🇲🇽 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
Pinned
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...
Reposted by 🇲🇽 Leonardo Collado-Torres
Issue 31 of RDM Weekly is out! 📬
➡️ OS resources in Comm Sciences @csdisseminate.bsky.social
➡️ RDA 25th Plenary Meeting Programme @researchdataall.bsky.social
➡️ Ask for R Help by Creating a Small Reproducible Example @libdrstats.bsky.social
and more!
rdmweekly.substack.com/p/rdm-weekly...
➡️ OS resources in Comm Sciences @csdisseminate.bsky.social
➡️ RDA 25th Plenary Meeting Programme @researchdataall.bsky.social
➡️ Ask for R Help by Creating a Small Reproducible Example @libdrstats.bsky.social
and more!
rdmweekly.substack.com/p/rdm-weekly...
RDM Weekly - Issue 031
A weekly roundup of Research Data Management resources.
rdmweekly.substack.com
February 3, 2026 at 2:05 PM
Issue 31 of RDM Weekly is out! 📬
➡️ OS resources in Comm Sciences @csdisseminate.bsky.social
➡️ RDA 25th Plenary Meeting Programme @researchdataall.bsky.social
➡️ Ask for R Help by Creating a Small Reproducible Example @libdrstats.bsky.social
and more!
rdmweekly.substack.com/p/rdm-weekly...
➡️ OS resources in Comm Sciences @csdisseminate.bsky.social
➡️ RDA 25th Plenary Meeting Programme @researchdataall.bsky.social
➡️ Ask for R Help by Creating a Small Reproducible Example @libdrstats.bsky.social
and more!
rdmweekly.substack.com/p/rdm-weekly...
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
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
February 3, 2026 at 5:21 AM
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
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
Reposted by 🇲🇽 Leonardo Collado-Torres
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)!
Check out their preprint (doi.org/10.1101/2024...) and our discussion (youtu.be/WKs-g4lXzZs)!
doi.org
January 8, 2026 at 6:00 PM
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)!
Check out their preprint (doi.org/10.1101/2024...) and our discussion (youtu.be/WKs-g4lXzZs)!
Reposted by 🇲🇽 Leonardo Collado-Torres
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
January 27, 2026 at 7:53 PM
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
Reposted by 🇲🇽 Leonardo Collado-Torres
you don't need to copy/paste from that preview! the rendered reprex, in a friendly md form, is already on your clipboard 😆
the htmlpreview is for your 👀, but the good stuff is on the clipboard waiting to be pasted in the relevant venue (default is github, but slack can also be requested)
the htmlpreview is for your 👀, but the good stuff is on the clipboard waiting to be pasted in the relevant venue (default is github, but slack can also be requested)
January 27, 2026 at 8:08 PM
you don't need to copy/paste from that preview! the rendered reprex, in a friendly md form, is already on your clipboard 😆
the htmlpreview is for your 👀, but the good stuff is on the clipboard waiting to be pasted in the relevant venue (default is github, but slack can also be requested)
the htmlpreview is for your 👀, but the good stuff is on the clipboard waiting to be pasted in the relevant venue (default is github, but slack can also be requested)
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
@jennybryan.bsky.social #RStats #reprex
January 27, 2026 at 8:16 PM
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
@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
@jennybryan.bsky.social
January 27, 2026 at 8:06 PM
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
@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
@jennybryan.bsky.social #RStats
January 27, 2026 at 7:58 PM
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
@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
@jennybryan.bsky.social #RStats
January 27, 2026 at 7:49 PM
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
@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
@jennybryan.bsky.social #RStats #reprex
January 27, 2026 at 7:44 PM
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
@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
January 27, 2026 at 7:41 PM
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
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
@jennybryan.bsky.social
#RStats #reprex #reproducibility #JHPCE
youtu.be/LfUFxHFhXTE
[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
youtu.be
January 27, 2026 at 5:00 PM
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
@jennybryan.bsky.social
#RStats #reprex #reproducibility #JHPCE
youtu.be/LfUFxHFhXTE
Reposted by 🇲🇽 Leonardo Collado-Torres
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 16, 2026 at 6:33 PM
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
Reposted by 🇲🇽 Leonardo Collado-Torres
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
Introductory look: youtu.be/xuCQZ5_5KB0
Reusable prompts: youtu.be/mlMl81xRI_M
#RStats #LLMs
January 16, 2026 at 6:22 PM
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
Introductory look: youtu.be/xuCQZ5_5KB0
Reusable prompts: youtu.be/mlMl81xRI_M
#RStats #LLMs
Reposted by 🇲🇽 Leonardo Collado-Torres
Honored to be appointed Chief Scientific Officer @lieberinstitute.bsky.social. LIBD is a uniquely collaborative place with extraordinary biological resources and a commitment to translation 🧠🔬🧪. Grateful to my colleagues and excited to help guide our next chapter!
www.libd.org/keri-martino...
www.libd.org/keri-martino...
Keri Martinowich, Ph.D., Chief Scientific Officer | The Lieber Institute for Brain Development | Research & Discovery
Lieber Institute for Brain Development Appoints Keri Martinowich, Ph.D., as Chief Scientific Officer Baltimore, MD (January 6, 2025) — The Lieber Institute for Brain Development (LIBD) announced the a...
www.libd.org
January 9, 2026 at 1:07 PM
Honored to be appointed Chief Scientific Officer @lieberinstitute.bsky.social. LIBD is a uniquely collaborative place with extraordinary biological resources and a commitment to translation 🧠🔬🧪. Grateful to my colleagues and excited to help guide our next chapter!
www.libd.org/keri-martino...
www.libd.org/keri-martino...
Reposted by 🇲🇽 Leonardo Collado-Torres
📊YEAR IN CHARTS📉📈
I pulled together 14 charts to summarize the trends that shaped business and the economy in 2025
My 3rd time in a row doing a year in charts for DealBook, this edition is the most robust one yet in both charts & text!
www.nytimes.com/2025/12/20/b...
🎁 link nyti.ms/3LdhNo3
I pulled together 14 charts to summarize the trends that shaped business and the economy in 2025
My 3rd time in a row doing a year in charts for DealBook, this edition is the most robust one yet in both charts & text!
www.nytimes.com/2025/12/20/b...
🎁 link nyti.ms/3LdhNo3
From A.I. to Tariffs, 14 Charts That Explain 2025
www.nytimes.com
December 20, 2025 at 3:31 PM
📊YEAR IN CHARTS📉📈
I pulled together 14 charts to summarize the trends that shaped business and the economy in 2025
My 3rd time in a row doing a year in charts for DealBook, this edition is the most robust one yet in both charts & text!
www.nytimes.com/2025/12/20/b...
🎁 link nyti.ms/3LdhNo3
I pulled together 14 charts to summarize the trends that shaped business and the economy in 2025
My 3rd time in a row doing a year in charts for DealBook, this edition is the most robust one yet in both charts & text!
www.nytimes.com/2025/12/20/b...
🎁 link nyti.ms/3LdhNo3
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!
And thanks for the apple 🍎 butter Kelsey from @lieberinstitute.bsky.social
End of year gifts 🎁 are well appreciated ^_^ Thank you again!
December 19, 2025 at 5:50 PM
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!
And thanks for the apple 🍎 butter Kelsey from @lieberinstitute.bsky.social
End of year gifts 🎁 are well appreciated ^_^ Thank you again!
Reposted by 🇲🇽 Leonardo Collado-Torres
2025 was an election “off-year”, but there were many consequential races. For those of us working elections it was hardly a year off!
Some of the key takeaways, brought to you by Caroline Soler, Alex Lemonides & me.
www.nytimes.com/interactive/...
and 🎁 a link, for the holidays: nyti.ms/4s5533p
Some of the key takeaways, brought to you by Caroline Soler, Alex Lemonides & me.
www.nytimes.com/interactive/...
and 🎁 a link, for the holidays: nyti.ms/4s5533p
Takeaways from an eventful 2025 election cycle
Takeaways from an eventful 2025 election cycle.
www.nytimes.com
December 19, 2025 at 4:22 PM
2025 was an election “off-year”, but there were many consequential races. For those of us working elections it was hardly a year off!
Some of the key takeaways, brought to you by Caroline Soler, Alex Lemonides & me.
www.nytimes.com/interactive/...
and 🎁 a link, for the holidays: nyti.ms/4s5533p
Some of the key takeaways, brought to you by Caroline Soler, Alex Lemonides & me.
www.nytimes.com/interactive/...
and 🎁 a link, for the holidays: nyti.ms/4s5533p
Reposted by 🇲🇽 Leonardo Collado-Torres
Cynthia @cynthiasc.bsky.social pasó de alumna de un curso de la CDSB a trabajar con uno de nuestros co-fundadores por 3 años en EEUU. Ahora Cynthia está de regreso en México 🇲🇽 y disponible para dar cursos, colaborar, proyectos como consultora, y mucho más
lcolladotor.github.io/es/authors/c...
lcolladotor.github.io/es/authors/c...
December 18, 2025 at 3:00 PM
Cynthia @cynthiasc.bsky.social pasó de alumna de un curso de la CDSB a trabajar con uno de nuestros co-fundadores por 3 años en EEUU. Ahora Cynthia está de regreso en México 🇲🇽 y disponible para dar cursos, colaborar, proyectos como consultora, y mucho más
lcolladotor.github.io/es/authors/c...
lcolladotor.github.io/es/authors/c...
I'd like to thank 🙏🏽 @cynthiasc.bsky.social for her 3 years at @lieberinstitute.bsky.social working in my team analyzing data generated by @kr-maynard.bsky.social et al.
Cynthia led our first foray into the world of multi-omics data (snRNA-seq + snATAC-seq)
#multiome #snRNAseq #scATACseq
Cynthia led our first foray into the world of multi-omics data (snRNA-seq + snATAC-seq)
#multiome #snRNAseq #scATACseq
December 17, 2025 at 11:24 PM
I'd like to thank 🙏🏽 @cynthiasc.bsky.social for her 3 years at @lieberinstitute.bsky.social working in my team analyzing data generated by @kr-maynard.bsky.social et al.
Cynthia led our first foray into the world of multi-omics data (snRNA-seq + snATAC-seq)
#multiome #snRNAseq #scATACseq
Cynthia led our first foray into the world of multi-omics data (snRNA-seq + snATAC-seq)
#multiome #snRNAseq #scATACseq
Reposted by 🇲🇽 Leonardo Collado-Torres
Really excited to share this new study - collaboration across several teams in our division @lieberinstitute.bsky.social, led by @lahuuki.bsky.social @kr-maynard.bsky.social @lcolladotor.bsky.social - congratulations to everyone! 🧠🔬👩🔬
Excited to share our latest preprint from @lieberinstitute.bsky.social spatial + single-cell RNA-seq map the ERC & explore how AD risk shapes gene expression doi.org/10.1101/2025...
Our major finding: “APOE E4 Alzheimer’s Risk Converges on an Oligodendrocyte Subtype in the Human Entorhinal Cortex”
Our major finding: “APOE E4 Alzheimer’s Risk Converges on an Oligodendrocyte Subtype in the Human Entorhinal Cortex”
December 11, 2025 at 12:58 PM
Really excited to share this new study - collaboration across several teams in our division @lieberinstitute.bsky.social, led by @lahuuki.bsky.social @kr-maynard.bsky.social @lcolladotor.bsky.social - congratulations to everyone! 🧠🔬👩🔬
When academic spam doesn’t know where you work (@lieberinstitute.bsky.social) or that the job as involves working with @kr-maynard.bsky.social and yourself hehehe 🤭
December 13, 2025 at 12:08 PM
When academic spam doesn’t know where you work (@lieberinstitute.bsky.social) or that the job as involves working with @kr-maynard.bsky.social and yourself hehehe 🤭
Reposted by 🇲🇽 Leonardo Collado-Torres
Excited to share our latest preprint from @lieberinstitute.bsky.social spatial + single-cell RNA-seq map the ERC & explore how AD risk shapes gene expression doi.org/10.1101/2025...
Our major finding: “APOE E4 Alzheimer’s Risk Converges on an Oligodendrocyte Subtype in the Human Entorhinal Cortex”
Our major finding: “APOE E4 Alzheimer’s Risk Converges on an Oligodendrocyte Subtype in the Human Entorhinal Cortex”
December 11, 2025 at 12:13 PM
Excited to share our latest preprint from @lieberinstitute.bsky.social spatial + single-cell RNA-seq map the ERC & explore how AD risk shapes gene expression doi.org/10.1101/2025...
Our major finding: “APOE E4 Alzheimer’s Risk Converges on an Oligodendrocyte Subtype in the Human Entorhinal Cortex”
Our major finding: “APOE E4 Alzheimer’s Risk Converges on an Oligodendrocyte Subtype in the Human Entorhinal Cortex”
[2025-10-16] What Makes a Good Data Visualization?
Here's a teaser video of @christinezhang.bsky.social's guest lecture for the "140.776 Statistical Computing" 💻 course that I instructed this year at @johnshopkinssph.bsky.social
Watch Christine's full guest lecture for free at youtu.be/SeLucCb05Dk
Here's a teaser video of @christinezhang.bsky.social's guest lecture for the "140.776 Statistical Computing" 💻 course that I instructed this year at @johnshopkinssph.bsky.social
Watch Christine's full guest lecture for free at youtu.be/SeLucCb05Dk
December 5, 2025 at 6:33 PM
[2025-10-16] What Makes a Good Data Visualization?
Here's a teaser video of @christinezhang.bsky.social's guest lecture for the "140.776 Statistical Computing" 💻 course that I instructed this year at @johnshopkinssph.bsky.social
Watch Christine's full guest lecture for free at youtu.be/SeLucCb05Dk
Here's a teaser video of @christinezhang.bsky.social's guest lecture for the "140.776 Statistical Computing" 💻 course that I instructed this year at @johnshopkinssph.bsky.social
Watch Christine's full guest lecture for free at youtu.be/SeLucCb05Dk
Reposted by 🇲🇽 Leonardo Collado-Torres
Clever approach - and I'll vouch - we've tried it, and it works.
Path to more rigorous experimental design for comparisons across individuals and biological sex within cohorts, and most importantly for me - saves us some $$$.
Path to more rigorous experimental design for comparisons across individuals and biological sex within cohorts, and most importantly for me - saves us some $$$.
New computational paper from the lab! Thanks to the reviewers for helping us improve this paper from the preprint version and Nucleic Acids Research for a smooth publication process.
Excited to share that our article on accurate sample deconvolution of pooled snRNA-seq data using sex-dependent gene expression patterns is live on NAR Genomics and Bioinformatics! 🎉
Check it out here: doi.org/10.1093/narg...
#NARGenomicsandBioinformatics #snRNAseq #Genomics #Bioinformatics
Check it out here: doi.org/10.1093/narg...
#NARGenomicsandBioinformatics #snRNAseq #Genomics #Bioinformatics
December 1, 2025 at 12:22 AM
Clever approach - and I'll vouch - we've tried it, and it works.
Path to more rigorous experimental design for comparisons across individuals and biological sex within cohorts, and most importantly for me - saves us some $$$.
Path to more rigorous experimental design for comparisons across individuals and biological sex within cohorts, and most importantly for me - saves us some $$$.