Dr Andrew Lonsdale

Dr Andrew Lonsdale

@lonsbio.bsky.social

Bioinformatics post-doc at @petermaccc.bsky.social in the @aliciao.bsky.social Lab. Keen believer in the benefit of side projects. He/Him. Work/Life: 💻💻💻💻💻 👨‍👩‍👧‍👧 👨‍👩‍👧‍👧

601 followers448 following99 posts

Dr Andrew Lonsdale reposted

Michelle Meier
@michellemeier.bsky.social

Equally happy and terrified to share my first preprint of my PhD! Turns out the order of your scRNA-seq QC pipeline matters more than we thought: removing ambient RNA before doublet detection can reduce doublet detection performance!

#SingleCell preprints@prepub-singlecell.bsky.social

Order Matters: Ambient RNA correction confounds doublet detection in single-cell RNA sequencing #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.64898/2026.10.13.758369v1

Dr Andrew Lonsdale reposted

BF Francis Ouellette
@bffo.bsky.social

From the @bioinfoadv.bsky.social journal | Phil Bourne (1953–2026): from small molecules to big data—the journey of a multifaceted visionary | #Bioinformatics #Pioneer @rcsbpdb.bsky.social @iscb.bsky.social #PLOSCBTSR #OpenScience #OpenAccess #DataScience |🧬🖥️🧪🔓❤️ ⬇️ academic.oup.com/bioinformati...

academic.oup.comPhil Bourne (1953–2026): from small molecules to big data—the journey of a multifaceted visionaryAbstract. Born in London in 1953 and raised in Australia, Phil Bourne spent over four decades in science moving across scales: from crystal structures to t

Dr Andrew Lonsdale reposted

Jovana Maksimovic
@jovmaksimovic.bsky.social

Gene fusions drive ~16% of all cancers & 50-70% of childhood ALL. But standard scRNA-seq can't see them — the assays aren't built to capture fusion breakpoints. We built a way to fix that. @aliciao.bsky.social @sadras-t.bsky.social @petermaccc.bsky.social @onjcri.org.au @10xgenomics.bsky.social 🧵

bioRxivpreprint@biorxivpreprint.bsky.social

Closing the fusion-detection gap in single-cell RNA-seq with a scalable, probe-based workflow https://www.biorxiv.org/content/10.64898/2026.08.26.747171v1

Dr Andrew Lonsdale
@lonsbio.bsky.social

The almost best thing about this is that Bioinformatics Twitter is back!

Phil Ewels@ewels.bsky.social

Super excited to be launching two things today: #RustQC 🦀🧬 and rewrites.bio 🚀 I used AI to rewrite 15 RNA-seq QC tools into a single Rust binary (I've never written any Rust). It ended up being over 60x faster. Here's the story 🧵 seqeralabs.github.io/RustQC/

seqeralabs.github.ioWelcome to RustQCFast quality control tools for sequencing data, written in Rust.

Dr Andrew Lonsdale reposted

Cancer Bioinformatics Australia
@cancerbioinfoau.bsky.social

🚨Two weeks to get your abstracts in! 🚨 cancerbioinformatics.au/abstracts

cancerbioinformatics.auCBA Abstract SubmissionAbsSS
Cancer Bioinformatics Australia@cancerbioinfoau.bsky.social

📣 Registrations and Abstract submissions are now open for Cancer Bioinformatics Australia 2026! Symposium Info: cancerbioinformatics.au Registrations (closes May 22nd): cancerbioinformatics.au/register Abstract submission (closes March 27th): cancerbioinformatics.au/abstracts

Dr Andrew Lonsdale
@lonsbio.bsky.social

Some background to this, and an example I think of Phil's attitudes towards fostering students and encouraging others. I never got a chance to meet Phil in person, but will share his act of generosity that helped myself and @hdashnow.bsky.social and I think had in indelible mark on our careers. 1/8

Thiago Carvalho@cyrilpedia.bsky.social

'Phil was also the founding Editor-in-Chief of PLOS Computational Biology, where he created the beloved Ten Simple Rules series. He was so prolific in the series that the meta-article “Ten Simple Rules for Writing a PLOS Ten Simple Rules Article” literally includes, as Rule 4: “Be Philip E. Bourne.”

blog.stephenturner.usRemembering Phil BournePersonal reflections on a legendary scientist, leader, builder, and mentor
View full thread
Dr Andrew Lonsdale
@lonsbio.bsky.social

And while it was true at the time that statistically speaking it helped to be PEB to publish a 10SR, I think the mark he has left on the community is that you no longer need to be him. He taught everyone how to do things and the attitude to have. 7/8

Dr Andrew Lonsdale
@lonsbio.bsky.social

Some background to this, and an example I think of Phil's attitudes towards fostering students and encouraging others. I never got a chance to meet Phil in person, but will share his act of generosity that helped myself and @hdashnow.bsky.social and I think had in indelible mark on our careers. 1/8

Thiago Carvalho@cyrilpedia.bsky.social

'Phil was also the founding Editor-in-Chief of PLOS Computational Biology, where he created the beloved Ten Simple Rules series. He was so prolific in the series that the meta-article “Ten Simple Rules for Writing a PLOS Ten Simple Rules Article” literally includes, as Rule 4: “Be Philip E. Bourne.”

blog.stephenturner.usRemembering Phil BournePersonal reflections on a legendary scientist, leader, builder, and mentor
View full thread
Dr Andrew Lonsdale
@lonsbio.bsky.social

- I inject comments about what you have written highlighted in italics - We all review the result and if we agree it gets submitted for consideration by another editor (who may of course reject it)" Phil noted that "not only is the article unorthodox so is the process - I love that!". 5/8

Dr Andrew Lonsdale
@lonsbio.bsky.social

We passed a few drafts back and forth and that was it! I have no doubt that Phil's involvement helped the publication in its journey, but read the article - Phil's commentary elevates that paper. I find those insights invaluable and with no false modesty, they are the best bits of the paper. 6/8

Dr Andrew Lonsdale
@lonsbio.bsky.social

Some background to this, and an example I think of Phil's attitudes towards fostering students and encouraging others. I never got a chance to meet Phil in person, but will share his act of generosity that helped myself and @hdashnow.bsky.social and I think had in indelible mark on our careers. 1/8

Thiago Carvalho@cyrilpedia.bsky.social

'Phil was also the founding Editor-in-Chief of PLOS Computational Biology, where he created the beloved Ten Simple Rules series. He was so prolific in the series that the meta-article “Ten Simple Rules for Writing a PLOS Ten Simple Rules Article” literally includes, as Rule 4: “Be Philip E. Bourne.”

blog.stephenturner.usRemembering Phil BournePersonal reflections on a legendary scientist, leader, builder, and mentor
View full thread
Dr Andrew Lonsdale
@lonsbio.bsky.social

"I cant recall ever laughing out loud at a PLOS submission but now I have. But laughter in a positive way - I agree this is a celebration of the series and I suggest the following. - I become an author (why deny the stats) - I make a few changes to the article and comments for you to consider 4/8

Dr Andrew Lonsdale
@lonsbio.bsky.social

Some background to this, and an example I think of Phil's attitudes towards fostering students and encouraging others. I never got a chance to meet Phil in person, but will share his act of generosity that helped myself and @hdashnow.bsky.social and I think had in indelible mark on our careers. 1/8

Thiago Carvalho@cyrilpedia.bsky.social

'Phil was also the founding Editor-in-Chief of PLOS Computational Biology, where he created the beloved Ten Simple Rules series. He was so prolific in the series that the meta-article “Ten Simple Rules for Writing a PLOS Ten Simple Rules Article” literally includes, as Rule 4: “Be Philip E. Bourne.”

blog.stephenturner.usRemembering Phil BournePersonal reflections on a legendary scientist, leader, builder, and mentor
Dr Andrew Lonsdale
@lonsbio.bsky.social

In 2014 a couple of rag tag PhD students from Melbourne, Australia, submitted a Presubmission Inquiry to PLOS Comp Bio - "Ten Simple Rules for a PLOS Ten Simple Rules". This was unsolicited. We hadn't written a 10SR, had no position of authority on a 10SR to speak from. 2/8

Dr Andrew Lonsdale reposted

Anthony Beckhouse
@antobeck.bsky.social

Join the local Melbourne #illumina Field Apps team to specialise in #Bioinformatics. It's a great team, you get to play with #DRAGEN and help customers get the best data for analysis. #genomics #multiomics #singlecell #spatial #transcriptome #epigenetics bit.ly/46o4sRj I can refer the right folks.

Dr Andrew Lonsdale
@lonsbio.bsky.social

Emotional rollercoaster at #LorneGenome today: - adipose tissue remembers being overweight in the transcriptome, nudging you back to weight gain after a loss - Meerkats reproductive success correlates with higher body mass I’m sure there is a lesson in there somewhere

Dr Andrew Lonsdale reposted

Stephen Turner
@stephenturner.us

Glad to see impact, significance, design as evaluation criteria. I once had a submission rejected from JOSS because my software had too few lines of code (still a little salty about that one). Good move all around 👏 blog.joss.theoj.org/2026/01/prep...

blog.joss.theoj.orgPreparing JOSS for a generative AI future: From code to human creativity and design | Journal of Open Source Software BlogBlog for the Journal of Open Source Software • <a href='https://joss.theoj.org'>https://joss.theoj.org</a>

Dr Andrew Lonsdale reposted

Jimmy Breen
@wessidepraxis.bsky.social

Thanks to the amazing Adelaide Bioinformatics community for making #ABACBS2025 an amazing event. We couldn’t have done it without you. A few more days of workshops to go before the festival finishes for another year 😀

Dr Andrew Lonsdale reposted

Phoebe Carr
@phoebecarr.bsky.social

Loved hearing from Dr. Wytamma Wirth about a deep learning approach to bacterial taxonomic clasification, BABET. The coolest part for me was hearing how tiny the database is! #ABACBS2025 ⚫️🔴 🔵⚪️