Lieber Institute for Brain Development

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

Teaching omics methods to LCG-UNAM students | L. Collado-Torres Notes from a second semester introductory class to the world of omics research techniques at LCG-UNAM. That is, my undergrad alma mater. Thank you for the invitation! Valentina Arias Ojeda is as teach...

New blog post: "Teaching #omics #methods to #LCG-UNAM students"

Thanks for inviting me @vaalarias.bsky.social and Dr Constance Auvynet ^_^

Blog post is available in both English and Spanish 🇲🇽

#genomics #scRNAseq #Visium #spatialomics @10xgenomics.bsky.social

lcolladotor.github.io/2025/03/07/t...

Immunolabeling for cell types in a tissue section of the human hippocampus

Images 🔬 from in progress pilot experiment 🤩 - immunolabeling in human hippocampus 🧠 for key cell types, which we are coupling w/ high-definition transcriptomics to assess molecular changes in local cellular niches during aging and neurodenerative disorders. Anatomical structure is so exquisite 👩‍🔬🧪

Super pleased to present the Hallock lab's second article, out now in Learning & Memory! In our first article, we found increased transcription of Apoe in a mouse attentional circuit. What is Apoe doing in this circuit? A super team of undergrads wanted to find out 👇 1/n

Congrats to Kasey and the @daylab.bsky.social team! Honored for our teams to have contributed to the project, showing conservation of enrichment of RELN in DRD1-MSNs in nucleus accumbens of human 🧠. Including an image from RNAscope experiments in that project as my #FluorescenceFriday 🔬🧪👩‍🔬

✨2025 #ResearchExcellenceAward✨ #SIRS

🧠🔬Honored to receive this award, recognizing my team’s impact on #schizophrenia research. It highlights the power of collaboration, uniting basic and clinical sciences. Grateful to learn from brilliant young scientists dedicated to improving patients’ lives.

At a bus stop

@isaacgs94.bsky.social: Are you Julio Collado?

Leo: no

I: 😥

L: I’m his son

I: <relief>

L: I’m Leo Collado

Isaac had seen me on social media. We already followed each other here 😅

Congrats on completing your PhD studies at @sangerinstitute.bsky.social Enjoy the celebrations! 🇲🇽

Our paper has sparked a lot of people asking me – so Keri, what’s the tldr – is there, or isn’t there, new neurons in the human hippocampus?

It's a little more complicated than a yes or no IMO.

Integrating Aversive Memories in the Basolateral Amygdala Decades of research have established a critical role of the basolateral complex of the amygdala (BLA) in the encoding and storage of aversive memories. Much of this work utilizes Pavlovian fear condit...

How are long-term memories stored in the amygdala? How are old memories integrated with new memories over time? We discuss this and more in a new review led by @JianfengLiu6 with @HugoBayer1 and @StephenMaren. www.biologicalpsychiatryjournal.com/article/S000...

Fluorescence microscopy of a tissue section from locus coeruleus of the human brain, labeling for tyrosine hydroxylase in green and phosphorylated Tau in magenta

Very honored to get to share work from our group here investigating impact of neuromelanin and Tau pathology on molecular signaling in the locus coeruleus amongst a fantastic collection of talks with really exciting functional genomics approaches to understanding human 🧠 development and disease