Charles Dussiau
@charlesdussiau.bsky.social
Postdoc at EMBL and DKFZ at Judith Zaugg and Mick Milsom labs
Computational Hematologist
Computational Hematologist
Reposted by Charles Dussiau
We’re recruiting a Research Engineer in #bioengineering
Join a dynamic multi-institute environment at @upcite.bsky.social to support cutting-edge work in #microfluidics #organoids & tissue #manufacture
Apply👇🏻 if you’re excited about interdisciplinary collaborative science🔬🧪⚗️🧑🔬
Join a dynamic multi-institute environment at @upcite.bsky.social to support cutting-edge work in #microfluidics #organoids & tissue #manufacture
Apply👇🏻 if you’re excited about interdisciplinary collaborative science🔬🧪⚗️🧑🔬
November 27, 2025 at 11:55 AM
We’re recruiting a Research Engineer in #bioengineering
Join a dynamic multi-institute environment at @upcite.bsky.social to support cutting-edge work in #microfluidics #organoids & tissue #manufacture
Apply👇🏻 if you’re excited about interdisciplinary collaborative science🔬🧪⚗️🧑🔬
Join a dynamic multi-institute environment at @upcite.bsky.social to support cutting-edge work in #microfluidics #organoids & tissue #manufacture
Apply👇🏻 if you’re excited about interdisciplinary collaborative science🔬🧪⚗️🧑🔬
Reposted by Charles Dussiau
“There were some cells in there that were very messed up”
In a technological tour-de-force, researchers have sequenced the whole genomes of more than 100 individual cells from one 74-year-old man
go.nature.com/44yj4MN
In a technological tour-de-force, researchers have sequenced the whole genomes of more than 100 individual cells from one 74-year-old man
go.nature.com/44yj4MN
We are all mosaics: vast genetic diversity found between cells in a single person
Technical advances allow researchers to trace the genetic changes that occur over time.
go.nature.com
November 26, 2025 at 9:28 AM
“There were some cells in there that were very messed up”
In a technological tour-de-force, researchers have sequenced the whole genomes of more than 100 individual cells from one 74-year-old man
go.nature.com/44yj4MN
In a technological tour-de-force, researchers have sequenced the whole genomes of more than 100 individual cells from one 74-year-old man
go.nature.com/44yj4MN
Reposted by Charles Dussiau
We are looking for a postdoc to join our team! If you're interested in translating a cutting edge genomics technology (www.nature.com/articles/s41...) to real-life applications in hematology, this is for you. We offer a unique working environment ON THE BEACH: recruitment.crg.eu/content/jobs...
November 20, 2025 at 9:36 AM
We are looking for a postdoc to join our team! If you're interested in translating a cutting edge genomics technology (www.nature.com/articles/s41...) to real-life applications in hematology, this is for you. We offer a unique working environment ON THE BEACH: recruitment.crg.eu/content/jobs...
Reposted by Charles Dussiau
Capsule: Comprehensive Reproducibility Framework for R and Bioinformatics Workflows github.com/SAADAT-Abu/C... ...Generates Docker containers, exports to Nextflow & Snakemake #Rstats
November 19, 2025 at 7:02 PM
Capsule: Comprehensive Reproducibility Framework for R and Bioinformatics Workflows github.com/SAADAT-Abu/C... ...Generates Docker containers, exports to Nextflow & Snakemake #Rstats
Reposted by Charles Dussiau
🚨 Excited to share our paper 📢 @natcomms.nature.com
We reveal how inflammation reshapes the human #bonemarrow niche 🦴, home of 🩸 stem cells, in the context of #clonalhematopoiesis and #myelodysplasia
An amazing journey with fantastic colleagues and collaborators, thank you all!
shorturl.at/ad0st
We reveal how inflammation reshapes the human #bonemarrow niche 🦴, home of 🩸 stem cells, in the context of #clonalhematopoiesis and #myelodysplasia
An amazing journey with fantastic colleagues and collaborators, thank you all!
shorturl.at/ad0st
November 19, 2025 at 8:12 PM
🚨 Excited to share our paper 📢 @natcomms.nature.com
We reveal how inflammation reshapes the human #bonemarrow niche 🦴, home of 🩸 stem cells, in the context of #clonalhematopoiesis and #myelodysplasia
An amazing journey with fantastic colleagues and collaborators, thank you all!
shorturl.at/ad0st
We reveal how inflammation reshapes the human #bonemarrow niche 🦴, home of 🩸 stem cells, in the context of #clonalhematopoiesis and #myelodysplasia
An amazing journey with fantastic colleagues and collaborators, thank you all!
shorturl.at/ad0st
Reposted by Charles Dussiau
Pre-print alert! And this one really is a must read for anyone that does spectral #flowcytometry. It is a complete, fully-automated spectral unmixing pipeline that reduces error up to 9000-fold.
Want to get a tough sample, like lung, looking like this? Read more!
www.biorxiv.org/content/10.1...
Want to get a tough sample, like lung, looking like this? Read more!
www.biorxiv.org/content/10.1...
October 28, 2025 at 8:06 AM
Pre-print alert! And this one really is a must read for anyone that does spectral #flowcytometry. It is a complete, fully-automated spectral unmixing pipeline that reduces error up to 9000-fold.
Want to get a tough sample, like lung, looking like this? Read more!
www.biorxiv.org/content/10.1...
Want to get a tough sample, like lung, looking like this? Read more!
www.biorxiv.org/content/10.1...
Reposted by Charles Dussiau
New “discrete state” model of hematopoiesis published in Nature Immunology. rdcu.be/eL8oO
We propose a hierarchical model of hematopoiesis where stable “discrete states” serve as key regulatory nodes.
We propose a hierarchical model of hematopoiesis where stable “discrete states” serve as key regulatory nodes.
A unified multimodal single-cell framework reveals a discrete state model of hematopoiesis in mice
Nature Immunology - Grimes and colleagues integrate multiomic features to create a framework that allows the isolation of discrete cell states across hematopoiesis and exploit the underlying gene...
rdcu.be
October 22, 2025 at 1:10 PM
New “discrete state” model of hematopoiesis published in Nature Immunology. rdcu.be/eL8oO
We propose a hierarchical model of hematopoiesis where stable “discrete states” serve as key regulatory nodes.
We propose a hierarchical model of hematopoiesis where stable “discrete states” serve as key regulatory nodes.
Reposted by Charles Dussiau
Interested in cellular plasticity? Come to my live virtual talk at the Night Science Seminar Series! Free register here: cassyni.com/events/ApfsK...
September 12, 2025 at 9:17 PM
Interested in cellular plasticity? Come to my live virtual talk at the Night Science Seminar Series! Free register here: cassyni.com/events/ApfsK...
Reposted by Charles Dussiau
Been digging through GEO for multiome single-cell data, frustrating how much is unusable 🫠 (missing annotations, frag files, raw data). Uploading properly takes effort, but it makes your dataset so much more impactful... Props to (most of) the authors who fixed things when I reached out, though 👍
September 12, 2025 at 1:33 AM
Been digging through GEO for multiome single-cell data, frustrating how much is unusable 🫠 (missing annotations, frag files, raw data). Uploading properly takes effort, but it makes your dataset so much more impactful... Props to (most of) the authors who fixed things when I reached out, though 👍
Reposted by Charles Dussiau
Imagine detecting bone marrow disorders without a painful aspiration! The PERIBLOOD clinical trial by CLISEQ Ltd., the Weizmann Institute of Science & Weizmann’s commercial arm Yeda will see if a blood draw & GEM-X #scRNAseq could help develop future diagnostics. https://bit.ly/46i7TrX
September 9, 2025 at 5:05 PM
Imagine detecting bone marrow disorders without a painful aspiration! The PERIBLOOD clinical trial by CLISEQ Ltd., the Weizmann Institute of Science & Weizmann’s commercial arm Yeda will see if a blood draw & GEM-X #scRNAseq could help develop future diagnostics. https://bit.ly/46i7TrX
Reposted by Charles Dussiau
You can also save money by cutting-costs and preventing waste. We do a low of flow cytometry, and retitrated antibodies for overnight staining, reducing costs ~100-fold while improving signal-to-noise and reproducibility
currentprotocols.onlinelibrary.wiley.com/doi/10.1002/...
currentprotocols.onlinelibrary.wiley.com/doi/10.1002/...
Do more with Less: Improving High Parameter Cytometry Through Overnight Staining
Recent advances in flow cytometry have allowed high-dimensional characterization of biological phenomena, enabling breakthroughs in a multitude of fields. Despite the appreciation of the unique prope...
currentprotocols.onlinelibrary.wiley.com
September 3, 2025 at 4:03 PM
You can also save money by cutting-costs and preventing waste. We do a low of flow cytometry, and retitrated antibodies for overnight staining, reducing costs ~100-fold while improving signal-to-noise and reproducibility
currentprotocols.onlinelibrary.wiley.com/doi/10.1002/...
currentprotocols.onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Charles Dussiau
Our new review is out in Trends in Cancer. We had fund writing this :) We discuss the roles of retrotransposons in immune modulation in normal and malignant
hematopoiesis. www.cell.com/trends/cance...
hematopoiesis. www.cell.com/trends/cance...
Reawakening retrotransposons: immune modulation in normal and malignant hematopoiesis
Retrotransposons are mobile repetitive elements that constitute around 43% of the
human genome. Normally silenced through epigenetic mechanisms, retrotransposons can
become reactivated in response to ...
www.cell.com
September 3, 2025 at 5:02 AM
Our new review is out in Trends in Cancer. We had fund writing this :) We discuss the roles of retrotransposons in immune modulation in normal and malignant
hematopoiesis. www.cell.com/trends/cance...
hematopoiesis. www.cell.com/trends/cance...
Reposted by Charles Dussiau
New online! Imaging-based multimodal profiling of single cells with STAMP
Imaging-based multimodal profiling of single cells with STAMP
Nature Reviews Genetics, Published online: 21 August 2025; doi:10.1038/s41576-025-00891-6In this Tools of the Trade article, Kellie Wise and Anna Pascual-Reguant introduce STAMP (single-cell transcriptomics analysis and multimodal profiling), which harnesses imaging to measure RNA and/or protein expression in fixed cells or nuclei.
www.nature.com
August 21, 2025 at 11:29 AM
New online! Imaging-based multimodal profiling of single cells with STAMP
Reposted by Charles Dussiau
I hoped a fully-featured #rstats ggplot-based heatmap package would show up one day. {ggalign} might be it. It's basically {patchwork} on steroids 🧪 yunuuuu.github.io/ggalign/
August 6, 2025 at 6:13 PM
I hoped a fully-featured #rstats ggplot-based heatmap package would show up one day. {ggalign} might be it. It's basically {patchwork} on steroids 🧪 yunuuuu.github.io/ggalign/
Reposted by Charles Dussiau
Did you ever wonder what insights hide in the multiplets that are usually discarded in flow cytometry? 🫧 Find out in the first publication of my PhD, now out in Nature Methods! www.nature.com/articles/s41... (1/4)
August 7, 2025 at 8:48 PM
Did you ever wonder what insights hide in the multiplets that are usually discarded in flow cytometry? 🫧 Find out in the first publication of my PhD, now out in Nature Methods! www.nature.com/articles/s41... (1/4)
Reposted by Charles Dussiau
Excited to share our latest paper @natmethods.nature.com
We present a high-throughput framework to map cellular interactions at ultra-high scale – broadly applicable from whole-organism immune response mapping to personalized therapy response prediction (1/4).
www.nature.com/articles/s41...
We present a high-throughput framework to map cellular interactions at ultra-high scale – broadly applicable from whole-organism immune response mapping to personalized therapy response prediction (1/4).
www.nature.com/articles/s41...
August 7, 2025 at 11:24 AM
Excited to share our latest paper @natmethods.nature.com
We present a high-throughput framework to map cellular interactions at ultra-high scale – broadly applicable from whole-organism immune response mapping to personalized therapy response prediction (1/4).
www.nature.com/articles/s41...
We present a high-throughput framework to map cellular interactions at ultra-high scale – broadly applicable from whole-organism immune response mapping to personalized therapy response prediction (1/4).
www.nature.com/articles/s41...
Reposted by Charles Dussiau
New paper from @elhamazizi.bsky.social, @bleilab.bsky.social & @danapeer.bsky.social labs: Decipher, a deep generative model to track disease trajectories in single-cell data.
📖 Read: bit.ly/4mufVnZ @columbiaseas.bsky.social @columbiacancer.bsky.social @mskcancercenter.bsky.social
📖 Read: bit.ly/4mufVnZ @columbiaseas.bsky.social @columbiacancer.bsky.social @mskcancercenter.bsky.social
Joint representation and visualization of derailed cell states with Decipher - Genome Biology
Biological insights often depend on comparing conditions such as disease and health. Yet, we lack effective computational tools for integrating single-cell genomics data across conditions or character...
bit.ly
August 5, 2025 at 4:11 PM
New paper from @elhamazizi.bsky.social, @bleilab.bsky.social & @danapeer.bsky.social labs: Decipher, a deep generative model to track disease trajectories in single-cell data.
📖 Read: bit.ly/4mufVnZ @columbiaseas.bsky.social @columbiacancer.bsky.social @mskcancercenter.bsky.social
📖 Read: bit.ly/4mufVnZ @columbiaseas.bsky.social @columbiacancer.bsky.social @mskcancercenter.bsky.social
Reposted by Charles Dussiau
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
August 4, 2025 at 1:52 PM
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
Reposted by Charles Dussiau
👏 Congratulations to Dr. Leïla Perié, team leader at @institutcurie.bsky.social who's been awarded an #ERC #ProofofConcept Grant for her project "VisioWell", the 1st accessible ex-vivo single-cell live-cell imaging device designed to analyse the dynamics of non-adherent cells.
#CellBio @cnrs.fr
#CellBio @cnrs.fr
July 23, 2025 at 9:52 AM
👏 Congratulations to Dr. Leïla Perié, team leader at @institutcurie.bsky.social who's been awarded an #ERC #ProofofConcept Grant for her project "VisioWell", the 1st accessible ex-vivo single-cell live-cell imaging device designed to analyse the dynamics of non-adherent cells.
#CellBio @cnrs.fr
#CellBio @cnrs.fr
Reposted by Charles Dussiau
Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1...
Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
July 22, 2025 at 9:59 PM
Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1...
Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
Reposted by Charles Dussiau
Benchmarking clustering, alignment, and integration methods for spatial transcriptomics - Genome Biology genomebiology.biomedcentral.com/articles/10.... 🧬🖥️ github.com/maiziezhoula...
July 23, 2025 at 6:30 PM
Benchmarking clustering, alignment, and integration methods for spatial transcriptomics - Genome Biology genomebiology.biomedcentral.com/articles/10.... 🧬🖥️ github.com/maiziezhoula...
Reposted by Charles Dussiau
The Commission is pushing for a massive increase in funding for Horizon Europe 2028-2034. If I understand correctly, Pillar I, which includes @erc.europa.eu and Marie Sklodowska Curie fellowships, would go from the current €25 billion to €44 billion. Let's hope it happens!
Very promising news on the next seven-year EU budget, with a proposed substantial increase for Horizon Europe including the ERC.
We are analysing the other parts of this proposal in more detail.
@Vonderleyen @EZaharievaEU
research-and-innovation.ec.europa.eu/news/all-res...
We are analysing the other parts of this proposal in more detail.
@Vonderleyen @EZaharievaEU
research-and-innovation.ec.europa.eu/news/all-res...
Horizon Europe 2028 - 2034: twice bigger, simpler, faster and more impactful
Research and innovation news alert: As part of the next long-term EU budget 2028-2034, the Commission is proposing to double the budget of the research and innovation framework programme to €175 billi...
research-and-innovation.ec.europa.eu
July 23, 2025 at 8:28 PM
The Commission is pushing for a massive increase in funding for Horizon Europe 2028-2034. If I understand correctly, Pillar I, which includes @erc.europa.eu and Marie Sklodowska Curie fellowships, would go from the current €25 billion to €44 billion. Let's hope it happens!
Reposted by Charles Dussiau
How does luspatercept relieve anemia in myelodysplastic syndromes?
Amit Verma & team discover splicing of erythroid transcription factor is associated with therapeutic response in MDS: buff.ly/KFd7ri7
Amit Verma & team discover splicing of erythroid transcription factor is associated with therapeutic response in MDS: buff.ly/KFd7ri7
July 11, 2025 at 1:20 PM
How does luspatercept relieve anemia in myelodysplastic syndromes?
Amit Verma & team discover splicing of erythroid transcription factor is associated with therapeutic response in MDS: buff.ly/KFd7ri7
Amit Verma & team discover splicing of erythroid transcription factor is associated with therapeutic response in MDS: buff.ly/KFd7ri7
Reposted by Charles Dussiau
H3K4me3 is a post-transcriptional histone mark | bioRxiv
www.biorxiv.org/content/10....
www.biorxiv.org/content/10....
July 11, 2025 at 2:15 PM
H3K4me3 is a post-transcriptional histone mark | bioRxiv
www.biorxiv.org/content/10....
www.biorxiv.org/content/10....
Reposted by Charles Dussiau
Spatial multi-omics reveals cell-type-specific nuclear compartments | Nature
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Spatial multi-omics reveals cell-type-specific nuclear compartments - Nature
A genomic barcoding scheme called two-layer DNA seqFISH+ enables the simultaneous mapping of more than 100,000 loci and has been used to identify cell-type-specific subnuclear compartments in the mous...
www.nature.com
June 27, 2025 at 5:54 AM
Spatial multi-omics reveals cell-type-specific nuclear compartments | Nature
www.nature.com/articles/s41...
www.nature.com/articles/s41...