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Kenny Pavan

@kennypavan.com
209 followers 182 following 93 posts

Science, nature photos, mental-health advocate, and star trek 🖖 PhD Candidate @ OHSU studying synaptic connectivity. myOwnOpinions=True

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Kenny Pavan @kennypavan.com · 17/08/2026
If only git worked locally 🤔
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Kenny Pavan @kennypavan.com · 12/04/2026
Obligatory national pet day post. She laughs at all my jokes despite the overwhelming evidence that she shouldn't.
A dog laughing while sitting in the park.
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Ming Tommy Tang @tommytang.bsky.social · 22/03/2026
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.
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Theo Sanderson @theo.io · 08/02/2026
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
bluesky-map.theo.io
Bluesky Map
Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.
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Kenny Pavan @kennypavan.com · 08/02/2026
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.
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David S. F. Portree @dsfpspacefl1ght.bsky.social · 08/01/2026
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
Mars Express image of Olympus Mons volcano showing frost, 2024
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PEERing into Science Podcast @peeringintoscience.bsky.social · 01/01/2026
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!
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Vollum Institute @volluminstitute.bsky.social · 30/12/2025
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
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scverse @scverse.bsky.social · 20/11/2025
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.
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Dirk Eddelbuettel @eddelbuettel.com · 26/10/2025
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...
Screenshot of blog post at https://dirk.eddelbuettel.com/blog/2025/10/26#duckdb-mlpack_0.0.2 announcing that mlpack is now a duckdb community extension
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Kenny Pavan @kennypavan.com · 26/08/2025
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...
sciencedirect.com
Human brain cell types shape host-rabies virus transcriptional interactions revealing a preexisting pro-viral astrocyte subpopulation
How virus-host cell interactions and innate immune antagonism shape neurotropic infection dynamics across diverse brain cell types is largely unknown.…
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Kenny Pavan @kennypavan.com · 06/05/2025
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
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Kenny Pavan @kennypavan.com · 24/03/2025
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...
github.com
GitHub - ArpiarSaundersLab/annsql: The AnnSQL package enables SQL based queries on AnnData objects.
The AnnSQL package enables SQL based queries on AnnData objects. - ArpiarSaundersLab/annsql
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Kenny Pavan @kennypavan.com · 04/02/2025
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
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Kenny Pavan @kennypavan.com · 29/01/2025
By extension, Wikipedia says DeepSeek trained on its data and asks for $5 donation.
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Albert Vilella, PhD. @albertvilella.bsky.social · 28/01/2025
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"
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Man in Business Suit Levitating @dfeldman.org · 23/01/2025
“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
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Kenny Pavan @kennypavan.com · 22/01/2025
The numbers speak for themselves. #startrek #startrekmemes #data #ML #AI 🖖
Commander Data from Star Trek The Next Generation as a change my mind meme stating "AI is just matrix multiplication. Change my mind."
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Kenny Pavan @kennypavan.com · 17/01/2025
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
A vending machine at OHSU Knight Cancer Research Building that is a pick up and dropoff for cancer risk screening.
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David Berenstein @davidberenstein.bsky.social · 15/01/2025
Smol-scale vector search doesn't need a dedicated vector database! You can simply use the Hugging Face Hub. code: buff.ly/4jfilpC build on DuckDB: buff.ly/4jgWAWl
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Kenny Pavan @kennypavan.com · 07/01/2025
It's refreshing to see a client-side javascript encryption package published in Bioinformatics. 🧬🖥️ #cybersecurity doi.org/10.1093/bioi...
doi.org
Crypt4GH-JS: Securely storing sensitive data online with client-side encryption
AbstractMotivation and results. Crypt4GH-JS is a browser-ready implementation of the Crypt4GH file encryption standard written in JavaScript. While having
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 06/01/2025
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...
Drake meme top text: "Training on shitty data scraped from the internet" bottom text "Training on shit"
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Vinny Costa @vincentcostaphd.bsky.social · 05/01/2025
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.
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Kenny Pavan @kennypavan.com · 02/01/2025
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...
An example R script showing how an AnnSQL database file can be accessed using R by using the DuckDB R API.
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Kenny Pavan @kennypavan.com · 22/12/2024
This is just the C to WebAssembly to HTML/CSS renderer I never knew I needed. www.nicbarker.com/clay
nicbarker.com
Clay - UI Layout Library
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Kenny Pavan @kennypavan.com · 21/12/2024
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...
biorxiv.org
Host and rabies virus gene expression is shaped by human brain cell type and reveals a preexisting pro-viral transcriptional state in astrocytes
Rabies virus (RABV) proteins play dual roles during the infection of complex neural tissue, the generation and spread of new virions and the active inhibition of cellular innate immune pathways, both ...
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Kenny Pavan @kennypavan.com · 06/12/2024
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
Tiny wood cabin surrounded by trees and covered in moss.
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Kenny Pavan @kennypavan.com · 05/12/2024
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...
academic.oup.com
Knowledge mining of brain connectivity in massive literature based on transfer learning
AbstractMotivation. Neuroscientists have long endeavored to map brain connectivity, yet the intricate nature of brain networks often leads them to concentr
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Kenny Pavan @kennypavan.com · 04/12/2024
Exciting project and roadmap. It will be fun to follow along with this ambitious timeline and scope. 🧪🖥️🧬 e11.bio/news/roadmap
e11.bio
E11 Bio Roadmap | E11 Bio
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Upol Ehsan | hiring PhDs for Fall'27 @upolehsan.bsky.social · 02/12/2024
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
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Kenny Pavan @kennypavan.com · 01/12/2024
Slide Number One... 🧬🖥️🧪🖖 #StarTrek #PhDLife #AcademicSky
Star Trek The Next Generation opening title, "We're Close to Generating Data."
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Tia N. Donaldson, PhD @tiandonaldson.bsky.social · 27/11/2024
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
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Upol Ehsan | hiring PhDs for Fall'27 @upolehsan.bsky.social · 25/11/2024
AI Ethics Committees: where we debate for months whether something is ethical, only for someone else to launch it anyway. #AI #AIethics #ResponsibleAI
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Kenny Pavan @kennypavan.com · 22/11/2024
Preparing for my first DAC meeting. Any pro-tips? 🧪🧬🖥️ #AcademicSky
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c0nc0rdance @c0nc0rdance.bsky.social · 12/08/2023
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 transcribed copy of this document:
https://www.mcsweeneys.net/articles/faq-the-snake-fight-portion-of-your-thesis-defense
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The PhD Place - Academic Community @thephdplace.bsky.social · 17/11/2024
A perfect thesis is never finished and a finished thesis is never perfect
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Jay Hennig @jhennig.bsky.social · 18/11/2024
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...
videocast.nih.gov
BRAIN NeuroAI Workshop
NIH BRAIN NeuroAI Workshop to inform and coordinate future BRAIN research strategies and priority areas to build on recent scientific advances at the intersection of neuroscience and artificial intell...
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Kenny Pavan @kennypavan.com · 19/11/2024
Actual footage of my models training when all the GPU nodes are occupied. 🧪 #Bioinformatics #MLSky #AISky #AcademicSky
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Eddie Pérez Claudio @edpclau.me · 19/11/2024
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
pitt.zoom.us
Video Conferencing, Web Conferencing, Webinars, Screen Sharing
Zoom is the leader in modern enterprise video communications, with an easy, reliable cloud platform for video and audio conferencing, chat, and webinars across mobile, desktop, and room systems. Zoom ...
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Jason Moore @moorejh.bsky.social · 19/11/2024
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
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Kenny Pavan @kennypavan.com · 19/11/2024
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
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Kenny Pavan @kennypavan.com · 18/11/2024
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
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Kenny Pavan @kennypavan.com · 18/11/2024
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
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Kenny Pavan @kennypavan.com · 18/11/2024
Hey #Bluesky, meet the good-est girl, Pond. #dogs #bordercollie #tricks
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Upol Ehsan | hiring PhDs for Fall'27 @upolehsan.bsky.social · 18/11/2024
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.
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Kenny Pavan @kennypavan.com · 17/11/2024
Peaceful vibes at Byodo-In temple prior to starting my program. Looking forward to sitting and breathing here again soon.
Byodo-In Temple
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Kenny Pavan @kennypavan.com · 17/11/2024
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.
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William Gunn @metasynthesis.net · 17/11/2024
Not that anyone in particular needs it, but here's a guide to good science communication. It's not all obvious! mikeyoungacademy.dk/how-to-be-kind-… 🧪
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Kenny Pavan @kennypavan.com · 17/11/2024
#Ai is out of control. Who do I write a letter to about this?
Branch with moss that looks like long hair and a smiling face.
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Kenny Pavan @kennypavan.com · 17/11/2024
Autumn hiking adventures in the #pnw
Bridge with surrounding foliage
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