rdcu.be/ePnoK
CellWhisperer: a multimodal AI that enables interactive scRNA-seq data exploration with natural-language conversations.
CellWhisperer: a multimodal AI that enables interactive scRNA-seq data exploration with natural-language conversations.
Multimodal learning enables chat-based exploration of single-cell data
Nature Biotechnology - CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.
rdcu.be
November 11, 2025 at 1:37 PM
rdcu.be/ePnoK
CellWhisperer: a multimodal AI that enables interactive scRNA-seq data exploration with natural-language conversations.
CellWhisperer: a multimodal AI that enables interactive scRNA-seq data exploration with natural-language conversations.
Phys: 'New molecular drivers of long COVID link nasal inflammation to lingering symptoms'
'Using state-of-the-art single-cell transcriptomics (scRNA-seq) combined with cell biology models, the scientists were able to decipher the cellular and molecular mechanisms..'
phys.org/news/2025-11...
'Using state-of-the-art single-cell transcriptomics (scRNA-seq) combined with cell biology models, the scientists were able to decipher the cellular and molecular mechanisms..'
phys.org/news/2025-11...
New molecular drivers of long COVID link nasal inflammation to lingering symptoms
A research team from the Research Center Borstel, Leibniz Lung Center (FZB), Kiel University (CAU), the University of Lübeck (UzL), and the University Medical Center Schleswig-Holstein (UKSH), togethe...
phys.org
November 7, 2025 at 4:59 PM
Phys: 'New molecular drivers of long COVID link nasal inflammation to lingering symptoms'
'Using state-of-the-art single-cell transcriptomics (scRNA-seq) combined with cell biology models, the scientists were able to decipher the cellular and molecular mechanisms..'
phys.org/news/2025-11...
'Using state-of-the-art single-cell transcriptomics (scRNA-seq) combined with cell biology models, the scientists were able to decipher the cellular and molecular mechanisms..'
phys.org/news/2025-11...
Pleased to see the official release of our research letter in @jci.org ! In my first-ever corresponding author publication, we leveraged a publicly available scRNA-seq dataset and asked how prostate cancer cells systemically reprogram the cells of the bone marrow. www.jci.org/articles/vie...
JCI -
Prostate tumor–mediated IFNG signaling primes myeloid cells in bone premetastatic niche for immunosuppressive IL-10 signaling
www.jci.org
November 10, 2025 at 5:57 PM
Pleased to see the official release of our research letter in @jci.org ! In my first-ever corresponding author publication, we leveraged a publicly available scRNA-seq dataset and asked how prostate cancer cells systemically reprogram the cells of the bone marrow. www.jci.org/articles/vie...
🧬 CellWhisperer introduces a chat-based way to explore scRNA-seq data. By enabling natural language analysis, it bridges biologists and bioinformaticians—paving the way for AI-driven bioinformatics assistants. (10/11)
November 11, 2025 at 12:52 PM
🧬 CellWhisperer introduces a chat-based way to explore scRNA-seq data. By enabling natural language analysis, it bridges biologists and bioinformaticians—paving the way for AI-driven bioinformatics assistants. (10/11)
Inferring the regulation dynamics of oscillatorynetworks from scRNA-seq data [new]
Inferred cell cycle positions enhance gene regulatory network inference, especially in early progenitor cells, by improving on temporal ordering.
Inferred cell cycle positions enhance gene regulatory network inference, especially in early progenitor cells, by improving on temporal ordering.
November 10, 2025 at 11:49 AM
Inferring the regulation dynamics of oscillatorynetworks from scRNA-seq data [new]
Inferred cell cycle positions enhance gene regulatory network inference, especially in early progenitor cells, by improving on temporal ordering.
Inferred cell cycle positions enhance gene regulatory network inference, especially in early progenitor cells, by improving on temporal ordering.
From Germany:
scRNA-seq reveals persistent aberrant differentiation of nasal epithelium driven by TNFα and TGFβ in post-COVID syndrome
www.nature.com/articles/s41...
Screenshot from latest Science for ME weekly update
#LongCovid #PASC
scRNA-seq reveals persistent aberrant differentiation of nasal epithelium driven by TNFα and TGFβ in post-COVID syndrome
www.nature.com/articles/s41...
Screenshot from latest Science for ME weekly update
#LongCovid #PASC
November 6, 2025 at 1:54 AM
From Germany:
scRNA-seq reveals persistent aberrant differentiation of nasal epithelium driven by TNFα and TGFβ in post-COVID syndrome
www.nature.com/articles/s41...
Screenshot from latest Science for ME weekly update
#LongCovid #PASC
scRNA-seq reveals persistent aberrant differentiation of nasal epithelium driven by TNFα and TGFβ in post-COVID syndrome
www.nature.com/articles/s41...
Screenshot from latest Science for ME weekly update
#LongCovid #PASC
'Here, we present a multi-organ single-cell atlas encompassing 23 fetal and adult organs, integrating scRNA-seq & scTCR-seq fm over 2.8 million immune cells across 15 second-trimester fetal & 4 adult donors.'
#Immunology
#Immunology
Systemic immune activity occurs during human immune system maturation
Profiling of immune cells from consecutive developmental time points in second-trimester
fetuses and adults reveals that immune activation, immune tolerance, and hematopoiesis
occur in a systemic way ...
www.cell.com
October 30, 2025 at 10:26 PM
'Here, we present a multi-organ single-cell atlas encompassing 23 fetal and adult organs, integrating scRNA-seq & scTCR-seq fm over 2.8 million immune cells across 15 second-trimester fetal & 4 adult donors.'
#Immunology
#Immunology
CytoTRACE 2: an interpretable deep-learning method that uses scRNA-seq data to predict absolute developmental potential across datasets.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Improved reconstruction of single-cell developmental potential with CytoTRACE 2 - Nature Methods
CytoTRACE 2 is an interpretable deep learning framework that leverages single-cell RNA sequencing data to predict absolute developmental potential across datasets.
www.nature.com
October 29, 2025 at 3:14 PM
CytoTRACE 2: an interpretable deep-learning method that uses scRNA-seq data to predict absolute developmental potential across datasets.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Excited to see our paper online! We combined scMS and scRNA-seq from the same plant cells 🌱 — a step toward true single-cell multi-omics in plants.
Overview 👇
Overview 👇
A research team from the @oconnorlab.bsky.social has made a breakthrough in elucidating the biosynthesis of plant natural products by combining scRNA-seq and scMS in the same plant cell. The study was published in @pnas.org. www.ice.mpg.de/516369/PR_Ka...
A glimpse into the cell factory: matching gene expression to metabolite production in single plant cells
A research team at the Max Planck Institute for Chemical Ecology has successfully combined single-cell RNA sequencing (scRNA-seq) and single-cell mass spectrometry (scMS) analysis on the same plant ce...
www.ice.mpg.de
October 27, 2025 at 6:32 PM
Excited to see our paper online! We combined scMS and scRNA-seq from the same plant cells 🌱 — a step toward true single-cell multi-omics in plants.
Overview 👇
Overview 👇
1/ If you're in bioinformatics, you're staring at matrices all day.
RNA-seq? Gene x sample.
scRNA-seq? Gene x cell.
Everything is a matrix.
But I never learned how to think in matrices. And I regret it.
RNA-seq? Gene x sample.
scRNA-seq? Gene x cell.
Everything is a matrix.
But I never learned how to think in matrices. And I regret it.
October 23, 2025 at 1:45 PM
1/ If you're in bioinformatics, you're staring at matrices all day.
RNA-seq? Gene x sample.
scRNA-seq? Gene x cell.
Everything is a matrix.
But I never learned how to think in matrices. And I regret it.
RNA-seq? Gene x sample.
scRNA-seq? Gene x cell.
Everything is a matrix.
But I never learned how to think in matrices. And I regret it.
11/
Key takeaways:
Bioinformatics is matrix math. Learn linear algebra basics.
Sparse matrices dominate scRNA-seq.
Tools abstract it, but understanding gives you control.
Watch StatQuest
Watch 3Blue1Brown
You won’t regret it. But you’ll regret not doing it sooner.
Key takeaways:
Bioinformatics is matrix math. Learn linear algebra basics.
Sparse matrices dominate scRNA-seq.
Tools abstract it, but understanding gives you control.
Watch StatQuest
Watch 3Blue1Brown
You won’t regret it. But you’ll regret not doing it sooner.
October 23, 2025 at 1:45 PM
11/
Key takeaways:
Bioinformatics is matrix math. Learn linear algebra basics.
Sparse matrices dominate scRNA-seq.
Tools abstract it, but understanding gives you control.
Watch StatQuest
Watch 3Blue1Brown
You won’t regret it. But you’ll regret not doing it sooner.
Key takeaways:
Bioinformatics is matrix math. Learn linear algebra basics.
Sparse matrices dominate scRNA-seq.
Tools abstract it, but understanding gives you control.
Watch StatQuest
Watch 3Blue1Brown
You won’t regret it. But you’ll regret not doing it sooner.
Explore zebrafish heart regeneration with precision: 8 stages mapped via Stereo-seq & scRNA-seq, unlocking cardiomyocyte secrets. Impressive regeneration! PMID:40253397, Nat Commun 2025, @NatureComms https://doi.org/10.1038/s41467-025-59070-0 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
An organ-wide spatiotemporal transcriptomic and cellular atlas of the regenerating zebrafish heart | Nature Communications
Adult zebrafish robustly regenerate injured hearts through a complex orchestration of molecular and cellular activities. However, this remarkable process, which is largely non-existent in humans, remains incompletely understood. Here, we utilize integrated spatial transcriptomics (Stereo-seq) and single-cell RNA-sequencing (scRNA-seq) to generate a spatially-resolved molecular and cellular atlas of regenerating zebrafish heart across eight stages. We characterize the cascade of cardiomyocyte cell states responsible for producing regenerated myocardium and explore a potential role for tpm4a in cardiomyocyte re-differentiation. Moreover, we uncover the activation of ifrd1 and atp6ap2 genes as a unique feature of regenerative hearts. Lastly, we reconstruct a 4D “virtual regenerating heart” comprising 569,896 cells/spots derived from 36 scRNA-seq libraries and 224 Stereo-seq slices. Our comprehensive atlas serves as a valuable resource to the cardiovascular and regeneration scientific comm
doi.org
October 20, 2025 at 6:10 AM
Look forward to sharing our work
@ahascience.bsky.social
#AHA25 From scRNA-seq to LLMs & AI-driven risk prediction, here’s how we’re decoding the intersection of cancer, immunity, & the heart. 💥👇 #CHIP #ICI #CardioOncology @yalecvrc.bsky.social @yalecancer.bsky.social
@Yale
@ahascience.bsky.social
#AHA25 From scRNA-seq to LLMs & AI-driven risk prediction, here’s how we’re decoding the intersection of cancer, immunity, & the heart. 💥👇 #CHIP #ICI #CardioOncology @yalecvrc.bsky.social @yalecancer.bsky.social
@Yale
October 19, 2025 at 4:57 PM
Look forward to sharing our work
@ahascience.bsky.social
#AHA25 From scRNA-seq to LLMs & AI-driven risk prediction, here’s how we’re decoding the intersection of cancer, immunity, & the heart. 💥👇 #CHIP #ICI #CardioOncology @yalecvrc.bsky.social @yalecancer.bsky.social
@Yale
@ahascience.bsky.social
#AHA25 From scRNA-seq to LLMs & AI-driven risk prediction, here’s how we’re decoding the intersection of cancer, immunity, & the heart. 💥👇 #CHIP #ICI #CardioOncology @yalecvrc.bsky.social @yalecancer.bsky.social
@Yale
Accelerating scRNA-seq analysis: automated cell type annotation using representation learning and vector search https://www.biorxiv.org/content/10.1101/2025.10.06.680787v1
October 8, 2025 at 8:47 AM
Accelerating scRNA-seq analysis: automated cell type annotation using representation learning and vector search https://www.biorxiv.org/content/10.1101/2025.10.06.680787v1
Very candid responses from Azim Surani here on his initially turbulent scientific journey, & accounts of genomic imprinting and the pioneering of mammalian scRNA-seq. Great to see this put together by Ashley Moffett & @geraldinejowett.bsky.social journals.biologists.com/dev/article/...
An interview with Azim Surani
Professor Azim Surani is the Director of Epigenomics and Germline Imprinting at the Gurdon Institute in Cambridge, UK. He is this year's recipient of both the prestigious Kyoto Prize and the Paul Ehrl...
journals.biologists.com
October 3, 2025 at 4:33 PM
Very candid responses from Azim Surani here on his initially turbulent scientific journey, & accounts of genomic imprinting and the pioneering of mammalian scRNA-seq. Great to see this put together by Ashley Moffett & @geraldinejowett.bsky.social journals.biologists.com/dev/article/...
First batch of scrna-seq data and I’m like a kid in a candy store!!
Awesome work by @annaschreiber.bsky.social and analysis by the amazing @lrizzardi.bsky.social !!
I can’t put it down!
Awesome work by @annaschreiber.bsky.social and analysis by the amazing @lrizzardi.bsky.social !!
I can’t put it down!
a cartoon of spongebob saying woot woot while holding a walkie talkie
ALT: a cartoon of spongebob saying woot woot while holding a walkie talkie
media.tenor.com
October 1, 2025 at 8:50 PM
First batch of scrna-seq data and I’m like a kid in a candy store!!
Awesome work by @annaschreiber.bsky.social and analysis by the amazing @lrizzardi.bsky.social !!
I can’t put it down!
Awesome work by @annaschreiber.bsky.social and analysis by the amazing @lrizzardi.bsky.social !!
I can’t put it down!
After vaccinating mice with these particles, researchers found that the vaccine accumulated in the lymph nodes- structures where B-cells encounter antigens and undergo rapid mutations that generate antibodies with high affinity for a particular antigen. This process takes place within clusters of
September 30, 2025 at 4:07 PM
After vaccinating mice with these particles, researchers found that the vaccine accumulated in the lymph nodes- structures where B-cells encounter antigens and undergo rapid mutations that generate antibodies with high affinity for a particular antigen. This process takes place within clusters of
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
💸 Stem cell culture that’s ~95% cheaper and weekend-free: a win-win for PIs and trainees!
Our revised manuscript is online at ORE: open-research-europe.ec.europa.eu/articles/4-1...
Benchmarked across cell lines & differentiation protocols, including scRNA-seq — with lessons for #cultivatedmeat too!
Our revised manuscript is online at ORE: open-research-europe.ec.europa.eu/articles/4-1...
Benchmarked across cell lines & differentiation protocols, including scRNA-seq — with lessons for #cultivatedmeat too!
open-research-europe.ec.europa.eu
September 20, 2025 at 2:41 PM
💸 Stem cell culture that’s ~95% cheaper and weekend-free: a win-win for PIs and trainees!
Our revised manuscript is online at ORE: open-research-europe.ec.europa.eu/articles/4-1...
Benchmarked across cell lines & differentiation protocols, including scRNA-seq — with lessons for #cultivatedmeat too!
Our revised manuscript is online at ORE: open-research-europe.ec.europa.eu/articles/4-1...
Benchmarked across cell lines & differentiation protocols, including scRNA-seq — with lessons for #cultivatedmeat too!
ScRNA-seq and scATAC-seq reveal that sertoli cell mediate spermatogenesis disorders through stage-specific communications in non-obstructive azoospermia https://www.biorxiv.org/content/10.1101/2024.04.09.588807v1
ScRNA-seq and scATAC-seq reveal that sertoli cell mediate spermatogenesis disorders through stage-specific communications in non-obstructive azoospermia https://www.biorxiv.org/content/10.1101/2024.04.09.588807v1
Non-obstructive azoospermia (NOA) belongs to male infertility due to spermatogenesis failure. Howeve
www.biorxiv.org
April 13, 2024 at 2:29 PM
ScRNA-seq and scATAC-seq reveal that sertoli cell mediate spermatogenesis disorders through stage-specific communications in non-obstructive azoospermia https://www.biorxiv.org/content/10.1101/2024.04.09.588807v1
To get a clearer picture we re-analyzed scRNA-seq datasets encompassing the SVZ, generated by the labs of F Doetsch (@doetschlab.bsky.social), A Martin Villalba, J Frisen, S Linnarsson (@slinnarsson.bsky.social), J Biernaskie, N Rajewsky, F Miller, A Alvarez Buylla and O Raineteau. (7/18)
November 17, 2024 at 8:16 PM
To get a clearer picture we re-analyzed scRNA-seq datasets encompassing the SVZ, generated by the labs of F Doetsch (@doetschlab.bsky.social), A Martin Villalba, J Frisen, S Linnarsson (@slinnarsson.bsky.social), J Biernaskie, N Rajewsky, F Miller, A Alvarez Buylla and O Raineteau. (7/18)
generates synthetic scRNA-seq dataset by a generator to replace the original dataset. Then, (2) we propose a single-step conditional diffusion generator named SCDG, which perform single-step gradient back-propagation to help scDD optimize [4/7 of https://arxiv.org/abs/2503.04357v1]
March 7, 2025 at 6:44 AM
generates synthetic scRNA-seq dataset by a generator to replace the original dataset. Then, (2) we propose a single-step conditional diffusion generator named SCDG, which perform single-step gradient back-propagation to help scDD optimize [4/7 of https://arxiv.org/abs/2503.04357v1]
Ever heard of Live-seq? Live-seq time-resolved transcriptomes of living cells can add directionality to scRNA datasets! www.cytosurge.com/cancer-cell-... Happy to discuss this any time!
March 11, 2025 at 10:35 AM
Ever heard of Live-seq? Live-seq time-resolved transcriptomes of living cells can add directionality to scRNA datasets! www.cytosurge.com/cancer-cell-... Happy to discuss this any time!
Expressing FKBP-enAsCas12a w/a guide library (to KO targets) then depleting the enzyme for ~48 hrs via dTag, guide RNA transcripts/barcodes accumulate & can be used to link each guide to a phenotype by scRNA-seq. Results w/depleted enAsCas12a look similar to cells expressing guides only (no enzyme).
December 9, 2024 at 1:05 PM
Expressing FKBP-enAsCas12a w/a guide library (to KO targets) then depleting the enzyme for ~48 hrs via dTag, guide RNA transcripts/barcodes accumulate & can be used to link each guide to a phenotype by scRNA-seq. Results w/depleted enAsCas12a look similar to cells expressing guides only (no enzyme).
STEGO.R: an application to aid in scRNA-seq and scTCR-seq processing and analysis. https://www.biorxiv.org/content/10.1101/2023.09.27.559702v1
STEGO.R: an application to aid in scRNA-seq and scTCR-seq processing and analysis. https://www.biorxiv.org/content/10.1101/2023.09.27.559702v1
Introduction: The hypervariable T cell receptor (TCR), created through somatic recombination, allows
www.biorxiv.org
September 30, 2023 at 12:48 AM
STEGO.R: an application to aid in scRNA-seq and scTCR-seq processing and analysis. https://www.biorxiv.org/content/10.1101/2023.09.27.559702v1