🚨Preprint alert! I'm excited to share a new preprint co-led with the talented @shkwon-bcmbneuro.bsky.social during my postdoc at @jhubiostat.bsky.social . In this project, we investigated the 𝐦𝐨𝐥𝐞𝐜𝐮𝐥𝐚𝐫 𝐩𝐚𝐭𝐡𝐨𝐥𝐨𝐠𝐲 𝐨𝐟 𝐬𝐜𝐡𝐢𝐳𝐨𝐩𝐡𝐫𝐞𝐧𝐢𝐚 𝐢𝐧 𝐝𝐥𝐏𝐅𝐂 𝐮𝐬𝐢𝐧𝐠 𝐭𝐡𝐞 𝐜𝐮𝐭𝐭𝐢𝐧𝐠-𝐞𝐝𝐠𝐞 𝐬𝐩𝐚𝐭𝐢𝐚𝐥 𝐦𝐮𝐥𝐭𝐢-𝐨𝐦𝐢𝐜𝐬 𝐚𝐩𝐩𝐫𝐨𝐚𝐜𝐡.

Sang Ho (Sangho) Kwon@shkwon-bcmbneuro.bsky.social · 6mo ago

FIRST post here on Bluesky - we’re excited to share that our large spatial transcriptomics study of the human dlPFC in schizophrenia is now available on bioRxiv📄: www.biorxiv.org/content/10.6... (1/9)

"Absurd ad hoc analysis pipelines are justified solely by their results, not by their logic. And once they are published, open code just makes things worse, because other researchers use the code to publish more rubbish."

Richard McElreath 🐈‍⬛@rmcelreath.bsky.social · last yr.

How can we reform science? I have some ideas. But I am not sure you’ll like them, because they don’t promise much. elevanth.org/blog/2025/07...

Yes, we should give you guidance up front. Also, as I frequently say, if you ever have a question about what your editor wants to see in a revision, ask us to review/approve a revision plan. I never want my authors losing sleep over my expectations. Truly.

Sometimes authors summarize their responses to 3-6 major points raised by the reviewers in their resub cover letters or at the top of their rebuttal letters. This is so super helpful to editors, because it brings us right up to speed after not having read the paper/reviews for months. THANKS!!

Inspiring read to understand where the genomics study of complex psychiatric disorder stands now. Very excited how spatial transcriptomics contributes enlightening mediating effect of genetic risk variants. Some cool work is brewing! www.nature.com/articles/s41...

Genomics of schizophrenia, bipolar disorder and major depressive disorder

Nature Reviews Genetics - Genomic advances have enhanced our understanding of schizophrenia, bipolar disorder and major depressive disorder, revealing genetic architectures and risk mechanisms...

nature.com

my work with @stephaniehicks.bsky.social and @boyiguo.bsky.social has been published in Biostatistics! tldr: the mean-variance bias exists in SRT data & impacts SVG detection. we propose #spoon, available on @bioconductor.bsky.social, to address this! pmc.ncbi.nlm.nih.gov/articles/PMC... 🤩

#SpotSweeper is now published! Check our journal club session summary of the pre-print version by @lahuuki.bsky.social The new features @boyiguo.bsky.social + @mictott.bsky.social added in this revised manuscript enhance the use cases for #SpotSweeper: 👀 #VisiumHD data! youtu.be/f72XcXmtkfw?...

[2024-09-04] Journal club on SpotSweeper

YouTube video by Leonardo Collado Torres

youtu.be

Michael Totty@mictott.bsky.social · last yr.

🚨 New paper published in @natmethods.nature.com! We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics. 📰 Paper : nature.com/articles/s41... 💻 Code: github.com/MicTott/Spot... 📈 Website: mictott.github.io/SpotSweeper/ 🧵👇

Great collaboration motivates methodological and biological innovation! Grateful for the opportunity to work together with @martinowk.bsky.social and @lieberinstitute.bsky.social, investigating the molecular pathology of neuropsychiatric disorder, coming soon! 😉

Keri Martinowich@martinowk.bsky.social · last yr.

Important methods development for spatial transcriptomics (ST) data from @mictott.bsky.social @boyiguo.bsky.social @stephaniehicks.bsky.social - congrats! Applying this method to our QC workflow has substantially improved many new ST datasets generated across diverse regions/tissues in the human 🧠

Important methods development for spatial transcriptomics (ST) data from @mictott.bsky.social @boyiguo.bsky.social @stephaniehicks.bsky.social - congrats! Applying this method to our QC workflow has substantially improved many new ST datasets generated across diverse regions/tissues in the human 🧠

Michael Totty@mictott.bsky.social · last yr.

🚨 New paper published in @natmethods.nature.com! We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics. 📰 Paper : nature.com/articles/s41... 💻 Code: github.com/MicTott/Spot... 📈 Website: mictott.github.io/SpotSweeper/ 🧵👇

Excited to announce that I'll start as a tenure-track assistant professor @uofuphs.bsky.social this fall. #BiostatsElevated The #GUOmics lab will focus on developing biologically informed machine learning methods to decode spatial and population-scale omics data. Look forward to exciting colabs!

🤔Could quality control create more harm than good? We explore this question in the context of #SRT. SpotSweeper is developed to combat implicit selection bias. Led by fellow rising star @mictott.bsky.social and collab with amazing mentor @stephaniehicks.bsky.social 👉: bsky.app/profile/mict...

Nature Methods@natmethods.nature.com · last yr.

Quality control matters in spatial transcriptomics. Check out this paper from Guo and colleagues on SpotSweeper that corrects for both local and regional artifacts across diverse technologies. www.nature.com/articles/s41...

Your yearly reminder to acknowledge the core facilities you use and their staff scientists in your papers. These scientists are a crucial part of the scientific ecosystem and to continue to exist they need tangible credit for their work. Plus their associated expertise adds credibility to your work.

"An open letter to graduate students and other procrastinators: it’s time to write" www.nature.com/articles/s41... Enjoyed reading the article, and reflect on my own writing workflow. Plan to include in my lab handbook as resources for trainees. #PDL#writing#comp-lab

An open letter to graduate students and other procrastinators: it’s time to write - Nature Biotechnology

Nature Biotechnology - An open letter to graduate students and other procrastinators: it’s time to write

nature.com

Excited to share a new algorithm that we have been working on over the last year. 💡 idea is to extend mutual nearest neighbors for #spatial data. We call it spatial mutual nearest neighbors (spatialMNN) 😄 Thank you @haowen-zhou.bsky.social @pratibha-panwar.bsky.social who led this work! 👏 🧬🖥️🧪

thank you @stephaniehicks.bsky.social and @boyiguo.bsky.social for your amazing mentorship on this project! so excited that this is finally out

Stephanie Hicks@stephaniehicks.bsky.social · 2y ago

Fantastic poster from @kinnaryshah.bsky.social tonight at #biodata24! She developed the spoon package to correct for the mean variance relationship in #spatial transcriptomics data #ProudPI #stats 🖥️🧬🧪🧠📈 Preprint: www.biorxiv.org/content/10.1... Software: www.bioconductor.org/packages/spoon