Lieber Institute for Brain Development

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We have several positions open at various levels (Research Assistant, Research Associate, Postdoctoral Fellow) across our highly interactive teams in the Division of Translational Neuroscience 🧠🔬🧪 @lieberinstitute.bsky.social

www.libd.org/careers/

Links to individual positions in the thread below.

Really proud of huge collaborative efforts from several teams in Translational Neuroscience Division @lieberinstitute.bsky.social w/ labs of @stephaniehicks.bsky.social and @alexisbattle.bsky.social to provide this resource on cell types and spatial organization in nucleus accumbens of human 🧠

so excited to share that our preprint characterizing the dorsal anterior cingulate cortex in post-mortem human brain from @lieberinstitute.bsky.social is out! we integrated matched SRT and snRNA-seq data to investigate agranularity and von Economo neurons

An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus - Nature Neuroscience The topographical organization of cells in the hippocampus reflects its ability to regulate mood and cognition. Here the authors generate a spatially resolved gene expression map in the human hippocam...

Excited to share this huge team effort collaboration supervised by Stephanie Page in Translational Neuroscience @lieberinstitute.bsky.social and @stephaniehicks.bsky.social @jhubiostat.bsky.social to generate a spatio-molecular resource of the hippocampus in human 🧠

www.nature.com/articles/s41...

Grateful to have started my dream postdoc with @kr-maynard.bsky.social this week 🤩 Thanks to @martinowk.bsky.social @lieberinstitute.bsky.social and everyone for such a warm welcome, and so happy to be part of the team! Excited for all the great science and memories to come in this next chapter 🧠🎉

Thanks to Heather Thomas and everyone on the @oneneurojhu.org team for coming over to @lieberinstitute.bsky.social to interview us and hear about research being conducted by our teams! 👩‍🔬🔬🧠🔵

OneNeuro's August #FotoFriday #FluorescenceFriday contest winner is "Cellular Subtype Composition of an Amphetamine-activated Ensemble in mPFC," by Suhaas Adiraju from @martinowk.bsky.social at the @lieberinstitute.bsky.social

View the complete gallery here: www.oneneurojhu.org/art/

(1/10) We’re excited to share our new preprint (doi.org/10.1101/2025...), which uncovers the spatiomolecular landscape of the human nucleus accumbens (NAc), by integrating snRNA-seq with Visium spatial transcriptomics across 10 control donors. 🧠 #NAcLIBD #snRNAseq #10xVisium

YouTube video by Leonardo Collado Torres [2025-08-13] Journal club: Cell-type deconvolution methods for spatial transcriptomics

Hi everyone! Check my journal club talk on the latest review paper: Cell-type deconvolution methods for spatial transcriptomics 🧬

🎥 www.youtube.com/watch?v=xDjF...
🛝 speakerdeck.com/manishabarse

@lieberinstitute.bsky.social #Bioinformatics #SpatialTranscriptomics #Cell-TypeDeconvolution

Welcome @heenadivecha.bsky.social to Bsky! ^_^

Heena is a great scientist who worked at @lieberinstitute.bsky.social before joining @jhu.edu as a PhD student, and who is now back doing her PhD with @kr-maynard.bsky.social at LIBD

🔁

YouTube video by Lieber Institute Dr. Leonardo Collado Torres | A Data Scientist Examines the Brain

Biostats assistant professor @lcolladotor.bsky.social is also an investigator @lieberinstitute.bsky.social where he leads the R/Bioconductor-powered Team Data Science group. Learn more about his work in the video below: www.youtube.com/watch?v=Rz4L...

Phenomenal talk from @hyejungwon.bsky.social who is visiting us @lieberinstitute.bsky.social for the day. Groundbreaking work w/ important implications and roadmap for using rapidly emerging information on psychiatric genetics to prioritize variants and understand their impact on 🧠 function

YouTube video by Leonardo Collado Torres [2025-06-13] Intro to data.table and dtplyr for data manipulation

Just covered the data.table and dtplyr packages at LIBD R Stats Club @libdrstats.bsky.social. Really useful to be able to write dplyr code and get data.table performance!

#rstats

youtu.be/D3u64PMlJSI

Great collaboration motivates methodological and biological innovation!

Grateful for the opportunity to work together with @martinowk.bsky.social and @lieberinstitute.bsky.social, investigating the molecular pathology of neuropsychiatric disorder, coming soon! 😉

App: r-graph-gallery.com/color-palett...

Special thanks to @emilhvitfeldt.bsky.social for the {paletteer} package and to the @libdrstats.bsky.social club for fostering these practical #bioinformatics tips!

YouTube video by Leonardo Collado Torres Choosing a Color Palette

🎨 Struggling to pick the perfect color palette for data visualizations? Check out walkthrough of interactive tools and the awesome {paletteer} package by @emilhvitfeldt.bsky.social !

🔗 youtu.be/9tAeTjVD7ns

Let’s make our plots both beautiful and accessible!
#RStats @libdrstats.bsky.social

YouTube video by Leonardo Collado Torres [2025-05-30] Reshaping data, Joining tables

Hi everyone! Check my beginner-friendly #RStats talk at @lieberinstitute.bsky.social on reshaping, joining, binding, & set ops- all #tidyverse way! Shared simple demo to handle data better!

🎥 youtu.be/5L133h_1SNo
🛝 speakerdeck.com/manishabarse...

@libdrstats.bsky.social #DataWrangling #DataScience

And response to the Matters Arising from the authors of the original paper here: www.nature.com/articles/s41...

False positives in study of memory-related gene expression - Nature Nature - False positives in study of memory-related gene expression

Important 'Matters Arising' from @neurome.bsky.social and Zhaoxia Yu discussing false positives due to multiple comparisons in large-scale gene expression data. I applaud Eran and others who consistently raise these issues for discussion in the community.

www.nature.com/articles/s41...

SpotSweeper: spatially aware quality control for spatial transcriptomics - Nature Methods SpotSweeper is a spatially aware method for quality control of spatially resolved transcriptomics data that corrects for spatial confounding missed by existing methods, including both local and region...

🚨 New paper published in @natmethods.nature.com!

We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics.

📰 Paper : nature.com/articles/s41...
💻 Code: github.com/MicTott/Spot...
📈 Website: mictott.github.io/SpotSweeper/

🧵👇

Important methods development for spatial transcriptomics (ST) data from @mictott.bsky.social @boyiguo.bsky.social @stephaniehicks.bsky.social - congrats!

Applying this method to our QC workflow has substantially improved many new ST datasets generated across diverse regions/tissues in the human 🧠

New career milestone: served on a @jhu.edu PhD thesis committee meeting for the first time 🙌🏽

Thanks @jef.works for inviting me! And thanks @mikeschatz.bsky.social @jihk.bsky.social for your guidance! Great to share this experience with Fred Tan as well ^_^

It’s exciting to talk about […]

YouTube video by Leonardo Collado Torres [2025-05-23] Introduction to dplyr for data manipulation

Do a lot of PCA? Interested in streamlining data wrangling? In a couple recent LIBD R Stats Club @libdrstats.bsky.social sessions I talk about PCAtools, and dplyr for beginners.

youtu.be/rClA0Ms-oOw
youtu.be/XIbraIgPt0M

#RStats

YouTube video by Leonardo Collado Torres [2025-05-21] Journal club on brain multiome papers

🔬 Diving into ATAC-seq workflows?
You've likely heard about Seurat, Signac, MACS2, Cicero, and chromVAR—core components in many workflows.
Here’s a quick overview I put together that showcases different approaches used across recent studies.
youtu.be/R5P8mGMXuIg?...
#SingleCell #Epigenomics #LIBD

Learning more about APOE differences in the cell types of the brain 🧠

I presented "APOE genotype determines cell-type-specific pathological landscape of Alzheimer’s disease" from @zhaonaa.bsky.social at our team journal club, check it out!

doi.org/10.1016/j.ne...

▶️ youtu.be/L4J9jFS-Pic

Kinnary Shah is a fourth-year PhD candidate and co-president of the Biostats Student Org. Learn more about Kinnary and two of her ongoing research projects, one with the @lieberinstitute.bsky.social, and one with @stephaniehicks.bsky.social, on our website:
publichealth.jhu.edu/departments/...

YouTube video by Leonardo Collado Torres [2025-04-11] Scaffolding R-Shiny apps with generative AI

Last month at @libdrstats.bsky.social LIBD #rstats club I showed a #GenAI multi-modal LLM prompting technique for planning and scaffolding a R-Shiny + bslib application, using Google AI Studio, with VisualStudio Code as the IDE for R development (only free tools).
youtu.be/7PA45mVxZ8M

"How are you using #AI to make your work easier?" That's a FAQ right now @lieberinstitute.bsky.social.

Last week I searched @adobe.com Premier Pro's AI features. I found at helpx.adobe.com/premiere-pro... that it can

* create a transcript + captions
* detect filler words
* detect pauses

In ~5 min

Recently @mbarse.bsky.social presented a journal club on a proof of concept methods paper by @daylab.bsky.social et al

The pre-print at doi.org/10.1101/2024... is well written and we are interested in applying this method to future @lieberinstitute.bsky.social data.

bsky.app/profile/mbar...

YouTube video by Leonardo Collado Torres [2025-05-02] pseudobulk analysis with pseudoBulkDGE()

Presented at @lieberinstitute.bsky.social #RStats club on pseudobulk analysis using pseudoBulkDGE()📊 A handy wrapper for DE analysis following OSCA guidelines-shared a demo & walked through the method!✨
🎥 youtu.be/0OkWBLyLrfg
🛝 speakerdeck.com/manishabarse...

@libdrstats.bsky.social #Bioinformatics