That is hot, even by Brisbane standards

Global equity of data is only possible when countries can have ownership and generate their own data. Data equity and access to infrastructure is so important. A great presentation by @ebi.embl.org Interim Director Dr. Joanna McEntyre @abacbs.bsky.social #ABACBS2025

🚨 Update to nohuman 🚨

While testing against the standard Kraken DB, I noticed Kraken was detecting far more human reads than nohuman. I realised Kraken masks low-complexity regions by default during DB construction and that setting had been left on in nohuman, leading to missing human reads.

Huge thanks to Chenxi Zhou for helping scale this approach to human sized genomes!

Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing Abstract. Polyadenylation is a dynamic process that is important in cellular physiology, which has implications in messenger RNA decay rates, translation e

A paper from @lachlanjmc.bsky.social Lachlan Coin, not active here for the past month, on Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing academic.oup.com/gigascience/...

La. regulators approve Entergy power plants for Meta’s AI data center Louisiana Public Service Commissioners voted four to one to approve Entergy’s three new gas plants to power Meta’s largest-ever data center.

Louisiana has to build three new natural gas power plants to accommodate the "AI" data center that Meta just crammed through because said center will use *Three Times* as much electricity (and, thus, attendant resources) as the *Entire City Of New Orleans*, every year.

Y'all this isn't sustainable.

A do-or-die moment for the scientific enterprise Reflecting on our paper “The entities enabling scientific fraud at scale are large, resilient, and growing rapidly”

Today, our article "The entities enabling scientific fraud at scale are large, resilient, and growing rapidly" is finally published in PNAS. I hope that it proves to be a wake-up-call for the whole scientific community.

reeserichardson.blog/2025/08/04/a...

We identify novel interferon stimulated transcripts and genes. We also found elongation of poly(A) tails of genes encoding ribosomal proteins in response to interferon stimulation (but not influenza infection), indicating this may be an important part of the innate immune response.

The Ferret is widely considered as the gold-standard animal model for influenza infection. Ferrets are infected with the same strains of Influenza that infect humans, and show similar symptoms (sneezing, fever)

Characterizing the transcriptomic response to interferon and infection in European Domestic Ferret respiratory tissues using long-read RNA sequencing The European domestic ferret (Mustela putorius furo) is considered the gold-standard small animal model for studying human and avian influenza virus infections. However, experimental characterization ...

Our latest preprint using long read nanopore sequencing to study Ferret transcriptomic response to infection and interferon stimulation, lead by Rubaiyea Farrukee and Jessie Chang www.biorxiv.org/content/10.1...

Characterisation of in vitro resistance selection against second-/last-line antibiotics in methicillin-resistant Staphylococcus aureus ATCC 43300 strain AbstractBackground and objectives. The increasing occurrence of MRSA clinical isolates harbouring reduced susceptibility to mainstay antibiotics has escala

New paper from our lab in collaboration with Blaskovich lab led by former Phd student Anggia Prasetyoputri using in vitro selection to identify drug resistance conferring murations in S. aureus academic.oup.com/jacamr/artic...

New preprint from @aleixcanalda.bsky.social on structural variation in TB and its role in evolution and drug resistance www.biorxiv.org/content/10.1...

As well as enriching for target host transcripts, we also show that it can be used to enrich for viral transcripts in infected cells, in this case SARS-Cov2

And can be used investigate differential isoform usage

The method provides ~10 fold enrichment across a range of different expression levels

Customizable host and viral transcript enrichment using CRISPR-Cas9 long-read sequencing for isoform discovery and validation Long-read RNA sequencing has been broadly utilized to examine the diversity of transcriptomes, understand differential expression and discover novel transcript isoforms. One of the major limitations o...

New preprint from the lab, describing an approach to enrichment of transcript isoforms for nanopore cDNA sequencing, using CRISPR-Cas9 www.biorxiv.org/content/10.1...

Customizable host and viral transcript enrichment using CRISPR-Cas9 long-read sequencing for isoform discovery and validation www.biorxiv.org/content/10.1101/2025.04....

I want to provide an overview and perspective of rare disease genomic testing, which is a real success story of science impacting health - a science which goes back over 100 years and yet is still striding forward and much more to come.

I should add that we decided to not report RNA modifications in this preprint as we use outdated R9.4 chemistry, and there are many modifications and many tools, which often given conflicting results. But this is also an exciting area for biomarker discovery.

Overall we think there is a lot of potential for finding new biomarkers of disease using native RNA sequencing. One thing to note is that nanopore direct RNA sequencing is quite a bit lower throughput than cDNA sequencing, so its still more expensive.

Even though we had a relatively small sample size (12), we also looked to find potential polyadenylation biomarkers of bacterial vs viral infection. Left panel shows normal gene expression count based biomarkers (reflecting what we saw with larger cDNA-seq study), right panel shows polyA biomarkers

After filtering likely artefacts, we found a modest number (594) of new transcript isoforms, including 9 new isoforms for IGLL5. We also looked for differential transcript usage, and found 4 genes with statistically significant differential transcript usage between bacterial and viral infection

We asked whether polyadenylation varied by pathway/function. This plot shows polyA tails of transcripts in significant GO molecular functions in a gene set enrichment analysis for median tail length (excluding mitochondrial genes)

Firstly we wanted to see if dRNA sequencing based gene counts were similar to cDNA based gene counts. The answer depends a lot on which analysis pipeline you use. Algorithms which use expectation maximisation seem to be better correlated (e.g. nanocount with kallisto)

To do this we re-sequenced left-over RNA from the same extraction for 12 samples which had been previously sequenced as part of a larger sepsis biomarker study using Illumina cDNA sequencing (www.thelancet.com/journals/lan...

Latest preprint from the lab: we asked whether native RNA sequencing (using nanopore sequencing) might be a successor to traditional cDNA sequencing for biomarker discovery in blood.

New report highlights the scientific impact of open source software Two of the scientists who won this year’s Nobel Prize for cracking the code of proteins’ intricate structures relied, in part, on a series of computing

“We don’t value software, data, and methods in the same way we value papers, even though those resources empower millions of scientists” 💯

www.statnews.com/sponsor/2024...

Genome size estimation from long read overlaps https://www.biorxiv.org/content/10.1101/2024.11.27.625777v1 Summary: Accurate genome size estimation is an important component of genomic analyses, though exist

Genome size estimation from long read overlaps www.biorxiv.org/content/10.1101/2024.11....

🌟 Excited to share my latest preprint with @lachlanjmc.bsky.social on @biorxivpreprint.bsky.social: "Genome size estimation from long read overlaps”! 🚀

Check it out here: doi.org/10.1101/2024...
And find the code here: github.com/mbhall88/lrge

🧵👇