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Doc Rowdy

@scrnaseq.bsky.social
330 followers 1.3K following 11 posts

JupyterLab is my Winamp visualizer.

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#SingleCell preprints @prepub-singlecell.bsky.social · 01/10/2026
Single-cell transcriptomics reveals life cycle and cell cycle gene expression dynamics during in vitro growth of two Leishmania species #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20…
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Doc Rowdy @scrnaseq.bsky.social · 01/10/2026
www.frontiersin.org/journals/imm... 👀📊
frontiersin.org
Frontiers | Ranitidine Inhibition of Breast Tumor Growth Is B Cell Dependent and Associated With an Enhanced Antitumor Antibody Response
Background: The histamine receptor 2 antagonist ranitidine is a commonly used, non-prescription, medication. It limits the development, growth and metastasis...
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MwahahahahahadScientist @mads100tist.bsky.social · 24/08/2023
The plot thickens
An X Y axis plot showing dots that get progressively thicker
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Jan Lammerding - Lab @lammerdinglab.bsky.social · 21/09/2026
Looking for a faculty position combining research in fundamental cell and molecular biology with therapeutic discovery? Join our amazing faculty at the @weillinstitute.bsky.social at Cornell University in Ithaca, New York. academicjobsonline.org/ajo/jobs/32657 Apply by Nov. 15! Please share!
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#SingleCell preprints @prepub-singlecell.bsky.social · 19/06/2026
Vibrational optoacoustic detection of lipid-membrane dynamics enables label-free imaging of cell membrane potential #SingleCell 🧪🧬🖥️ www.biorxiv.org/content/10.64898/20…
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Cenk Celik @cenkcelik.bsky.social · 12/06/2026
Are you interested in learning multiomics analysis for your project? Join me for a hands-on workshop at Bilimler Köyü (Village of Sciences) in Foça, İzmir for a week. #spatialtranscriptomics #scrnaseq
Life at the single-cell and spatial resolution.
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Australian BioCommons @ausbiocommons.bsky.social · 15/06/2026
Upskill in #scRNAseq! Our July workshop covers QC, normalisation, and clustering in R. Learn the ‘why’ behind the workflow with expert facilitators. Applications close 13 July: www.biocommons.org.au/events/scrna... #NCRISImpact #SingleCell
biocommons.org.au
WORKSHOP: Single cell RNAseq analysis in R — Australian BioCommons
Analysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell RNAseq analysis using a number of tool. More information Apply
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Paola A. Marignani @pmarignani.bsky.social · 17/03/2026
💨☕👩‍💻Excited to share our recent discovery. Tumour suppressors LKB1 and SMARCA4 working together to regulate gene expression, acting as a nexus between metabolism and chromatin remodelling. #LungCancer #CancerResearch #Epigenetics #Metabolism #LKB1 #SMARCA4 www.frontiersin.org/journals/cel...
frontiersin.org
Frontiers | Tumor suppressors LKB1 and SMARCA4 functionally interact to regulate gene expression across diverse biological processes in lung cancer
IntroductionThe tumor suppressor kinase liver kinase B1 (LKB1) is known to regulate the activity of the metabolic sensor AMP-activated protein kinase (AMPK),...
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Jean de Lima @jeandelima.bsky.social · 07/03/2026
Excited to share our work published in @cp-immunity.bsky.social! We investigated the role of HIF-1α in CD4 T cells using #Xenium spatial transcriptomics in infected lungs containing #TertiaryLymphoidStructures (TLS) (1/10). www.cell.com/immunity/ful...
cell.com
HIF-1α+ CD4+ T cells coordinate a tissue-resident immune cell network in the lung
Tertiary lymphoid structures are critical components of tissue immunity, necessitating better understanding of their organization and immune functions. De Lima et al. investigate the spatial and tempo...
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Earlham Institute @earlhaminst.bsky.social · 16/03/2026
🆕 New Study: Scientists working on a Gut Cell Atlas have conducted #singlecell #RNAseq on intestinal cells, discovering clusters of immune and endothelial cells localise around scar tissue in the submucosa. 🧬💻 ➡️ buff.ly/0Y9bpZN @uoe-igc.bsky.social @helmsleytrust.bsky.social #CellAtlas #scRNAseq
buff.ly
New study maps cellular mechanisms driving fibrosis in Crohn's Disease
Researchers at the Earlham Institute, the University of Edinburgh and Heriot-Watt University have analysed gut cells to understand the drivers behind fibrosis (scarring), a common complication in Crohn’s Disease affecting 10-20% of patients.
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 09/02/2026
🚀 Course: Advanced Python for Data Science & Bioinformatics 📅 23–26 March | 🌍 Online Ready to level up your Python skills for biology? Dive into data wrangling, BioPython, visualization & machine learning, and build an end-to-end project 🐍📊🧬 www.physalia-courses.org/courses-work... #Python
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Mega, regular edition @megamaniaco.bsky.social · 25/02/2026
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James Lingford @jameslingford.bsky.social · 27/02/2026
A minimal PyTorch re-implementation of AlphaFold2 github.com/ChrisHayduk/... We need more stuff like this. The incentive is to always be making the new groundbreaking tool, while maintenance + improvement of "old" tools gets left behind. But there is still heaps to be gained in "old" tools
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PLOS Biology @plosbiology.org · 25/02/2026
The process of #PeerReview is vital to contemporary science, but is also under enormous strain. @carlbergstrom.com & Kevin Gross use mathematical models to dissect the threats to the long-term viability of peer review, suggesting ways to stabilize it @plosbiology.org 🧪 plos.io/4kR02bo
The Vatican Museums' Bramante Staircase provides a striking visual metaphor for a vicious feedback cycle in scholarly publishing: rising paper submissions across an expanding landscape of journals strains the limited supply of volunteer peer review labor, which in turn makes editorial decisions less predictable and encourages authors to submit their work more ambitiously, increasing the burden on peer reviewers further still. Image credit: Carl T. Bergstrom
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Danai Vagiaki @danaivagiaki.bsky.social · 08/02/2026
As scRNA-seq cohorts grow in scale (e.g. FinnGen, TenK10K), so does the need for methods that can handle millions of cells from thousands of donors. LIVI's scalable design enables systematic trans-eQTL discovery in such datasets, revealing cellular mechanisms underlying complex disease risk. 11/n
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Stegle Lab @steglelab.bsky.social · 10/02/2026
Working on trans-eQTL mapping with population-scale scRNA-seq? Meet LIVI, our latest framework that enables efficient trans-eQTL mapping at single-cell resolution across cohorts of hundreds to thousands of donors. Preprint: doi.org/10.64898/202... Summary in the 🧵 below by @danaivagiaki.bsky.social
doi.org
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 17/02/2026
Allele-specific splicing modulates protein isoforms and Alzheimer's risk www.biorxiv.org/content/10.64898/20…
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bioinfoblogs @bioinfoblogs.bsky.social · 17/02/2026
📝 Researchers identify potential immune evasion mechanism in premalignant lung lesions ✍️ RNA-Seq Blog
rna-seqblog.com
Researchers identify potential immune evasion mechanism in premalignant lung lesions
Article de RNA-Seq Blog
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bioinfoblogs @bioinfoblogs.bsky.social · 14/02/2026
📝 Nanopore sequencing of intact aminoacylated tRNAs ✍️ RNA-Seq Blog
rna-seqblog.com
Nanopore sequencing of intact aminoacylated tRNAs
Article de RNA-Seq Blog
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Science Magazine @science.org · 11/02/2026
When asked to draw a scientist, school-age kids in the United States are increasingly sketching women, according to a study from 2018. Read more on #WomenInScienceDay: scim.ag/4qFrPON
A child drawing of a female scientist. The hedline is: What does a scientist look like? Children are drawing women more than ever before
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Torsten Seemann @torstenseemann.bsky.social · 09/02/2026
A LaTeX package to add coffee strains to your documents😆 framagit.org/Pathe/coffee...
framagit.org
Patrick / coffeestains · GitLab
This package provides an essential feature to LaTeX that has been missing for too long. It adds a coffee stain to your documents. A lot of time can...
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Stephen Turner @stephenturner.us · 06/02/2026
Biological data governance in an age of AI www.science.org/doi/10.1126/... #biosecurity
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Karen K. Ho @karenho.bsky.social · 05/02/2026
the Epstein files are really devastating because they remind me of how many girls and women miss out on professional opportunities, mentorship and careers because of how many powerful, rich and influential men only view girls and women — and interactions with them — through the lens of sex
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Doc Rowdy @scrnaseq.bsky.social · 04/02/2026
"Both research papers and salami can be cut into multiple, smaller pieces." Insightful. en.wikipedia.org/wiki/Least_p...
en.wikipedia.org
Least publishable unit - Wikipedia
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Louise Huuki-Myers @lahuuki.bsky.social · 04/11/2025
Proud to announce our paper ‘Transcriptomic Analysis of the Human Habenula in Schizophrenia’ from @lieberinstitute.bsky.social is the cover article for the November issue of the American Journal of Psychiatry! 🧠 #HabenulaLIBD #snRNAseq #Habenula doi.org/10.1176/appi...
doi.org
Transcriptomic Analysis of the Human Habenula in Schizophrenia | American Journal of Psychiatry
Objective: The objective of this study was to define the molecular neuroanatomy of the human habenula (Hb) and identify transcriptomic differences between brains of individuals with schizophrenia and ...
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bioRxiv Genetics @biorxiv-genetic.bsky.social · 03/02/2026
A Most Powerful Test for Gene-Gene Interaction in the Presence of Main Effects www.biorxiv.org/content/10.64898/20…
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Stevoisiak @stevoisiak.bsky.social · 03/02/2026
I made a filterlist for uBlock Origin to remove Generative AI features on websites. Includes blocks for * Google AI Summaries * YouTube Ask button & chat summaries * GitHub Copilot * Facebook AI chat * X's Grok buttons * Deviantart DreamUp * Booru AI images * And more github.com/Stevoisiak/S...
Google with AI buttonsGoogle without AI buttons
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Pavel @spavel.bsky.social · 01/02/2026
Person: say, i am alive.

Computer: I am alive.

Person: oh my god.
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Nikolai Slavov @slavov-n.bsky.social · 01/02/2026
A reminder that proteins are highly dynamic molecules. 🟧 We have made much progress in measuring & predicting static protein structures, but the dynamics that animate life remain challenging to measure & model.
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Stephen Turner @stephenturner.us · 31/01/2026
Guide to multi-omics integration with toy examples: supervised latent components (DIABLO), unsupervised shared/partial/unique structure (DIVAS), VAEs/conditional VAEs, and key baselines (MOFA, JIVE, SNF) with practical tips + code. github.com/Trhova/Multi...
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Stephen Turner @stephenturner.us · 30/01/2026
Advancing regulatory variant effect prediction with AlphaGenome www.nature.com/articles/s41... 🧬💻🧪 Code: github.com/google-deepm... Author roundtable: www.youtube.com/watch?v=V8lh...
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Doc Rowdy @scrnaseq.bsky.social · 30/01/2026
This preprint combines cell-line scRNA-seq reanalysis with bulk LUAD checks in cBioPortal. The cross-dataset consistency for metabolic and cell cycle terms is encouraging.
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Florian Jug @florianjug.bsky.social · 28/12/2025
🚨 Alarm!!! 🚨 AI/ML course for microscopy image analysis!!! 🧐 In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!? 20 students, ~14 TAs and lecturers 🗓️ June 4-18 2026 ✍️ Jan 15 2026 ✍️ 🔁 pls!! www.janelia.org/you-janelia/...
janelia.org
Deep Learning for Microscopy Image Analysis
Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,
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Michael Hoffman @michaelhoffman.bsky.social · 01/12/2025
My fists
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callista yee @csybio.bsky.social · 26/11/2025
I was lucky enough to inherit a bunch of racks where a graduate student had labelled all of them with Rack jokes 😂, perfect. I am dead at Racksputin.
microcentrifuge tube racks with Rack names
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Doc Rowdy @scrnaseq.bsky.social · 26/11/2025
Most of what makes cells functionally distinct happens at the post-transcriptional level, but we spent a decade obsessing over transcriptomics. scRNAseq is powerful precisely because it's incomplete. It forces us to think about what it doesn't capture.
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Jovana Maksimovic @jovmaksimovic.bsky.social · 26/11/2025
Great work by Hengxin Pan presenting at #abacbs2025 from @nadia-davidson.bsky.social lab @wehi-research.bsky.social CONCERTDR: an R package with a comprehensive suite of tools for drug response data analysis github.com/DavidsonGrou...
github.com
GitHub - DavidsonGroup/CONCERT_DR: CONCERT_drug repurposing
CONCERT_drug repurposing. Contribute to DavidsonGroup/CONCERT_DR development by creating an account on GitHub.
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Nature @nature.com · 25/11/2025
Nature research paper: Semantic design of functional de novo genes from a genomic language model go.nature.com/48uEnAn
go.nature.com
Semantic design of functional de novo genes from a genomic language model - Nature
By learning a semantics of gene function based on genomic context, the genomic language model Evo autocompletes DNA prompts to generate novel genes encoding protein and RNA molecules with defined activities, whose sequences generalize beyond those found in nature.
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Doc Rowdy @scrnaseq.bsky.social · 25/11/2025
scRNAseq forced us to realize that cell types we'd carefully defined in textbooks for decades were meaningless—they were just convenient categories drawn around the densest clusters in transcriptional space. Nature doesn't actually sort cells that way.
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Doc Rowdy @scrnaseq.bsky.social · 25/11/2025
Single-cell RNA-seq is younger than the iPhone. 🤯 The first bona fide scRNA-seq transcriptomes were published in 2009 by Tang et al., who sequenced individual mouse cells and showed you could capture a whole transcriptome from a single cell. From “sci-fi” to standard tool in just over a decade...
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 17/11/2025
We have started the course on #scRNAseq using R and @bioconductor.bsky.social with Jacques Serizay @almeidasilvaf.bsky.social & an international cohort of attendees working on very different cool projects. #singlecell #RNAseq #Genomics #Bioinformatics
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Ming Tommy Tang @tommytang.bsky.social · 16/11/2025
1/  Mapping quantitative data to color www.nature.com/articles/nm...
nature.com
Mapping quantitative data to color
Nature Methods - Data structure informs choice of color maps.
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