From standing at the lab bench preparing the very first single-cell libraries for these samples, to finally seeing this work published, this has been an unforgettable journey.🥹 🧬✨ #scRNAseq #Microbiome #Genomics
Took 2 years & endless discussions/customized bioinformatics pipelines/Genomic validations...and finally happy reading..@IGIBSocial
Intracellular microbial shifts during COVID-19 infection and longitudinal recovery revealed by single-cell RNA sequencing.. cell.com/iscience/fulltext/S…
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Code and pipeline are open source: github.com/czbiohub-sf/compa…
Paper: journals.plos.org/ploscompbi…
Need help with your single-cell workflows? trinobia.com/contact/
#RNAvelocity #scRNAseq #Bioinformatics #SingleCell #ComputationalBiology
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You've run your scRNA-seq experiment. Now you want to know where your cells are heading. You reach for RNA velocity — but which method do you use, and does it actually matter?
Turns out: yes, quite a lot.
#RNAvelocity #scRNAseq #Bioinformatics #SingleCell #Genomics
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Master scRNA-seq dimensionality reduction! 📊🧬 Join @OmicsLogic's 4-Day Workshop to unlock cell patterns using PCA, t-SNE, and UMAP. Get hands-on experience with Cell Ranger & Seurat workflows.
📅 July 13–16, 2026 🚀 Register: forms.gle/38PniyAJuZC7567N6
#scRNAseq #Bioinformatics
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Using trephine biopsy and #scRNAseq, this study reveals key cellular and molecular features of the bone marrow microenvironment in #Autoimmune #HemolyticAnemia, advancing understanding of disease mechanisms. @LaStatale
#STTT #OpenAccess: doi.org/10.1038/s41392-025-0…
ALT Bone marrow microenvironment in autoimmune hemolytic anemia: from trephine biopsy to single cell RNA sequencing
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Available as open-source R Python package and a web server.
Paper: doi.org/10.1038/s42003-026-1…
Tool: github.com/cafferychen777/mL…
Working on single-cell analysis at your institute? trinobia.com/contact/
#scRNAseq #Bioinformatics
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Single LLMs can annotate cell types. They can also hallucinate them. 56% of initial predictions in a new study were classified as hallucinations. What if you make multiple LLMs deliberate until they agree?
nature.com/articles/s42003-0…
#scRNAseq #Bioinformatics #LLM #AI
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Paul Geeleher retweeted
Jun 10
Self-supervised learning on observational scRNAseq especially with naive reconstruction or masking losses will never deliver a causal model of gene regulation. It will learn statistical structure in expression space, not the mechanisms that generate regulatory change. 1/
Jun 10
18 months after posting this tweet, the AI for science commentariat is still proclaiming the death of single-cell scaling laws on the basis of... {checks notes}... a model sweep ranging from 1 million to a whopping 10 million parameters. (but unlike 18 months ago, these proclamations now come wrapped in premium AI-written slop, giving them a glittering verisimilitude of rigor)
left as an exercise for the reader: generalize from this example to a meta-update about how epistemically adversarial the scientific environment we're operating in is (for extra credit, partial out the effects of mood affiliation and status deferral)
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Herbert B Schiller retweeted
Jun 11
13. In conclusion, if you want a scRNAseq normalization method to best satisfy
- depth norm
- variance stabilization
- monotonicity
Run PFlogPF (package coming soon).
The code is available here: github.com/pachterlab/BHGP_2…
The manuscript is available here: biorxiv.org/content/10.1101/…
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Want to run scRNA-seq analysis on your own data? Or bring a customized workshop to your research group?
Get in touch with Trinobia. We tailor courses to your team's level and datasets.
🔗 trinobia.com/contact/
#scRNAseq #Bioinformatics #ComputationalBiology #CancerResearch
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We just wrapped up a hands-on scRNA-seq data analysis workshop for PhD students at @DKFZ 🎉
From experimental design to biological interpretation, researchers worked through the complete single-cell analysis journey.
#scRNAseq #SingleCellRNAseq #Bioinformatics #
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Jun 11
11. And the method that does satisfy all three isn't new. It's the centered log-ratio, from 1982! This transform has been available for 40 years, passed over in hundreds of thousands of scRNAseq studies for methods that perform poorly with respect to these desiderata.
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Azimazade et al. developed an explainable machine learning (XML) pipeline to study associations between clinical outcomes and in silico estimated cell types within the TIME of over 5,000 METABRIC and TCGA samples from patients with breast cancer. In estrogen receptor-positive samples, macrophages correlated positively with pathological complete responses after neoadjuvant chemotherapy, but negatively with relapse-free survival. Imaging mass cytometry and scRNAseq data demonstrated that HLA-ABC macrophages accumulated in the vicinity of HLA-ABChi epithelial cells and were associated with Tregs and TEX cells. bit.ly/4uteIkj
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Jun 11
Cellecta’s Single-Cell CRISPR Screening Service (Perturb-Seq, CRISP-Seq, CROP-Seq) lets you study how genetic perturbations reshape mRNA expression at the single-cell level—using 10X Chromium scRNA-Seq.
- Analyze 100 gene perturbations in a single pooled experiment
- Combine CRISPR KO, CRISPRi, or CRISPRa with single-cell profiling
- Discover regulators and pathways missed in bulk screens
Turn complex cellular responses into actionable insights.
Get a quote at: cellecta.com/products/single…
#SingleCellCRISPR #PerturbSeq #CRISPRScreening #FunctionalGenomics #scRNASeq #Cellecta #GeneEditing #10XGenomics
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CDK4/6
Endothelial Cell Cycle
#ArterioVenousMalformation
#HereditaryHemorrhagicTelangiectasia
Evidence from
👉Fucci2🐭 (fluorescent cell cycle reporter) Retina BMP9/10 blocking Ab
👉🐭Retina BMP9/10 blocking Ab
Palbociclib CDK4/6i
Restores retinal venous EC planar polarity
Quenches elevated glycolysis genes, TCA cycle genes & OXPHOS
👉🐭EC ALK1 KO Retina Brain
Palbociclib
⏬Retinal AVM hypervascularity
⏬Basilar/middle cerebral arteryφ
⏬Lung vascular permeability (latex leakage)
Partially restore retinal AV differentiation (scRNAseq)
⏬Retinal VEGF signal
Augment Retinal BMP9/10 signal
👉👤HHT2 (ALK1) Skin biopsy
#SciArt
@Gael_Genet @HirschiLab @CircAHA 2024
ahajournals.org/doi/full/10.…
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