got like 350+ applications for one bioinformatics position open on my team in 1 week. Never seen this happen in my entire career! This is going to take some effort to sort out. Will be interesting to see the response to a second, slightly more senior biofx one opening up next week.

Me three months ago:

Scientists Discover Gene Responsible For Eating Whole Goddamn Bag Of Chips theonion.com/scienti...

Reading up on the (apparently?) new organelle discovered in mammalian cell lines — Hemifusomes. Pretty neat. www.nature.com/articles/s41... But the top comment on Reddit hits home. 🤣😭

So this week at the Genomic Standards Consortium meeting in Cambridge - I asked the audience towards the end of my talk: Anyone know of any research that aims to detect fraud or data falsification in the #genomics field? A auditorium full of global leaders in the field, zero hands raised #GSC25

NIH wants to hear from you. No really. Request for Information on Maximizing Research Funds by Limiting Allowable Publishing Costs grants.nih.gov/grants/guide...

Really good meeting! Glad I made the trip - met tons of new people and learned about quite a few things I didn’t know before! #GSC25 Genomic Standards Consortium, Cambridge UK.

Fun fact: SRA processes 45TB of genomics data daily. 160PB data total 35M sequencing datasets 😱

FWIW // It irks me that when at a conference 1/2 the attendees are working, laptops open, and not paying attention. Some of these speakers have literally traveled 1/2 way around the world to give a 20 minute talk - but many of the KOLs here are already checked out…

Group leader positions in @sangerinstitute.bsky.social Cellular Genomics, led by @mhaniffa.bsky.social, to decode and recode human tissues. Broad net - clinical research, in vitro models, single cell, AI. Vibrant, supportive community. Please share! sanger.wd103.myworkdayjobs.com/en-GB/Wellco...

Absolutely incredible talk by @laraurban42.bsky.social at #GSC25 on the use of @nanoporetech.com data to estimate the viability of bacteria directly from samples - based on ML modeling of squiggle data directly. 😱 #genomics #bioinformatics

Does anyone know if you can query RefSeq and parse the status codes w/o downloading ALL of it in genbank format first and then grep'ing those lines? Image from RefSeq docs, but AFAIK you can't directly query the "COMMENT" field with NCBI's esearch or RESTapi... #bioinformatics #help

Motherfucking wind farms…