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
A pre-trained large generative model for translating single-cell transcriptomes to proteomes www.nature.com/articles/s41... 🧬🖥️🧪 github.com/TencentAILab...
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
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...
@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
🔗 doi.org/10.1093/molbev/msaf229
#evobio #molbio
October 24, 2025 at 9:29 AM
@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
🔗 doi.org/10.1093/molbev/msaf229
#evobio #molbio
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
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...
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...
Taming the reference genome jungle: the refget sequence collection standard. #ReferenceGenomes #Transcriptomes #SequenceCollectionStandards #GA4GH @biorxiv-genomic.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 21, 2025 at 8:31 AM
Taming the reference genome jungle: the refget sequence collection standard. #ReferenceGenomes #Transcriptomes #SequenceCollectionStandards #GA4GH @biorxiv-genomic.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
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...
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.
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
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
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
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
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
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!
The goal was to understand biogeography, so we sequenced transcriptomes for the new species, and several others, and built the largest-yet Caenorhabditis phylogeny. The most common Pohnpeian species (C. pwilidak sp nov) is sister to a Hawaiian endemic clade!
September 24, 2025 at 8:33 PM
The goal was to understand biogeography, so we sequenced transcriptomes for the new species, and several others, and built the largest-yet Caenorhabditis phylogeny. The most common Pohnpeian species (C. pwilidak sp nov) is sister to a Hawaiian endemic clade!
Heitzmann et al. compared brain transcriptomes of four sexual genotypes of the African pygmy mouse, showing how sex and neo-sex chromosomes impacted transcriptomes to reflect their transmission mode, evolutionary trajectories, and genomic conflicts.
🔗 doi.org/10.1093/molbev/msaf208
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf208
#evobio #molbio
September 23, 2025 at 9:15 AM
Heitzmann et al. compared brain transcriptomes of four sexual genotypes of the African pygmy mouse, showing how sex and neo-sex chromosomes impacted transcriptomes to reflect their transmission mode, evolutionary trajectories, and genomic conflicts.
🔗 doi.org/10.1093/molbev/msaf208
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf208
#evobio #molbio
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
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
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...
by @GrrlScientist
#evolution #GeneExpression🧬 #transcriptomes #cervidae🦌🦬🦒 #headgear #SciComm🧪 www.forbes.com/sites/grrlsc...
May 27, 2024 at 10:29 AM
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...
by @GrrlScientist
#evolution #GeneExpression🧬 #transcriptomes #cervidae🦌🦬🦒 #headgear #SciComm🧪 www.forbes.com/sites/grrlsc...
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.
Novel framework enables accurate gene fusion detection in long-read cancer transcriptomes; reduces false positives.
February 28, 2025 at 2:54 PM
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.
Novel framework enables accurate gene fusion detection in long-read cancer transcriptomes; reduces false positives.
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
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
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 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
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 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
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
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions https://pubmed.ncbi.nlm.nih.gov/38829048/
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
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
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?
Are there meaningfully lifted over gene annotations / exon coordinates / transcriptomes / population variant datasets / cancer hotspot datasets / &c?
October 25, 2024 at 2:51 PM
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?
Are there meaningfully lifted over gene annotations / exon coordinates / transcriptomes / population variant datasets / cancer hotspot datasets / &c?
Meta-analysis of the brain transcriptomes of multiple genetic mouse models of schizophrenia highlights dysregulation in striatum and thalamus https://www.biorxiv.org/content/10.1101/2025.03.26.645496v1
March 29, 2025 at 10:15 AM
Meta-analysis of the brain transcriptomes of multiple genetic mouse models of schizophrenia highlights dysregulation in striatum and thalamus https://www.biorxiv.org/content/10.1101/2025.03.26.645496v1
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!
2/🧬Using Slide-seq, we built a high-resolution atlas of ovarian aging, profiling 601,831 spots across 68 spatial transcriptomes. This captured the development & interactions of 345 oocytes, 653 follicles, and 234 corpora lutea in their native tissue context.
December 18, 2024 at 2:32 PM
2/🧬Using Slide-seq, we built a high-resolution atlas of ovarian aging, profiling 601,831 spots across 68 spatial transcriptomes. This captured the development & interactions of 345 oocytes, 653 follicles, and 234 corpora lutea in their native tissue context.
tweeted this earlier but had a chance to go through. very cool suite of tools and new methodology, TAPIN-seq, to molecularly characterize the transcriptomes of cells we can trace in the fly visual system. broadly applicable too! https://www.biorxiv.org/content/early/2018/08/05/385476
December 5, 2024 at 5:58 AM
tweeted this earlier but had a chance to go through. very cool suite of tools and new methodology, TAPIN-seq, to molecularly characterize the transcriptomes of cells we can trace in the fly visual system. broadly applicable too! https://www.biorxiv.org/content/early/2018/08/05/385476
📢Job Opening! 🧪🖥️🧬👩🔬
Ready to hire qualified candidates to map #RNA modifications in human transcriptomes using #nanopore direct sequencing.
Dr. Ya-Ming Hou at Thomas Jefferson University
houlaboratory.com/research
#HigherEd #EDUSky #AcademicSky #STS
Ready to hire qualified candidates to map #RNA modifications in human transcriptomes using #nanopore direct sequencing.
Dr. Ya-Ming Hou at Thomas Jefferson University
houlaboratory.com/research
#HigherEd #EDUSky #AcademicSky #STS
August 4, 2025 at 2:28 PM
📢Job Opening! 🧪🖥️🧬👩🔬
Ready to hire qualified candidates to map #RNA modifications in human transcriptomes using #nanopore direct sequencing.
Dr. Ya-Ming Hou at Thomas Jefferson University
houlaboratory.com/research
#HigherEd #EDUSky #AcademicSky #STS
Ready to hire qualified candidates to map #RNA modifications in human transcriptomes using #nanopore direct sequencing.
Dr. Ya-Ming Hou at Thomas Jefferson University
houlaboratory.com/research
#HigherEd #EDUSky #AcademicSky #STS