1st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...

Complete Mutagenesis of the Genome and Proteome of ΦX174

The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...

biorxiv.org

New GWAS of Fibromyalgia identified 26 loci and found an HTT inframe indel (same gene as Huntington's disease [HD]). Howevere, the Fibromyalgia variant isn't associated with HD, the HD CAG repeat isn't associated with Fibromyalgia, and they aren't in LD. www.nature.com/articles/s41...

In this collaboration with the Gokcumen lab, @alberaqil.bsky.social developed a method based on interchromosomal linkage disequilibrium to detect false positive trans-eQTLs, showcased on GTEx and MAGE. The approach could be used to filter other trans molecular QTLs, which may be similarly impacted.

Gokcumen Lab@gokcumenlab.bsky.social · last wk.

New paper with @rajivmccoy.bsky.social @ajhgnews.bsky.social. Bottom line: Polymorphic gene duplications absent in the reference genome can produce spurious trans-eQTLs, and we propose a method to identify these false positives. authors.elsevier.com/c/1nWChgeXHnOF

Toward generalizable and interpretable AI in regulatory genomics www.nature.com/articles/s41... rdcu.be/fwcdT 🧬💻🧪

Toward generalizable and interpretable AI in regulatory genomics - Nature Genetics

This Review surveys the current landscape of genomic artificial intelligence through the lens of sequence-to-function models, examining how architectural choices, training data, prediction tasks, mode...

nature.com

I’m starting a new job this fall! I will be launching a new lab to develop AI methods to predict disease risk and progression using the nationwide biomedical research datasets here in Finland.

All experience hath shewn, that mankind are more disposed to suffer, while evils are sufferable, than to right themselves by abolishing the forms to which they are accustomed. But...it is their right, it is their duty, to throw off such Government, and to provide new Guards for their future security

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...

Incorporating responsiveness into the Activity-by-Contact model improves prediction of native regulation and explains 2 long-observed phenomena: 1) Why are housekeeping genes often insensitive to distal enhancers? 2) How do enhancers skip active genes?

Genes with responsive promoters are regulated by more enhancers and sensitive to their perturbation. Genes with non-responsive promoters (many housekeeping genes) are insensitive to and skipped by enhancers.

Yes; I think QEDs idea of an AI-based "impact" prediction / metric is a bad idea. This is true for all of the reasons Pedro mentioned but also, because "impact" metrics, in general, and as a whole, are bad ideas, not goals. They are largely counterproductive to good science & should be abandoned.

Pedro Beltrao@pedrobeltrao.bsky.social · last mo.

@qedscience.bsky.social has come up with a really controversial idea - an AI score for scientific impact. This trained score correlates with the impact factor of published preprints and the binning of papers into discrete quality bins accessed by independent scientists. Backlash in 3, 2, 1... (more)

Happy to share that this work led by @mihkeljesse.bsky.social has now been published at PLOS Genetics! journals.plos.org/plosgenetics... A couple of thoughts below.

Ultra-fast genetic colocalisation across millions of association signals

Author summary Over 90% of human genetic variants associated with human traits and diseases lie in non-coding regions of the genome, making it difficult to interpret the mechanisms by which these vari...

journals.plos.org

@mihkeljesse.bsky.social · 11mo ago

After 1.5 years of work in @kauralasoo.bsky.social’s lab, we finally published my preprint! We introduce gpu-coloc, a GPU-accelerated implementation of coloc, show comparability to CLPP and aim to provide practical guidelines. Now accessible on BioRxiv: www.biorxiv.org/content/10.1...

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

Huge congratulations to @mihkeljesse.bsky.social for such a well-deserved award!

European Society of Human Genetics@eshg.bsky.social · 2mo ago

#eshg2026 Best poster awards Best Poster in Basic Research: Mihkel Jesse (Tartu, Estonia) Best Poster in Clinical Research: Francesco Pintus (Turin, Italy) Look at these posters on the Virtual Conference Platform 💻️

Congratulations @jelisavetadzi.bsky.social! Lovely to see brilliant and hardworking PhD students getting such well-deserved recognition ❤️

European Society of Human Genetics@eshg.bsky.social · 2mo ago

#eshg2026 Vienna Medical Academy Award: Best presentation in translational genetic reserach/therapy of genetic diseases. Jelisaveta Džigurski (Tartu, Estonia)

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease. Details below careersearch.stanford.edu/jobs/computa... Plz RT

Unfortunately I have to miss #ESHG2026 this year, but do check out this lighting talk (and poster!) from the brilliant @mihkeljesse.bsky.social! Mihkel did this work during his BSc (!) studies in my lab. Preprint available at: www.biorxiv.org/content/10.1....

Atlas "We have created a comprehensive resource of both common and low-frequency genetic variants associated with 249 metabolic traits in up to 619,372 individuals across multiple ancestry groups.' www.nature.com/articles/s41...

Excited to release #OpenSplice - the impact of >500,000 mutations on the alternative splicing of 600 human exons www.biorxiv.org/content/10.6... Led by @gioia-quarantani.bsky.social + funded by @opentargets.org ‬ @sangerinstitute.bsky.social @crg.eu #cshlsymp26 #RNA2026 @rnasociety.bsky.social

1\ Excited to finally share some of my PhD work: OpenSplice! We measured how >590,000 mutations affect exon inclusion across 600 human exons, creating a resource to study splicing regulation, benchmark variant effect predictors, and support variant interpretation.

bioRxiv Genomics@biorxiv-genomic.bsky.social · 2mo ago

OpenSplice: the impact of half a million mutations on the alternative splicing of 600 human exons https://www.biorxiv.org/content/10.64898/2026.05.22.727141v1

🧬 Join us at the 25th International Gene Forum – with stellar speakers from around the world (again)! Register now to secure your spot! 📅 August 25–26, 2026 📍 Estonian National Museum, Tartu, Estonia 🌐 Information & registration: www.geneforum.ee #Geneforum2026 #Geneforum

OpenSplice: the impact of half a million mutations on the alternative splicing of 600 human exons https://www.biorxiv.org/content/10.64898/2026.05.22.727141v1

"Genetic analysis of circulating metabolic traits in 619,372 individuals" www.nature.com/articles/s41... Congrats to the teams of Priit Palta and @kauralasoo.bsky.social

Genetic analysis of circulating metabolic traits in 619,372 individuals - Nature

A genome-wide association study combining data from the Estonian Biobank and the UK Biobank identifies many common and low-frequency locus–metabolic trait associations, enabling the identification of ...

nature.com

Kaur Alasoo@kauralasoo.bsky.social · 2y ago

Happy to share our most recent GWAS meta-analysis of 249 circulating metabolic biomarkers (Nightingale Health platform) in up to 619,372 individuals. www.medrxiv.org/content/10.1...

Genetic analysis of circulating metabolic traits in 619,372 individuals @nature.com @kauralasoo.bsky.social @unitartupress.bsky.social www.nature.com/articles/s41...

tinyurl.com/reuxynmc Very excited to see this work I was a small part of published! We analysed two large scale colocalisation datasets: OpenTargets data and an analysis of immune-mediated disease GWAS/immune cell eQTLs seeking to understand the "colocalisation gap". Some highlights:

Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluation

Author summary Most of the genetic variants associated with complex traits are located outside genes, limiting functional interpretation. Genetic colocalisation helps identify candidate causal genes b...

journals.plos.org

Hi Genetics/Comp-Bio community 👋 Interested in mentoring a comp-bio research student in East Africa over the summer? Do you have any experience in bioinformatics, biostats, genome/RNA-seq analyses, ML, or metagenomics? We'd love to have you as a mentor in our new program! 🧵 (1/n)

Our wiggleplotr package (www.bioconductor.org/packages/rel...) can now import RNA-seq read coverage from parquet format in addition to bigWig (think multi-sample bigWig). This has a large impact on reducing IO, because we can extract regional read coverage from e.g. 500 samples in 1 file operation.

Michael Love@mikelove.bsky.social · 3mo ago

Bioconductor 3.23 is released! Thanks to the core team for all the hard work that goes into a release, and to the package reviewers. The lab has a bunch of updates in here that I'll post in 🧵 over the next few days:

NEWS: The ERC Scientific Council has listened to the concerns from members of the research community about changes to the re-submission rules, intended to manage the surge in demand for grants. The Scientific Council will readjust some of the changes: link.europa.eu/TBqRQJ

ERC Scientific Council readjusts rules for reapplication

The ERC Scientific Council has listened to the concerns from members of the research community about the recent announcement on changes to the re-submission rules. The changes, intended to manage the ...

link.europa.eu

Academia feels increasingly like playing Monkey Island, if you miss something as absurd as picking up a rubber chicken with a pulley in the first scene, you only realize much later that you’re stuck and can’t pass to the next stage (👇 see below 1/3) www.science.org/content/arti...

Abrupt change to European funder’s rules leaves researchers shut out

Flood of proposals to European Research Council—perhaps unleashed by AI—means unsuccessful applicants must wait longer to reapply

science.org

Great interview here with @kauralasoo.bsky.social on genetics research and collaborative science. blog.cs.ut.ee/2025/10/06/k...

We are so excited to see our work out in @nature.com! We present a multi-omic single-cell atlas of 12 organs in human fetal development, explore the enhancer landscape, use deep learning to infer rules of transcription factor activity, and interpret non-coding variants in complex traits: #GeneReg 🧬🖥️

John Greally@greally.bsky.social · 4mo ago

This @anshulkundaje.bsky.social, Kyle Fahr and William Greenleaf paper is finally out, we've been following it for a while in its preprint form, phenomenal work. www.nature.com/articles/s41...