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Here is the transcriptomics insight: the bulk RNA-seq (Fig 1), single-cell RNA-seq (Fig. 2), spatial transcriptomics (Fig. 3), and the original organ (Fig. 4). (Feel free to cite with image credit to Bo Xia)

seqLens: optimizing language models for genomic predictions biorxiv.org/content/10.110…

In this blog post, we show how chromatin accessibility can be profiled with minimal processing using nanopore sequencing – preserving native structure and capturing rich signal. Read it here: epi2me.nanoporetech.com/chromatin-acc-…

Single-Nucleus Transcriptomics Reveals How Tissue Context Shapes the Circadian Transcriptome of the Arabidopsis Leaf biorxiv.org/content/10.110… #biorxiv_plants

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986

Our latest paper is out in its final form in The Plant Cell We show that in plants the same DNA sequence can act as an insulator or silencer depending on the surrounding regulatory context. Read the full paper at: doi.org/10.1093/plcell…

BioFMs aren’t just for humans 🦠 BGI plugs NT-50M & Evo‑7B embeddings into a cross‑attention boost, stacks a lightweight ensemble 👀 Gets 97.5 % accuracy at spotting soil probiotics from only 100 genome snippets

Our study on COmapper using nanopore long-read sequencing is now published online! (see New Phytologist New Phytologist : Phytologistnph.onlinelibrary.wiley.com/doi/10.1111/np…) Congratulations to lead author Dohwan Byun, soon-to-be Dr. Namil Son, and the co-authors!

I'M BLOWN AWAY. Andrej Karpathy just explained Software 3.0 at YC. BIG IDEAS: English is coding. AI is electricity. And, build for LLMs, not just people. Key takeaways:

Meet The Speakers of the Single-Cell Approaches in Plant Biology GRC Conference! To Apply to the GRC: lnkd.in/gvkMxuKR To Learn More About Dr. Nobori's Research: tatsuyanobori.com

Part 2 of my series on the shifting DNA sequencing landscape is out🧬 I explore the 3 major emerging sequencing platforms: Roche's SBX, Oxford Nanopore, and PacBio's HIFI This next phase invites new technical/philosophical questions on completeness, interpretation & application

KeyGene Single pollen nuclei sequencing: profiling of meiotic recombination keygene.com/single-pollen-…

Machine learning to predict de novo protein–protein interactions cell.com/trends/biotech…

New Resource: "Transcription factor binding divergence drives transcriptional and phenotypic variation in maize" rdcu.be/esSwW Genome-wide comparative analysis of DNA binding for 200 transcription factors in two maize inbred lines.

New OA Article: "Single-cell transcriptomics reveal how root tissues adapt to soil stress" rdcu.be/esLU8 With News & Views: "Environmental cues shape root barriers" rdcu.be/esSRh

Illumina to Acquire SomaLogic Assets from Standard BioTools for up to $425M | GenomeWeb genomeweb.com/sequencing/ill…

Will we ever get an updated Oxford Nanopore ASIC? The launch of the mk1d with nothing but improved temperature control and USB-C makes it clear that it is not any time soon...

Introducing AlphaGenome: an AI model to help scientists better understand our DNA – the instruction manual for life 🧬 Researchers can now quickly predict what impact genetic changes could have - helping to generate new hypotheses and drive biological discoveries. ↓

Food For Thought On ONT's Proteomics Push 🧬🖥️ omicsomics.blogspot.com/2025/06/food-f…

The reference-free pangenome of Arabidopsis thaliana biorxiv.org/content/10.110… #biorxiv_genomic