Lieber Institute for Brain Development

Thanks to all my @lieberinstitute.bsky.social and external colleagues who helped me with my first 🇺🇸 National Institutes of Health (NIH) R01 grant resubmission ^^ and those who wrote support letters for it

Hopefully it’ll do well on this second round! Fingers crossed 🤞🏽

#ESI

Talk submission video for Posit Conf 2026 #RStats

«Organizing your data science team to be efficient, adaptive to new developments, and resilient to turnover rate»

URLs:
1. lcolladotor.github.io/bioc_team_ds/
2. research.libd.org/rstatsclub/
3. github.com/LieberInstit...

#OpenSource #Bioconductor

New postdoctoral opportunity @lieberinstitute.bsky.social working w/ @tsawada1.bsky.social and our Molecular Neurogenetics team using human induced pluripotent stem cells to investigate molecular, cellular and neuroendocrine mechanisms by which impaired placental function impacts brain development

We sincerely thank #NIMH #NIGMS & @lieberinstitute.bsky.social for supporting this work and are deeply grateful to the donors and their families, whose generosity made this research possible.

Again, we’re very excited to share this work with the community and look forward what comes next 🤩 (9/9)

FIRST post here on Bluesky - we’re excited to share that our large spatial transcriptomics study of the human dlPFC in schizophrenia is now available on bioRxiv📄: www.biorxiv.org/content/10.6... (1/9)

Microscopy image showing pink fill in neurons stained for tyrosine hydroxylase in a section of mouse brain tissue

For #FluorescenceFriday - unmistakably the blue spot 🔵 (locus coeruleus) - here labeled in a section of the mouse brain in pink with tyrosine hydroxylase (TH) 🔬🧠🧪

Image credit to the @lieberinstitute.bsky.social Circuits team - @jorge-miranda.bsky.social @rehg-j.bsky.social

Is schizophrenia associated with accelerated aging?

In our new paper, we find evidence for consistently faster aging in schizophrenia, though not among unaffected siblings nor clinical high-risk youth

doi.org/10.1017/S003...

New paper out on cortistatin neurons and their role in regulating fear and cortical hyperexcitability in the prelimbic cortex! This one has been a fun ride 🧵 www.biorxiv.org/content/10.6...

Congrats to @aaronsalisbury.bsky.social and @mictott.bsky.social on this exciting project initially designed to mechanistically investigate a molecular association with PTSD that we observed in postmortem human brain tissue. Fun🧵below explaining the scientific rational and findings from Michael!

@lieberinstitute.bsky.social @jhubiostat.bsky.social

lcolladotor.github.io/rnaseq_LCG-U... is looking ready for next week!

We'll have the most guest presenters ever this year with @meli-mq99.bsky.social @gabrielramirezv.bsky.social @mariagtac.bsky.social & @daiannaglez.bsky.social 🙌🏽

See you soon at LCG-UNAM! 🇲🇽

#RStats @bioconductor.bsky.social

Spatially resolved molecular sex differences at single-cell resolution in the adult human ventromedial and arcuate hypothalamus The ventromedial hypothalamus (VMH) and arcuate (ARC) nuclei of the hypothalamus play critical roles in regulating metabolism and behavior. Here, Mulvey et al. create a focused spatial transcriptomic ...

Now online! @lieberinstitute.bsky.social & @jhubiostat.bsky.social collaboration generating important resource (Visium & Xenium) on molecular organization of human hypothalamus w/ cool findings associating sex differential expression to neuropsychiatric disorders 🧠🔬🧪
www.cell.com/cell-reports...

@nick-eagles.bsky.social concluded that scratch space location matters significantly for performance 💾⚡. He explained his motivation: he had a real use case with hundreds of millions of rows 📊 that originally took

Full length video: youtu.be/ikumz_QLZiE
#RStats #dplyr #duckplyr #rpolars #data.table

@nick-eagles.bsky.social introduced his presentation on benchmarking #dplyr alternatives 📊💻. He planned to review public benchmarks of various data manipulation packages 📦 as well as his own custom benchmark results 🔬

Full length 🎥: youtu.be/ikumz_QLZiE
#RStats #dplyr #duckplyr #rpolars #data.table

@geopertea.bsky.social discussed how the AI provides semantic understanding of code 🧠💻, showing how objects are generated from different parts of the codebase 🔗. He acknowledged that you can do this manually too 👨‍💻, and sometimes manual inspection might ...

#RStats #PositronIDE @posit.co

@geopertea.bsky.social showed his chat history 📜 and explained a useful use case: he asked the AI to look into a repository 🔍 and tell him what methods they were using for calculations 🧮. Basically, he had the AI read the code and summarize it for him 📝✨.

#RStats #Positron #PositronAI

@geopertea.bsky.social explained how you can add your own custom agents 🤖 to #Positron & showed the interactive way to configure them 🛠️. He demonstrated how the "plan" agent is defined, noting that it doesn't use any file mod tools 📝❌ - it's specifically designed for planning purposes 📋

#RStats

@geopertea.bsky.social demonstrated setting up #Positron IDE 💻 by first detecting local interpreters and updating extensions 🔧. He showed how to login to @github.com to activate GitHub Copilot connectivity 🤖 for the Positron assistant. During the new installation, the app provides an...

#RStats

I explained why including context is crucial 📚! I pointed out that someone could just paste code like "GRanges from 1 to 1000 plus..." but then I would be confused 😕 asking "where does this function come from? What package is this from?" 📦❓

@jennybryan.bsky.social #RStats #reprex

I demonstrated running a #reprex in a fresh #RStats session 💻 & opened it in my browser 🌐. It showed the 📦 loading with all its messages, then the function itself. I pointed out that I had made a syntax error: I missed the colon before the plus sign ➕❌, which caused an error

@jennybryan.bsky.social

I explained how the reprex workflow helps with collaboration 🤝! I described a scenario where I ask a question about why the mean is 2.5 and not 3, and Nina wants to help by running the same code 💻. She can easily copy-paste the #reprex output and it actually runs ✅!

@jennybryan.bsky.social #RStats

I demonstrated how to use the #reprex package 📦! I loaded it and explained the workflow: I copied lines of code from my console (pretending Leo has a question ❓), then ran the reprex() function without any arguments 💻.

@jennybryan.bsky.social #RStats

I explained how a common problem makes it harder for people to get help 😤. People often think they've provided everything needed - posting their code online 💻, showing how to recreate objects, sharing all the code they ran, and even including the output 📊.

@jennybryan.bsky.social #RStats #reprex

I explained the common problem people encounter when asking for coding help 🤔. I showed how someone might copy code they ran, paste it, ask a question. I was setting up to explain what's wrong with this approach ❌ of sharing code for troubleshooting purposes💻 #RStats #reprex @jennybryan.bsky.social

[2020-04-03] How to ask for R help by creating a small reproducible example (edited on 2026-01-27) YouTube video by Leonardo Collado Torres

I re-edited this 2020 video using Adobe Premier Pro's features for removing filler words, pauses, and text-based editing. In total it went down from 20:53 min to 12:41. I hope that you get to (re-)enjoy it ^_^.

@jennybryan.bsky.social

#RStats #reprex #reproducibility #JHPCE

youtu.be/LfUFxHFhXTE

A colleague Geo @geopertea.bsky.social found out a cool trick to get Positron working with full support at our computing cluster JHPCE (remote file explorer, Positron assistant seeing the remote R session). Game changer for my work at LIBD! Check out his demo video (youtu.be/CnmaJG8VPp8) #positron

In a recent journal club, I covered the SOFA paper by @wkhuber.bsky.social and colleagues. It's especially cool how you can guide the factorization approach with known covariates.

Check out their preprint (doi.org/10.1101/2024...) and our discussion (youtu.be/WKs-g4lXzZs)!

Cells in culture stained with antibodies - mix of green, purples and pinks

Was just reviewing a slide deck, and came across this lovely image on the title slide. I don't even know what it is, but its 🤩 and I missed #FluorescenceFriday, so let me add some 🔬beauty to your night 🧠🧪👩‍🔬

Image credit to Stephanie Page and the Imaging Development team @lieberinstitute.bsky.social

Lots has evolved since these R Stats sessions @libdrstats.bsky.social, but we touch on the hot topic of integrating LLMs into data science, mostly with Github Copilot, in a couple sessions--

Introductory look: youtu.be/xuCQZ5_5KB0
Reusable prompts: youtu.be/mlMl81xRI_M

#RStats #LLMs

👋 #ACNP2026! I'm Keri - @lieberinstitute.bsky.social CSO and long-time @acnporg.bsky.social mtg attendee. Happy to chat emerging translational neuroscience approaches, human 🧠 omics, LC 🔵, and hiPSC models. I ❤️ to talk fonts, neuro trivia and why white wine spritzers are the perfect conference drink

Thanks for the mug @jhubiostat.bsky.social!

And thanks for the apple 🍎 butter Kelsey from @lieberinstitute.bsky.social

End of year gifts 🎁 are well appreciated ^_^ Thank you again!