This is a really important issue - pubmed and other websites distort authorship contributions by only using the first/last author instead of honouring the "equal contributions" designation. This has real-life impact and disincentivises team science:
Ludwig @oxfordcancer.bsky.social’s Sabrina James presented her research at #AACR2026 in a poster titled “Unexpected identification of tumor-infiltrating H. pylori or human papillomavirus (HPV) 16 in three exceptional responders in immunochemotherapy-treated esophageal cancer.”
#CanSky #OncoSky
Good piece. “If your problem with open access is that commercial publishers are hoovering up all the money, design open access interventions that specifically prevent commercial publishers from receiving your money.”
Pleased to share our review on chromosomal instability (CIN) and aneuploidy in cancer, led by Amanda Mennie. Now out @annualreviews.bsky.social!
www.annualreviews.org/content/jour...
The Oxford Tube express coach is reinstating its White City stop, dropped in March’s timetable change in favour of a new Acton stop for the Elizabeth Line, after passenger feedback. White City will be a request stop, requiring passengers to ring the bell to alight. www.oxfordtube.com/service-upda...
I wrote an essay. It’s about gain-of-function mutations. And penguins. Also ion channels, chihuahuas, the film Alien, recycled cardboard, and the Apollonian mind. Oh, and muffins.
Thanks to the editors of #GENETICS @genetics-gsa.bsky.social for letting me take some stylistic liberties. 1/2
Positron plus JupyterHub logo, with the Posit logo in the corner.
We are thrilled to announce that Positron Server is now available for academic use via JupyterHub!
This gives students a robust #RStats & #Python data science IDE without needing a local install or new infrastructure.
Learn more: positron.posit.co/blog/posts/2...
But shall this crazed old man be tamely suffered to drag a whole ship’s company down to doom with him?
Do you want to move to Oxford and join our lab? There is a computational biologist position open atm to develop and implement tools to analyse TE expression in single cell long read data and more. Apply! #TEsky #UniversityofOxford #postdoc
The DNA Polymerase Meeting is a biennial international conference that brings together scientists from around the globe to discuss the latest discoveries in the field of DNA polymerases and their role in DNA replication and repair. Topics will span from fundamental mechanistic insights into polymerase structure and function to cutting-edge applications in biotechnology, medicine, and synthetic biology. DNA polymerases are not only essential for maintaining genome integrity under diverse cellular conditions, but they have also become indispensable tools in molecular biology and technology—powering PCR, sequencing, genome editing, aptamer generation and diagnostic innovations. The past seven conferences held in Ascona, Madrid, Cambridge, Biarritz, Leiden, Stockholm, and Warsaw were extremely successful, fostering collaborations and advancing the field. We are delighted to continue this tradition with the upcoming meeting in Paris, scheduled for Sep 28th to Oct 1st 2026.
🧬 8th DNA Polymerases Meeting
📅 28 Sept – 1 Oct 2026, Paris
An international conference on DNA polymerases: replication, repair, genome integrity, and applications in PCR, sequencing, genome editing and diagnostics.
Register now ↘️ www.8th-dna-polymerases.conferences-pasteur.org
Rastair: an integrated variant and methylation caller www.biorxiv.org/content/10.64898/2026.03...
The @daphnejacksontr.bsky.social fellowships have an emphasis on specific advanced research, scientific, engineering and/or creative techniques, alongside mentoring and training that fully equips those undertaking them to return to a technical professional career.
📍 All details here: t.ly/ehbF9
Rastair is freely available as source code (and compilation is easy 😉), via Docker, conda or as pre-compiled binaries. If you want to learn more, check the website:
www.rastair.com
Upset plot showing the overlap in CpG positions called by rastair vs DRAGEN and MethylDackel. Rastair calls a substantial number of CpGs that are not reported by either of the other two.
Sankey plot showing how "CpG" positions uniquely called by rastair are reported by Illumina's DRAGEN: nearly 1M are not called at all (coverage/base-quality cut-off differences etc). The rest are "de-novo" CPGs where the C/G part is reported in the CX file, and the N>C/G part is reported in the VCF only
By calling variants first, rastair identifies nearly 1M additional CpG positions in an average human genome where a SNP turns a CpH into a CpG 🤯 AFAIK, no other caller currently does this cleanly, not even Illumina's DRAGEN, which reports the C and the G part of a "de-novo CpG" in 2 files 🙈
Runtime over input dataset size: lower is better. Rastair is much faster than other tools, and rastair with GPU is the fastest of them all.
F1 score over coverage. Rastair's F1 score for input with more than 30x coverage is better than TVC and Biscuit, and very close to tools run on clean WGS data
Rastair comes with optional GPU acceleration which makes it ~ 2x faster than the CPU version, and about 10x faster than any WGS variant caller. Meanwhile, F1 scores are very close to top-of-the-line callers.
🎉New preprint out today! We present rastair - an ultra-fast SNP and methylation caller for TAPS or 5-Base data. Rastair takes less than 1h to process e.g. a 50x 5-Base dataset, yet SNP call accuracy is nearly identical to GATK on WGS data 🔥
Free park and ride bus travel has been extended until at least the end of May 2026.
The offer is being funded by the income from the temporary congestion charge. Further investment plans will be discussed by cabinet at a public meeting later this spring.
➡️ news.oxfordshire.gov.uk/free-park-an...
For all the talk of how the new Archbishop is progressive, the fact she did this speaks volumes anyhow far the church still has to go. Also we need to remove them from the Lords. Obviously.
A bit more than a month after 2.1, we now released Rastair 2.1, a #rust tool that detects variants and methylated positions from TAPS and 5base sequence reads. 2.1 adds GPU support and a bunch of other performance optimizations that I'm quite proud of! www.rastair.com
Rising sun shining through pine trees at the villa Borghese in Rome
Morning mist in Rome 🤩
Looking forward to presenting our recent work on platelet-derived cfDNA at the 1st meeting of the Italian Society for Liquid Biopsy in Rome today!
Have some extra time this weekend? Check out this Founders Podcast episode on our founder Daniel K. Ludwig:
podcasts.apple.com/us/podcast/t...
#CanSky #OncoSky
Heading to # AGBT in Orlando tomorrow! Ping me if you're there, too - would love to meet up!
Looks a lot like AI slop. We're so doomed...
Modeling the evolutionary dynamics of clonal hematopoiesis @natgenet.nature.com @moffittnews.bsky.social
www.nature.com/articles/s41...
Have you ever once seen the New York Times quote Trump like this?
Three UK research councils suspend funding opportunities
“Temporary block on grant applications by MRC, BBSRC and EPSRC heightens concerns over funding cuts”
Many congratulations to Lauren Murphy!
