scRNA-seq has partly ruined murmurations for me...
Witness the mesmerizing murmuration of starlings in Italy, a stunning display of nature's coordination and beauty as they dance through the sky in unison.
April 23, 2026 at 9:30 AM
scRNA-seq has partly ruined murmurations for me...
Today we report single-cell APEX-seq (scAPEX-seq)—a method for unbiased mapping of subcellular transcriptomes at single-cell resolution. It reveals cell states invisible to standard scRNA-seq and identifies regulators of CAR T function that improve solid tumor killing.
tinyurl.com/32pf6b8p
tinyurl.com/32pf6b8p
March 18, 2026 at 11:40 AM
Today we report single-cell APEX-seq (scAPEX-seq)—a method for unbiased mapping of subcellular transcriptomes at single-cell resolution. It reveals cell states invisible to standard scRNA-seq and identifies regulators of CAR T function that improve solid tumor killing.
tinyurl.com/32pf6b8p
tinyurl.com/32pf6b8p
Tumor-reactive T cell receptors are rapidly identified from lymphocyte scRNA-seq data go.nature.com/49O5INm
rdcu.be/d8L1u
rdcu.be/d8L1u
Prediction of tumor-reactive T cell receptors from scRNA-seq data for personalized T cell therapy - Nature Biotechnology
Tumor-reactive T cell receptors are rapidly identified from lymphocyte scRNA-seq data.
go.nature.com
February 13, 2025 at 6:21 PM
Tumor-reactive T cell receptors are rapidly identified from lymphocyte scRNA-seq data go.nature.com/49O5INm
rdcu.be/d8L1u
rdcu.be/d8L1u
I’m really happy to present #SCALPEL, a new #Nextflow tool to quantify transcript isoforms at the single-cell level using conventional 3’ scRNA-seq data #scRNA-seq #single-cell #tools #isoforms
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Quantification of transcript isoforms at the single-cell level using SCALPEL - Nature Communications
Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...
www.nature.com
July 14, 2025 at 10:31 AM
I’m really happy to present #SCALPEL, a new #Nextflow tool to quantify transcript isoforms at the single-cell level using conventional 3’ scRNA-seq data #scRNA-seq #single-cell #tools #isoforms
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Millions of PBMCs have been analyzed by scRNA-seq. Have we seen it all ?
We profiled thousands of single PBMCs — proteomes and transcriptomes side by side — and uncovered functional coordination undetectable in the deepest scRNA-seq we could perform.
www.biorxiv.org/content/10.6...
1/
We profiled thousands of single PBMCs — proteomes and transcriptomes side by side — and uncovered functional coordination undetectable in the deepest scRNA-seq we could perform.
www.biorxiv.org/content/10.6...
1/
September 15, 2026 at 11:48 AM
Millions of PBMCs have been analyzed by scRNA-seq. Have we seen it all ?
We profiled thousands of single PBMCs — proteomes and transcriptomes side by side — and uncovered functional coordination undetectable in the deepest scRNA-seq we could perform.
www.biorxiv.org/content/10.6...
1/
We profiled thousands of single PBMCs — proteomes and transcriptomes side by side — and uncovered functional coordination undetectable in the deepest scRNA-seq we could perform.
www.biorxiv.org/content/10.6...
1/
It's here! new preprint: Gravlax, an annotation-independent molecular evidence archive for scRNA-seq.
A count matrix freezes one annotation. Molecules never change. Instead, gravlax keeps the evidence. Requantify, query, and discover under any annotation. 🧵
www.biorxiv.org/content/10.6...
A count matrix freezes one annotation. Molecules never change. Instead, gravlax keeps the evidence. Requantify, query, and discover under any annotation. 🧵
www.biorxiv.org/content/10.6...
September 21, 2026 at 3:52 PM
It's here! new preprint: Gravlax, an annotation-independent molecular evidence archive for scRNA-seq.
A count matrix freezes one annotation. Molecules never change. Instead, gravlax keeps the evidence. Requantify, query, and discover under any annotation. 🧵
www.biorxiv.org/content/10.6...
A count matrix freezes one annotation. Molecules never change. Instead, gravlax keeps the evidence. Requantify, query, and discover under any annotation. 🧵
www.biorxiv.org/content/10.6...
Neuron programming! Pro-neural TFs + 480 morphogen conditions + scRNA-seq --> Diverse iN subtypes of forebrain, midbrain, hindbrain, spinal cord, and PNS. @hsiuchuanlin.bsky.social @jasperjanssens.bsky.social and Treutlein Lab! @science.org www.science.org/doi/10.1126/... #NGN2 #ASCL1
July 11, 2025 at 8:59 PM
Neuron programming! Pro-neural TFs + 480 morphogen conditions + scRNA-seq --> Diverse iN subtypes of forebrain, midbrain, hindbrain, spinal cord, and PNS. @hsiuchuanlin.bsky.social @jasperjanssens.bsky.social and Treutlein Lab! @science.org www.science.org/doi/10.1126/... #NGN2 #ASCL1
Check out the BAR's Single Cell Data Portal at bar.utoronto.ca/single_cell_..., in beta. There's a curated list of scRNA-seq datasets with viewer links, our own CellxGene instance for exploring 14 datasets from 6 papers, and a new tool, SUPeR Viewer! Thanks to PCA and C-SPIRIT for input.
September 24, 2026 at 7:31 PM
Check out the BAR's Single Cell Data Portal at bar.utoronto.ca/single_cell_..., in beta. There's a curated list of scRNA-seq datasets with viewer links, our own CellxGene instance for exploring 14 datasets from 6 papers, and a new tool, SUPeR Viewer! Thanks to PCA and C-SPIRIT for input.
Cell type-specific interaction analysis using doublets in scRNA-seq
Cell type-specific interaction analysis using doublets in scRNA-seq
AbstractSummary. Doublets are usually considered an unwanted artifact of single-cell RNA-sequencing (scRNA-seq) and are only identified in datasets for the
academic.oup.com
December 19, 2024 at 7:26 PM
Cell type-specific interaction analysis using doublets in scRNA-seq
This Registered Report from @fabiantheis.bsky.social and colleagues evaluates feature selection methods and provides guidance on how feature selections impact scRNA-seq integration analysis.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Feature selection methods affect the performance of scRNA-seq data integration and querying - Nature Methods
This Registered Report presents a benchmarking study evaluating the impact of feature selection on scRNA-seq integration.
www.nature.com
March 13, 2025 at 6:23 PM
This Registered Report from @fabiantheis.bsky.social and colleagues evaluates feature selection methods and provides guidance on how feature selections impact scRNA-seq integration analysis.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
My postdoc work at Treutlein lab and @graycamplab.bsky.social with @jasperjanssens.bsky.social is out in @science.org ! We screen for neuron subtypes using pro-neural TFs + morphogen combinations + scRNA-seq and profiled over 700,000 cells in 480 conditions. www.science.org/doi/10.1126/...
July 12, 2025 at 10:11 PM
My postdoc work at Treutlein lab and @graycamplab.bsky.social with @jasperjanssens.bsky.social is out in @science.org ! We screen for neuron subtypes using pro-neural TFs + morphogen combinations + scRNA-seq and profiled over 700,000 cells in 480 conditions. www.science.org/doi/10.1126/...
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...
bmcgenomics.biomedcentral.com
December 3, 2024 at 8:38 AM
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
📣 new preprint multimodal atlas. Imaging + scRNA, 57M cells. 🧬🔬
Cells are complex dynamical systems — but most ways we measure them destroy them. We asked: how does live imaging compare to scRNA-seq, the field’s gold std?
The answer surprised us 🧵
www.biorxiv.org/content/10.6...
Cells are complex dynamical systems — but most ways we measure them destroy them. We asked: how does live imaging compare to scRNA-seq, the field’s gold std?
The answer surprised us 🧵
www.biorxiv.org/content/10.6...
June 3, 2026 at 9:23 PM
📣 new preprint multimodal atlas. Imaging + scRNA, 57M cells. 🧬🔬
Cells are complex dynamical systems — but most ways we measure them destroy them. We asked: how does live imaging compare to scRNA-seq, the field’s gold std?
The answer surprised us 🧵
www.biorxiv.org/content/10.6...
Cells are complex dynamical systems — but most ways we measure them destroy them. We asked: how does live imaging compare to scRNA-seq, the field’s gold std?
The answer surprised us 🧵
www.biorxiv.org/content/10.6...
Our new contribution to the quest to find causal GWAS genes! Sam Ghatan from my lab at @nygenome.org led a systematic comparison of eQTLs and CRISPRi+scRNA-seq screens. TL;DR: they provide highly complementary insights, with ortogonal pros and cons. 🧵👇
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
May 6, 2025 at 5:01 PM
Our new contribution to the quest to find causal GWAS genes! Sam Ghatan from my lab at @nygenome.org led a systematic comparison of eQTLs and CRISPRi+scRNA-seq screens. TL;DR: they provide highly complementary insights, with ortogonal pros and cons. 🧵👇
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Most transcriptomics studies sample ~0.001% of a mouse. Which region do we choose? Often: we guess.
Meet DISCO-seq 🤗 flipping the order: RNA-preserving clearing → whole-organ/whole-body 3D imaging → pick ROIs in 3D → unbiased scRNA-seq.
Preprint: www.biorxiv.org/content/10.6...
Meet DISCO-seq 🤗 flipping the order: RNA-preserving clearing → whole-organ/whole-body 3D imaging → pick ROIs in 3D → unbiased scRNA-seq.
Preprint: www.biorxiv.org/content/10.6...
December 18, 2025 at 2:46 PM
Most transcriptomics studies sample ~0.001% of a mouse. Which region do we choose? Often: we guess.
Meet DISCO-seq 🤗 flipping the order: RNA-preserving clearing → whole-organ/whole-body 3D imaging → pick ROIs in 3D → unbiased scRNA-seq.
Preprint: www.biorxiv.org/content/10.6...
Meet DISCO-seq 🤗 flipping the order: RNA-preserving clearing → whole-organ/whole-body 3D imaging → pick ROIs in 3D → unbiased scRNA-seq.
Preprint: www.biorxiv.org/content/10.6...
Excited to share our study on spatio-temporal reconstruction of cardiac scar formation led by Andy Chan. We combine scRNA-seq with spatial transcriptomics to resolve the fibrotic niche and the niche of dedifferentiating cardiomyocytes.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 16, 2024 at 12:26 PM
Excited to share our study on spatio-temporal reconstruction of cardiac scar formation led by Andy Chan. We combine scRNA-seq with spatial transcriptomics to resolve the fibrotic niche and the niche of dedifferentiating cardiomyocytes.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Eine schwere COVID19-Erkrankung steht im Zusammenhang mit dysregulierten Immunreaktionen. Dexamethason wirkt, indem es den fehlgeleiteten Status bestimmter Immunzellen, sogenannter Monozyten, neu verdrahtet.
July 3, 2024 at 10:17 PM
Eine schwere COVID19-Erkrankung steht im Zusammenhang mit dysregulierten Immunreaktionen. Dexamethason wirkt, indem es den fehlgeleiteten Status bestimmter Immunzellen, sogenannter Monozyten, neu verdrahtet.
scRNA-seq has revolutionized biology, but it’s not without challenges. We uncovered significant quality issues in widely used reference cell atlases like the Human Cell Atlas and Tabula Sapiens. Up to 85% of cells in some datasets are low-quality or misidentified!
2/8
2/8
December 3, 2024 at 8:38 AM
scRNA-seq has revolutionized biology, but it’s not without challenges. We uncovered significant quality issues in widely used reference cell atlases like the Human Cell Atlas and Tabula Sapiens. Up to 85% of cells in some datasets are low-quality or misidentified!
2/8
2/8
🧵 Bioinformatics: Keeping Up with Rapidly Advancing Technologies
1/ Bioinformatics evolves fast. Just as we catch up with single-cell RNA-seq (scRNA-seq), spatial transcriptomics arrives with new challenges.
1/ Bioinformatics evolves fast. Just as we catch up with single-cell RNA-seq (scRNA-seq), spatial transcriptomics arrives with new challenges.
March 31, 2025 at 1:15 PM
🧵 Bioinformatics: Keeping Up with Rapidly Advancing Technologies
1/ Bioinformatics evolves fast. Just as we catch up with single-cell RNA-seq (scRNA-seq), spatial transcriptomics arrives with new challenges.
1/ Bioinformatics evolves fast. Just as we catch up with single-cell RNA-seq (scRNA-seq), spatial transcriptomics arrives with new challenges.
Interested in how to infer tumour microenvironment ecosystems from scRNA-seq atlases?
I'll be at #AACR25 presenting in the ED06 session this Friday 3-4.30pm.
Otherwise would love to meet to chat science for anyone on here attending
Preprint: www.biorxiv.org/content/10.1...
I'll be at #AACR25 presenting in the ED06 session this Friday 3-4.30pm.
Otherwise would love to meet to chat science for anyone on here attending
Preprint: www.biorxiv.org/content/10.1...
April 22, 2025 at 2:43 PM
Interested in how to infer tumour microenvironment ecosystems from scRNA-seq atlases?
I'll be at #AACR25 presenting in the ED06 session this Friday 3-4.30pm.
Otherwise would love to meet to chat science for anyone on here attending
Preprint: www.biorxiv.org/content/10.1...
I'll be at #AACR25 presenting in the ED06 session this Friday 3-4.30pm.
Otherwise would love to meet to chat science for anyone on here attending
Preprint: www.biorxiv.org/content/10.1...
How accurate are 'gene regulatory networks' inferred from scRNA-seq data?
This comprehensive analysis in @naturemethods.bsky.social concludes:
1. The areas under the precision-recall curve are moderate
2. Methods not using pseudotime-ordered cells are more accurate
This comprehensive analysis in @naturemethods.bsky.social concludes:
1. The areas under the precision-recall curve are moderate
2. Methods not using pseudotime-ordered cells are more accurate
April 14, 2025 at 11:44 AM
How accurate are 'gene regulatory networks' inferred from scRNA-seq data?
This comprehensive analysis in @naturemethods.bsky.social concludes:
1. The areas under the precision-recall curve are moderate
2. Methods not using pseudotime-ordered cells are more accurate
This comprehensive analysis in @naturemethods.bsky.social concludes:
1. The areas under the precision-recall curve are moderate
2. Methods not using pseudotime-ordered cells are more accurate
📢 new preprint alert: So so excited to share our analysis on the impact of common and rare variants on single-cell gene expression in blood, using WGS and scRNA-seq data from nearly 2,000 individuals and 5.4m cells as part of TenK10K phase 1 🧬 www.medrxiv.org/content/10.1...
🧵👇 (1/n)
🧵👇 (1/n)
March 24, 2025 at 7:47 AM
📢 new preprint alert: So so excited to share our analysis on the impact of common and rare variants on single-cell gene expression in blood, using WGS and scRNA-seq data from nearly 2,000 individuals and 5.4m cells as part of TenK10K phase 1 🧬 www.medrxiv.org/content/10.1...
🧵👇 (1/n)
🧵👇 (1/n)
To investigate Merkel cell regeneration, we generated a scRNA-seq dataset at several points of adult skin regeneration following dermal appendage injury
September 22, 2026 at 8:41 PM
To investigate Merkel cell regeneration, we generated a scRNA-seq dataset at several points of adult skin regeneration following dermal appendage injury
New preprint! 🐛 Root-knot nematodes hijack root cells, turning them into feeding sites and making plants very sick. Using a cross-species scRNA-seq approach we mapped this process and show how this knowledge can be used to engineer resistant crops.🌱 A summary🧵 :
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 10, 2025 at 2:30 PM
New preprint! 🐛 Root-knot nematodes hijack root cells, turning them into feeding sites and making plants very sick. Using a cross-species scRNA-seq approach we mapped this process and show how this knowledge can be used to engineer resistant crops.🌱 A summary🧵 :
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
scRNA-seq data sets exploding in number and size - check out scanpy & anndata for >1b cells: new experimental update includes APIs for scaling with dask from anndata, integrated with lots of scanpy and rapids-singlecell functions.
gist.github.com/ilan-gold/98...
gist.github.com/ilan-gold/98...
December 11, 2024 at 3:48 PM
scRNA-seq data sets exploding in number and size - check out scanpy & anndata for >1b cells: new experimental update includes APIs for scaling with dask from anndata, integrated with lots of scanpy and rapids-singlecell functions.
gist.github.com/ilan-gold/98...
gist.github.com/ilan-gold/98...