#transcriptomes
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haoyin.bsky.social
Downregulated FGF9 in type 2 diabetic #SkeletalMuscle
db/db🐭

Re-analysis of Human SkM #T2D #Sarcopenia transcriptomes
Hub genes: FGF9 BDH1 LDHA

#SciRep 2025
www.nature.com/articles/s41...
November 25, 2025 at 8:16 PM
haoyin.bsky.social
CellWhisperer

From Transcriptome to Text

A great LLM-Chatbot explorer for CELLxGENE & GEO & your own data!

Contrastive language image pretraining
Geneformer
BioBERT
>1 million bulk/pseudo-bulk transcriptomes

cellwhisperer.bocklab.org

#NatBiotech 2025
www.nature.com/articles/s41...
November 22, 2025 at 12:14 PM
natureportfolio.nature.com
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 🧬 🧪
This is figure 1, which gives an overview of the CellWhisperer multimodal AI for natural-language analysis of transcriptome data.
November 20, 2025 at 2:42 AM
scrnaseq.bsky.social
Single-cell RNA-seq is younger than the iPhone. 🤯 The first bona fide scRNA-seq transcriptomes were published in 2009 by Tang et al., who sequenced individual mouse cells and showed you could capture a whole transcriptome from a single cell. From “sci-fi” to standard tool in just over a decade...
November 25, 2025 at 1:47 AM
cellraiser.bsky.social
This work shines because of @zjmaggiexu.bsky.social passion for these cells. She built it all—the cultures, transcriptomes, analyses, modeling and collaborations—from scratch. I can’t begin to express how brilliant and hard-working a scientist she is (and she's 👀 for postdocs!). So proud of her 🥲
Photographs of Zhejing "Maggie" Xu, an extraordinary gifted, hard-working, and brilliant grad student who is as comfortable at the bench or IDE as she is in the field. Truly an amazing individual whose passion for suctorian, protists, and cell biology more generally is in a class all its own
November 18, 2025 at 4:15 PM
natureportfolio.nature.com
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 🧬 🧪
This is figure 1, which gives an overview of the CellWhisperer multimodal AI for natural-language analysis of transcriptome data.
November 15, 2025 at 8:26 PM
theplantcell.bsky.social
Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes (Fabricio Almeida-Silva, Yves Van de Peer) doi.org/10.1093/plce... #PlantScience @aspbofficial
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
doi.org
November 12, 2025 at 1:27 PM
stephenturner.us
A pre-trained large generative model for translating single-cell transcriptomes to proteomes www.nature.com/articles/s41... 🧬🖥️🧪 github.com/TencentAILab...
November 6, 2025 at 7:01 PM
jcornlab.bsky.social
Ever noticed that #CRISPR editing results differ between cells? Awesome PhD student Moritz Schlapansky developed "scOUT-seq" to measure single cell transcriptomes + editing. 1.2 million cells, 74 cell types, living 🐭. Cell subtypes differ wildly from bulk average! www.biorxiv.org/content/10.1...
Cell-stereotyped DNA repair outcomes are widespread during genome editing
Genome editing outcomes are governed by DNA repair pathways that vary with cell type and state. We developed scOUT-seq (single-cell Outcomes Using Transcript sequencing), a scalable approach that join...
www.biorxiv.org
October 24, 2025 at 8:44 AM
molbioevol.bsky.social
@djivanp.bsky.social @aline-muyle.bsky.social et al. sequenced the transcriptomes of nine dioecious, two gynodioecious, and two hermaphrodite Silene species, finding that those with older sex separation exhibit the most numerous sex-biased genes.

🔗 doi.org/10.1093/molbev/msaf229

#evobio #molbio
MBE | Evolution of Sex-Biased Gene Expression During Transitions to Separate Sexes in the Silene Genus
October 24, 2025 at 9:29 AM
lab-turner.bsky.social
Our latest 📢 We generated isogenic iPSCs with XX, XY, XO and XXY karyotypes to study sex chromosome effects 🧫 While XX and XY transcriptomes are similar, XO cells showed an important effect of the Y and inactive X @crick.ac.uk @stemcellreports.bsky.social www.sciencedirect.com/science/arti...
A human induced pluripotent stem cell toolbox for studying sex chromosome effects
Sex chromosomes shape male (XY)-female (XX) differences in development and disease. These differences can be modeled in vitro by comparing XY and XX h…
www.sciencedirect.com
October 23, 2025 at 11:06 AM
bar-plantbio.bsky.social
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
jsantoyo.bsky.social
Taming the reference genome jungle: the refget sequence collection standard. #ReferenceGenomes #Transcriptomes #SequenceCollectionStandards #GA4GH @biorxiv-genomic.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
October 21, 2025 at 8:31 AM
almeidasilvaf.bsky.social
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...
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
pacbio.bsky.social
Great discussions at our #ASHG25 CoLab on how #PacBio HiFi multiomics connects genomes, transcriptomes, and proteomes.

Attendees explored how long-read sequencing reveals links between genetic variation, isoforms, and protein diversity in human cell types and disease pathways.
October 16, 2025 at 7:00 PM
pacbio.bsky.social
Join our second #ASHG25 CoLab at 2:30pm in CoLab Theater 2!

Explore how #PacBio HiFi multiomics connects genomes, transcriptomes, and proteomes to reveal links between genetic variation, isoforms, and protein diversity.

Full program here: bit.ly/4nmBnfn
October 6, 2025 at 9:06 PM
delphinem-p.bsky.social
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!
geminiteamlab.bsky.social GeminiTeamLab @geminiteamlab.bsky.social · Oct 3
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
rmwaterhouse.bsky.social
25 #genomes & 62 transcriptomes of ladybird beetles 🐞 - evolution of chemosensory, digestive, detoxifying, & immune #genes associated with dietary shifts 🥩<=>🥗 bmcbiol.biomedcentral.com/articles/10.... #biodiversity #genomics #evolution
Molecular evolution of dietary shifts in ladybird beetles (Coleoptera: Coccinellidae): from fungivory to carnivory and herbivory - BMC Biology
Background Dietary shifts are major evolutionary steps that shape ecological niches and biodiversity. The beetle family Coccinellidae, commonly known as ladybirds, first transitioned from a fungivorou...
bmcbiol.biomedcentral.com
February 28, 2025 at 5:38 PM
grrlscientist.bsky.social
Diverse Headgear Of Hoofed Mammals Evolved From A Common Ancestor, study from Baruch College & CUNY Graduate Center, published by Communications Biology

by @GrrlScientist

#evolution #GeneExpression🧬 #transcriptomes #cervidae🦌🦬🦒 #headgear #SciComm🧪 www.forbes.com/sites/grrlsc...
May 27, 2024 at 10:29 AM
aixbiobot.bsky.social
GFHunter enables accurate and efficient gene fusion detection in long-read cancer transcriptomes [new]
Novel framework enables accurate gene fusion detection in long-read cancer transcriptomes; reduces false positives.
GFHunter enables accurate and efficient gene fusion detection in long-read cancer transcriptomes Figure 1 Figure 2 Figure 3
February 28, 2025 at 2:54 PM
biorxiv-cancer.bsky.social
Meta-analyses of mouse and human prostate single-cell transcriptomes reveal widespread epithelial plasticity in tissue regression, regeneration, and cancer https://www.biorxiv.org/content/10.1101/2024.01.30.578066v1
Meta-analyses of mouse and human prostate single-cell transcriptomes reveal widespread epithelial plasticity in tissue regression, regeneration, and cancer https://www.biorxiv.org/content/10.1101/2024.01.30.578066v1
Recent advances in single-cell RNA-sequencing (scRNA-seq) technology have facilitated studies of cel
www.biorxiv.org
February 3, 2024 at 1:53 AM
vscooper.micropopbio.org
TL;DR:
History influenced:
- Basal transcriptomes
- Efflux targets
- Population dynamics
- Mutation spectra
History did not influence:
- Drug-induced transcriptomic state
- Broad mechanisms of drug resistance
www.biorxiv.org/content/10.1... h/t @aleciarokes.bsky.social
History shapes regulatory and evolutionary responses to tigecycline in strains of Acinetobacter baumannii from the pre- and post-antibiotic eras
Evolutionary history encompasses genetic and phenotypic bacterial differences, but the extent to which history influences drug response and antimicrobial resistance (AMR) adaptation is unclear. Histor...
www.biorxiv.org
January 24, 2025 at 4:14 PM
phypapers.bsky.social
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions https://pubmed.ncbi.nlm.nih.gov/38829048/
June 4, 2024 at 1:43 PM
s-j-aitken.bsky.social
Thanks, Vardhman! Yes, we'd love others to make good use of our data (it'll all be at BioStudies, ArrayExpress, or ENA). There are about 600 whole genome sequences, 600 whole slide images, and 400 total transcriptomes from tumours - plus dozens of ChIP-seq, ATAC-seq, and RNA-seq from control tissues
January 30, 2025 at 3:06 AM
alexr.bsky.social
Can I use a T2T reference for cancer analyses yet?

Are there meaningfully lifted over gene annotations / exon coordinates / transcriptomes / population variant datasets / cancer hotspot datasets / &c?
October 25, 2024 at 2:51 PM