Impressive work from @saschalaubinger.bsky.social and colleagues, describing molecular and phenotypic footprints of climate in transcriptomes of native Arabidopsis thaliana.
#plantscience
www.biorxiv.org/content/10.6...
#plantscience
www.biorxiv.org/content/10.6...
March 8, 2026 at 8:08 AM
Impressive work from @saschalaubinger.bsky.social and colleagues, describing molecular and phenotypic footprints of climate in transcriptomes of native Arabidopsis thaliana.
#plantscience
www.biorxiv.org/content/10.6...
#plantscience
www.biorxiv.org/content/10.6...
Francesco Cicconardi talk on single cell transcriptomes of Heliconiini butterfly brains @tibbe-evolneuro.bsky.social #ESEB2025 SYMPOSIUM 17.2
August 18, 2025 at 1:22 PM
Francesco Cicconardi talk on single cell transcriptomes of Heliconiini butterfly brains @tibbe-evolneuro.bsky.social #ESEB2025 SYMPOSIUM 17.2
Our paper on the evolution (duplicated) gene expression divergence in spatially resolved plant transcriptomes is now out @theplantcell.bsky.social
w/ @yvdp.bsky.social
#PlantSci #Evolution
academic.oup.com/plcell/advan...
w/ @yvdp.bsky.social
#PlantSci #Evolution
academic.oup.com/plcell/advan...
Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes
After gene and genome duplications, expression divergence across cell types is not random, and it can be explained by a combination of gene age, gene funct
academic.oup.com
October 16, 2025 at 11:20 AM
Our paper on the evolution (duplicated) gene expression divergence in spatially resolved plant transcriptomes is now out @theplantcell.bsky.social
w/ @yvdp.bsky.social
#PlantSci #Evolution
academic.oup.com/plcell/advan...
w/ @yvdp.bsky.social
#PlantSci #Evolution
academic.oup.com/plcell/advan...
I use transcriptomics to study the host response to emerging virus infection. I’ve seen a lot of chaotic transcriptomes. The only transcriptomic chaos here is everything having to do with data acquisition, analysis, & interpretation
Folks, the situation with the latest anti-vaccine preprint making the rounds is way worse than initially assessed. There's even a dash of plagiarism!
reeserichardson.blog/2025/07/28/n...
reeserichardson.blog/2025/07/28/n...
No, mRNA vaccines do not cause “transcriptomic chaos”
A review of a recent anti-vaccine preprint
reeserichardson.blog
July 29, 2025 at 10:36 AM
I use transcriptomics to study the host response to emerging virus infection. I’ve seen a lot of chaotic transcriptomes. The only transcriptomic chaos here is everything having to do with data acquisition, analysis, & interpretation
Now published!!!! www.nature.com/articles/s41...
April 28, 2025 at 12:48 PM
Now published!!!! www.nature.com/articles/s41...
@camillemrcht.bsky.social present the Transipedia project that index human transcriptomes for biomedical research at #DSB2026
February 18, 2026 at 4:34 PM
@camillemrcht.bsky.social present the Transipedia project that index human transcriptomes for biomedical research at #DSB2026
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
New preprint from our lab, spearheaded by @maelledaunesse.bsky.social and in collaboration with Diego Villar!
In which we ask, can we detect joint signatures suggestive of positive selection on transcriptomes and epigenomes?
In which we ask, can we detect joint signatures suggestive of positive selection on transcriptomes and epigenomes?
We've just released our new preprint! 🐀✨
doi.org/10.1101/2025...
How do gene expression and regulation evolve during adaptation? And how can we tell adaptive shifts apart from simple drift?
@camilleberthelot.bsky.social
👇 A short thread on what we found in African mole-rats.
doi.org/10.1101/2025...
How do gene expression and regulation evolve during adaptation? And how can we tell adaptive shifts apart from simple drift?
@camilleberthelot.bsky.social
👇 A short thread on what we found in African mole-rats.
Coordinated shifts in gene expression and regulation during mole-rat evolution
Changes in gene expression and regulation are central to mammalian phenotypic evolution. Yet, distinguishing adaptive gene expression shifts from neutral divergence remains challenging. Here, we integ...
doi.org
December 4, 2025 at 4:50 PM
New preprint from our lab, spearheaded by @maelledaunesse.bsky.social and in collaboration with Diego Villar!
In which we ask, can we detect joint signatures suggestive of positive selection on transcriptomes and epigenomes?
In which we ask, can we detect joint signatures suggestive of positive selection on transcriptomes and epigenomes?
We’re unwrapping a new method today at @mskcancercenter.bsky.social. Led by Sydney Blattman, Nabih Maslah, and @austinv11.com with @danapeer.bsky.social, @ronanchaligne.bsky.social and @10xgenomics.bsky.social, we present GIFT: Genotyping In Fixed Transcriptomes www.biorxiv.org/content/10.6... 1/n
www.biorxiv.org
April 13, 2026 at 3:13 PM
We’re unwrapping a new method today at @mskcancercenter.bsky.social. Led by Sydney Blattman, Nabih Maslah, and @austinv11.com with @danapeer.bsky.social, @ronanchaligne.bsky.social and @10xgenomics.bsky.social, we present GIFT: Genotyping In Fixed Transcriptomes www.biorxiv.org/content/10.6... 1/n
🧠📈 Now available on the Allen Brain Cell Atlas - aging mouse brain data!
Explore the most comprehensive and detailed single-cell dataset of the aged and young adult mouse brain. Contains 1.2 million high-quality, single-cell transcriptomes.
🔭 Explore: knowledge.brain-map.org/abcatlas?def...
Explore the most comprehensive and detailed single-cell dataset of the aged and young adult mouse brain. Contains 1.2 million high-quality, single-cell transcriptomes.
🔭 Explore: knowledge.brain-map.org/abcatlas?def...
January 28, 2025 at 10:28 PM
🧠📈 Now available on the Allen Brain Cell Atlas - aging mouse brain data!
Explore the most comprehensive and detailed single-cell dataset of the aged and young adult mouse brain. Contains 1.2 million high-quality, single-cell transcriptomes.
🔭 Explore: knowledge.brain-map.org/abcatlas?def...
Explore the most comprehensive and detailed single-cell dataset of the aged and young adult mouse brain. Contains 1.2 million high-quality, single-cell transcriptomes.
🔭 Explore: knowledge.brain-map.org/abcatlas?def...
The main project of my PhD 🧬🔬 is out: we developed single-cell lentiMPRA, a lentivirus-based method to measure enhancer activity and transcriptomes at single-cell resolution. We then applied sc-lentiMPRA to fully synthetic enhancers 🧩...
🔗 doi.org/10.64898/202...
🔗 doi.org/10.64898/202...
doi.org
March 4, 2026 at 10:25 AM
The main project of my PhD 🧬🔬 is out: we developed single-cell lentiMPRA, a lentivirus-based method to measure enhancer activity and transcriptomes at single-cell resolution. We then applied sc-lentiMPRA to fully synthetic enhancers 🧩...
🔗 doi.org/10.64898/202...
🔗 doi.org/10.64898/202...
Splicing was discovered in adenoviruses, but was thought to be only anecdotal in plant viruses... We may need to revisit plant viral transcriptomes and proteomes!
How do geminiviruses maximize their limited coding capacity? Our recent preprint uncovers splicing of viral transcripts as one more strategy used by this viral family. We show that RNA splicing is prevalent in the geminivirus TYLCV — and required for infectivity! www.biorxiv.org/content/10.1...
Pervasive splicing in a plant DNA virus
Viruses maximize their limited coding space through strategies that increase transcript and protein diversity. In mammalian viruses, splicing is a well-established mechanism for proteome expansion, ye...
www.biorxiv.org
October 3, 2025 at 8:57 PM
Splicing was discovered in adenoviruses, but was thought to be only anecdotal in plant viruses... We may need to revisit plant viral transcriptomes and proteomes!
Great to see this paper in all its glory online: link.springer.com/article/10.1...
A huge effort from Gordon and the team at @pjkeelinglab.bsky.social!
Phylogenomic tree of Cercozoa based on single-cell transcriptomes from 100 uncultured cells
@ubcbotany.bsky.social @science.ubc.ca
A huge effort from Gordon and the team at @pjkeelinglab.bsky.social!
Phylogenomic tree of Cercozoa based on single-cell transcriptomes from 100 uncultured cells
@ubcbotany.bsky.social @science.ubc.ca
Phylogenomic tree of Cercozoa based on single-cell transcriptomes from 100 uncultured cells - BMC Biology
Background Cercozoa are single-celled eukaryotes (protists) and are part of the supergroup Rhizaria. Cercozoans have vastly different morphologies and are defined by their phylogenetic affinity. While...
link.springer.com
February 26, 2026 at 10:38 AM
Great to see this paper in all its glory online: link.springer.com/article/10.1...
A huge effort from Gordon and the team at @pjkeelinglab.bsky.social!
Phylogenomic tree of Cercozoa based on single-cell transcriptomes from 100 uncultured cells
@ubcbotany.bsky.social @science.ubc.ca
A huge effort from Gordon and the team at @pjkeelinglab.bsky.social!
Phylogenomic tree of Cercozoa based on single-cell transcriptomes from 100 uncultured cells
@ubcbotany.bsky.social @science.ubc.ca
Very happy to see our work out examining guard cell transcriptomes over the course of a slowly developing drought. Thanks to @bradylabs.bsky.social and @kaisakajala.bsky.social for the inspiration, way back in Davis in 2013! The data are available in bar.utoronto.ca/eplant & doi.org/10.1093/plce...
October 22, 2025 at 4:56 PM
Very happy to see our work out examining guard cell transcriptomes over the course of a slowly developing drought. Thanks to @bradylabs.bsky.social and @kaisakajala.bsky.social for the inspiration, way back in Davis in 2013! The data are available in bar.utoronto.ca/eplant & doi.org/10.1093/plce...
2) adult neuron transcriptomes show that some neurons are similar, likely in their functions, and diverge from their lineages;
December 5, 2024 at 2:19 PM
2) adult neuron transcriptomes show that some neurons are similar, likely in their functions, and diverge from their lineages;
New Article: "Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls" rdcu.be/eiWNF
Fern transcriptomes reveal repeated whole-genome duplications, unique gene families and distinct lignocellulosic evolution... #PlantScience
Fern transcriptomes reveal repeated whole-genome duplications, unique gene families and distinct lignocellulosic evolution... #PlantScience
April 23, 2025 at 11:14 AM
New Article: "Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls" rdcu.be/eiWNF
Fern transcriptomes reveal repeated whole-genome duplications, unique gene families and distinct lignocellulosic evolution... #PlantScience
Fern transcriptomes reveal repeated whole-genome duplications, unique gene families and distinct lignocellulosic evolution... #PlantScience
Nature research paper: Connecting single-cell transcriptomes to projectomes in the mouse visual cortex
go.nature.com/4vHbkDH
go.nature.com/4vHbkDH
Connecting single-cell transcriptomes to projectomes in the mouse visual cortex - Nature
In the mouse visual cortex, multimodal cell-type definitions, gene expression patterns and cell location predict long-range projection targets of excitatory neurons, linking transcriptomic identity with morphological, electrophysiological and circuit-level properties.
go.nature.com
July 4, 2026 at 12:31 PM
Nature research paper: Connecting single-cell transcriptomes to projectomes in the mouse visual cortex
go.nature.com/4vHbkDH
go.nature.com/4vHbkDH
Yiliang Ding - in the AI session - extracting information from 1000 plant transcriptomes/RNA sequences using foundational models - finding functional motifs with no a priori knowledge
@yiliangding.bsky.social #icar2025 #plantbiology
@yiliangding.bsky.social #icar2025 #plantbiology
June 17, 2025 at 2:41 PM
Yiliang Ding - in the AI session - extracting information from 1000 plant transcriptomes/RNA sequences using foundational models - finding functional motifs with no a priori knowledge
@yiliangding.bsky.social #icar2025 #plantbiology
@yiliangding.bsky.social #icar2025 #plantbiology
A paper in Nature Biotechnology presents CellWhisperer, which uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data. go.nature.com/3XqzItR 🧬 🧪
November 15, 2025 at 8:26 PM
A paper in Nature Biotechnology presents CellWhisperer, which uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data. go.nature.com/3XqzItR 🧬 🧪
Originalpublikation: www.nature.com/articles/s42...
Plants grown in Apollo lunar regolith present stress-associated transcriptomes that inform prospects for lunar exploration - Communications Biology
Arabidopsis plants were seeded onto lunar soil samples taken directly from the Apollo 11, 12, and 17 missions. Transcriptomic analyses reveal that plants grown in lunar soil differentially express gen...
www.nature.com
September 1, 2025 at 8:44 AM
Originalpublikation: www.nature.com/articles/s42...
On behalf of 108 colleagues and friends from 11 countries, thrilled to share the first paper from our 100 #Diatom Genomes Project (100DGP). Just out @plosbiology.org | @norwichmicro.bsky.social | @ueaenv.bsky.social | @jgi.doe.gov
doi.org/10.1371/jour...
doi.org/10.1371/jour...
The 100 Diatom Genomes Project
This Community Page presents the 100 Diatom Genomes Project, which aims to sequence the genomes and transcriptomes of 100 diatom species across major lineages, life forms and ecological strategies. Th...
doi.org
September 1, 2026 at 6:47 PM
On behalf of 108 colleagues and friends from 11 countries, thrilled to share the first paper from our 100 #Diatom Genomes Project (100DGP). Just out @plosbiology.org | @norwichmicro.bsky.social | @ueaenv.bsky.social | @jgi.doe.gov
doi.org/10.1371/jour...
doi.org/10.1371/jour...
"HPRC2 contributes 460 haplotypes that together capture over 99% of common variation observed in the All of Us Research Program v8 cohort"
Also, coordinate system, transcriptomes,..
Also, coordinate system, transcriptomes,..
HPRC2: A human pangenome reference with near-complete coverage of common genetic variation https://www.biorxiv.org/content/10.64898/2026.07.21.739710v1
July 22, 2026 at 8:42 AM
"HPRC2 contributes 460 haplotypes that together capture over 99% of common variation observed in the All of Us Research Program v8 cohort"
Also, coordinate system, transcriptomes,..
Also, coordinate system, transcriptomes,..
What a MASSIVE scientific undertaking 🤩
Stephens et al. inferred orthogroups for over 100 scleractinia reference genomes/transcriptomes - 228 datasets total!
I can only begin to imagine what incredible insights can be gained from this 🪸🧬🧪
#popgen #evolution #coralreefs #phylogentics #EvoBio
Stephens et al. inferred orthogroups for over 100 scleractinia reference genomes/transcriptomes - 228 datasets total!
I can only begin to imagine what incredible insights can be gained from this 🪸🧬🧪
#popgen #evolution #coralreefs #phylogentics #EvoBio
Stephens, Kulczyk & @bhattacharyalab.bsky.social suggest that dark genes (those with no ascribable biological function) in stony corals originated via bursts of lineage-specific duplication, often from genes with known functions.
🔗 doi.org/10.1093/gbe/evag072
#genome #evolution #corals
🔗 doi.org/10.1093/gbe/evag072
#genome #evolution #corals
April 9, 2026 at 8:15 PM
What a MASSIVE scientific undertaking 🤩
Stephens et al. inferred orthogroups for over 100 scleractinia reference genomes/transcriptomes - 228 datasets total!
I can only begin to imagine what incredible insights can be gained from this 🪸🧬🧪
#popgen #evolution #coralreefs #phylogentics #EvoBio
Stephens et al. inferred orthogroups for over 100 scleractinia reference genomes/transcriptomes - 228 datasets total!
I can only begin to imagine what incredible insights can be gained from this 🪸🧬🧪
#popgen #evolution #coralreefs #phylogentics #EvoBio