Obligatory national pet day post. She laughs at all my jokes despite the overwhelming evidence that she shouldn't.

1/ Hot take: deep learning is overkill for 90% of bioinformatics problems. I've watched teams spend months building neural networks that get outperformed by XGBoost trained in an afternoon. Here's why simpler models keep winning.

I made a map of 3.4 million Bluesky users - see if you can find yourself! bluesky-map.theo.io I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail

there’s nothing better than reaching into a bag of pistachios and pulling out one that’s already open... ...there’s also nothing worse than reaching into that same bag and pulling out just an empty shell.

In the difficult years ahead, we should remember that the snows of Olympus lie silent beneath the stars, waiting for our grandchildren. - Arthur C. Clarke

Happy new year nerds! Episode 2 is out! Go listen to my conversation with Dr. Swetha Murthy and learn how she found her confidence through her science 🧬 Available now everywhere you listen to podcasts!

Austin Schubert (Saunders Lab) won "Most Innovative Approach" at the Cure SYNGAP1 conference. His poster was titled "Brain–wide discovery of when, where, and how SYNGAP1 haploinsufficiency alters neurodevelopment through single cell RNA profiling.” cc: @trill-nye.bsky.social @your-arpy.bsky.social

Full house for our Bi[o]hub workshop on Day 3! Communities aren’t just built, they are co-created. Together, we’re shaping an open, connected world of all-things-single-cell research, where sharing tools and ideas drives discovery.

duckdb-mlpack 0.0.2: mlpack is now a duckdb community extension Bringing mlpack machine learning to duckdb SQL dirk.eddelbuettel.com/blog/2025/10...

Huge congratulations to my awesome lab mates, @your-arpy.bsky.social, and their collaborators @pasteur.fr on publishing their new paper showing how rabies hijacks brain cells and revealing a rare astrocyte subtype that boosts viral transcription 🧪 #SingleCell www.sciencedirect.com/science/arti...

Happy to share my first publication! AnnSQL leverages DuckDB to create a relational database based on each AnnData layer, enabling fast queries on massive, atlas-sized single-cell datasets. 🧬🖥️ #Bioinformatics #SingleCell #DuckDb

𝗔𝗻𝗻𝗦𝗤𝗟 v1 has landed! Explore atlas sized single-cell datasets, with minimal resources using SQL that's powered by the #DuckDb database engine. #SingleCell 🧬 🖥️ 🖖 github.com/ArpiarSaunde...

I spend way too much time converting AnnData objects into Seurat objects and haven't found a tool or pipeline that just works, while retaining all data layers. What are some tools or pipelines to ease this process? 🧬 🖥️ #SingleCell

By extension, Wikipedia says DeepSeek trained on its data and asks for $5 donation.

Learning about some of the magic behind the #DeepSeek R1 paper: "Optimisations actually began at chip level, below even CUDA, with DeepSeek engineers writing assembly language to overcome H800 bandwidth throttling. This in itself is an extraordinary technical feat"

“It’s easier to fool a man than to convince him that he’s been fooled.” - Mark Twain Well, someone tried to tell me that Mark Twain never actually said that, but I don’t believe them

The numbers speak for themselves. #startrek #startrekmemes #data #ML #AI 🖖

Remember when vending machines were just for snacks? Happy to see OHSU researchers spearheading this screening program to help improve cancer early detection. www.healthyoregonproject.com 🧪 #healthtech #genomics

Smol-scale vector search doesn't need a dedicated vector database! You can simply use the Hugging Face Hub. code: https://buff.ly/4jfilpC build on DuckDB: https://buff.ly/4jgWAWl

It's refreshing to see a client-side javascript encryption package published in Bioinformatics. 🧬🖥️ #cybersecurity doi.org/10.1093/bioi...

METAGENE-1: a 7B parameter autoregressive transformer model trained on over 1.5T DNA and RNA base pairs sequenced from wastewater samples. @oliu-io.bsky.social @samsja19.bsky.social @shangshang-wang.bsky.social @jefftk.com @willieneis.bsky.social metagene.ai/metagene-1-p...

Everyone can go home for the rest of year b/c @marlenecohen.bsky.social & colleagues just won 2025. The “everything is everywhere” & “brain areas are a myth” crowd should go bake a humble pie, chug some Pepto-Bismol, & shut their pie holes until they have fully digested this tour de force.

Let's talk about inte𝗥operability. The Python based AnnSQL package transforms AnnData objects into easily shareable persistent databases. Using the DuckDB R package, you can easily open these databases to run fast, easy queries 🧬🖥️🧪 #SingleCell #R #inteRoperability www.biorxiv.org/content/10.1...

This is just the C to WebAssembly to HTML/CSS renderer I never knew I needed. www.nicbarker.com/clay

Congrats to @your-arpy.bsky.social, my awesome lab mates and their collaborators at @pasteur.fr who just dropped a new preprint exploring how rabies hijacks brain cells and uncovered a rare astrocyte subtype that amplifies viral mRNA 🧬🖥️🧪 #neuroskyence #genomics www.biorxiv.org/content/10.1...

Stumbled upon this cozy cabin while hiking in the serene forests near the Oregon coast. Awful wifi, but we left a stellar review anyway. 📷🌳🪵 #Oregon #Photography

Nice approach to mining regional connectivity along with a fluid user-interface for exploration of regional gene, disease, cell type, and NT; along with easy access to the literature for validation. #NeuroSky #NeuroAI #MLSky #BioInformatics #Neuroscience 🧬🖥️🧠 academic.oup.com/bioinformati...

Exciting project and roadmap. It will be fun to follow along with this ambitious timeline and scope. 🧪🖥️🧬 e11.bio/news/roadmap

The Human-centered Explainable AI (#HCXAI) workshop will be back at #CHI2025 for the FIFTH time in a row! This year will be better than ever before. We're ready--the only missing piece is YOU! 🔗 hcxai.jimdosite.com Please share + help us get the word out. #academicSky #academia #AI #HCI 1/2

Slide Number One... 🧬🖥️🧪🖖 #StarTrek #PhDLife #AcademicSky

Dear grad students, Don’t go into the lab tomorrow. Put the thesis away. That data analysis can wait too. Spend time with your loved ones/take a day of rest. The science will be there when you get back. Sincerely, A retired grad student

AI Ethics Committees: where we debate for months whether something is ethical, only for someone else to launch it anyway. #AI #AIethics #ResponsibleAI

Preparing for my first DAC meeting. Any pro-tips? 🧪🧬🖥️ #AcademicSky

I feel like the academic community doesn't talk enough about the tradition of fighting a snake during your thesis defense. Given its importance, we should spend more time on it in grad school. For example: Tactical Snake Fighting 101 should be taught in year 1 of PhD programs. Anyone agree?

A perfect thesis is never finished and a finished thesis is never perfect

Just noticed the videos from the BRAIN NeuroAI workshops are online now, in case you missed them: videocast.nih.gov/watch=55160 videocast.nih.gov/watch=55262 n4solutionsllc.com/brain-neuroa...

Actual footage of my models training when all the GPU nodes are occupied. 🧪 #Bioinformatics #MLSky #AISky #AcademicSky

Join UPitt's Biomedical Informatics Colloquium this Friday November 22! We'll have a talk on how to leverage machine learning to predict palliative care needs in patients with chronic diseases by Prof. Li Zhou, MD, PhD. pitt.zoom.us/webinar/regi... #ClinicalInformatics #MedSky #AcademicSky

In this paper, we did our best to review scant literature on feature selection in machine learning using knowledge graphs academic.oup.com/bib/article/... #machinelearning #bioinformatics

How do you recharge your mind and body during lunch in academia? I've noticed some skip lunch entirely or eat quickly as a necessary transaction, while others take time to enjoy food and company. What creative ways do you rebalance during your break? 🧪 #AcademicSky #Science #Research #Lunch

In academia, mental health is your oxygen mask. Like on an airplane, we’re reminded to put on our own mask first before helping others. What daily practices help you prioritize mental health and promote a healthier, supportive research environment for all? 🧪#AcademicSky

When writing a paper, what tips, habits, or routines do you all swear by to boost productivity, maintain balance, and keep the process enjoyable? 🧪 #academicsky #science #research #mentalhealth

Hey #Bluesky, meet the good-est girl, Pond. #dogs #bordercollie #tricks

Grant applications: Convince us your idea is so groundbreaking it borders on sorcery—in 500 words. Then explain exactly how you'll pull off this miracle with no money, no staff, and a timeline shorter than a fruit fly's lifespan—in 300 words. Bonus points if you don’t cry.

Peaceful vibes at Byodo-In temple prior to starting my program. Looking forward to sitting and breathing here again soon.

Hi #AcademicSky! I'm acclimating to the high altitude here #bluesky. I'm a PhD candidate researching multimodal and high-throughput methods to explore synaptic connectivity through viral tropism. I'm actively developing artificial learning methods and visual tools to understand biological learning.

Not that anyone in particular needs it, but here's a guide to good science communication. It's not all obvious! https://mikeyoungacademy.dk/how-to-be-kind-on-social-media-a-guide-for-scientists/ 🧪

#Ai is out of control. Who do I write a letter to about this?

Autumn hiking adventures in the #pnw

Meet AnnSQL, a Python package for lightening fast querying of massive single-cell datasets. The needs of the many (cells) outweigh the needs of the few 🖖 #bioinformatics #genomics #python #sql #duckdb #firstpost www.biorxiv.org/content/10.1...