Not sure where my genomics people are after the demise of twitter. The de novo transcriptome assembly crew will hopefully find this useful @titus.idyll.org @johnwares.bsky.social @idworkin.bsky.social arxiv.org/abs/2610.37031
pyTransRate: reference-free quality assessment of de novo transcriptome assemblies with current aligners and quantifiers
Summary: The original software TransRate scores a de novo transcriptome assembly by mapping the reads it was built from back to it, with no reference required. Its last release (1.0.3) depends on Ruby...
arxiv.org
November 3, 2026 at 1:00 PM
Not sure where my genomics people are after the demise of twitter. The de novo transcriptome assembly crew will hopefully find this useful @titus.idyll.org @johnwares.bsky.social @idworkin.bsky.social arxiv.org/abs/2610.37031
Refining RNA-Seq Transcriptome Profiles with Transcript-Specific Minimal-Shared Regions https://www.biorxiv.org/content/10.64898/2026.10.28.762701v1
November 3, 2026 at 6:47 AM
Refining RNA-Seq Transcriptome Profiles with Transcript-Specific Minimal-Shared Regions https://www.biorxiv.org/content/10.64898/2026.10.28.762701v1
In case you missed it––interesting @jxbotany.bsky.social paper about #Agricultural #Plastics and their effects on the #Rhizosphere #microbiome and #Plant #transcriptome from last year. #PlantScience doi.org/10.1093/jxb/...
Agri-plastics in soils drive changes in the rhizosphere bacterial community and plant transcriptome in Arabidopsis
The presence of microplastics does not affect Arabidopsis growth but alters rhizobacterial communities and leads to transcriptional changes, suggesting tha
doi.org
November 2, 2026 at 12:26 PM
In case you missed it––interesting @jxbotany.bsky.social paper about #Agricultural #Plastics and their effects on the #Rhizosphere #microbiome and #Plant #transcriptome from last year. #PlantScience doi.org/10.1093/jxb/...
Transcriptome analysis provides insights into candidate genetic regulators of birch response to salt stress https://www.biorxiv.org/content/10.64898/2026.10.29.762967v1
November 2, 2026 at 5:01 PM
Transcriptome analysis provides insights into candidate genetic regulators of birch response to salt stress https://www.biorxiv.org/content/10.64898/2026.10.29.762967v1
The poly-A kits capture the mRNA entirely, whereas the Flex kits are focused on parts of the Human transcriptome.
November 2, 2026 at 12:45 PM
The poly-A kits capture the mRNA entirely, whereas the Flex kits are focused on parts of the Human transcriptome.
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS. In a new paper, we find that TWAS gets the sign wrong around 20-30% of the time!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
High false sign rates in transcriptome-wide association studies - Nature Genetics
This study finds that the direction of effect captured by transcriptome-wide association studies is often reversed relative to the true biological mechanism, suggesting that caution is needed when int...
www.nature.com
October 29, 2026 at 2:57 PM
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS. In a new paper, we find that TWAS gets the sign wrong around 20-30% of the time!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
tWhEEL: a transcript-aware workflow for quantifying CRISPR knockout feasibility using transcriptome assembly https://www.biorxiv.org/content/10.64898/2026.10.27.762389v1
November 1, 2026 at 2:48 AM
tWhEEL: a transcript-aware workflow for quantifying CRISPR knockout feasibility using transcriptome assembly https://www.biorxiv.org/content/10.64898/2026.10.27.762389v1
A conserved thermodynamic signature links transcriptome organization to growth state https://www.biorxiv.org/content/10.64898/2026.11.03.764118v1
November 4, 2026 at 10:47 PM
A conserved thermodynamic signature links transcriptome organization to growth state https://www.biorxiv.org/content/10.64898/2026.11.03.764118v1
A conserved thermodynamic signature links transcriptome organization to growth state https://www.biorxiv.org/content/10.64898/2026.11.03.764118v1
November 4, 2026 at 10:47 PM
A conserved thermodynamic signature links transcriptome organization to growth state https://www.biorxiv.org/content/10.64898/2026.11.03.764118v1
RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure https://www.biorxiv.org/content/10.64898/2026.11.02.763788v1
November 4, 2026 at 8:46 AM
RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure https://www.biorxiv.org/content/10.64898/2026.11.02.763788v1
RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure https://www.biorxiv.org/content/10.64898/2026.11.02.763788v1
November 4, 2026 at 8:46 AM
RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure https://www.biorxiv.org/content/10.64898/2026.11.02.763788v1
A single-nucleus multiome profiling reveals the regulatory programs driving plant nematode–induced syncytium
Tarek Hewezi, et al.
nph.onlinelibrary.wiley.com/doi/10.1111/...
#PlantScience
Tarek Hewezi, et al.
nph.onlinelibrary.wiley.com/doi/10.1111/...
#PlantScience
October 30, 2026 at 10:41 PM
A single-nucleus multiome profiling reveals the regulatory programs driving plant nematode–induced syncytium
Tarek Hewezi, et al.
nph.onlinelibrary.wiley.com/doi/10.1111/...
#PlantScience
Tarek Hewezi, et al.
nph.onlinelibrary.wiley.com/doi/10.1111/...
#PlantScience
Super excited to see this work by @kutaydeniz.bsky.social now published in Science!
doi.org/10.1126/science.aeg1125
doi.org/10.1126/science.aeg1125
Whole-body single-cell atlas of an adult vertebrate, Danionella cerebrum
A complete cell type transcriptome atlas of a vertebrate could promote understanding of animal cell type composition, organization, and evolution. The miniaturized, transparent, and regenerative teleo...
doi.org
October 30, 2026 at 12:55 AM
Super excited to see this work by @kutaydeniz.bsky.social now published in Science!
doi.org/10.1126/science.aeg1125
doi.org/10.1126/science.aeg1125
DNA demethylases constrain multigenerational methylome and transcriptome divergence https://www.biorxiv.org/content/10.64898/2026.10.29.762914v1
October 30, 2026 at 3:00 PM
DNA demethylases constrain multigenerational methylome and transcriptome divergence https://www.biorxiv.org/content/10.64898/2026.10.29.762914v1
Refining RNA-Seq Transcriptome Profiles with Transcript-Specific Minimal-Shared Regions https://www.biorxiv.org/content/10.64898/2026.10.28.762701v1
November 3, 2026 at 6:47 AM
Refining RNA-Seq Transcriptome Profiles with Transcript-Specific Minimal-Shared Regions https://www.biorxiv.org/content/10.64898/2026.10.28.762701v1
What is a body made of? Many great studies have identified, characterized, and cataloged cell types across organisms. New in @science.org, we take this question to the scale of an entire adult vertebrate, opening organism-wide biology at single-cell resolution: tinyurl.com/3fbkwp4d; #ScienceResearch
Whole-body single-cell atlas of an adult vertebrate, Danionella cerebrum
A complete cell type transcriptome atlas of a vertebrate could promote understanding of animal cell type composition, organization, and evolution. The miniaturized, transparent, and regenerative teleo...
tinyurl.com
October 30, 2026 at 11:51 PM
What is a body made of? Many great studies have identified, characterized, and cataloged cell types across organisms. New in @science.org, we take this question to the scale of an entire adult vertebrate, opening organism-wide biology at single-cell resolution: tinyurl.com/3fbkwp4d; #ScienceResearch
🌱🧬 Plants vary widely in specialised metabolites—even within populations.
Pangenomes and pantranscriptomes move beyond single references to capture this diversity and trace metabolic pathways underlying stress resilience. #plantscience @bpucker.bsky.social onlinelibrary.wiley.com/doi/10.1111/...
Pangenomes and pantranscriptomes move beyond single references to capture this diversity and trace metabolic pathways underlying stress resilience. #plantscience @bpucker.bsky.social onlinelibrary.wiley.com/doi/10.1111/...
Elucidating and exploring specialised plant metabolism through a pangenomic and pantranscriptomic lens
Past studies of plant specialised metabolism have largely missed the biochemical diversity within plant populations due to being limited to a single-reference genome or transcriptome. In this review,....
onlinelibrary.wiley.com
November 4, 2026 at 8:35 AM
🌱🧬 Plants vary widely in specialised metabolites—even within populations.
Pangenomes and pantranscriptomes move beyond single references to capture this diversity and trace metabolic pathways underlying stress resilience. #plantscience @bpucker.bsky.social onlinelibrary.wiley.com/doi/10.1111/...
Pangenomes and pantranscriptomes move beyond single references to capture this diversity and trace metabolic pathways underlying stress resilience. #plantscience @bpucker.bsky.social onlinelibrary.wiley.com/doi/10.1111/...
A single-cell multimodal foundation model enables cross modality analysis between transcriptome and chromatin https://www.biorxiv.org/content/10.64898/2026.10.28.762297v1
November 3, 2026 at 1:46 AM
A single-cell multimodal foundation model enables cross modality analysis between transcriptome and chromatin https://www.biorxiv.org/content/10.64898/2026.10.28.762297v1
Transcriptome analysis provides insights into candidate genetic regulators of birch response to salt stress https://www.biorxiv.org/content/10.64898/2026.10.29.762967v1
November 2, 2026 at 5:01 PM
Transcriptome analysis provides insights into candidate genetic regulators of birch response to salt stress https://www.biorxiv.org/content/10.64898/2026.10.29.762967v1
Refining RNA-Seq Transcriptome Profiles with Transcript-Specific Minimal-Shared Regions #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.64898/2026.10.28.762701v1
https://www.biorxiv.org/content/10.64898/2026.10.28.762701v1
November 3, 2026 at 8:01 AM
Refining RNA-Seq Transcriptome Profiles with Transcript-Specific Minimal-Shared Regions #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.64898/2026.10.28.762701v1
https://www.biorxiv.org/content/10.64898/2026.10.28.762701v1
A single-cell multimodal foundation model enables cross modality analysis between transcriptome and chromatin https://www.biorxiv.org/content/10.64898/2026.10.28.762297v1
November 3, 2026 at 1:46 AM
A single-cell multimodal foundation model enables cross modality analysis between transcriptome and chromatin https://www.biorxiv.org/content/10.64898/2026.10.28.762297v1
Excited to post my lab's latest pre-print, led by the phenomenal Anna Dmitrieva!
Anna asked the question - what happens to epigenetic inheritance when you lose (almost) all DNA demethylation activity?
www.biorxiv.org/content/10.6...
Anna asked the question - what happens to epigenetic inheritance when you lose (almost) all DNA demethylation activity?
www.biorxiv.org/content/10.6...
DNA demethylases constrain multigenerational methylome and transcriptome divergence
In plants, animals and fungi, DNA methylation is important for the silencing of repetitive DNA and impacts the expression of a subset of genes. DNA methylation landscapes exhibit a high degree of stab...
www.biorxiv.org
October 30, 2026 at 6:06 PM
Excited to post my lab's latest pre-print, led by the phenomenal Anna Dmitrieva!
Anna asked the question - what happens to epigenetic inheritance when you lose (almost) all DNA demethylation activity?
www.biorxiv.org/content/10.6...
Anna asked the question - what happens to epigenetic inheritance when you lose (almost) all DNA demethylation activity?
www.biorxiv.org/content/10.6...
Top2All: Benchmarking sparse-to-transcriptome reconstruction from high-expression profiles across sex- and sex-steroid-defined conditions https://www.biorxiv.org/content/10.64898/2026.10.31.763361v1
November 3, 2026 at 7:47 AM
Top2All: Benchmarking sparse-to-transcriptome reconstruction from high-expression profiles across sex- and sex-steroid-defined conditions https://www.biorxiv.org/content/10.64898/2026.10.31.763361v1
Top2All: Benchmarking sparse-to-transcriptome reconstruction from high-expression profiles across sex- and sex-steroid-defined conditions https://www.biorxiv.org/content/10.64898/2026.10.31.763361v1
November 3, 2026 at 7:47 AM
Top2All: Benchmarking sparse-to-transcriptome reconstruction from high-expression profiles across sex- and sex-steroid-defined conditions https://www.biorxiv.org/content/10.64898/2026.10.31.763361v1
A single-cell multimodal foundation model enables cross modality analysis between transcriptome and chromatin #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.10.28.762297v1
https://www.biorxiv.org/content/10.64898/2026.10.28.762297v1
November 3, 2026 at 2:00 AM
A single-cell multimodal foundation model enables cross modality analysis between transcriptome and chromatin #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.10.28.762297v1
https://www.biorxiv.org/content/10.64898/2026.10.28.762297v1