Exciting work! A mitochondrial perspective of scRNAseq datasets!
New year, new version of mitoXplorer 3.0 (mitoxplorer3.ibdm.univ-amu.fr) : mine your single-cell RNA-seq data from a mitochondrial perspective by creating cell-type specific pseudo-bulks or by looking at mitochondrial variability on single-cell level. Check it out at doi: doi.org/10.1101/2024...
mitoXplorer 3.0, a web tool for exploring mitochondrial dynamics in single-cell RNA-seq data
Mitochondria are important eukaryotic organelles, best known for their function in ATP production and in cellular metabolism and signalling. It is widely accepted that their structure, composition and...
doi.org
January 9, 2025 at 8:24 AM
Exciting work! A mitochondrial perspective of scRNAseq datasets!
🌱 When a root cell undergoes symmetric division, are the daughter cells actually identical? By combining live-cell imaging and scRNAseq we discovered a new cell state with uneven BR activity. Read our full paper in Cell: doi.org/10.1016/j.ce... @nvukas.bsky.social @trevormnolan.bsky.social
March 10, 2025 at 2:58 PM
🌱 When a root cell undergoes symmetric division, are the daughter cells actually identical? By combining live-cell imaging and scRNAseq we discovered a new cell state with uneven BR activity. Read our full paper in Cell: doi.org/10.1016/j.ce... @nvukas.bsky.social @trevormnolan.bsky.social
Dynamic visualization of the RNA velocity flows during #zebrafish development 🧪🧬
#genomics #scRNAseq #sciart #scicom #biology #zebrahub
#devbio
more at www.cell.com/cell/fulltex...
#genomics #scRNAseq #sciart #scicom #biology #zebrahub
#devbio
more at www.cell.com/cell/fulltex...
November 22, 2024 at 1:56 AM
Dynamic visualization of the RNA velocity flows during #zebrafish development 🧪🧬
#genomics #scRNAseq #sciart #scicom #biology #zebrahub
#devbio
more at www.cell.com/cell/fulltex...
#genomics #scRNAseq #sciart #scicom #biology #zebrahub
#devbio
more at www.cell.com/cell/fulltex...
Out now in Dev Cell! scRNAseq trajectories describe the cascade of gene expression as cells differentiate, but turning them into a clear understanding of the underlying biology of a cell type's development remains challenging. authors.elsevier.com/c/1k9qj5Sx5g... (1/)
November 26, 2024 at 3:49 PM
Out now in Dev Cell! scRNAseq trajectories describe the cascade of gene expression as cells differentiate, but turning them into a clear understanding of the underlying biology of a cell type's development remains challenging. authors.elsevier.com/c/1k9qj5Sx5g... (1/)
Awesome talk from @akshayjg.bsky.social at the Jornades de Bioinformàtica i Genòmica presenying our work on Alzheimer's disease using iPSCs and scRNAseq.
December 19, 2025 at 11:06 AM
Awesome talk from @akshayjg.bsky.social at the Jornades de Bioinformàtica i Genòmica presenying our work on Alzheimer's disease using iPSCs and scRNAseq.
Pipeline release! nf-core/scrnaseq v2.4.1 - nf-core/scrnaseq 2.4.1!
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/2.4.1
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/2.4.1
October 2, 2023 at 12:18 PM
Pipeline release! nf-core/scrnaseq v2.4.1 - nf-core/scrnaseq 2.4.1!
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/2.4.1
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/2.4.1
scnanoseq nf-co.re/scrnaseq: an nf-core [Nextflow] pipeline for Oxford Nanopore single-cell RNA-sequencing www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/nf-core/scna...
April 11, 2025 at 8:00 PM
scnanoseq nf-co.re/scrnaseq: an nf-core [Nextflow] pipeline for Oxford Nanopore single-cell RNA-sequencing www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/nf-core/scna...
Pipeline release! nf-core/scrnaseq v4.0.0 - 4.0.0!
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/4.0.0
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/4.0.0
March 11, 2025 at 8:05 AM
Pipeline release! nf-core/scrnaseq v4.0.0 - 4.0.0!
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/4.0.0
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/4.0.0
Big news: Our #Zebrahub paper is out in #Cell!
A timecourse atlas of zebrafish embryonic development combining #scRNAseq & #lightsheet, to undersdand progenitor dynamics.
📄 Read: cell.com/cell/fulltex...
🌐 Explore: zebrahub.sf.czbiohub.org
#DevBio #Biology #Zebrafish Big thanks to all authors!
A timecourse atlas of zebrafish embryonic development combining #scRNAseq & #lightsheet, to undersdand progenitor dynamics.
📄 Read: cell.com/cell/fulltex...
🌐 Explore: zebrahub.sf.czbiohub.org
#DevBio #Biology #Zebrafish Big thanks to all authors!
November 17, 2024 at 8:47 PM
Big news: Our #Zebrahub paper is out in #Cell!
A timecourse atlas of zebrafish embryonic development combining #scRNAseq & #lightsheet, to undersdand progenitor dynamics.
📄 Read: cell.com/cell/fulltex...
🌐 Explore: zebrahub.sf.czbiohub.org
#DevBio #Biology #Zebrafish Big thanks to all authors!
A timecourse atlas of zebrafish embryonic development combining #scRNAseq & #lightsheet, to undersdand progenitor dynamics.
📄 Read: cell.com/cell/fulltex...
🌐 Explore: zebrahub.sf.czbiohub.org
#DevBio #Biology #Zebrafish Big thanks to all authors!
David Hall & @vectorimmunity.bsky.social highlight @merklinglab.bsky.social & colleagues’ Cell Genomics article on #mosquito cellular responses in #midgut & #fatbody after #bloodfeeding. #Aedes #aegypti #scRNAseq #Metabolomics @iastateresearch.bsky.social
authors.elsevier.com/a/1lbEr5Eb1x...
authors.elsevier.com/a/1lbEr5Eb1x...
August 13, 2025 at 11:49 AM
David Hall & @vectorimmunity.bsky.social highlight @merklinglab.bsky.social & colleagues’ Cell Genomics article on #mosquito cellular responses in #midgut & #fatbody after #bloodfeeding. #Aedes #aegypti #scRNAseq #Metabolomics @iastateresearch.bsky.social
authors.elsevier.com/a/1lbEr5Eb1x...
authors.elsevier.com/a/1lbEr5Eb1x...
A valuable step toward connecting atlas-scale single-cell data with ocular biology and precision ophthalmology.
#SingleCell #scRNAseq #Ophthalmology #Transcriptomics #CellAtlas
#SingleCell #scRNAseq #Ophthalmology #Transcriptomics #CellAtlas
September 30, 2026 at 3:25 AM
A valuable step toward connecting atlas-scale single-cell data with ocular biology and precision ophthalmology.
#SingleCell #scRNAseq #Ophthalmology #Transcriptomics #CellAtlas
#SingleCell #scRNAseq #Ophthalmology #Transcriptomics #CellAtlas
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.
My R35 MIRA grant is officially funded. The Gurney Lab lives for another 5 years! This will allow us to push our awesome work on scRNAseq during phage infection even further and develop a better understanding of how phage sociality and gene essentiality is impacted by the environment and host.
August 28, 2026 at 6:09 PM
My R35 MIRA grant is officially funded. The Gurney Lab lives for another 5 years! This will allow us to push our awesome work on scRNAseq during phage infection even further and develop a better understanding of how phage sociality and gene essentiality is impacted by the environment and host.
I've posted the notes/slides for my computational biology class at github.com/pachterlab/B... Topics were chosen based on appearing in >=3 bio areas, although for focus examples are all drawn from #scRNAseq. Homeworks include both theory and exploration of data (via GoogleColab).
September 22, 2023 at 1:55 PM
I've posted the notes/slides for my computational biology class at github.com/pachterlab/B... Topics were chosen based on appearing in >=3 bio areas, although for focus examples are all drawn from #scRNAseq. Homeworks include both theory and exploration of data (via GoogleColab).
Whole-body Single-cell Spatial transcriptomic atlas of adult Danionella ~1 cm long
scRNAseq
MERFISH (500-gene)
HCR
Endothelial cell podxl+ (Fig S8)
Vascular vs Visceral mural cell (Fig S10)
Peter Reddien lab bioRxiv 2026
www.biorxiv.org/content/10.6...
scRNAseq
MERFISH (500-gene)
HCR
Endothelial cell podxl+ (Fig S8)
Vascular vs Visceral mural cell (Fig S10)
Peter Reddien lab bioRxiv 2026
www.biorxiv.org/content/10.6...
February 10, 2026 at 12:57 PM
Whole-body Single-cell Spatial transcriptomic atlas of adult Danionella ~1 cm long
scRNAseq
MERFISH (500-gene)
HCR
Endothelial cell podxl+ (Fig S8)
Vascular vs Visceral mural cell (Fig S10)
Peter Reddien lab bioRxiv 2026
www.biorxiv.org/content/10.6...
scRNAseq
MERFISH (500-gene)
HCR
Endothelial cell podxl+ (Fig S8)
Vascular vs Visceral mural cell (Fig S10)
Peter Reddien lab bioRxiv 2026
www.biorxiv.org/content/10.6...
We just released IRIS (7+yrs project), a tech we believe will transform cell biology by pairing high-resolution cell images with matched #scRNAseq, letting us interpret cellular form by its molecular ground truth.
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
December 2, 2025 at 2:18 PM
We just released IRIS (7+yrs project), a tech we believe will transform cell biology by pairing high-resolution cell images with matched #scRNAseq, letting us interpret cellular form by its molecular ground truth.
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
Our manuscript describing #MatriCom, a web application we developed in collaboration with @valerioizzi.bsky.social to infer #ECM communication systems from #scRNASeq datasets is now available on @biorxivpreprint.bsky.social!
MatriCom: a scRNA-Seq data mining tool to infer ECM-ECM and cell-ECM communication systems https://www.biorxiv.org/content/10.1101/2024.12.10.627834v1
December 17, 2024 at 3:18 AM
Our manuscript describing #MatriCom, a web application we developed in collaboration with @valerioizzi.bsky.social to infer #ECM communication systems from #scRNASeq datasets is now available on @biorxivpreprint.bsky.social!
And @erinsauve.bsky.social received a best poster award at #ICPvR for her P. vivax scRNAseq work!
February 14, 2025 at 12:32 PM
And @erinsauve.bsky.social received a best poster award at #ICPvR for her P. vivax scRNAseq work!
This looks like an incredible way to analyse scRNaseq. While I have concerns over the way this could be used, AI approach to interacting with scRNAseq could be a game changer for drawing meaning for our ever increasingly complex datasets: Cell Whisperer #ImmunoSky
cellwhisperer.bocklab.org
cellwhisperer.bocklab.org
CellWhisperer: Unlocking the Language of Cells
cellwhisperer.bocklab.org
October 18, 2024 at 10:49 PM
This looks like an incredible way to analyse scRNaseq. While I have concerns over the way this could be used, AI approach to interacting with scRNAseq could be a game changer for drawing meaning for our ever increasingly complex datasets: Cell Whisperer #ImmunoSky
cellwhisperer.bocklab.org
cellwhisperer.bocklab.org
And epigenetic hulk smashing every papers. With a preference for scRNAseq papers
November 14, 2024 at 8:38 PM
And epigenetic hulk smashing every papers. With a preference for scRNAseq papers
A funded postdoctoral position is available at the IBPS, Sorbonne
University/CNRS/INSERM in Paris, to investigate the
formation of the olfactory organ in zebrafish.
We are looking for an postdoctoral researcher with expertise in transcriptomics
and bioinformatics, (scRNAseq analysis).
University/CNRS/INSERM in Paris, to investigate the
formation of the olfactory organ in zebrafish.
We are looking for an postdoctoral researcher with expertise in transcriptomics
and bioinformatics, (scRNAseq analysis).
September 24, 2026 at 9:15 AM
A funded postdoctoral position is available at the IBPS, Sorbonne
University/CNRS/INSERM in Paris, to investigate the
formation of the olfactory organ in zebrafish.
We are looking for an postdoctoral researcher with expertise in transcriptomics
and bioinformatics, (scRNAseq analysis).
University/CNRS/INSERM in Paris, to investigate the
formation of the olfactory organ in zebrafish.
We are looking for an postdoctoral researcher with expertise in transcriptomics
and bioinformatics, (scRNAseq analysis).
Today, we report that chronic intermittent fasting impairs beta-cell maturation and function in adolescent mice. Using scRNAseq, we delineated a "maturation score" for beta-cells. Long-term IF good if you're older, might be harmful if you are still developing!
👇
www.cell.com/cell-reports...
👇
www.cell.com/cell-reports...
January 19, 2025 at 11:37 AM
Today, we report that chronic intermittent fasting impairs beta-cell maturation and function in adolescent mice. Using scRNAseq, we delineated a "maturation score" for beta-cells. Long-term IF good if you're older, might be harmful if you are still developing!
👇
www.cell.com/cell-reports...
👇
www.cell.com/cell-reports...
Proximal Ascending aorta is made of #SmoothMuscleCell of dual lineage origins
Luminal side: Wnt1+ #CardiacNeuralCrest
Abluminal side: Mef2c+ #SecondHeartField
Their transcript profiles by scRNAseq + snATACseq👇
#AortaEd
#ATVB 2024 @ahajournals.bsky.social
www.ahajournals.org/doi/10.1161/...
Luminal side: Wnt1+ #CardiacNeuralCrest
Abluminal side: Mef2c+ #SecondHeartField
Their transcript profiles by scRNAseq + snATACseq👇
#AortaEd
#ATVB 2024 @ahajournals.bsky.social
www.ahajournals.org/doi/10.1161/...
January 26, 2025 at 1:39 PM
Proximal Ascending aorta is made of #SmoothMuscleCell of dual lineage origins
Luminal side: Wnt1+ #CardiacNeuralCrest
Abluminal side: Mef2c+ #SecondHeartField
Their transcript profiles by scRNAseq + snATACseq👇
#AortaEd
#ATVB 2024 @ahajournals.bsky.social
www.ahajournals.org/doi/10.1161/...
Luminal side: Wnt1+ #CardiacNeuralCrest
Abluminal side: Mef2c+ #SecondHeartField
Their transcript profiles by scRNAseq + snATACseq👇
#AortaEd
#ATVB 2024 @ahajournals.bsky.social
www.ahajournals.org/doi/10.1161/...
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...
In our latest study in @cp-immunity.bsky.social, we followed dynamics of vaccine-specific Tfh cells for 60+ weeks after immunization.
authors.elsevier.com/a/1m3mV3qNrU...
We captured >500,000 CD4 T cells including >36,000 vaccine-specific Tfh by scRNAseq, giving an unprecedented longitudinal detail.
authors.elsevier.com/a/1m3mV3qNrU...
We captured >500,000 CD4 T cells including >36,000 vaccine-specific Tfh by scRNAseq, giving an unprecedented longitudinal detail.
November 12, 2025 at 7:45 PM
In our latest study in @cp-immunity.bsky.social, we followed dynamics of vaccine-specific Tfh cells for 60+ weeks after immunization.
authors.elsevier.com/a/1m3mV3qNrU...
We captured >500,000 CD4 T cells including >36,000 vaccine-specific Tfh by scRNAseq, giving an unprecedented longitudinal detail.
authors.elsevier.com/a/1m3mV3qNrU...
We captured >500,000 CD4 T cells including >36,000 vaccine-specific Tfh by scRNAseq, giving an unprecedented longitudinal detail.