Kenny Pavan
@kennypavan.com
Science, nature photos, mental-health advocate, and star trek 🖖
Bioinformatics | ML | PhD Candidate @ OHSU studying synaptic connectivity.
myOwnOpinions=True
Bioinformatics | ML | PhD Candidate @ OHSU studying synaptic connectivity.
myOwnOpinions=True
Pinned
Kenny Pavan
@kennypavan.com
· Nov 18
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
Reposted by Kenny Pavan
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...
Bringing mlpack machine learning to duckdb SQL
dirk.eddelbuettel.com/blog/2025/10...
October 26, 2025 at 1:58 PM
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...
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...
www.sciencedirect.com/science/arti...
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.…
www.sciencedirect.com
August 26, 2025 at 3:31 PM
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...
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
#Bioinformatics #SingleCell #DuckDb
🔍 Recently published in Bioinformatics Advances: "AnnSQL: A Python SQL-based package for fast large-scale single-cell genomics analysis using minimal computational resources"
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf105
Authors: @kennypavan.com and @your-arpy.bsky.social
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf105
Authors: @kennypavan.com and @your-arpy.bsky.social
May 6, 2025 at 2:20 PM
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
#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...
github.com/ArpiarSaunde...
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
github.com
March 24, 2025 at 5:29 PM
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/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
February 4, 2025 at 8:45 PM
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.
January 29, 2025 at 4:58 PM
By extension, Wikipedia says DeepSeek trained on its data and asks for $5 donation.
Reposted by Kenny Pavan
“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
Well, someone tried to tell me that Mark Twain never actually said that, but I don’t believe them
January 23, 2025 at 2:28 PM
“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
Well, someone tried to tell me that Mark Twain never actually said that, but I don’t believe them
January 22, 2025 at 4:45 AM
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
www.healthyoregonproject.com
🧪 #healthtech #genomics
January 17, 2025 at 8:53 PM
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
www.healthyoregonproject.com
🧪 #healthtech #genomics
Reposted by Kenny Pavan
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
You can simply use the Hugging Face Hub.
code: https://buff.ly/4jfilpC
build on DuckDB: https://buff.ly/4jgWAWl
January 15, 2025 at 1:00 PM
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
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...
doi.org/10.1093/bioi...
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
doi.org
January 7, 2025 at 7:16 PM
It's refreshing to see a client-side javascript encryption package published in Bioinformatics. 🧬🖥️ #cybersecurity
doi.org/10.1093/bioi...
doi.org/10.1093/bioi...
Reposted by Kenny Pavan
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...
@oliu-io.bsky.social @samsja19.bsky.social @shangshang-wang.bsky.social @jefftk.com @willieneis.bsky.social
metagene.ai/metagene-1-p...
January 6, 2025 at 10:19 PM
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...
@oliu-io.bsky.social @samsja19.bsky.social @shangshang-wang.bsky.social @jefftk.com @willieneis.bsky.social
metagene.ai/metagene-1-p...
Reposted by Kenny Pavan
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.
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.
New results for a new year! “Linking neural population formatting to function” describes our modern take on an old question: how can we understand the contribution of a brain area to behavior?
www.biorxiv.org/content/10.1...
🧠👩🏻🔬🧪🧵
#neuroskyence
1/
www.biorxiv.org/content/10.1...
🧠👩🏻🔬🧪🧵
#neuroskyence
1/
Linking neural population formatting to function
Animals capable of complex behaviors tend to have more distinct brain areas than simpler organisms, and artificial networks that perform many tasks tend to self-organize into modules (1-3). This sugge...
www.biorxiv.org
January 5, 2025 at 2:41 AM
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.
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...
www.biorxiv.org/content/10.1...
January 2, 2025 at 5:37 PM
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...
www.biorxiv.org/content/10.1...
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...
#neuroskyence #genomics
www.biorxiv.org/content/10.1...
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 ...
www.biorxiv.org
December 21, 2024 at 9:54 PM
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...
#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
#Oregon #Photography
December 6, 2024 at 2:07 AM
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
#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...
#NeuroSky #NeuroAI #MLSky #BioInformatics #Neuroscience 🧬🖥️🧠
academic.oup.com/bioinformati...
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
academic.oup.com
December 5, 2024 at 9:33 PM
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...
#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
e11.bio/news/roadmap
E11 Bio Roadmap | E11 Bio
e11.bio
December 4, 2024 at 12:39 AM
Exciting project and roadmap. It will be fun to follow along with this ambitious timeline and scope. 🧪🖥️🧬
e11.bio/news/roadmap
e11.bio/news/roadmap
Reposted by Kenny Pavan
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
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
December 2, 2024 at 6:35 PM
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
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
December 1, 2024 at 12:41 AM
Reposted by Kenny Pavan
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
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
November 27, 2024 at 6:13 PM
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
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
Reposted by Kenny Pavan
AI Ethics Committees: where we debate for months whether something is ethical, only for someone else to launch it anyway.
#AI #AIethics #ResponsibleAI
#AI #AIethics #ResponsibleAI
November 25, 2024 at 5:35 PM
AI Ethics Committees: where we debate for months whether something is ethical, only for someone else to launch it anyway.
#AI #AIethics #ResponsibleAI
#AI #AIethics #ResponsibleAI
Preparing for my first DAC meeting. Any pro-tips? 🧪🧬🖥️ #AcademicSky
November 22, 2024 at 8:00 PM
Preparing for my first DAC meeting. Any pro-tips? 🧪🧬🖥️ #AcademicSky