BaDoi Phan

This weekend I walked to at graduation to end my 8 years in Pittsburgh. This was supported by mentors and friends including
Andreas Pfenning and Ruby Holland.

To top it off, a major PhD dissertation project with
@wrstauffer.bsky.social
is now published in Neuron! bit.ly/4ktg1v1

I'm excited to be matched to at @stanfordanes.bsky.social, an excellent program, and future home for me to continue my career as a physician scientist caring for the people from where I grew up. 🧑🏻‍⚕️👨🏽‍🔬 #doubledocs

list of banned keywords

🚨BREAKING. From a program officer at the National Science Foundation, a list of keywords that can cause a grant to be pulled. I will be sharing screenshots of these keywords along with a decision tree. Please share widely. This is a crisis for academic freedom & science.

I'm teaching single-cell data analysis in #Rstats this Spring 2025
@FAESatNIH_EDU
! 📊

Two-course series:
Updated Seurat v5 tutorials
+ multi-modal analysis
+ spatial transcriptomics content
Real datasets & self-directed projects

Register @ tinyurl.com/FAESscBioS2025
#bioinformatics #scRNA

Cell Type Specific Enhancers for Dorsolateral Prefrontal Cortex The dorsolateral prefrontal cortex (DLPFC) is crucial to primate cognitive functions, but a paucity of cell type specific tools limits studies of DLPFC neurocomputational principles. Therefore, we set...

tinyurl.com/nphpfcenh

Cell Type Specific Enhancers for Dorsolateral Prefrontal Cortex The dorsolateral prefrontal cortex (DLPFC) is crucial to primate cognitive functions, but a paucity of cell type specific tools limits studies of DLPFC neurocomputational principles. Therefore, we set...

Ack! The copy paste from twitter failed me. Here’s the most important part of the thread: tinyurl.com/nphpfcenh

🌟 15/15 Impact: These tools enable new experiments in primate cognition & potential therapies. Grateful to both labs & collaborators for support! DM for questions! /end

🧩 14/15 Biggest achievement: Built pipeline to identify & validate cell-specific tools in primates. Years of work and a huge team effort but worth it! 😮‍💨

🔮 13/15 What's next:
- Studying cognitive circuits
- Developing targeted therapies
- Understanding disorders
Just getting started!

🎓 12/15 Proud to share resources, contact
@wrstauffer
for details:
- Primate DLPFC cell atlas🧬
- Our ML models💻
- Validated viral toolbox 🧰 🦠
All available to accelerate research! #OpenScience

⚠️ 11/15 We're transparent about limitations:
- Some baseline non-specific expression
- Promoter needs optimization
- Viral crosstalk issues in multiplexing
More work ahead!

🐭 10/15 Surprising discovery: Our primate enhancers worked in mouse cortex too! Evolution conserved these regulatory elements 🧬 #evolution

🔍 9/15 Our validation pipeline:
- Multiplexed screening first
- Single injections to confirm
- Functional testing
Rigorous approach pays off!

🧪 8/15 Key finding: Getting specificity right depends on:
- Viral titer (concentration matters!)
- Capsid choice
- Injection parameters
Details matter!

⚡️ 7/15 Most exciting part: Used RMacL3-01 to express ChR2. Could control L2/3 neurons with light! First time achieving this specificity in primate DLPFC 🔦 #optogenetics

🔋 6/15 Best performers:
- Our RMacL3-01: Targets L2/3 projection neurons (77% specific!)
- RMacL5ET-01: Hits L5 extra long-range projection neurons
Proud of these results! 🎯

🎯 5/15 Our viral toolbox: Created AAVs with these enhancers. Like GPS-guided delivery trucks for genes! Tested different viral capsids (PHP.eB, 2YF, X1.1) to optimize delivery 🚛

🤖 4/15 The cool part: We developed ML models (SNAIL) to scan thousands of DNA regions & predict enhancers. Turned a needle-in-haystack problem into a targeted search! #MachineLearning

🧬 3/15 Our approach: We used snRNA-seq & ATAC-seq from rhesus DLPFC. Found 11 excitatory & 10 inhibitory neuron types conserved in humans🧑🏽‍🦲and rodents🐭! Each with unique molecular fingerprints 🎯 #genomics

🔬 2/15 The challenge: How do we study specific neuron types in primate brains? Prior to our work, we lacked tools to target DLPFC neurons, especially in a cell-type specific way #Neuroscience

🧠 1/15 First bsky post and preprint alert! Part 4 of my thesis work is now online🎓🕺📜! We created tools to study specific neuron types in primate prefrontal cortex to be able to study complex thinking! Let's break down this work from the Stauffer (Pitt 🐵) and Pfenning (CMU🧬) labs🧵.

I made a systems neuroscience starter pack, focused on experimentalists who study the brain at the level of populations of neurons!

Also want to be on the list? Reply or DM me a picture of your ephys rig or 2p setup and I'll add you 🤭

go.bsky.app/UiqX7ry

I made a starter pack for neuroscience folks but I just saw that it’s capped at 150 people. Sorry if I missed anyone! Maybe #neuroscience folks should start making subfield starter packs? 🧪

go.bsky.app/Q69XurQ

A starter pack! Some of my favorite women in neuroscience (sorry if I forgot you, I will add!)

go.bsky.app/SCFmKoC

As an #R user both in #Rstudio and #Terminal, I have been known to change my IDE color panel to look like the #Matrix 😎💻💊

Yass 👏🏽

I have money on those being subtypes the medial shell NAcc islands of NUDAP MSNs 😉. #addiction #neurobiology

Microscopy image of human brain with fluorescently labeled cell markers

Doing a #MicroscopyMonday because I’m just so excited about these images of D1R sub -populations in nucleus accumbens of human brain 🧠🔬🤩

Hi Everyone 👋 Been slow to migrate over here but here I am! Neuroscientist studying addiction stress, circuits and molecules across the lifespan. Prof and Vice Chair of Neurobio and Assoc Director of the Kahlert Institute for Addiction Medicine.