Thrilled to share that our scE2G paper is now published in Nature Genetics! www.nature.com/articles/s41... scE2G predicts enhancer-gene regulatory interactions from single-cell data with state-of-the-art performance. Amazing work led by @mayayayas.bsky.social and @613weilin.bsky.social!

Mapping enhancer–gene regulatory interactions from single-cell data - Nature Genetics

scE2G is a family of models that predict enhancer–gene regulatory interactions from single-cell datasets and enable mapping of these interactions across diverse cell types and tissues.

nature.com

Jesse Engreitz@jengreitz.bsky.social · 2d ago

Update: scE2G is now online at Nature Genetics! Since the preprint, we added a new benchmark on a fully held-out CRISPR dataset. scE2G continues to show state-of-the-art performance, reinforcing that it generalizes well nature.com/articles/s41588-026-02695-8 1/

New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...

I dag toppar SVT.se med en Lancet-studie från 2021: kylan dödar fler än värmen. Att den dyker upp just nu är ingen slump. Varje gång någon skriver om uppvärmning och dödsfall översköljs tråden av mindre konton som länkar den. Jag har sett det i flera år.

We're recruiting! An open functional genomics postdoc position at @scilifelab-ngi.bsky.social / my lab / Robert Månsson lab. Top notch environment for technology and applications development in lovely Stockholm. Please spread the word or apply if interested: www.kth.se/lediga-jobb/...

🔥 Does switching to a pangenome reference actually improve your association study? We tested it, and the answer is yes, measurably. Our preprint is online now: "Pangenome-based human genome analysis improves trait association and genomic prediction": doi.org/10.64898/202...

Pangenome-based human genome analysis improves trait association and genomic prediction

The Human Pangenome Reference Consortium has generated 462 open-access reference genomes and a variation graph that represents differences among them, providing a substrate for pangenome-based analysi...

doi.org

For those interested in PacBio's SPRQ-Nx chemistry and reusable SMRT Cells: in the Genome of Sweden project, we moved from 2 to 3 acquisitions per SMRT Cell in June. The results are impressive—we’re now approaching 400 Gb HiFi yield from a single SMRT Cell!

How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

Next at #VALT2026: Juan Francisco Cervilla on evaluating gene fusion expression in B-ALL at single-cell resolution, using long reads to resolve fusion transcripts cell by cell. #LongTREC #lrRNAseq #FusionGenes

Excited to share our ‘perspective’ on significant impact long-read sequencing technologies, genome assemblies and better (AI-assisted) interpretation-tools will bring to our field of medical genetics – as we are entering an era of “near-perfect genome sequencing”. www.nature.com/articles/s41...

Near-perfect genome sequencing in medical genetics - Nature Genetics

This Perspective introduces near-perfect genome sequencing, which encompasses diploid genome assembly, pangenome references and artificial intelligence-driven variant interpretation, and proposes a ro...

nature.com

Let me be explicit. The massive heat waves we're seeing around the world more extreme and frequent due to human-caused #climatechange. And these heat waves are going to continue to worsen because of our failure to reduce carbon pollution. Just one of the many costs of #climate change.

Joint profiling of chromatin and splicing in the brain uncovers shared and distinct patterns go.nature.com/3IKlcJn rdcu.be/fpONd

Combined single-cell profiling of chromatin–transcriptome and splicing across brain cell types, regions and disease state - Nature Biotechnology

Joint profiling of chromatin and splicing in the brain uncovers shared and distinct patterns.

go.nature.com

SciLifeLab Planetary Biology invites researchers across Sweden to submit their existing eDNA/metabarcoding extraction and library-preparation protocols for development into production-scale workflows. Read more and apply: www.scilifelab.se/news/planeta...

Planetary Biology Call for eDNA/Metabarcoding Protocol Pilots

The SciLifeLab Planetary Biology Capability (PB Capability) invites researchers across Sweden to propose ideas that will drive significant advancements in environmental life sciences, are based on the...

scilifelab.se

The FDA's new draft guidance on genome editing safety highlights why detecting large indels and chromosomal abnormalities is critical, where short-reads fall short. HiFi sequencing offers >99.9% accuracy to characterize all editing outcomes. Learn more: bit.ly/49ZpV4S

Nice to the new UCSC genome browser track with SNV frequencies from around the world - including 1000 Swedish genomes from the SweGen project www.nature.com/articles/ejh...

Next up, Adam Ameur shares that long-read WGS efforts are ongoing in Sweden for population genomics and clinical diagnostics. They bridge these projects by using a joint analysis framework and shared variant databases. #ESHG2026 #PacBio #ESHG

These are beta test results of PacBio's reusable SMRT-cells, run on human blood DNA from the "Genome of Sweden" project. Results have been really impressive so far, with an average >250Gb per SMRT-cell over 2 acquisitions. We are now about to expand to 3 acquisitions

PacBio@pacbio.bsky.social · 2mo ago

Sharing results from a beta test of PacBio’s SPRQ-Nx reusable SMRT cells using two acquisitions! This increased SMRT cell throughput reduces sequencing costs for large human WGS projects. #ESHG2026 #PacBio #ESHG

New blog post! I analyse the new hac@v6.0.0 basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...

T2T assemblies for nearly all major Y chromosome haplogroups courtesy of a collab between @humanpangenome.bsky.social and HGSVC! What was once the hardest human chromosome to finish can now be routinely assembled thanks to ONT + Verkko www.biorxiv.org/content/10.6...

Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures https://www.biorxiv.org/content/10.64898/2026.06.03.729890v1

Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...

a few nice updates from Boris on Anthropic's fossil-fuelled chatbot www.linkedin.com/posts/bgamaz...

"Researchers found undisturbed primary forests store 83% more carbon per acre than the managed forests that are replacing them." This study is "shocking" - as in "we've been lied to by the forest industry" and... it's not in our climate models. sustainability.stanford.edu/news/shockin...

A ‘shocking’ carbon discovery in Sweden’s forests

A new study finds old-growth forests in Sweden store far more carbon than the industrial tree plantations that are rapidly replacing them, with soil accounting for most of the difference. Protecting u...

sustainability.stanford.edu

The new long read cDNA kit by @nanoporetech.com is a major upgrade (and improvement!), substantially increasing read length, with a strong impact on transcript discovery and quantification. We @goekelab.bsky.social have tested this in the beta release, more updates soon #nanoporeconf

#NanoporeConf My Nanopore Notes for London Calling 2026 are stacking up, but I need to go to sleep shortly. Not sure if I'll be awake for a 4am tech talk, but we'll see.... gringer.gitlab.io/presentation...

📣 The ELIXIR-coordinated EU project, #B1MGplus, is conducting a survey on 💡 the use, access, governance and sustainability of #genomicdata and related services. Provide your insights to 🎯 support the development of a sustainable European genomic data infrastructure. 👉 https://loom.ly/4uSHoak

The preliminary #VALT Scientific Programme was published last week! longtrec.eu/VALT/ Check the selected Talks and Flash talks! 👉 Still in time to join us at what is shaping up to be a super event! : lnkd.in/eXPG_6cY

Expressions of interest are invited for this comprehensive course, equipping you with the skills and knowledge needed to design, perform, and analyse #longread #singlecell RNA-seq experiments from end to end. 🗓️ 17 - 19 November 2026 Register interest below! ⤵️

Single-cell Long-read Bioinformatics: from Data Generation to Visualisation

Hands on training in long‑read single‑cell RNA‑seq, from experimental design to data interpretation

buff.ly

Last call to register for our gene editing webinar! Short reads and PCR bias can hide critical editing outcomes. Join us to see how amplification free #PacBio HiFi sequencing and PureTarget provide a complete view of #CRISPR edits. Register here: bit.ly/4mbDW4i

A new preprint comparing short and long-read technologies for human WGS www.biorxiv.org/content/10.6...

#oopsie Anthropic secretly installs spyware when you install Claude Desktop www.thatprivacyguy.com/blog/anthrop...

Anthropic secretly installs spyware when you install Claude Desktop — That Privacy Guy!

Anthropic's Claude Desktop silently installs a Native Messaging bridge into seven Chromium browsers, including browsers Anthropic's own documentation says it does not support, and browsers the user ha...

thatprivacyguy.com