🎉 New year, new paper! Alfred, my first PhD student, just published his very first paper - and it’s featured on the cover of the first issue of @orgbiomolchem.rsc.org this year! 🥳 pubs.rsc.org/en/content/a... A thread 🧵 about what Alfred did and what the paper is all about 👇 1/🧵

This is winter in #Gaza. People are facing a third winter of cold temperatures, torrential rain and heavy winds after being repeatedly forcibly displaced. Conditions have destroyed and flooded the makeshift shelters people are living in.

Sequencing Instrumrnt Outlook 2026 My observations & predictions on sequencing instrument companies 🧬🖥️ omicsomics.blogspot.com/2026/01/sequ...

WATCH: MSF Executive Director @sana.msf.ca speaks to CTV about vital humanitarian activities in #Palestine at risk from Israeli registration rules. MSF provides a vast amount of life-saving healthcare, yet even this is not enough to meet the overwhelming needs of people in #Gaza.

MSF Australia on Israel ban of aid orgs to Gaza for antisemitism - "Impossible to replace ... 100,000 trauma surgeries, and delivered 10,000 babies." @sstephanietrann.bsky.social also on Israel's Aussie antisemites blacklist #auspol michaelwest.com.au/israel-bans-...

Blog post: Just quit Quitting projects in science is hard, but we should be doing a lot more of it. open.substack.com/pub/arjunraj...

I've been thinking about the "virtual cell" concept and wanted to write up a few thoughts. Specifically on how I think the prior experience in GWAS informs the most likely way these models will be useful. andrewcarroll.github.io/2025/12/23/t...

579 high-quality human genomes from @humanpangenome.bsky.social, Arab Pangenome and individual papers (CHM13, CN1, KSA001, I002C, YAO and KOREF1). Sequences available in the AGC format (3.7GB) and FM-index in the ropebwt3 format (20.3GB). For details, see github.com/lh3/human-asm

Three decades of biodiversity data, published one decade after we started the project! Our new paper in @NatureComms shows how airborne eDNA from archived aerosol filters can track ecosystem changes across the tree of life—2700+ genera, weekly resolution, 34 years. www.nature.com/articles/s41...

Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...

Excited to share new preprint led by Sergio Salas on “unassigned RNAs” in imaging-based spatial transcriptomics. Across technologies, 30-40% of transcripts fall outside segmentation, & many show structured, biologically meaningful extrasomatic patterns. 📄 www.biorxiv.org/content/10.6...

Excited to share our final accepted version of the CiFi method out today: www.nature.com/articles/s41...

Looking for a postdoc in computational biology? We are looking for a postdoc candidate apply for the fellowship 'Juan de la Cierva' for a project on long-read transcriptomics, multiomics, spatial transcriptomics, single-cell long-reads. Deadline is approaching!! (December 10th)

Human gene maps contain major blind spots that leaves out a vast majority of the world's biological diversity, according to a new study led by the CRG's @rodericguigo.bsky.social with @bsc-cns.bsky.social. The researchers uncovered tens of thousands of new transcripts and entirely new genes.

Mapping single-cell diploid chromatin fiber architectures using DAF-seq - @uwgenome.bsky.social @uwdeptmedicine.bsky.social go.nature.com/4rFTAHy

Climate models have performed extraordinary well (especially given the complexity involved). Climate contrarians on the other hand, not so much. Listed +30 predictions ⬇️. Anyone obvious missing? @katharinehayhoe.com @michaelemann.bsky.social mathsnilsson.se/2025/11/30/c...

COP30 overpromised, underdelivered, empowered distractions, backtracked on issues and once again gave big oil and big ag a free pass. Unfortunately, the suspicions of climate scientists (here in Brazil and abroad) were confirmed again.

This is a very exciting opportunity to connect researchers working on RNA data analysis issues. I can´t wait to see this community growing!!! @bcbhubcsic.bsky.social @i2sysbio.es @hitseq.bsky.social @conesalab.bsky.social

We are excited to announce our most recent preprint “Single-cell long-read sequencing of the experience-induced transcriptome” (www.biorxiv.org/content/10.1...) led by @sheridan in collaboration with Richard Huganir. A few highlights:

The world’s oldest #RNA extracted from #WoollyMammoth: “gives us a completely different picture” ↓ 🧪⚒️ Woolly mammoth preserved in the Siberian permafrost for nearly 40,000 years sequenced. 🖥️ 🧬 www.youtube.com/watch?v=tHQv... Weekend reading: www.scilifelab.se/news/worlds-...

Great to see our new preprint our. Thanks for everybody of the HiFi Solves EMEA consortium for their valuable contribution - this study was driven by the wonderful @bartvds.bsky.social @radboudumc.bsky.social! Exciting to show clinical utility of lrGS in multi-center study.

About fifteen years ago, scientists at SciLifeLab and @umeaplantsciencecentre.se teamed up to sequence the enormous spruce genome 🧪 🖥️ 🧬 youtu.be/5eO0C3tDNDM Featured here: @forsbergnilsson.bsky.social (UU), Pär Ingvarsson (SLU, prev. @umeauniversitet.bsky.social) & Björn Nystedt (@nbis.se)

Excited to see our work featured! We evaluated PureTarget for verification of CRISPR-Cas9 genome editing outcomes, with great results. Read more in the publication spotlight by @pacbio.bsky.social and in our preprint: www.biorxiv.org/content/10.1... www.pacb.com/blog/publica...

Heart ‘blueprint’ made openly available in unique resource 🧪 A detailed map showing how different groups of cells are arranged and how they interact in fetal #HeartDevelopment, now published by SciLifeLab and KTH researchers. ↓ www.scilifelab.se/news/cellula... #OpenAccess #SpatialTranscriptomics

Improving long-read somatic structural variant calling with pangenome and de novo personal genome assembly https://www.biorxiv.org/content/10.1101/2025.10.28.685154v1

We’re thrilled to announce the first symposium dedicated to #LongReadsTranscriptomics, taking place in Valencia, Spain! More information available at: 👉 longtrec.eu/VALT/ Meet the #LongReadsTranscriptomics community, connect with experts, and explore the latest advances in this research area.

I am looking to get my hands on some #Illumina 5-base methylation data - does anyone have a bam file that I could use for some testing? Please RT for reach!

We investigated Constellation from Illumina @bcmhgsc.bsky.social for rare disease cases @gregor-research.bsky.social from @bcmhouston.bsky.social. We tested HG002-4 & sequenced 21 families. We could detangle complex SV & other interesting findings described here: www.medrxiv.org/content/10.1...

Just in time for #ASHG2025, a new FinnGen public data release is live! This release features the first clinical laboratory value association results. Analyses cover 383 lab measurements (OMOPIDs) with data from ≥1,000 participants each. Access the results here: www.finngen.fi/en/access_re...

PacBio: $300 Genome Via Chemistry Update 🧬🖥️ omicsomics.blogspot.com/2025/10/pacb...

New preprint for sequencing enthusiasts!🧬💻 We benchmarked Element Biosciences’ AVITI against Illumina NovaSeq, with validation using PacBio Revio. All platforms are available at NGI Sweden! Great work led by Pontus Höijer and Robert Månsson. www.biorxiv.org/content/10.1...

Last week we were in the Washington Post for our characterization of Robertsonian chromosomes. This week we are entering our 10th day of being shut down and all of our research is on hold. To help me feel not-so-bad, here is a thread of some studies we released right before the shutdown 🧵 [1/n]...

Some thoughts on the blossoming of genomic medicine stimulated by the excellent @ga4gh.org meeting in lovely Uppsala Sweden. www.linkedin.com/pulse/though...

Now published! Our paper on: (1) Accurate sequencing of sperm at scale (2) Positive selection of spermatogenesis driver mutations across the exome (3) Offspring disease risks from male reproductive aging [1/n] www.nature.com/articles/s41...

We're hiring! My team at @nygenome.org is looking for a statistical genetics postdoc to decipher functional architecture of complex diseases from cutting-edge CRISPR+scRNA-seq data, with @nevillesanjana.bsky.social lab. Happy to meet at #ASHG25, apply here jobs.silkroad.com/NYGenome/Car...

Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin

We are hiring a postdoctoral researcher to identify genes involved in frontotemporal dementia using short- and long-read sequencing data. More information is available at jobs.vib.be/j/124543/pos....

This is a big advance, folks. We've never had a disease-modifying drug for this devastating inherited disease www.science.org/content/arti... www.washingtonpost.com/health/2025/... www.economist.com/science-and-...

Hey all! Now that i've left my position at UQ, I thought I would leverage my network here to see if anyone has leads on environmental genomics, biotech, marine policy positions in the US/Canada/Australia/Europe. I'd love to speak with anyone in those fields re openings, worthwhile recruiters, etc.

I'm super excited to announce the new PureTarget kits from @pacbio.bsky.social are out! We have a new carrier screening panel and updated repeat expansion panels plus variant calling software to support both. Press release - www.pacb.com/press_releas...

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

What is the benefit of a T2T reference instead of GRCh38 for population-scale sequencing projects? Read all about it in our latest paper. Special thanks to Daniel Schmitz for leading this work, which involved reanalysis of 1000 samples! genome.cshlp.org/content/earl...

To "accelerate high-impact, curiosity-led research and innovation, and to facilitate breakthroughs" - let me tell you my students using genAI are NOT curious and what it is accelerated so far is lying, cheating and data fabrication

Excited to share our latest preprint: LongBench—a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches. www.biorxiv.org/content/10.1...

Our first PacBio Revio run with over 140Gb average HiFi yield! This was for a pool of 16 human WGS libraries across 8 SMRTcells, giving >20x coverage per sample. We're running these samples as part of the "Genome of Sweden" project 🧬🇸🇪

Today people went around my neighborhood in north east London spray painting St George’s crosses onto people’s homes. Many of these houses have non British people living in them. This is getting very dark, very quick.

Couldn’t be prouder of this collaboration on targeted long-read sequencing for pharmacogenomics! #PGx

New blog post – A quick look at Roche's SBX lh3.github.io/2025/09/11/a...

New preprint! With PureTarget we achieved >1000× coverage of targets with ~5kb PacBio reads at QV39. This enabled high-resolution analysis of CRISPR-Cas9 outcomes Key finding: Some CRISPR-mutations may only emerge in the second generation, due to germ cell mosaicism www.biorxiv.org/content/10.1...

Long-read single-cell genome, transcriptome and open chromatin profiling links genotype to phenotypes. https://www.biorxiv.org/content/10.1101/2025.09.08.674950v1