BioAI Weekly: Sept 15 - 22 📊 This week: 203 articles analyzed, 36 community posts tracked, 10 trending topics identified Full article here: genomely.substack.com/p/bioai-week... An overview 🧵 below 👇 #AI #machinelearning #llms

Codex made my #software ~3.5x faster per #FASTA entry!💥 Previous version 🔵. #Codex optimized in 🟠 Beyond my use case, this suggests that tools like Codex can be used to solve a major issue in #bioinformatics — the long-term stability of software🛠️, which threatens scientific reproducibility.

one of the most epic accounts, @bernoid.bsky.social bsky.app/profile/bern...

Really wish I could use polls on BlueSky 🥺 CC @bsky.app

BioAI Weekly Sept 08-15 @genomelybio.bsky.social posts weekly on AIxBio news. This week, we examined & summarized 210 articles, 33 community posts (eg, from Reddit), and 10 trending topics (eg, from Bluesky) open.substack.com/pub/genomely...

How come different people giving the same prompt to ChatGPT get different answers? A new article from ThinkingMachines explains why LLMs are nondeterministic, and it largely comes down to how parallelization and precision are handled. 🧵

996 starts to take hold in SF. Is this the beginning of a broader shift? 🧐

Small LLMs are underrated - they can run locally on laptops/phones - no API costs or rate limits - full privacy & control - fast inference for real-time apps - perfect for specialized tasks/subagents The future will be a combination of 100B+ parameter models and those in the 7B-25B range

Major overhaul on my personal website is now live! jlsteenwyk.com

University of Calgary is hiring a tier I CRC professorship in crop genomics. Come work in one of the most beautiful corners of the world! careers.ucalgary.ca/jobs/1668764...

New short paper from our lab @currentbiology.bsky.social, in which we discover of a new mode of cell motility for choanoflagellates: flagellar gliding. www.cell.com/current-biol... - A 🧵

There's a lot happening in AI, and we made a way to keep up. @genomelybio.bsky.social will now post weekly reports about AI (& beyond). Eg, we examined & summarized 166 articles, 56 community posts (eg, from Reddit), and 10 trending topics (eg, from Bluesky) genomely.substack.com/p/ai-weekly-...

The LSRF post-doc fellowship is open (due Oct 31)! The LSRF is a supportive and kind community. We *always* celebrate each other. On a personal level, they've always greeted me with open arms and an abundance of kindness. If you are thinking of applying and have questions, feel free to reach out!

Still blows my mind that the only 2% codes of the ~3 billion base pair human genome encodes for proteins! The discovery that the other 98% isn't junk happened when I was in undergrad, and it is cool to have seen so much progress in understanding this vast space of non-coding DNA

I love seeing research entities (univs and institutes) having industry collaborations. The two can really achieve a lot together

JOB ALERT @bertuzzilab.bsky.social is recruiting 2 Research Associates for a project on Mucorales! Very exciting and can definitely recommend working with this group ☺️ www.jobs.manchester.ac.uk/Job/JobDetai...

Quantum computing could revolutionize phylogenetic inference by exploring vast tree spaces! Imagine reconstructing evolutionary histories from massive genomics datasets in minutes, not months. Quantum algorithms + life's complexity would equal unprecedented insights into biology 🧬

We're hiring a tech for a project focused on the impact of genetic background on genetics and evolution. If you like doing lots of microbial evolution experiments and are good at bioinformatics/computation, this might be for you. aprecruit.ucsf.edu/JPF05782

You: Write a bluesky-style post about life in academia and biotech Model: I'll do that tomorrow

Alexa has ordered items from reporters saying “Alexa, order..” FYI @kevinroose.com & @caseynewton.bsky.social🙃 A news anchor once reported about a kid buying a dollhouse w/ Alexa, & said “I love the little girl, saying ‘Alexa ordered me a dollhouse’” Well, dollhouses were ordered in many homes 😆

ClipKIT now supports Python versions 3.9 to 3.13 ClipKIT is easy to download and install via pip! pypi.org/project/clip...

New ClipKIT feature! Users can now control how many threads are being used by ClipKIT with the -t / --threads argument. Default is single-thread. Documentation has been updated accordingly. jlsteenwyk.com/ClipKIT/adva...

Want to acquire #ExM images like this and help us understand the true extent of cytoskeletal diversity across the tree of life? This position might be for you! embl.wd103.myworkdayjobs.com/en-US/EMBL/j... With @dudinlab.bsky.social @embl.org @biology-unige.bsky.social @moorefound.bsky.social

Stunning image of a mammal (the eastern quoll) that glows✨ under UV light💡 📷: Ben Alldridge, reported in the @nature.com briefing #nature #neature #marsupial

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Excited to share that I will be a co-director for the upcoming Workshop on Phylogenomics @evomics.bsky.social, alongside the amazing main team lead @rosafernandez.bsky.social and Erin K. Molloy We are putting together an amazing workshop with details to come - can't wait to share it with everyone!🥳

Starter packs are a helpful mechanism to grow community The "Genomics, Evolution, and More" starter pack is my attempt to help foster connection pt1: go.bsky.app/JjvzkWU pt2: go.bsky.app/31tXVEC pt3: go.bsky.app/Rb2VW9m If you want to be included in the starter pack, I would be happy to add you!

NEW publication: Super happy to see the ClipKIT web application now published in Nucleic Acids Research @narjournal.bsky.social!! Trim your alignments for FREE on us :D Application: clipkit.genomelybio.com#/ Manuscript: academic.oup.com/nar/article/... #phylogenetics #evolution #bioinformatics

Another TechBio Berkeley Meetup on the way! 📅 Tues, July 22 | 5:30–7:30 PM 📍 Berkeley, CA (register to see location) Network with biotech builders, scientists & founders over brews. RSVP Now: lu.ma/n3boihud

NEW pub: The role of metabolism in shaping #enzyme structures over 400 million years. Now out in @nature.com Super grateful to have played a small role in this project - congrats to lead/corr authors Oliver, Benjamin, and Markus! www.nature.com/articles/s41... #alphafold #evolution #genomics

High throughput biochemical assessment of 200 orthologs reveals temperature-associated functional differences Such an impressive blend of wet- and dry-lab www.science.org/doi/10.1126/...

And that's a wrap for the 10th "Choanoflagellates & Friends" workshop at our own @pasteur.fr, the only conference where you award a baguette for the best talk. What a privilege to be part of such a vibrant, passionate and generous community. The future of our field is bright!

Awesome GUI for ClipKit. Use this application to get rid of your ambiguous regions when setting up Phylogenetic analysis! academic.oup.com/nar/advance-...

ClipKIT in the browser: fast online trimming of multiple sequence alignments for phylogenetics https://pubmed.ncbi.nlm.nih.gov/40260744/

such a stunning cover!! 🤩🤩🤩 Congrats @jameststroud.bsky.social, @wcratcliff.bsky.social and the others involved! bsky.app/profile/wcra...

Please consider nominating deserving colleagues (including yourselves) who would be excellent candidates for five open positions on the Council, including Nominations for President-elect, Secretary, Treasurer, and 2 Councilors. Please share widely! @official-smbe.bsky.social

New report shows that NIH grants fueled $95 billion in economic activity and 407,782 jobs in 2024. That's not to mention the countless lives that biomedical research has saved. Show me a better investment than that. www.forbes.com/sites/michae...

Google has dominated search for years. To see OpenAI/ChatGPT take over 4% in two years is remarkable

A hearty welcome to @rokaslab.bsky.social!! Antonis is now part of thee Genomics, Evolution, and More pt3 starter pack go.bsky.app/Rb2VW9m Quickly connect with others in the Genomics community by checking out the pt1 (go.bsky.app/JjvzkWU) and pt2 (go.bsky.app/31tXVEC) starter packs!

Users can now specify their own taxon and sequence delimiters in OrthoSNAP as of v1.3.2 using the -d / --delimiter argument journals.plos.org/plosbiology/...

An issue with length limits of sequence headers has now been resolved in OrthoHMM v 0.1.1 🥳 bsky.app/profile/jlst...

Part 3 of the "Genomics, Evolution, and More" starter pack is now available go.bsky.app/Rb2VW9m and includes the likes of @abigailllind.bsky.social and @planaria1.bsky.social! 🧬🥳🧬🥳 Don't forget to check out pts 1 and 2! Pt 1: go.bsky.app/JjvzkWU Pt 2: go.bsky.app/31tXVEC bsky.app/profile/jlst...

A laid-back lab gives me a productivity boost. Loving good tunes, great ideas, and incredible teams #LabLife #ChillScience

"The combined electricity consumption of the AI and cryptocurrency industries reached 460 terawatt-hours (TWh) in 2022, accounting for about 2% of the global total energy consumption." 😮 www.science.org/doi/10.1126/...

Elated to share the PhyKIT protocols manuscript appeared on the cover of Current Protocols🥳🥳🥳 bsky.app/profile/jlst...

U.S. businesses that sold goods and services to USAID are in limbo, including American farms dealing in rice, wheat and soybeans purchased as food aid.

There is a lot left to explore in evolutionary genomics. The data is there; more is being generated. The software is there; more tools are being engineered. These are exciting times!

The Matrix is a great movie. AI safety is something we should all be talking about more seriously in academia, especially given that many important AI-related advances are happening at our desks

My heart goes out to the lab animals that have passed