🇲🇽 Leonardo Collado-Torres

YouTube video by Leonardo Collado Torres [2025-07-18] Plots in Python with seaborn and plotnine

Hot take: ggplot2 is better than any plotting option available in Python-- but I discuss a couple options in Python at an R Stats Club session @libdrstats.bsky.social linked below. I personally use plotnine, since it's essentially a port of ggplot2 for Python.

youtu.be/xK9UNcOfjnI

Congratulations to our habenula team! We've learned a lot about working in this tiny brain region. Here we characterize the molecular signatures of human habenula cell types and transcriptomic changes associated with schizophrenia. Stay tuned 👀 for more exciting habenula findings in the near future.

Patterns of neural activity in prelimbic cortex neurons correlate with attentional behavior in the rodent continuous performance test - Translational Psychiatry Translational Psychiatry - Patterns of neural activity in prelimbic cortex neurons correlate with attentional behavior in the rodent continuous performance test

Happy to share that our paper characterizing PrL dynamics during sustained attention is finally out. This work was a collaboration between the @martinowk.bsky.social and Greg Carr groups at @lieberinstitute.bsky.social . www.nature.com/articles/s41...

#Calicumimaging #miniscopes #rCPT #PrL

I just completed my first radio 📻 interview ^_^

You'll be able to listen to it next Friday or so at www.iheart.com/podcast/269-.... Thanks Clau from iHeartRadio Miami's "Estamos Contigo" podcast for reaching out!

I'll be talking in Spanish about our recent #HabenulaLIBD 📜

bsky.app/profile/lcol...

Tiny Brain Region May Hold Clues to Schizophrenia, Scientists Say | The Lieber Institute for Brain Development | Research & Discovery What the Study Found Scientists have long searched for what goes wrong in the brains of people with schizophrenia. Now, researchers at the Lieber Institute for Brain Development in Baltimore may have ...

Para más, checa los anuncios de @lieberinstitute.bsky.social

🔗 www.libd.org/tiny-brain-r...
🔗 www.libd.org/inside-the-h...

además del comunicado de prensa de la Asociación Americana de Psiquiatría

🔗 www.psychiatry.org/News-room/Ne...

¡Y gracias a @lahuuki.bsky.social por el hilo 🧵 original!

Unlocking the Molecular Secrets of the Human Habenula | American Journal of Psychiatry PsychiatryOnline.org is the platform for all American Psychiatric Association Publishing journals, DSM, and bestselling textbooks, as well as APA Practice Guidelines, and continuing medical education.

Gracias a @nataliematosin.bsky.social y Sophie Debs por resaltar nuestro trabajo en su editorial “Desbloqueando los Secretos Moleculares de la Habénula Humana”

🔗 doi.org/10.1176/appi...

2025 LIBD lcolladotor data science team TL;DR A recap of recent work from our R Bioconductor-powered Team Data Science group at the Lieber Institute for Data Science. Team website: https://lcol…

Estos datos servirán para trabajo futuro sobre cambios moleculares que ocurren en #Habénula en enfermedades 🧠🧬 Mantén un 👀 abierto en @lieberinstitute.bsky.social para nuevos resultados de Hb de datos transcriptómicos con resolución espacial @10xgenomics.bsky.social

speakerdeck.com/lahuuki/2025...

GitHub - LieberInstitute/Habenula_Pilot: habenulaPilot project code repository habenulaPilot project code repository. Contribute to LieberInstitute/Habenula_Pilot development by creating an account on GitHub.

Nuestros datos de #Habénula y de expresión diferencial pueden ser explorados vía sitios web interactivos 💻 #DatosLibres #iSEE 👀

github.com/LieberInstit...

Usamos análisis de #eQTL para examinar como los SNPs se relacionan a la expresión génica en #Habénula. 7 genes eQTLs fueron identificados como GDEs, y 16 eSNPs como SNPs de riesgo a la esquizofrenia en GWAS. 9 nuevos genes fueron colocalizados con el riesgo genético de esquizofrenia

Investigamos si los GDEs que encontramos eran únicos a la #Habénula vs otras regiones del cerebro con estudios de esquizofrenia (núcleo caudado, giro dentado, dlPFC, hipocampo) y encontramos que 75% de los GDEs eran únicos a la habénula 🦄

Este análisis identificó 173 genes diferencialmente expresión (GDEs; DEGs en inglés) entre donadores control y los afectados por esquizofrenia. Algunos de estos GDEs (como HES5) apoyan la hipótesis del neurodesarrollo de la esquizofrenia 🌋

Para refinar la señal de habénula del vecino tálamo utilizamos nuestros datos de #snRNAseq para #deconvolución de nuestras muestras a granel #bulkRNA, estimando así la proporción de Hb. Estas proporciones las usamos para controlar diferencias en disecciones en el análisis de expresión diferencial 📊

También analizamos tejido enriquecido en Hb de donadores control o con esquizofrenia usando secuenciación masiva de ARN, generando un set de datos único para identificar cambios moleculares asociados a la enfermedad. ACP (PCA🇺🇸) de datos #bulkRNA de otras regiones muestran que la Hb es un caso aparte

Para contextualizar, integramos nuestros datos de #snRNAseq de Hb humana con datos #singlecell previamente publicados de Hb de ratón por el laboratorio de @gstuber.bsky.social. Algunos grupos de células neuronales como las LHb.2 enriquecidas por OPRM1 en humano aparecen conservadas entre especies 🐁

Usamos hibridación fluorescente in situ de molécula única #RNAScope y HALO de @indicalabs.bsky.social para visualizar la organización espacial de estas poblaciones neuronales de la Habénula humana. 🔬 Por ejemplo, neuronas MHb.2 que expresan CHAT se agruparon de forma separada de otras células de MHb

Creamos un mapa molecular con #snRNAseq de la Hb humana para entender la diversidad neuronal a un nivel molecular en esta región del cerebro única. Nuestros datos de 7 donadores control produjeron 16 mil núcleos y 17 grupos celulares, incluyendo 7 poblaciones neuronales laterales y 3 medias en Hb 🧪

¡Gracias a nuestros colaboradores del Instituto Lieber para el Desarrollo del Cerebro por su dedicación y arduo trabajo en este proyecto! 🧑‍🔬 #HabenulaLIBD @freneegf.bsky.social @nick-eagles.bsky.social @lahuuki.bsky.social @kr-maynard.bsky.social de la división lidereada por @martinowk.bsky.social

Acá va en español 🇲🇽
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"¡Estamos orgullosos de anunciar que nuestro artículo ‘Análisis Transcriptómico de la Habénula Humana en Esquizofrenia’ es el artículo de portada de la edición de noviembre del American Journal of Psychiatry!" 🧠 #HabenulaLIBD #snRNAseq #Habénula doi.org/10.1176/appi...

Tiny Brain Region May Hold Clues to Schizophrenia, Scientists Say | The Lieber Institute for Brain Development | Research & Discovery What the Study Found Scientists have long searched for what goes wrong in the brains of people with schizophrenia. Now, researchers at the Lieber Institute for Brain Development in Baltimore may have ...

Biostats professor @lcolladotor.bsky.social, along with his colleagues from @lieberinstitute.bsky.social, have created the first detailed molecular map of the human habenula, and with it gained new insights into its role in schizophrenia. Read the original study: psychiatryonline.org/doi/10.1176/...

Excited to share that the second project from my time at @lieberinstitute.bsky.social with @lcolladotor.bsky.social is now published! This was such a rewarding collaboration to be part of. 💡🧠
Huge congrats to @lahuuki.bsky.social and all co-authors!

#OpenData and #OpenCode from our latest @lieberinstitute.bsky.social project

Lots of #RStats and @bioconductor.bsky.social code inside of that repository!

#OpenScience

Congrats to @lahuuki.bsky.social and many members of @kr-maynard.bsky.social and @lcolladotor.bsky.social teams in our division who contributed to this study! Really excited to see this paper now published with contribution of data resources for molecular profiles of human habenula cell types 🧠🔬🧪

Transcriptomic Analysis of the Human Habenula in Schizophrenia | American Journal of Psychiatry Objective: The objective of this study was to define the molecular neuroanatomy of the human habenula (Hb) and identify transcriptomic differences between brains of individuals with schizophrenia and ...

Proud to announce our paper ‘Transcriptomic Analysis of the Human Habenula in Schizophrenia’ from @lieberinstitute.bsky.social is the cover article for the November issue of the American Journal of Psychiatry! 🧠 #HabenulaLIBD #snRNAseq #Habenula doi.org/10.1176/appi...

Finally, we made 2 web tools to share to this unprecedently large human LC xscriptomic data. A 3rd (that visualizes high-res H&E and NM with and spatial gene xpr.) on the way (last URL). We hope these help the #bluespot #LC #catecholamines community! Tools at: research.libd.org/LFF_spatial_... (7/8)

Impact of Alzheimer's disease risk factors and local neuromelanin content on the transcriptomic landscape of the human locus coeruleus The locus coeruleus (LC) is a small noradrenergic nucleus in the dorsal pons that sends projections across the brain regulating sleep, arousal, attention, stress responses, and some forms of cognition...

Got with the times + made a BSky to share our new, large-scale spatial RNAseq study of adult human #locuscoeruleus! Co-1st auth and cryostat wizard @heenadivecha.bsky.social squeezed 85 tissue sections into 43 Visium arrays. (1/8)

www.biorxiv.org/content/10.1...

Excited to share our newest project using spatial transcriptomics with novel image analysis approaches to investigate the impact of biological risk factors for Alzheimer's disease (AD) - APOE haplotype, sex, and genomic ancestry - on molecular states in the locus coeruleus (LC 🔵) of the human 🧠.

A title slide reading "Practical AI for data science" and my name and title.

I'll be keynoting at R/Pharma a week from today! The conference is free and virtual. I'll be focused on the mundane use cases of LLMs for wrangling data with #rstats, and the content should feel applicable for folks outside of pharma—come through. :)

Register: events.zoom.us/ev/Ai-geyS63...

Lieber Institute For Brain Development - Staff Scientist I, Translational Neuroscience A little about us:The Lieber Institute for Brain Development (LIBD) was established in 2010 to plot a new course in biomedical research that would change the lives of individuals affected with develop...

We are hiring for a PhD-level Staff Scientist to join our teams in the Translational Neuroscience Division @lieberinstitute.bsky.social. This is an exciting opportunity to work at the intersection of human 🧠 neuroanatomy and molecular neuroscience

recruiting.paylocity.com/recruiting/j...

Thanks again Weiqiang Zhou & Margaret Taub for organizing the "Current Topics in Biostatistics" seminar series for 1st year @jhubiostat.bsky.social students

While my notes (docs.google.com/document/d/1...) were similar, the questions and discussion lead me to talk about more about team organization

crafted -> crafting 😅