One of the curiosities of genomics history is that James Watson was vehemently against cDNA sequencing (for ESTs), and fought with Craig Venter & Bernadine Healy who championed it. Tl;dr Watson ended up resigning from the HGP, Venter plowed ahead... and we now have #scRNAseq.
November 9, 2025 at 9:41 PM
One of the curiosities of genomics history is that James Watson was vehemently against cDNA sequencing (for ESTs), and fought with Craig Venter & Bernadine Healy who championed it. Tl;dr Watson ended up resigning from the HGP, Venter plowed ahead... and we now have #scRNAseq.
What a glorious day--waking up to see this lovely preprint that does it all--a comprehensive scRNAseq atlas of leaf development, hints at the txn of new cell types, and great hypotheses about how GRNs may differ among related TFs
(and in other news, some hope for American Democracy)
(and in other news, some hope for American Democracy)
1/ Preprint alert:
🌾 The developing leaf of the wild grass Brachypodium distachyon at single-cell resolution
👉 doi.org/10.1101/2025...
A 70k-cell single-cell RNA-seq atlas of the developing grass leaf—from the shoot meristem to mature leaf tissues. @cerealcell.bsky.social @lbmountain.bsky.social
🌾 The developing leaf of the wild grass Brachypodium distachyon at single-cell resolution
👉 doi.org/10.1101/2025...
A 70k-cell single-cell RNA-seq atlas of the developing grass leaf—from the shoot meristem to mature leaf tissues. @cerealcell.bsky.social @lbmountain.bsky.social
November 5, 2025 at 2:16 PM
What a glorious day--waking up to see this lovely preprint that does it all--a comprehensive scRNAseq atlas of leaf development, hints at the txn of new cell types, and great hypotheses about how GRNs may differ among related TFs
(and in other news, some hope for American Democracy)
(and in other news, some hope for American Democracy)
Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding
The formation of neural circuits depends on the precise spatial and temporal organisation of neuronal populations during development. In the vertebrate spinal cord, progenitors are patterned into mole...
www.biorxiv.org
October 26, 2025 at 5:15 PM
Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
🎉 Big congrats to Philipp Janssen for defending his PhD! 🎓
He’s been a key part of the lab, contributing to many projects, including scRNAseq background and cross-species cell type comparisons, and always ready with new ideas (& coffee).
We’re sad to see him go but excited to see what comes next!
He’s been a key part of the lab, contributing to many projects, including scRNAseq background and cross-species cell type comparisons, and always ready with new ideas (& coffee).
We’re sad to see him go but excited to see what comes next!
October 13, 2025 at 10:45 AM
🎉 Big congrats to Philipp Janssen for defending his PhD! 🎓
He’s been a key part of the lab, contributing to many projects, including scRNAseq background and cross-species cell type comparisons, and always ready with new ideas (& coffee).
We’re sad to see him go but excited to see what comes next!
He’s been a key part of the lab, contributing to many projects, including scRNAseq background and cross-species cell type comparisons, and always ready with new ideas (& coffee).
We’re sad to see him go but excited to see what comes next!
Great insights from "Life Science Industry Meets Data Science 2025" #BiotechnetSwitzerland.
@dossola.bsky.social
One concept came up a few times: "Lots of Data ≠ Lots of Information". This rings especially true in #NGS and #scRNAseq, where massive datasets often yield vague correlations. 👇
@dossola.bsky.social
One concept came up a few times: "Lots of Data ≠ Lots of Information". This rings especially true in #NGS and #scRNAseq, where massive datasets often yield vague correlations. 👇
October 3, 2025 at 7:59 AM
Great insights from "Life Science Industry Meets Data Science 2025" #BiotechnetSwitzerland.
@dossola.bsky.social
One concept came up a few times: "Lots of Data ≠ Lots of Information". This rings especially true in #NGS and #scRNAseq, where massive datasets often yield vague correlations. 👇
@dossola.bsky.social
One concept came up a few times: "Lots of Data ≠ Lots of Information". This rings especially true in #NGS and #scRNAseq, where massive datasets often yield vague correlations. 👇
Proud to see our work finally out exploring spermatogenesis, X-chromosome activity and meiotic drive in the stalk-eyed fly!
journals.plos.org/plosgenetics...
#scRNAseq #Evolution #Selfishgene
@plos.org @sheffielduni.bsky.social @nerc-eof.bsky.social
journals.plos.org/plosgenetics...
#scRNAseq #Evolution #Selfishgene
@plos.org @sheffielduni.bsky.social @nerc-eof.bsky.social
Single-cell consequences of X-linked meiotic drive in stalk-eyed flies
Author summary Meiotic drivers, a class of selfish gene, are frequently located on sex chromosomes and have dramatic impacts on gamete development. However, our understanding of their molecular conseq...
journals.plos.org
October 1, 2025 at 3:20 PM
Proud to see our work finally out exploring spermatogenesis, X-chromosome activity and meiotic drive in the stalk-eyed fly!
journals.plos.org/plosgenetics...
#scRNAseq #Evolution #Selfishgene
@plos.org @sheffielduni.bsky.social @nerc-eof.bsky.social
journals.plos.org/plosgenetics...
#scRNAseq #Evolution #Selfishgene
@plos.org @sheffielduni.bsky.social @nerc-eof.bsky.social
📢 The #Danioheart atlas webpage has been updated.
In addition to the whole dataset (>34,000 zebrafish heart cells across 10 developmental stages) we now provide subclusters of each major cardiac cell population. #zebrafish #heart #scRNAseq
@stainierlab.bsky.social
www.mpi-hlr.de/danioheartat...
In addition to the whole dataset (>34,000 zebrafish heart cells across 10 developmental stages) we now provide subclusters of each major cardiac cell population. #zebrafish #heart #scRNAseq
@stainierlab.bsky.social
www.mpi-hlr.de/danioheartat...
danioheartatlas
www.mpi-hlr.de
October 1, 2025 at 10:18 AM
📢 The #Danioheart atlas webpage has been updated.
In addition to the whole dataset (>34,000 zebrafish heart cells across 10 developmental stages) we now provide subclusters of each major cardiac cell population. #zebrafish #heart #scRNAseq
@stainierlab.bsky.social
www.mpi-hlr.de/danioheartat...
In addition to the whole dataset (>34,000 zebrafish heart cells across 10 developmental stages) we now provide subclusters of each major cardiac cell population. #zebrafish #heart #scRNAseq
@stainierlab.bsky.social
www.mpi-hlr.de/danioheartat...
Regionalized & Sex-dependent scRNAseq of 🐭Aorta
Carotid
Aortic Arch
Descending Thoracic
Abdominal Aortic #SmoothMuscleCell
Arch
#SecondHeartField vs #NeuralCrest SMC
339 Regional SMC mRNA features ➡️ cardiovascular trait GWAS
#AortaEd
#NatCardiovascRes 2025
www.nature.com/articles/s44...
Carotid
Aortic Arch
Descending Thoracic
Abdominal Aortic #SmoothMuscleCell
Arch
#SecondHeartField vs #NeuralCrest SMC
339 Regional SMC mRNA features ➡️ cardiovascular trait GWAS
#AortaEd
#NatCardiovascRes 2025
www.nature.com/articles/s44...
September 30, 2025 at 10:48 AM
Regionalized & Sex-dependent scRNAseq of 🐭Aorta
Carotid
Aortic Arch
Descending Thoracic
Abdominal Aortic #SmoothMuscleCell
Arch
#SecondHeartField vs #NeuralCrest SMC
339 Regional SMC mRNA features ➡️ cardiovascular trait GWAS
#AortaEd
#NatCardiovascRes 2025
www.nature.com/articles/s44...
Carotid
Aortic Arch
Descending Thoracic
Abdominal Aortic #SmoothMuscleCell
Arch
#SecondHeartField vs #NeuralCrest SMC
339 Regional SMC mRNA features ➡️ cardiovascular trait GWAS
#AortaEd
#NatCardiovascRes 2025
www.nature.com/articles/s44...
New BCR reconstruction tool for scRNA-seq: assembles full heavy & light chains and annotates constant regions. Check it out:
www.biorxiv.org/content/10.1...
#scRNAseq #immunology
www.biorxiv.org/content/10.1...
#scRNAseq #immunology
GATHeR: Graph-based Accurate Tool for Immunoglobulin HEavy- and Light-chain Reconstruction
Recovering full-length, paired B-cell receptor (BCR) sequences from scRNA-seq reads remains difficult, especially in naive and memory B cells where immunoglobulin transcripts are sparse. Current metho...
www.biorxiv.org
September 22, 2025 at 4:50 AM
New BCR reconstruction tool for scRNA-seq: assembles full heavy & light chains and annotates constant regions. Check it out:
www.biorxiv.org/content/10.1...
#scRNAseq #immunology
www.biorxiv.org/content/10.1...
#scRNAseq #immunology
About scRNAseq, they trained on a separate dataset and tested on OpenProblems benchmark. They picked 1 from 22 train-sets by manual inspection (no reasoning)🤔 Best result applies BBKNN to ComBat-corrected PCA embeddings rather than raw PCA. Could this “double normalization” risk overfitting?✨🧪 #AI4S
Just spotted this paper saying their tree search/genetic algorithm writes better bioinformatics software than SOTA. Does batch correction of scRNAseq, and covid hospitalisation estim.
Noth outside my wheelhouse. Does anyone have expertise and energy to look at it?
arxiv.org/abs/2509.06503
Noth outside my wheelhouse. Does anyone have expertise and energy to look at it?
arxiv.org/abs/2509.06503
An AI system to help scientists write expert-level empirical software
The cycle of scientific discovery is frequently bottlenecked by the slow, manual creation of software to support computational experiments. To address this, we present an AI system that creates expert...
arxiv.org
September 10, 2025 at 3:35 AM
About scRNAseq, they trained on a separate dataset and tested on OpenProblems benchmark. They picked 1 from 22 train-sets by manual inspection (no reasoning)🤔 Best result applies BBKNN to ComBat-corrected PCA embeddings rather than raw PCA. Could this “double normalization” risk overfitting?✨🧪 #AI4S
Characterising the periodontal granulation tissue using scRNAseq. https://www.biorxiv.org/content/10.1101/2025.01.13.632112v1
January 15, 2025 at 3:53 PM
Characterising the periodontal granulation tissue using scRNAseq. https://www.biorxiv.org/content/10.1101/2025.01.13.632112v1
Massive congratulations to Harriet Banks who successfully defended her PhD thesis this afternoon. Harriet’s thesis explored biological mechanisms underlying anti-TNF response in a T-cell/macrophage Co-culture model using scRNAseq. #veryproudsupervisor
November 22, 2024 at 8:03 PM
Massive congratulations to Harriet Banks who successfully defended her PhD thesis this afternoon. Harriet’s thesis explored biological mechanisms underlying anti-TNF response in a T-cell/macrophage Co-culture model using scRNAseq. #veryproudsupervisor
#Ferroptosis of #MuscleStemCell in Myopathy #PeripheralArteryDisease
scRNAseq CD56+ MuSC
4 perfused/thigh vs 4 ischemic/calf muscle👤
Interesting Lipofuscin stain pattern
Ferroptosis also in non-satellite cells?🤔
Ulka Sachdev lab #ATVB 2023
www.ahajournals.org/doi/abs/10.1...
scRNAseq CD56+ MuSC
4 perfused/thigh vs 4 ischemic/calf muscle👤
Interesting Lipofuscin stain pattern
Ferroptosis also in non-satellite cells?🤔
Ulka Sachdev lab #ATVB 2023
www.ahajournals.org/doi/abs/10.1...
November 11, 2023 at 8:03 PM
#Ferroptosis of #MuscleStemCell in Myopathy #PeripheralArteryDisease
scRNAseq CD56+ MuSC
4 perfused/thigh vs 4 ischemic/calf muscle👤
Interesting Lipofuscin stain pattern
Ferroptosis also in non-satellite cells?🤔
Ulka Sachdev lab #ATVB 2023
www.ahajournals.org/doi/abs/10.1...
scRNAseq CD56+ MuSC
4 perfused/thigh vs 4 ischemic/calf muscle👤
Interesting Lipofuscin stain pattern
Ferroptosis also in non-satellite cells?🤔
Ulka Sachdev lab #ATVB 2023
www.ahajournals.org/doi/abs/10.1...
MuMu: a sample multiplexing protocol for droplet-based simultaneous single nuclei RNA- and ATAC-seq systems. #SingleNuclei #MultiplexingProtocol #10X #scRNAseq #scATACseq @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 1, 2024 at 7:41 PM
MuMu: a sample multiplexing protocol for droplet-based simultaneous single nuclei RNA- and ATAC-seq systems. #SingleNuclei #MultiplexingProtocol #10X #scRNAseq #scATACseq @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
UMIche features:
🧠 mclUMI (Markov clustering)
🧬 Homotrimer UMI support (majority vote & set cover)
🧪 scRNA-seq simulation (DeepConvCVAE)
📊 Visual analytics
A step forward in deduplication accuracy & benchmarking.
#UMI #scRNAseq #bioinformatics
🧠 mclUMI (Markov clustering)
🧬 Homotrimer UMI support (majority vote & set cover)
🧪 scRNA-seq simulation (DeepConvCVAE)
📊 Visual analytics
A step forward in deduplication accuracy & benchmarking.
#UMI #scRNAseq #bioinformatics
May 6, 2025 at 9:19 AM
UMIche features:
🧠 mclUMI (Markov clustering)
🧬 Homotrimer UMI support (majority vote & set cover)
🧪 scRNA-seq simulation (DeepConvCVAE)
📊 Visual analytics
A step forward in deduplication accuracy & benchmarking.
#UMI #scRNAseq #bioinformatics
🧠 mclUMI (Markov clustering)
🧬 Homotrimer UMI support (majority vote & set cover)
🧪 scRNA-seq simulation (DeepConvCVAE)
📊 Visual analytics
A step forward in deduplication accuracy & benchmarking.
#UMI #scRNAseq #bioinformatics
Drs. @kylessmith.bsky.social, Yiran Li, and a team in @doctorpauln77.bsky.social's lab at @sjcenos.bsky.social analyzed previously published #scRNAseq data and found no evidence of transitional cerebellar progenitors.
Read the article: go.nature.com/46iVgyl
Listen to the discussion: bit.ly/3IGfUP1
Read the article: go.nature.com/46iVgyl
Listen to the discussion: bit.ly/3IGfUP1
July 25, 2025 at 6:54 PM
Drs. @kylessmith.bsky.social, Yiran Li, and a team in @doctorpauln77.bsky.social's lab at @sjcenos.bsky.social analyzed previously published #scRNAseq data and found no evidence of transitional cerebellar progenitors.
Read the article: go.nature.com/46iVgyl
Listen to the discussion: bit.ly/3IGfUP1
Read the article: go.nature.com/46iVgyl
Listen to the discussion: bit.ly/3IGfUP1
Single cell and spatial alternative splicing analysis with Nanopore long read sequencing. #SingleCell #scRNAseq #AlternativeSplicing #LongReads #Sequencing @nanoporetech.com @natcomms.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
July 29, 2025 at 5:51 PM
Single cell and spatial alternative splicing analysis with Nanopore long read sequencing. #SingleCell #scRNAseq #AlternativeSplicing #LongReads #Sequencing @nanoporetech.com @natcomms.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Chevreul: an R bioconductor package for exploratory analysis of full-length single cell sequencing. #SingleCell #scRNAseq #Bioconductor #GigaByte
gigabytejournal.com/articles/158
gigabytejournal.com/articles/158
July 28, 2025 at 10:30 AM
Chevreul: an R bioconductor package for exploratory analysis of full-length single cell sequencing. #SingleCell #scRNAseq #Bioconductor #GigaByte
gigabytejournal.com/articles/158
gigabytejournal.com/articles/158
Ageing
#TenaLab @cabd-upo-csic.bsky.social @anaburgos.bsky.social (Killifish/ scRNAseq/ Aging)
https://www.biorxiv.org/content/10.1101/2025.03.24.645095
Special Topics
@aburger2009.bsky.social (Data Reporting/ Metadata/ AI)
https://osf.io/preprints/osf/kvn2x (27/34)
#TenaLab @cabd-upo-csic.bsky.social @anaburgos.bsky.social (Killifish/ scRNAseq/ Aging)
https://www.biorxiv.org/content/10.1101/2025.03.24.645095
Special Topics
@aburger2009.bsky.social (Data Reporting/ Metadata/ AI)
https://osf.io/preprints/osf/kvn2x (27/34)
April 9, 2025 at 7:30 PM
Ageing
#TenaLab @cabd-upo-csic.bsky.social @anaburgos.bsky.social (Killifish/ scRNAseq/ Aging)
https://www.biorxiv.org/content/10.1101/2025.03.24.645095
Special Topics
@aburger2009.bsky.social (Data Reporting/ Metadata/ AI)
https://osf.io/preprints/osf/kvn2x (27/34)
#TenaLab @cabd-upo-csic.bsky.social @anaburgos.bsky.social (Killifish/ scRNAseq/ Aging)
https://www.biorxiv.org/content/10.1101/2025.03.24.645095
Special Topics
@aburger2009.bsky.social (Data Reporting/ Metadata/ AI)
https://osf.io/preprints/osf/kvn2x (27/34)
A couple of people who joined our online workshop on scRNAseq found out about it via ChatGPT and I don't entirely know what to make of that.
June 25, 2025 at 12:59 AM
A couple of people who joined our online workshop on scRNAseq found out about it via ChatGPT and I don't entirely know what to make of that.
#NeuralStemCells (NSCs) & ependymal cells (ECs) are derived from #RadialGlialCells. This study uses #scRNAseq to characterize cell fate trajectories in the developing #VentricularZone, identifying TFEB as a regulator of the NSC/EPC balance @plosbiology.org 🧪 plos.io/3HbrsJG
August 1, 2025 at 8:29 AM
#NeuralStemCells (NSCs) & ependymal cells (ECs) are derived from #RadialGlialCells. This study uses #scRNAseq to characterize cell fate trajectories in the developing #VentricularZone, identifying TFEB as a regulator of the NSC/EPC balance @plosbiology.org 🧪 plos.io/3HbrsJG
A comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae1186/7924191 🧬🖥️🧪 https://github.com/danledinh/scRNAseq-repo
December 17, 2024 at 7:30 PM
A comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae1186/7924191 🧬🖥️🧪 https://github.com/danledinh/scRNAseq-repo
🧬 Are single-cell atlases complete? This was an interesting one to do: www.biorxiv.org/content/10.1... #scRNAseq #single-cell #atlas #cell #biodiversity #biostatistics
www.biorxiv.org
March 5, 2025 at 1:35 PM
🧬 Are single-cell atlases complete? This was an interesting one to do: www.biorxiv.org/content/10.1... #scRNAseq #single-cell #atlas #cell #biodiversity #biostatistics
On average, the diagnostic genes defining immune cells (natural killer cells, fibroblasts, B cells, etc) experience stronger selection than the diagnostic genes for cells involved in other biological processes. We do this for multiple tissues (scRNAseq from gut, liver, pronephros, and gills)
December 10, 2024 at 1:20 PM
On average, the diagnostic genes defining immune cells (natural killer cells, fibroblasts, B cells, etc) experience stronger selection than the diagnostic genes for cells involved in other biological processes. We do this for multiple tissues (scRNAseq from gut, liver, pronephros, and gills)