Yashar Zeighami

WeRTogether-useR!2025Keynote We R Together Yanina Bellini Saibene useR! 2025 Duke University How to learn, use and improve a programming language as a community

Still smiling after my keynote abt Community at #useR2025 💜

Huge thanks to the organizing team for the invite, and to everyone who joined, asked questions, and shared their thoughts — you made it truly special!

Slides docs.google.com/presentation...

Video: www.youtube.com/live/CTTvTQ-...
#rstats

Mapping cerebral blood perfusion and its links to multi-scale brain organization across the human lifespan | doi.org/10.1371/jour...

How does blood perfusion map onto canonical features of brain structure and function? @asafarahani.bsky.social investigates @plosbiology.org ⤵️

Hey #AAIC25 !
Today I'll be sharing our research on the mediating effect of WMH on spontaneous brain activity during aging! 🧠
Join me on poster 430!
@ameliemetz.bsky.social @dadarmahsa.bsky.social @yasharneuro.bsky.social @roqamoqa.bsky.social

Individual response to lifestyle interventions: a pooled analysis of three long-term weight loss trials AbstractAims. We explored the manifestations of individual weight loss (WL) response to long-term lifestyle interventions on cardiometabolic risk.Methods a

A healthy lifestyle in intervention clinical trials for weight loss, even without long term weight loss (only achieved in ~33%), led to improvement of key cardiometabolic factors
academic.oup.com/eurjpc/advan...

Vascular risk factors mediate the relationship between education and white matter hyperintensities https://www.medrxiv.org/content/10.1101/2025.06.03.25328899v1

Gray matter microstructure from in-vivo diffusion MRI reflects post-mortem neuropathology severity and clinical progression of Alzheimer's disease https://www.medrxiv.org/content/10.1101/2025.05.30.25328630v1

Sex Differences in Vulnerability to Tau Pathology: Impact on Cognitive Decline https://www.medrxiv.org/content/10.1101/2025.05.25.25328324v1

Congrats to HBHL-funded researcher & 2022 HBHL New Faculty Recruit @dadarmahsa.bsky.social on being awarded the President’s Prize for Outstanding Emerging Researchers at the 2025 @mcgill.ca @healthsciences.mcgill.ca Convocation Ceremony! Well deserved. 👏

🔗 reporter.mcgill.ca/mcgills-pres...

#SpatialTranscriptomics #BatchCorrelation

SpaBatch

Align multi-slice sequencing-based spatial data
Visium ST Stereo-seq

#VariationalGraphAutoEncoder
Masked data augmentation

vs STG3Net STAligner SEDR DeepST SpaGIC STitch3D

bioRxiv 2025
www.biorxiv.org/content/10.1...

(1/6) Thrilled to share our triple-N dataset (Non-human Primate Neural Responses to Natural Scenes)! It captures thousands of high-level visual neuron responses in macaques to natural scenes using #Neuropixels.

New paper in Imaging Neuroscience by Gustavo Chau Loo Kung, Jennifer A. McNab, et al:

Non-parametric prediction of brain MRI microstructure using transfer learning

doi.org/10.1162/imag...

Sneak peek from first poster session at #HBHLSymposium2025 📸

With over 100 trainees presenting their innovative research on brain health, it's a great opportunity to explore new perspectives and pioneering work from the next generation of researchers! 🖼️🎓 @healthsciences.mcgill.ca

A Multi-Scale Neuron Morphometry Dataset from Peta-voxel Mouse Whole-Brain Images - Scientific Data Scientific Data - A Multi-Scale Neuron Morphometry Dataset from Peta-voxel Mouse Whole-Brain Images

A Multi-Scale Neuron Morphometry Dataset from Peta-voxel Mouse Whole-Brain Images | Scientific Data www.nature.com/articles/s41...

@maximoprado.bsky.social and @mallarchak.bsky.social present their @westernubrainscan.bsky.social supported work on early biomarkers for development and monitoring of effective disease-modifying therapies at the #hbhlsymposium2025. @hbhlmcgill.bsky.social @westernu.bsky.social

Up next at #HBHLSymposium2025, @maximoprado.bsky.social & @mallarchak.bsky.social discussed their Initiative for Translational Neuroscience (ITN) collaboration & unpacked how early biomarkers help develop & monitor better treatments for neurodegenerative diseases. 🧪

@westernuresearch.bsky.social

Bar chart showing 651 NSF-funded research projects, with total terminated days in dark grey or red, completed days in light grey or red. Red highlights projects listed by Ted Cruz as "neo-Marxist class warfare propaganda".

For #TidyTuesday this week, we're looking at data on terminations of NSF grants 📊

🎨 Using colour to highlight one category
📈 Transparency to highlight the important data
✍️ Annotations instead of a legend for transparency

#RStats #ggplot2 #DataViz

Title slide: Trust the process? (Causal) Mediation analysis

Decision flowchart "So you want to conduct a mediation analysis"

This Thursday I will give a talk on (causal) mediation analysis -- happy to have finally worked out what I want to tell people.
And happy to pilot a new mode of slide sharing: just putting them on my website (juliarohrer.com/resources/)

You've heard of the many analysts projects, right?

Scholars give the same dataset/question to a bunch of researchers & they still get different answers.

Why is that?

Data cleaning!

This is consistent with Gelman's "garden of forking paths." Small coding decisions often drive results.

Neuroblox: A biomimetic brain modeling platform to test interventions and generate new scientific insights.
www.neuroblox.org
#neuroscience

Dissection of blood–brain barrier dysfunction through CSF PDGFRβ and amyloid, tau, neuroinflammation, and synaptic CSF biomarkers in neurodegenerative disorders CSF PDGFRβ, a candidate biomarker of BBB dysfunction, is increased in the early stages of neurodegenerative disorders, in association with neuroinflammation and axonal and synaptic damage.

www.thelancet.com/journals/ebi...

Epigenetic (methylation, biological) age is associated with increased risk of dementia and brain structural changes (including atrophy). From UK Biobank's 280,000 participants, ~4,800 cases of dementia over 14-year follow-up
www.neurology.org/doi/10.1212/...

Are you tired of getting signal dropout in your gradient echo EPI for spinal cord fMRI applications? Check out this new shimming study by Bréheret, D'Astous, Ma, Stockmann 🚀

👉 doi.org/10.1002/mrm....

Awesome opportunity to work on women’s brain health with an absolute star — pls repost

C-SIDE
Cell type-specific inference of differential expression in #SpatialTranscriptomics

👉Work for both Sequencing- & Imaging-based ST
👉Need single-cell reference
👉Histological features as covariates
👉Pixel-based Segmentation-free DEA

@naturemethods.bsky.social 2022
www.nature.com/articles/s41...

New paper in Imaging Neuroscience by Jack A. Reeves, Ferdinand Schweser, et al:

IRONMAP: Iron network mapping and analysis protocol for detecting over-time brain iron abnormalities in neurological disease

doi.org/10.1162/imag...

New paper in Imaging Neuroscience by Rebecca G. Clements, Molly G. Bright, et al:

Quantitative mapping of cerebrovascular reactivity amplitude and delay with breath-hold BOLD fMRI when end-tidal CO2 quality is low

doi.org/10.1162/imag...

@christopherjwhyte.bsky.social and I introduce a novel data-driven framework to evaluate >200 connectivity-based neural correlates of consciousness! Results are used to quantitatively compare predictions from neurodynamical models tailored to theoretic predictions.

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

Hey #ADPD2025 , I'm happy to present our work on characterizing brain atrophy and cerebrovascular pathology in Frontotemporal Dementia subtypes!

Tomorrow, April 5, 9:40am, Hall F2, session: Mechanisms and Clinical Trials in FTD, ALS, and Neurodegeneration 02

Multi-modal Monte Carlo MRI simulator of tissue microstructure | bioRxiv www.biorxiv.org/content/10.1...

The CNeuroMod longitudinal brain and spine structural protocol

🧠📊 Just out: a deeply sample structural brain and spine dataset from the cneuromod.ca team, now published in Imaging Neuroscience! led by Mathieu Boudreau and Julien Cohen-Adad. 📰 Paper here: lnkd.in/ewXA3dED 1/🧵