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🇲🇽 Leonardo Collado-Torres

@lcolladotor.bsky.social
4.1K followers 2.9K following 452 posts

#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 lcolladotor.github.io

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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 30/09/2026
140.776 - Statistical Computing at @jhubiostat.bsky.social @johnshopkinssph.bsky.social Lecture 09 summary lcolladotor.github.io/jhustatcompu... #RStats #DataScience
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 25/09/2026
140.776 - Statistical Computing at @jhubiostat.bsky.social @johnshopkinssph.bsky.social Lecture 08 summary lcolladotor.github.io/jhustatcompu... #RStats #DataScience
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Kristina Killgrove @killgrove.bsky.social · 22/09/2026
The newly discovered cuneiform tablet fragment contains text from a section of the Treaty of Kadesh related to the treatment of Hittite and Egyptian refugees in the Bronze Age (circa 1269 BC). 🧪🏺
livescience.com
'We have found traces of peace, thousands of years old': Fragment of world's oldest known peace treaty found in Turkey
Archaeologists excavating in the ancient Hittite capital of Hattusha have uncovered a fragment of the world's oldest peace treaty, signed around 1269 B.C.
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 22/09/2026
140.776 - Statistical Computing at @jhubiostat.bsky.social @johnshopkinssph.bsky.social Lecture 07 summary lcolladotor.github.io/jhustatcompu... Guest speaker: @nick-eagles.bsky.social from @lieberinstitute.bsky.social #RStats #DataScience #PositAssistant #AIcoding #Claude
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 18/09/2026
140.776 - Statistical Computing at @jhubiostat.bsky.social @johnshopkinssph.bsky.social Lecture 06 summary lcolladotor.github.io/jhustatcompu... #RStats #DataScience #ggplot2 #DataViz
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Renee García-Flores @freneegf.bsky.social · 16/09/2026
After a few more sprints between rooms and more great talks, we finished the day with the keynote by @christinezhang.bsky.social, Graphics Editor at The NYT. She’s part of the team behind many of the graphs the NYT times used on election night in 2024. (I was fangirling cuz she is so cool 😅)
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Renee García-Flores @freneegf.bsky.social · 16/09/2026
Day 1 of talks at posit::conf(2026) started with keynote speakers @sara-altman.bsky.social and @simonpcouch.com They talked about Posit’s efforts on building AI tools that are correct (trustworthy) while staying convenient (straightforward and intuitive). slides: pos.it/keynote #PositConf2026
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Renee García-Flores @freneegf.bsky.social · 14/09/2026
Woo! posit::conf(2026) started this morning, and I am super happy and grateful to be a Posit Opportunity Scholar this year! I am starting the week attending the Modern R Workflow Workshop taught by @jennybryan.bsky.social and @hadley.nz #PositConf2026
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 15/09/2026
140.776 - Statistical Computing at @jhubiostat.bsky.social @johnshopkinssph.bsky.social Lecture 05 summary lcolladotor.github.io/jhustatcompu... Full notes at gist.github.com/lcolladotor/... #RStats #DataScience #postcards #dplyr #tidyr
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Christine Zhang @christinezhang.bsky.social · 13/09/2026
Headed to Houston for #positconf! I can’t overstate the impact that @posit.co’s opensource products & packages (RStudio, Positron, tidyverse) have had on me as a journalist & data nerd 🤓 Thrilled/terrified to be giving a keynote presentation on Tues. If you’re there, say hello! conf.posit.co/2026/
Keynote Session by Christine Zhang, Graphics Editor at The New York Times: How to Be Clear When You Can’t Be Certain
Sometimes, data visualization is about using charts to illustrate a key point or conclusion gleaned from analyzing the data. But what if you’re not sure what the conclusion is? Presenting examples from news reporting on the topics of elections, polling and economics, I will talk about how I have grappled with uncertainty and how to communicate it to the public.
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 14/09/2026
We are excited to host @areal25.bsky.social at @lieberinstitute.bsky.social In prep, my team did a journal club on the #BigBrain project preprint "Mapping genetic effects on splicing [...]" doi.org/10.1101/2025... from the @trajnp.bsky.social & @davidaknowles.bsky.social labs youtu.be/iVyVcAgPZW8
youtu.be
[2026-09-02] Journal club on "Mapping genetic effects on splicing [...]" aka BigBrain project
YouTube video by Leonardo Collado Torres
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Bernie Mulvey @berniejmulvey.bsky.social · 11/09/2026
Excited to share work with cryostat wizard @heenadivecha.bsky.social looking at gene expression in my favorite brain region (LC) in adult postmortem brain! (Long URL to spare the trouble of identifying cars, buses, beds in 5x5 pixel imgs). (1/x) link.springer.com/epdf/10.1007...
link.springer.com
Molecular programs in human locus coeruleus link APOE and neuromelanin to Alzheimer’s vulnerability
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Jorge Miranda Barrientos @jorge-miranda.bsky.social · 11/09/2026
A little bit of what we are doing in the circuits group at @lieberinstitute.bsky.social. An Amphetamine recruited ensemble in the mPFC tagged with mCherry. Credits to Suhaas Adiraju (Grad student) and @danolivares.bsky.social. #fluorescencefriday
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 08/09/2026
140.776 - Statistical Computing at @jhubiostat.bsky.social @johnshopkinssph.bsky.social Lecture 03 summary lcolladotor.github.io/jhustatcompu... #RStats #DataScience #quarto
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 03/09/2026
140.776 - Statistical Computing at @jhubiostat.bsky.social @johnshopkinssph.bsky.social Lecture 2 summary #RStats #DataScience #git #GitHub #Reproducibility @jennybryan.bsky.social
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 03/09/2026
140.776 - Statistical Computing at @jhubiostat.bsky.social @johnshopkinssph.bsky.social Lecture 1 summary #RStats #DataScience
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Vinny Costa @vincentcostaphd.bsky.social · 28/08/2026
Like I have mentioned before spatial neurobiology is very hard. @svitlanabach.bsky.social makes the impossible seem routine.
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 23/08/2026
The last 3 years of my PhD I worked with LIBD data and was co-advised by @aejaffe.bsky.social. Then on 2016-08-22, #10YearsAgo today, I started my job at @lieberinstitute.bsky.social. The decision to stay on wasn’t the easiest but it felt like the best one for me: one I’m glad that I said yes to.
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Jorge Miranda Barrientos @jorge-miranda.bsky.social · 14/08/2026
Coming back from another amazing GRC frontal cortex. So proud of Suhaas Adiraju who presented some of the work we are doing at @lieberinstitute.bsky.social about Amphetamine ensembles within the mPFC.
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Bioconductor @bioconductor.bsky.social · 13/08/2026
🌟Thank you, R consortium, for supporting the Bioconductor community and helping make BioC2026 possible. R Consortium's mission is to support the R Foundation and organizations that develop, maintain, distribute & use R by identifying, developing & implementing infrastructure projects. #BioC2026
Thank you message for BioC2026 acknowledging R Consortium as a Silver Sponsor, featuring the Bioconductor logo, large colorful "THANK YOU" text, a boxed R Consortium logo with a "SILVER SPONSOR" badge, rainbow-colored raised-arms figures, and the line "Your generosity helped bring our community
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Keri Martinowich @martinowk.bsky.social · 31/07/2026
Congratulations @robinmagnard.bsky.social @daiannaglez.bsky.social and everyone involved from @kr-maynard.bsky.social @triciajanak.bsky.social @lcolladotor.bsky.social teams! Excited to see you all get this paper published and excited for the next steps and follow up studies!
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Jorge Miranda Barrientos @jorge-miranda.bsky.social · 30/07/2026
I am so thrilled to share that i was selected to received the 2026 BBRF young investigator grant from the @bbrfoundation.bsky.social. This is meaningful for me. Thanks so much to @martinowk.bsky.social and the @lieberinstitute.bsky.social for all the support.
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Robin Magnard @robinmagnard.bsky.social · 30/07/2026
The dataset is openly shared and available for download here 👇 github.com/LieberInstit...
github.com
GitHub - LieberInstitute/fentanyl_rat_hb_amy
Contribute to LieberInstitute/fentanyl_rat_hb_amy development by creating an account on GitHub.
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Robin Magnard @robinmagnard.bsky.social · 30/07/2026
It was great working with @daiannaglez.bsky.social on this study! This is the first paper from a collaboration between @triciajanak.bsky.social, @lcolladotor.bsky.social and @kr-maynard.bsky.social labs! Stay tuned for our single-cell profiling follow-up in both males and females!
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Robin Magnard @robinmagnard.bsky.social · 30/07/2026
Integration with existing rodent and human single-cell datasets linked these changes to specific neuronal, glial and vascular cell types. In the amygdala, upregulated genes overlapped with schizophrenia risk genes, while downregulated genes were enriched for substance use disorder risk genes.
The left and middle heatmaps link amygdala differentially expressed gene groups to enriched cell types in mouse and human single-cell datasets. The right heatmap compares habenula and amygdala gene groups with genes associated with disorders in large human genetic studies, known as genome-wide association studies (GWAS). Upregulated amygdala genes overlapped with schizophrenia-associated genes, while downregulated genes overlapped with substance-use-disorder-associated genes.
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Robin Magnard @robinmagnard.bsky.social · 30/07/2026
Bulk RNA-seq found 453 differentially expressed genes in the habenula and 3,041 in the amygdala. Upregulated genes: synaptic transmission and ion conductance in the habenula; metabolic and vesicular functions in the amygdala. Downregulated genes: extracellular matrix functions in both regions.
The upper heatmap shows log-fold changes for genes uniquely or jointly differentially expressed in the habenula and amygdala, separated into upregulated and downregulated groups. The lower matrix links these gene groups to enriched Gene Ontology terms in biological-process, cellular-component, and molecular-function categories. Shared downregulated genes are prominently associated with extracellular-matrix and glial functions.
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Robin Magnard @robinmagnard.bsky.social · 30/07/2026
🧠🧬 What are the effects of intravenous fentanyl self-administration on the habenula and amygdala transcriptomes? In our new Addiction Biology paper, we addressed this question using a chronic long-access model in rats! Here are some highlights 🧵👇 Paper 👉 dx.doi.org/10.1111/adb....
dx.doi.org
Transcriptional Response to Chronic Long‐Access Fentanyl Self‐Administration in Rat Habenula and Amygdala
Chronic intravenous long-access fentanyl self-administration in rats produced transcriptional remodeling in the habenula and amygdala. Bulk RNA-sequencing identified 453 habenula and 3,041 amygdala d...
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Keri Martinowich @martinowk.bsky.social · 16/07/2026
Was HOT 🌞 yesterday for long standing @lieberinstitute.bsky.social annual 🦀 feast tradition. Thanks to everyone on our teams who came out to celebrate another year of accomplishments, community and great science!
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Prashanthi Ravichandran @prashanthi-ravi.bsky.social · 02/07/2026
(1/10) We’re excited to share our recently published study www.sciencedirect.com/science/arti... which uncovers the spatiomolecular landscape of the human NAc, a key reward structure by integrating snRNA-seq with Visium spatial transcriptomics. 🧠 #NAcLIBD #snRNAseq #10xVisium
sciencedirect.com
Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbens
The nucleus accumbens (NAc) is a key component of the mesolimbic dopamine system that is implicated in several neuropsychiatric disorders. The NAc con…
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Kristen Maynard @kr-maynard.bsky.social · 02/07/2026
Excited to share our new study characterizing spatial gene expression in the human NAc led by @prashanthi-ravi.bsky.social @svitlanabach.bsky.social @rphillips3.bsky.social in collaboration with @martinowk.bsky.social @stephaniehicks.bsky.social @alexisbattle.bsky.social @lcolladotor.bsky.social.
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 29/06/2026
Me pregunto si conocen a alguien en #Guatemala 🇬🇹 que trabaje con datos de transcriptómica ( #scRNAseq #RNAseq #SpatialTranscriptomics) y/o use R y en especial #Bioconductor. Para ver si puedo coordinar y a dar una plática por allá. ¡Gracias! #RStats #RStatsES #ARNsec
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 06/06/2026
New team photos! 2026 version with @mbarse.bsky.social, @lahuuki.bsky.social, @nick-eagles.bsky.social ^^. We also have remote member contributors 🗺️ (@daiannaglez.bsky.social, @melo-mq99.bsky.social, @gabrielramirezv.bsky.social, from LCG UNAM). Thank you @martinowk.bsky.social for hosting us!
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Robin Magnard @robinmagnard.bsky.social · 15/05/2026
Thrilled about our new @janaklab.bsky.social paper now out in @npp-journal.bsky.social🧠⚡ Action-sequence termination cues evoke mesolimbic dopamine activity that drives habit-like behavior. Thanks to Tricia Janak, @younavandaele.bsky.social, and @yfcheng.bsky.social! www.nature.com/articles/s41...
nature.com
Sequence termination cues drive automated habit-like strategy via dopamine-mediated processes - Neuropsychopharmacology
Neuropsychopharmacology - Sequence termination cues drive automated habit-like strategy via dopamine-mediated processes
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elizabethginexi.bsky.social @elizabethginexi.bsky.social · 29/05/2026
Summary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule. Russell Vought is going destroy American Science. elizabethginexi.substack.com/p/summary-of...
elizabethginexi.substack.com
Summary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule
Russell Vought is going destroy American Science
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 26/05/2026
Si conocen a mexicano/as 🇲🇽 en @jhu.edu (o afiliada/os) y/o profesionistas en Baltimore, avísenme. Organizo un grupo de WA de mexas en Balto que estoy buscando revivir. Voy a aprovechar que estoy organizando una fiesta con mariachis 🎺 🎤 y así intentar fomentar nuestra pequeña comunidad. ¡Gracias!
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Emily R. Trunnell, Ph.D. @ertrunnell.bsky.social · 24/05/2026
Schizophrenia’s defining features—perception, thought, cognition—are inseparable from human language and self-awareness. These cannot be reproduced in other animals. Yesterday, in SAO's #WorldSchizophreniaDay article, we celebrated the research that's moving in a different direction. #SCZ #SCZDay
A graphic with a cartoon drawing of a person with their head in their hands. Squiggles surround their head, signifying mental health struggles. The text reads: "Studying schizophrenia across scales with human biology. Schizophrenia Awareness Day. May 22, 2026." The SAO logo is in the bottom right corner.
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Stephen Turner @stephenturner.us · 20/05/2026
Lots of cognitive dissonance from reading Nature today
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Abigail Goben @hedgielib.bsky.social · 20/05/2026
It's NIH grant season and I'm talking to a number of researchers with questions about the new DMSP form. Let us briefly marinate in the nonsense. (1/)
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rOpenSci @handle.invalid · 13/05/2026
✍️ 15 Years of rOpenSci, and We’re Just Getting Started 🎉 by The rOpenSci Team rOpenSci turns 15! 🎉 We're celebrating all year long, starting with three virtual community events on June. Come connect, reflect, and help shape the next 15 years […] [Original post on hachyderm.io]
Retro pixel-art graphic celebrating rOpenSci's 15th anniversary. The text 'rOpenSci' appears at the top in pixel font, flanked by three pixel-art balloons. A browser window frames the central message: '15 YEARS / TRANSFORMING OPEN SCIENCE' in bold pixel letters, overlaid on the rOpenSci geometric network pattern. A pixel badge reads 'OMG'. A pixel folder and sparkle icons complete the design. Made in Canva by Yani using a template design by Lauren Creatives
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Keri Martinowich @martinowk.bsky.social · 08/05/2026
Reading thank you letters from the kids after doing a Career Day presentation at my kids elementary school, and totally chuffed by some responses: -I think you are 37 -You are so smart, you must make a million dollars -Thanks to you, I'm in love with my brain -You are cool and so is your brain :)
A title slide for a presentation to elementary school students about neuroscientists
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Molly Schumer @mollyschumer.bsky.social · 08/05/2026
@gpreising.bsky.social is a long read rock star and is looking for postdocs or industry positions! bsky.app/profile/lcol...
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 08/05/2026
Alexis @alexisbattle.bsky.social did an awesome introduction for Jonathan’s @jkpritch.bsky.social for his #BoG2026 keynote! That was reaaaally good! 👏🏽 👏🏽 @cshlmeetings.bsky.social
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 08/05/2026
En #BoG2026 hubo varixs mexicanxs 🇲🇽 o científicxs trabajando con datos de México🇲🇽 Me da gusto 😊 aprender de sus contribuciones a la ciencia. Esta vez hubo proyectos del Mexican Biobank doi.org/10.1038/s415... @cshlmeetings.bsky.social @valenomics.bsky.social Ana @xavierrocarada.bsky.social Irepan
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Taylor Head, PhD @taylorhead.bsky.social · 06/05/2026
Excited to present a poster at #bog26 this evening starting at 7:30pm! Come by poster #108 to learn about some motivating and preliminary work on a novel method to fine-map causal isoforms in TWAS leveraging tissue-specific long-read RNA-seq evidence.
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Taylor Head, PhD @taylorhead.bsky.social · 06/05/2026
Shout-out to @seantbres.bsky.social who will be presenting some really interesting work at #bog26 this evening! Using long-read, isoform-resolved placental transcriptomics, this work shows how PFAS exposure impacts placental transcriptional networks and imprinting (poster #70)
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 08/05/2026
Mohamed @mabuelanin.bsky.social included a super cute slide about microtus radiation (referring to new species not ☢️) 🦫🐀 They used #CiFi cifi.dennislab.org which they developed recently. Got chromosome-level scaffolds including several T2T genome 🧬 cases #BoG2026 @cshlmeetings.bsky.social
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 08/05/2026
Arang Rhie from @aphillippy.bsky.social ’s lab told us about there is hidden structural variation on the human acrocentric chromosomes This project benefited from UK Biobank using all hg38 sequences (chrUn_…) More available at doi.org/10.64898/202... #BoG2026 @cshlmeetings.bsky.social
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 08/05/2026
Winston @timp0.bsky.social is guiding us through a #DNAm journey starting with his paper with @kasperdhansen.bsky.social from 2011 Nowadays with @pacbio.bsky.social and @nanoporetech.com long read DNA data you get DNAm for free! 5mC, 5hmC, brain 🧠 etc 🐇 🕳️ #BoG2026 @cshlmeetings.bsky.social
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Rob Patro @robp.bsky.social · 08/05/2026
Very interesting! We looked at using perplexity to evaluate quantification estimates in the absence of a ground truth (link.springer.com/article/10.1...). Our inspiration was NLP. I think it's a potentially very useful metric overall.
link.springer.com
Perplexity: evaluating transcript abundance estimation in the absence of ground truth - Algorithms for Molecular Biology
Background There has been rapid development of probabilistic models and inference methods for transcript abundance estimation from RNA-seq data. These models aim to accurately estimate transcript-leve...
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 08/05/2026
Nilah Ioannidis kickstarted #BoG2026 ’s Friday by guiding us through their explorations of how DNA 🧬 sequence prediction models actually perform with unseen sequences Goal: use these models in the clinic for personal genomics to predict individual molecular changes @cshlmeetings.bsky.social
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