iiinova — where your digital self keeps evolving

Reposted by Dr Andrew Lonsdale

Jovana Maksimovic @jovmaksimovic.bsky.social · 31/08/2026

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 🧵

1169

Dr Andrew Lonsdale @lonsbio.bsky.social · 10/07/2026

Prompts are available from the corresponding author upon reasonable request.

053

Reposted by Dr Andrew Lonsdale

Cancer Bioinformatics Australia @cancerbioinfoau.bsky.social · 21/05/2026

🎶 One Day More! 🎶 Poster presentations at Cancer Bioinformatics Australia are still open until tomorrow, Friday, May 22nd. abstracts.cancerbioinformatics.au

static.klipy.com

One Day More

Alt: GIF from Les Miserables, chorus of One Day More

031

Reposted by Dr Andrew Lonsdale

Lorne Genome Conference, Australia @lornegenome.bsky.social · 30/04/2026

Lorne Genome 2027 will be held 14 to 17th February in Lorne Australia. Our invited speakers will include Karen Arndt, Neil Brockdorff, Laura Banaszynski and Fides Zenk.

Lorne Genome 2027 Poster: 14 to 17th February, at Lorne Australia. Background shows the coast off Lorne. Invited speakers include Karen Arndt, Neil Brockdorff, Laura Banaszynski and Fides Zenk.

0107

Dr Andrew Lonsdale @lonsbio.bsky.social · 14/04/2026

With the heavy discounting on the first year of .bio domains right now, how can we not? It is decidedly not well-considered, but I will accept debate only in the form of a pull request compbiovs.bio

compbiovs.bio

computational biology vs bioinformatics

274

Dr Andrew Lonsdale @lonsbio.bsky.social · 12/04/2026

That took longer than I thought to put into words! I'll end by saying that the more I think in this, the less sure I am, but wonder if replacing "rewrite" with "fork of original code" helps in thinking about what to do - and what not to.

100

Dr Andrew Lonsdale @lonsbio.bsky.social · 12/04/2026

If an LLM can help add a new functionality in the rewrite language, it could probably do the same for the original language, and it might be nice to submit a PR to the original open source repo to maintain parity.

100

Dr Andrew Lonsdale @lonsbio.bsky.social · 12/04/2026

For the preprint threshold question, I guess my main query is what to do with novel contributions - a 5.6 or an extension to 5.5 "Contribute upstream responsibly" in the manifesto. Should (and will) extensions to the original make it upstream? and is this one criteria to meet for a preprint?

100

Dr Andrew Lonsdale @lonsbio.bsky.social · 12/04/2026

The recent JOSS update on what needs to be done to reach their publication benchmark was interesting I thought, blog.joss.theoj.org/2026/01/prep... and I really appreciate rewrites.bio for starting this conversation as well.

blog.joss.theoj.org

Preparing JOSS for a generative AI future: From code to human creativity and design | Journal of Open Source Software Blog

Blog for the Journal of Open Source Software • <a href='https://joss.theoj.org'>https://joss.theoj.org</a>

100

Dr Andrew Lonsdale @lonsbio.bsky.social · 12/04/2026

I totally agree there needs to be space for the careful human-driven rewrite, but worry along the lines of @katholt.bsky.social that there will be flood of inhuman ones that drown them out. The journal level will be important to filter genuine contributions, but preprints are a different beast.

100

Dr Andrew Lonsdale @lonsbio.bsky.social · 12/04/2026

Sorry, I guess that is what I meant - is there line for a rewrite to get to, to justify a preprint? I don't have any answers, and it gets murkier if it is a rewrite+, with the + being some new (and hopefully non-trivial) features that maintain backwards compatibility.

100

Dr Andrew Lonsdale @lonsbio.bsky.social · 11/04/2026

One thing I keep asking myself is where preprints of the rewrites sit. Easier to produce and get out there, and how they'll sit in the ecosystem?

100

Dr Andrew Lonsdale @lonsbio.bsky.social · 11/04/2026

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

Sickos meme, with "rewrites.bio flamewars" caption

1153

Dr Andrew Lonsdale @lonsbio.bsky.social · 14/03/2026

Irrespective of the validity of any of the arguments in this announcement (posit.co/blog/introdu...), this is how it *feels*

"Introducing AI in RStudio" on top of the You Were The Chosen One meme from Star Wars

110

Reposted by Dr Andrew Lonsdale

Cancer Bioinformatics Australia @cancerbioinfoau.bsky.social · 13/03/2026

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

cancerbioinformatics.au

CBA Abstract Submission

AbsSS

011

Reposted by Dr Andrew Lonsdale

Stephen Turner @stephenturner.us · 09/03/2026

Remembering Phil Bourne. Personal reflections on a legendary scientist, leader, builder, and mentor. blog.stephenturner.us/p/rememberin...

blog.stephenturner.us

Remembering Phil Bourne

Personal reflections on a legendary scientist, leader, builder, and mentor

83521

Dr Andrew Lonsdale @lonsbio.bsky.social · 10/03/2026

The community was enriched for his legacy, and is lessened by his passing. Vale Phil. 8/8

030

Dr Andrew Lonsdale @lonsbio.bsky.social · 10/03/2026

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

150

Dr Andrew Lonsdale @lonsbio.bsky.social · 10/03/2026

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

120

Dr Andrew Lonsdale @lonsbio.bsky.social · 10/03/2026

- 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

120

Dr Andrew Lonsdale @lonsbio.bsky.social · 10/03/2026

"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

120

Dr Andrew Lonsdale @lonsbio.bsky.social · 10/03/2026

We'd just read a lot of them in our journal club. It could have very easily been desk rejected and not ever seen the light of day. Instead, it was received in the best way. Phil's email response to our inquiry directly aligns with the opening line of the paper: journals.plos.org/ploscompbiol... 3/8

journals.plos.org

Ten Simple Rules for Writing a PLOS Ten Simple Rules Article

130

Dr Andrew Lonsdale @lonsbio.bsky.social · 10/03/2026

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

120

Dr Andrew Lonsdale @lonsbio.bsky.social · 10/03/2026

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

1127

Reposted by Dr Andrew Lonsdale

Peter MacCallum Cancer Centre @petermaccc.bsky.social · 24/02/2026

We’re proud to celebrate Dr Aparna Rao, Dr Deborah Meyran and Associate Professor Safeera Hussainy, who have been awarded the 2026 Lea Medals. Read more: www.petermac.org/about-us/new...

092

Reposted by Dr Andrew Lonsdale

Anthony Beckhouse @antobeck.bsky.social · 23/02/2026

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.

043

Reposted by Dr Andrew Lonsdale

Lorne Genome Conference, Australia @lornegenome.bsky.social · 18/02/2026

2026 Winner of the Lorne Genome Julian Wells Medal: Christine Wells (no relation!) @stemcellsystems.bsky.social congratulations, well deserved!!

1135

Dr Andrew Lonsdale @lonsbio.bsky.social · 17/02/2026

Almost literally too late, but here is a feed for BlueSky to collate #LorneGenome posts that blends mentions of Lorne + Genome along with posts from @lornegenome.bsky.social Should still work next year though! bsky.app/profile/did:...

141

Dr Andrew Lonsdale @lonsbio.bsky.social · 17/02/2026

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

060

Dr Andrew Lonsdale @lonsbio.bsky.social · 17/02/2026

Can only tag @antobeck.bsky.social here on BlueSky to say that the #Illumina coffee cart is once again the quiet hero of #LorneGenome

141

Reposted by Dr Andrew Lonsdale

EMBL-EBI @ebi.embl.org · 10/02/2026

We’re hiring: Research Group Leader in computational biology. Are you generating more research ideas than you can explore? Lead cutting-edge AI & biology research at EMBL-EBI. Apply by 11 April 2026: embl.wd103.myworkdayjobs.com/en-US/EMBL/j... #ScienceCareers @ewaldlab.org @embl.org

03950

Dr Andrew Lonsdale @lonsbio.bsky.social · 19/01/2026

My probably wrong 2c is that I once spent a long time in a similar situation to learn that .yaml and .yml were treated very differently by the program I was using, and to check the filenames or extensions between working and non-working aren't the issue in some weird way

000

Dr Andrew Lonsdale @lonsbio.bsky.social · 19/01/2026

Sounds like a version of "Spot It!"? math.mit.edu/research/hig...

math.mit.edu

120

Reposted by Dr Andrew Lonsdale

nf-core @nf-co.re · 14/01/2026

New blog post! nf-core and AI nf-co.re/blog/2026/statement-on-ai

042

Reposted by Dr Andrew Lonsdale

Stephen Turner @stephenturner.us · 11/01/2026

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.org

Preparing JOSS for a generative AI future: From code to human creativity and design | Journal of Open Source Software Blog

Blog for the Journal of Open Source Software • <a href='https://joss.theoj.org'>https://joss.theoj.org</a>

053

Dr Andrew Lonsdale @lonsbio.bsky.social · 18/12/2025

Every guide to GenAI in research ends up being: And now that you know how it's done……. Don't do it.

010

Reposted by Dr Andrew Lonsdale

Cancer Bioinformatics Australia @cancerbioinfoau.bsky.social · 18/12/2025

📣 Save The Date for Cancer Bioinformatics Australia 2026! 📣 CBA will be back in 2026 on June 5th, this time in Brisbane! It will feature oral and poster presentations, networking opportunities, and high-profile invited national and international speakers. Further info: cancerbioinformatics.au

Flyer with a picture of Brisbane detailing CBA 2026.

013

Reposted by Dr Andrew Lonsdale

Feargal Ryan @feargalr.bsky.social · 28/11/2025

That’s a wrap! Huge thank you to everyone who joined us for #ABACBS2025 & a big shout-out to the Adelaide bioinfo community who worked their butts off. Couldn’t have asked for a better crew or a better venue than Adelaide Oval. @wessidepraxis.bsky.social @linsalrob.bsky.social

0239

Dr Andrew Lonsdale @lonsbio.bsky.social · 28/11/2025

I enjoyed making this with you all much more than this photo would imply - I did not know we were linking arms! #wasmodic #abacbs2025

190

Reposted by Dr Andrew Lonsdale

Jovana Maksimovic @jovmaksimovic.bsky.social · 26/11/2025

It's not just because @torstenseemann.bsky.social is a bioinformatics legend but this may be my favourite #abacbs2025 poster because I'm a #trek tragic 🖖

03810

Reposted by Dr Andrew Lonsdale

Jimmy Breen @wessidepraxis.bsky.social · 26/11/2025

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 😀

1307

Reposted by Dr Andrew Lonsdale

Alicia Oshlack @aliciao.bsky.social · 25/11/2025

Awesome talk by @jovmaksimovic.bsky.social one detecting fusions in single cells with probes designed for 10X Flex. If I do say so myself 😜 #ABACBS2025

1203

Dr Andrew Lonsdale @lonsbio.bsky.social · 26/11/2025

Haha Thanks! Putting the “Ted Lasso of Australian Bioinformatics” on my speaker bio!

060

Dr Andrew Lonsdale @lonsbio.bsky.social · 26/11/2025

I wasn’t going to single you out in my speech @hdashnow.bsky.social but our @combine1.bsky.social shenanigans are a big part of my success!

040