iiinova — where your digital self keeps evolving

Adam Ameur @adameur.bsky.social · 29/09/2026

The early bird deadline for #LRUA26 is tomorrow, September 30. So make sure to register if you haven't already: lrua.se We have a fantastic lineup of speakers and are looking forward to bringing the long-read community together in Uppsala!

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Megan Dennis @mydennis.bsky.social · 29/09/2026

We are recruiting at the assistant professor level ~ Ideal candidates have expertise in genomics and/or biochemistry, applying emerging experimental, computational, AI-driven methods to answer mechanistic questions in human health. Please share! First review 10/30. recruit.ucdavis.edu/JPF07832

recruit.ucdavis.edu

Assistant Professor- Biochemistry and Molecular Medicine

University of California, Davis is hiring. Apply now!

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Juliet E McKenna @julietemckenna.bsky.social · 28/09/2026

I just read a third or possibly fourth news article where the reality of an 'AI has discovered something marvellous!' story turns out to be GenAI somehow accessed material it had no permissions for, which was the outcome of an expert's years of work, and presented it without attribution. GenAI lies.

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Adam Ameur @adameur.bsky.social · 16/09/2026

What happens after genome editing? Using PacBio PureTarget sequencing (>1000× coverage), we resolved CRISPR-Cas9 on-target and off-target outcomes at high resolution. In zebrafish, this revealed widespread mosaicism and edits transmitted to the offspring 🧬 🧪 link.springer.com/article/10.1...

link.springer.com

Accurate characterization of CRISPR-Cas9 genome editing outcomes and mosaicism with near-perfect long reads - Genome Medicine

Background Genetic mosaicism is a well-recognized consequence of CRISPR–Cas9 genome editing, yet its characterization remains challenging, especially when it involves low-frequency structural variants...

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Rada-Iglesias Lab @radaiglesiaslab.bsky.social · 01/09/2026

Have you ever wondered why developmental genes are often regulated by enhancers located at long distances? In this @natgenet.nature.com perspective, we speculate that long-range enhancer positioning may provide regulatory properties essential for proper gene expression www.nature.com/articles/s41...

nature.com

Mechanisms and functional implications of long-range enhancer-dependent gene regulation - Nature Genetics

Development depends on gene regulation by enhancers across long genomic distances. This Perspective discusses mechanisms enabling long-range enhancer–promoter communication and the potential advantage...

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Adam Ameur @adameur.bsky.social · 25/08/2026

LRUA26 abstract submission deadline extended to September 2! Don't miss this unique opportunity to present your long-read sequencing work as an oral or poster presentation, in the beautiful Uppsala University Main Building. For registration, abstract submission, and more info, visit: lrua.se

lrua.se

Long-Read Sequencing Uppsala, November 2–4, 2026

#LRUA26: Empower your research with long-read sequencing technologies and connect with experts, peers, and industry leaders in Uppsala this November.

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European Society of Human Genetics @eshg.bsky.social · 21/08/2026

🧬 Repeat-expansion disorders remain challenging to resolve with conventional approaches. New Perspective explores how LRS can capture repeat size, composition, mosaicism and methylation - and its growing role in research and clinical diagnostics. 👉https://www.nature.com/articles/s41588-026-02694-9

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Guillaume Holley @guillaumeolesan.bsky.social · 20/08/2026

I am delighted to present with @hannespetur.bsky.social our new study on the Icelandic pangenome reference HPRC-ICE. This work goes all the way from pangenome construction to disease association! (1/7) www.nature.com/articles/s41...

nature.com

An Icelandic pangenome reference - Nature

Newly developed methods enable construction of Icelandic haplotypes and mapping of population-scale short reads to a pangenome by reducing reference bias and improving discovery in low-mappability reg...

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Adam Ameur @adameur.bsky.social · 20/08/2026

🎉Our review on the use of long-read sequencing in tandem repeat disorders is out!🧬💻 Grateful to be part of this team effort. We're only starting to understand the role of repeats in human disease and long-reads will help unlock future discoveries www.nature.com/articles/s41...

nature.com

Toward the clinical application of long-read sequencing in repeat-expansion disorders - Nature Genetics

This Perspective by the LRS-RED consortium discusses methodological, bioinformatic and diagnostic advances in long-read sequencing (LRS) for repeat-expansion disorders, highlighting the potential of L...

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Adam Ameur @adameur.bsky.social · 10/08/2026

Submit your abstract for #LRUA26! Don't miss this unique opportunity to share your long-read sequencing research with leading experts. Oral and poster presentations will be selected from submitted abstracts. For registration and abstract submission: lrua.se Deadline: August 26

lrua.se

Long-Read Sequencing Uppsala, November 2–4, 2026

#LRUA26: Empower your research with long-read sequencing technologies and connect with experts, peers, and industry leaders in Uppsala this November.

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Albert Vilella, PhD. @albertvilella.bsky.social · 07/08/2026

Both NGS long-reads companies in the stock market, Oxford @nanoporetech.com and @pacbio.bsky.social have now presented H1 2026 results, and I give an analysis of where they are and where they might be going from now on in this piece on my Substack albertvilella.substack.com/p/ngs-long-r...

albertvilella.substack.com

NGS Long Reads H1 2026 financials for PacBio and Oxford Nanopore

And more announcements from both companies

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Robin Andersson @randersson.bsky.social · 05/08/2026

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!

nature.com

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.

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Jay Shendure @jshendure.bsky.social · 30/07/2026

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...

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Victor Pressfeldt @vpressfeldt.bsky.social · 24/07/2026

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.

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Tuuli Lappalainen @tuuliel.bsky.social · 10/07/2026

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/...

kth.se

KTH | Postdoc in genomics

KTH jobs is where you search for jobs at www.kth.se.

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Shuangjia Lu @lushjia.bsky.social · 07/07/2026

🔥 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...

doi.org

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...

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Adam Ameur @adameur.bsky.social · 03/07/2026

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!

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Andrew Carroll @acarroll.bsky.social · 01/07/2026

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...

andrewcarroll.github.io

The Best of Both Worlds - Assessing MiniBWA

Recently, Heng Li released MiniBWA (GitHub) alongside a paper by Heng Li and Nils Homer describing the method (paper). MiniBWA builds on the approaches in Minimap2 (also by Heng Li), but falls back on...

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LongTREC @longtrec.bsky.social · 29/06/2026

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

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Alex Hoischen @ahoischen.bsky.social · 26/06/2026

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...

nature.com

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...

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Peter Gleick @petergleick.bsky.social · 24/06/2026

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.

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NBIS @nbis.se · 22/06/2026

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...

scilifelab.se

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...

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PacBio @pacbio.bsky.social · 17/06/2026

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

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Adam Ameur @adameur.bsky.social · 17/06/2026

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...

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PacBio @pacbio.bsky.social · 14/06/2026

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

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Adam Ameur @adameur.bsky.social · 14/06/2026

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

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Ryan Wick @rrwick.bsky.social · 11/06/2026

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...

rrwick.github.io

Dorado v2.0.0: no more sup?

a blog for miscellaneous bioinformatics stuff

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Adam Phillippy @aphillippy.bsky.social · 08/06/2026

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...

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bioRxiv Genomics @biorxiv-genomic.bsky.social · 06/06/2026

Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures www.biorxiv.org/content/10.64898/20…

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Heng Li @lh3lh3.bsky.social · 30/05/2026

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...

biorxiv.org

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Ketan Joshi @ketanjoshi.co · 26/05/2026

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

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Svante Thunberg @svantethunberg.bsky.social · 23/05/2026

"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...

sustainability.stanford.edu

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...

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Jonathan Göke @jonathangoeke.bsky.social · 22/05/2026

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

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David Eccles 🌻🇵🇸7x🩹🛡️ @gringene.org · 20/05/2026

#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...

gringer.gitlab.io

London Calling 2026 - Presentation Notes and Other Things

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ELIXIR Europe @elixir-europe.org · 15/05/2026

📣 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. 👉 loom.ly/4uSHoak

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LongTREC @longtrec.bsky.social · 11/05/2026

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

longtrec.eu

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Earlham Institute @earlhaminst.bsky.social · 28/04/2026

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! ⤵️

buff.ly

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

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PacBio @pacbio.bsky.social · 26/04/2026

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

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Adam Ameur @adameur.bsky.social · 24/04/2026

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

biorxiv.org

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Heng Li @lh3lh3.bsky.social · 17/04/2026

Blog post on "The AI Rewrite Dilemma": lh3.github.io/2026/04/17/t...

lh3.github.io

The AI Rewrite Dilemma

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Krystle J McLaughlin @biophyskrys.bsky.social · 17/04/2026

As a scientist, I am here to report that this headline is indeed accurate as I am in fact STUNNED!! Wow. This is incredible. 🧪 "Newly discovered bacterial defense system challenges genetic code’s central dogma.": www.science.org/content/arti...

Screenshot of Science commentary articleL Scientists stunned by ‘fundamentally new way’ life produces DNA.
Newly discovered bacterial defense system challenges genetic code’s central dogma. Image: In a newly discovered bacterial defense system, paired strands of DNA (orange and cyan) are synthesized by two enzymes: One (yellow) uses an RNA template (beige) to guide the assembly of the nucleotide bases that make up DNA, while a second, highly unusual enzyme (light blue) uses its own amino acids as a template."

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Steven Robbins @stevenjrobbins.bsky.social · 09/04/2026

Given a discussion on another thread, thought it might be useful to start a separate thread on how users are achieving higher ONT yields—extraction kits, size selection, sample type, basic stats, etc. Anyone welcome to chime in. @acritschristoph.bsky.social @kirk3gaard.bsky.social

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Adam Ameur @adameur.bsky.social · 09/04/2026

📣Registration and abstract submission now open for the Long‑Read Sequencing Uppsala 2026 meeting, taking place November 2–4! For abstract submission, registration, and the preliminary program, please visit the conference website: 👉 lrua.se

lrua.se

Long-Read Sequencing Uppsala, November 2–4, 2026

#LRUA26: Empower your research with long-read sequencing technologies and connect with experts, peers, and industry leaders in Uppsala this November.

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European Society of Human Genetics @eshg.bsky.social · 31/03/2026

Hello from Gothenburg! 🇸🇪 The ESHG team is at the last Site visit in Gothenburg to go through all the details for the conference #eshg2026. Looking forward to seeing you there! Register and join us on-site in June: 2026.eshg.org/registration/

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Adam Ameur @adameur.bsky.social · 24/03/2026

What's the current best strategy to sequence complete transcripts in the ~20kb range? Should we attempt generating full length cDNA, or go for direct RNA on ONT? I suppose it will be a challenge in any case..

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