🇲🇽 Leonardo Collado-Torres
@lcolladotor.bsky.social
#RStats @Bioconductor.bsky.social/🧠 genomics @lieberinstitute.bsky.social + Asst. Prof. @jhubiostat.bsky.social/@lcgunam @jtleek.bsky.social @aejaffe.bsky.social alumni/ @libdrstats.bsky.social @CDSBMexico.bsky.social
http://lcolladotor.github.io
http://lcolladotor.github.io
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...
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...
November 7, 2025 at 3:58 PM
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...
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...
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
November 5, 2025 at 11:47 PM
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 🦄
November 5, 2025 at 11:47 PM
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 🌋
November 5, 2025 at 11:47 PM
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 📊
November 5, 2025 at 11:47 PM
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
November 5, 2025 at 11:47 PM
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 🐁
November 5, 2025 at 11:47 PM
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
November 5, 2025 at 11:47 PM
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 🧪
November 5, 2025 at 11:47 PM
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
November 5, 2025 at 11:47 PM
¡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
Thank you very much @christinezhang.bsky.social for taking the time to share your experience with us! I’m sure that everyone who attended your talk or sees the recording will benefit from it when crafted their own data visualizations 🎨
Feel free to come visit us in Baltimore 🦀 whenever you want ^^
Feel free to come visit us in Baltimore 🦀 whenever you want ^^
October 24, 2025 at 7:30 PM
Thank you very much @christinezhang.bsky.social for taking the time to share your experience with us! I’m sure that everyone who attended your talk or sees the recording will benefit from it when crafted their own data visualizations 🎨
Feel free to come visit us in Baltimore 🦀 whenever you want ^^
Feel free to come visit us in Baltimore 🦀 whenever you want ^^
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 […]
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 […]
June 3, 2025 at 9:40 PM
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 […]
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 […]
At a bus stop
@isaacgs94.bsky.social: Are you Julio Collado?
Leo: no
I: 😥
L: I’m his son
I:
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! 🇲🇽
@isaacgs94.bsky.social: Are you Julio Collado?
Leo: no
I: 😥
L: I’m his son
I:
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! 🇲🇽
March 30, 2025 at 10:48 PM
At a bus stop
@isaacgs94.bsky.social: Are you Julio Collado?
Leo: no
I: 😥
L: I’m his son
I:
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! 🇲🇽
@isaacgs94.bsky.social: Are you Julio Collado?
Leo: no
I: 😥
L: I’m his son
I:
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! 🇲🇽
New blog post: Initial impressions from testing Posit Connect
lcolladotor.github.io/2025/03/14/i...
I describe our use case and why I think that Posit Connect will be helpful for our @lieberinstitute.bsky.social work moving forward
@posit.co #RStats #shiny #shinyapps #spatialLIBD #iSEE
lcolladotor.github.io/2025/03/14/i...
I describe our use case and why I think that Posit Connect will be helpful for our @lieberinstitute.bsky.social work moving forward
@posit.co #RStats #shiny #shinyapps #spatialLIBD #iSEE
March 14, 2025 at 8:11 PM
New blog post: Initial impressions from testing Posit Connect
lcolladotor.github.io/2025/03/14/i...
I describe our use case and why I think that Posit Connect will be helpful for our @lieberinstitute.bsky.social work moving forward
@posit.co #RStats #shiny #shinyapps #spatialLIBD #iSEE
lcolladotor.github.io/2025/03/14/i...
I describe our use case and why I think that Posit Connect will be helpful for our @lieberinstitute.bsky.social work moving forward
@posit.co #RStats #shiny #shinyapps #spatialLIBD #iSEE
Check our recent video "[2025-01-29] R/Bioconductor-powered Team Data Science: TLDR version 2025"
youtu.be/alL-g2roXxM
We go over what analyses our @lieberinstitute.bsky.social has expertise on 💻
Slides orchestrated by @lahuuki.bsky.social at speakerdeck.com/lahuuki/2025...
👥 go.bsky.app/53gy4UP
youtu.be/alL-g2roXxM
We go over what analyses our @lieberinstitute.bsky.social has expertise on 💻
Slides orchestrated by @lahuuki.bsky.social at speakerdeck.com/lahuuki/2025...
👥 go.bsky.app/53gy4UP
February 12, 2025 at 9:35 PM
Check our recent video "[2025-01-29] R/Bioconductor-powered Team Data Science: TLDR version 2025"
youtu.be/alL-g2roXxM
We go over what analyses our @lieberinstitute.bsky.social has expertise on 💻
Slides orchestrated by @lahuuki.bsky.social at speakerdeck.com/lahuuki/2025...
👥 go.bsky.app/53gy4UP
youtu.be/alL-g2roXxM
We go over what analyses our @lieberinstitute.bsky.social has expertise on 💻
Slides orchestrated by @lahuuki.bsky.social at speakerdeck.com/lahuuki/2025...
👥 go.bsky.app/53gy4UP
Feeling ready for the @jhubiostat.bsky.social BSO (Biostats Student Org) Cultural Potluck! 🗺️
It's great to see current students re-implement the Cultural Mixers @mandymejia.bsky.social & I ran in 2012-~2015 lcolladotor.github.io/2013/11/20/s...
📸 with @mgschiavon.bsky.social @surh.bsky.social
It's great to see current students re-implement the Cultural Mixers @mandymejia.bsky.social & I ran in 2012-~2015 lcolladotor.github.io/2013/11/20/s...
📸 with @mgschiavon.bsky.social @surh.bsky.social
February 7, 2025 at 3:54 PM
Feeling ready for the @jhubiostat.bsky.social BSO (Biostats Student Org) Cultural Potluck! 🗺️
It's great to see current students re-implement the Cultural Mixers @mandymejia.bsky.social & I ran in 2012-~2015 lcolladotor.github.io/2013/11/20/s...
📸 with @mgschiavon.bsky.social @surh.bsky.social
It's great to see current students re-implement the Cultural Mixers @mandymejia.bsky.social & I ran in 2012-~2015 lcolladotor.github.io/2013/11/20/s...
📸 with @mgschiavon.bsky.social @surh.bsky.social
Thank very much @freneegf.bsky.social for teaching #LCG-UNAM students how to make their own websites with:
* RStudio project +
* Git repo +
* GitHub website using the #postcards #rstats 📦 by @seankross.com
It's been great to be part of your academic journey!
lcolladotor.github.io/rnaseq_LCG-U...
* RStudio project +
* Git repo +
* GitHub website using the #postcards #rstats 📦 by @seankross.com
It's been great to be part of your academic journey!
lcolladotor.github.io/rnaseq_LCG-U...
January 31, 2025 at 8:42 PM
Thank very much @freneegf.bsky.social for teaching #LCG-UNAM students how to make their own websites with:
* RStudio project +
* Git repo +
* GitHub website using the #postcards #rstats 📦 by @seankross.com
It's been great to be part of your academic journey!
lcolladotor.github.io/rnaseq_LCG-U...
* RStudio project +
* Git repo +
* GitHub website using the #postcards #rstats 📦 by @seankross.com
It's been great to be part of your academic journey!
lcolladotor.github.io/rnaseq_LCG-U...
FYI ⚠️
“you may want to arrange your travel plans—especially if travel is nonessential—to return to the U.S. no later than January 19.”
@johnshopkinssph.bsky.social
ois.jhu.edu/travel-infor...
“you may want to arrange your travel plans—especially if travel is nonessential—to return to the U.S. no later than January 19.”
@johnshopkinssph.bsky.social
ois.jhu.edu/travel-infor...
December 17, 2024 at 3:20 PM
FYI ⚠️
“you may want to arrange your travel plans—especially if travel is nonessential—to return to the U.S. no later than January 19.”
@johnshopkinssph.bsky.social
ois.jhu.edu/travel-infor...
“you may want to arrange your travel plans—especially if travel is nonessential—to return to the U.S. no later than January 19.”
@johnshopkinssph.bsky.social
ois.jhu.edu/travel-infor...
I didn't know how many GitHub issues I have opened throughout the years (or other stats). Though it was never a goal, I'm getting close to 1,000! ^_^ Mostly #RStats issues & documenting tasks for my team
Although github-readme-stats.vercel.app/api/top-lang... says that I mostly write html code :P
Although github-readme-stats.vercel.app/api/top-lang... says that I mostly write html code :P
December 10, 2024 at 7:56 PM
I didn't know how many GitHub issues I have opened throughout the years (or other stats). Though it was never a goal, I'm getting close to 1,000! ^_^ Mostly #RStats issues & documenting tasks for my team
Although github-readme-stats.vercel.app/api/top-lang... says that I mostly write html code :P
Although github-readme-stats.vercel.app/api/top-lang... says that I mostly write html code :P
I just copied Marcel Ramos (@mramos148.bsky.social) from @bioconductor.bsky.social core and edited my GitHub profile to display stats thanks to @anuraghazra.bsky.social's excellent github.com/anuraghazra/...
raw.githubusercontent.com/LiNk-NY/LiNK... --> github.com/lcolladotor/...
raw.githubusercontent.com/LiNk-NY/LiNK... --> github.com/lcolladotor/...
December 10, 2024 at 7:52 PM
I just copied Marcel Ramos (@mramos148.bsky.social) from @bioconductor.bsky.social core and edited my GitHub profile to display stats thanks to @anuraghazra.bsky.social's excellent github.com/anuraghazra/...
raw.githubusercontent.com/LiNk-NY/LiNK... --> github.com/lcolladotor/...
raw.githubusercontent.com/LiNk-NY/LiNK... --> github.com/lcolladotor/...
Sean et al found that #Cell2location did a great job with batch effect correction for spot deconvolution
We’ve also used C2L with @lieberinstitute.bsky.social data
#SpatialBiology
We’ve also used C2L with @lieberinstitute.bsky.social data
#SpatialBiology
December 5, 2024 at 11:57 PM
Sean et al found that #Cell2location did a great job with batch effect correction for spot deconvolution
We’ve also used C2L with @lieberinstitute.bsky.social data
#SpatialBiology
We’ve also used C2L with @lieberinstitute.bsky.social data
#SpatialBiology
Sean Houghton is now closing day 2 of track 1 at #SpatialBiology
Using Visium, Xenium, and Hyperion data
Using Visium, Xenium, and Hyperion data
December 5, 2024 at 11:57 PM
Sean Houghton is now closing day 2 of track 1 at #SpatialBiology
Using Visium, Xenium, and Hyperion data
Using Visium, Xenium, and Hyperion data
They can also find relay networks. Like A —> B —> C instead of just A —> B and B —> C. I missed getting a photo of this great slide!
The image below is from a previous slide showing how the results from #CellNEST can be visualized 🎨
I’m looking forward to the paper 📜!
#SpatialBiology
The image below is from a previous slide showing how the results from #CellNEST can be visualized 🎨
I’m looking forward to the paper 📜!
#SpatialBiology
December 5, 2024 at 11:44 PM
They can also find relay networks. Like A —> B —> C instead of just A —> B and B —> C. I missed getting a photo of this great slide!
The image below is from a previous slide showing how the results from #CellNEST can be visualized 🎨
I’m looking forward to the paper 📜!
#SpatialBiology
The image below is from a previous slide showing how the results from #CellNEST can be visualized 🎨
I’m looking forward to the paper 📜!
#SpatialBiology
Greg et al are working on a biological model where it’s known that there are many cell interactions and were excited to get results that matched what they expected
That’s great to see! It’s hard to validate cell to cell communication results 😣
#SpatialBiology
That’s great to see! It’s hard to validate cell to cell communication results 😣
#SpatialBiology
December 5, 2024 at 11:40 PM
Greg et al are working on a biological model where it’s known that there are many cell interactions and were excited to get results that matched what they expected
That’s great to see! It’s hard to validate cell to cell communication results 😣
#SpatialBiology
That’s great to see! It’s hard to validate cell to cell communication results 😣
#SpatialBiology