Pretty neat to see our paper - led by @kr-maynard.bsky.social @lcolladotor.bsky.social on the 2021 list of most cited neuroscience papers 🧠🔬🧪 www.thetransmitter.org/publishing/w...

The most-cited neuroscience papers from the past 30 years

Highly cited papers reflect the surge in artificial-intelligence research in the field and other technical advances.

thetransmitter.org

We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor”!

Helena Lucia Crowell@helucro.bsky.social · 9mo ago

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA. Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions). It’s been a joy working with you @estellayixingdong.bsky.social!

I am very excited to share this book! It has been so much to collaborate on the project. We hope you find it useful!

Helena Lucia Crowell@helucro.bsky.social · 9mo ago

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA. Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions). It’s been a joy working with you @estellayixingdong.bsky.social!

Orchestrating Spatial Transcriptomics Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.11.20.688607v1

Orchestrating Spatial Transcriptomics Analysis with Bioconductor (including interoperability with Python) Paper: www.biorxiv.org/content/10.1... Book: bioconductor.org/books/OSTA/ #Rstats

Whether you're new to bioinformatics or a seasoned pro, OSTA covers everything that you need to know about spatial transcriptomics data analysis spanning both sequencing and imaging-based technologies within the Bioconductor framework 👨‍💻🧬 Congrats to all the authors on this huge effort!

Helena Lucia Crowell@helucro.bsky.social · 9mo ago

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA. Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions). It’s been a joy working with you @estellayixingdong.bsky.social!

Honored to have gotten to be a part of this! I vividly remember the very early days of spatial transcriptomics when we were all scratching our heads over what to do with all this new data! It's come a long way - congrats @helucro.bsky.social @lmweber.bsky.social and everyone who contributed to this!

Helena Lucia Crowell@helucro.bsky.social · 9mo ago

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA. Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions). It’s been a joy working with you @estellayixingdong.bsky.social!

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA. Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions). It’s been a joy working with you @estellayixingdong.bsky.social!

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 9mo ago

Orchestrating Spatial Transcriptomics Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.11.20.688607v1

so excited to share that our preprint characterizing the dorsal anterior cingulate cortex in post-mortem human brain from @lieberinstitute.bsky.social is out! we integrated matched SRT and snRNA-seq data to investigate agranularity and von Economo neurons

Winter in Western Australia ☀️

Going from methods dev to full on cancer bio has been tough. All the more excited to see this out at last— www.biorxiv.org/content/10.1... @pascual-reguant.bsky.social @brukerspatial.bsky.social @hoheyn.bsky.social

Tracing colorectal malignancy transformation from cell to tissue scale

The transformation of normal intestinal epithelium into colorectal cancer (CRC) involves coordinated changes across molecular, cellular, and architectural scales; yet, how these layers integrate remai...

biorxiv.org

Update: We greatly revised our paper and renamed it “Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta”. We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases. arxiv.org/abs/2412.01561

Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta

Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can gi...

arxiv.org

Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind

Very excited to see this important work out led by the talented @mictott.bsky.social @boyiguo.bsky.social @jhubiostat.bsky.social! 🧪🧬🖥️

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/ 🧵👇

🚨 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/ 🧵👇

SpotSweeper: spatially aware quality control for spatial transcriptomics - Nature Methods

SpotSweeper is a spatially aware method for quality control of spatially resolved transcriptomics data that corrects for spatial confounding missed by existing methods, including both local and region...

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... 🤩

Feels like a social media tipping point might have happened 🐦🔵

This morning I'm teaching an intro to single cell data science! Feeling very appreciative to all the amazing developers in the #Bioconductor and open science #rstats communities! #Genomics 🖥️ 🧬 #stats 👩‍🔬 🔗 stephaniehicks.com/singlecellde...

One last visit to Washington DC before I leave for Boston 🇺🇸

Hello world 🙂🌤️