@themaklin.bsky.social
I do statistics, bacterial (meta)genomics and bioinformatics software development. Researcher @ University of Oslo
Strain displacement in microbiomes via ecological competition
Cool @natmicrobiol.nature.com publication by @erikbakkeren.bsky.social
@vit-pi.bsky.social @meganleeny.bsky.social @microscape.bsky.social & Kevin Foster
www.nature.com/articles/s41...
If you're interested in using pangenome graphs for comparative genomics, check out my webinar, part of EMBL-EBI's "Concepts, methods, and resources in pangenomics" series, available on-demand: www.ebi.ac.uk/training/eve...
06.11.2025 11:40 — 👍 16 🔁 11 💬 1 📌 0
E. coli can spread as quickly as swine flu, new research reveals. 🦠
For the first time, scientists can predict the rate at which gut bacteria pass between people — a major step towards tackling antibiotic-resistant infections.
Read here ⤵️
sanger.ac.uk/news_item/ad...
This. Also: We’ve no idea how much groundbreaking research we might actually be missing out on when core research doesn’t have the opportunity to gradually unfold, take place without being tailored to surface claims about high impact and fantastic deliverables.
05.11.2025 06:45 — 👍 29 🔁 7 💬 1 📌 0
So happy to share this! Bacteriocins were first discovered over 100 years ago, but what do they actually do? We look at >1000 bacteriocin plasmids and find links to virulence and antimicrobial resistance, and frequent bacteriocin sharing in Enterobacteriaceae.
www.nature.com/articles/s41...
The amount of AI generated art in slides at this conference, primarily used by older scientists, is killing me. Scientists please. Don’t use these ai platforms to make your figures or slides. They look bad and I have yet to see them meaningfully improve the message of talks.
31.10.2025 03:09 — 👍 1775 🔁 362 💬 39 📌 31🔊 Applications for the tenure-track illuminate global challenge fellowships at Queen’s are now open!
Comes with 5 years protected research time, a PhD studentship, & 60k start-up. I had one of these before getting my FLF, happy to chat to anyone interested!
www.qub.ac.uk/Research/fel...
22-Oct 2022 headline from The Economist A new paper claims SARS-CoV-2 bears signs of genetic engineering But it has yet to be peer reviewed. And others strongly disagree
🧵Remember the preprint claiming SARS-CoV-2 has a "synthetic fingerprint"?
It said a restriction map was "extremely unlikely to have arisen by random evolution.”
I took its claims seriously.
The "synthetic fingerprint" hypothesis collapses. My new preprint explains why.
arxiv.org/abs/2510.23833
Looks like OpenFold3 has been formally released in a public "preview". Not quite on parity with AlphaFold3 on a few benchmarks shown, in particular for antibody interactions. All info on the github link. I am sure we will hear more about this from the developers github.com/aqlaboratory...
28.10.2025 09:30 — 👍 50 🔁 20 💬 2 📌 0
1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...
21.10.2025 20:00 — 👍 44 🔁 24 💬 1 📌 2
This particular figure was quite striking - physical microscopy of the E. coli genome. Somehow we run these tangles mess through pores (often not breaking them over significant distances) and render them into reliable representation of whole genomic compartments.
🧫🦠
taas ajankohtanen vasemmisto.fi/liity-jasene...
14.10.2025 09:48 — 👍 6 🔁 0 💬 0 📌 0
Cover of The Lancet, Oct 11 issue. The quote, "Melioidosis is a disease so neglected it is not on WHO's list of Neglected Tropical Diseases."
Melioidosis—it's a fatal but preventable infection. Why is it not classed as a Neglected Tropical Disease (NTD)? Sophie Cousins reports in The Lancet.
Read in the latest issue 👉 tinyurl.com/zz65vbup
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
Our new systematic review is now out! Briefly, temporal multi-omic data and analyses are crucially needed to improve our understanding of microbiomes. Also, often the omics layers are not analyzed in an integrative way, even while such methods exist.
academic.oup.com/bib/article/...
New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers.
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
Obsessed with this Journal of Immaterial Science article 🔥
08.10.2025 08:56 — 👍 65 🔁 11 💬 3 📌 4
New preprint!
Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠
Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!
An epic effort by Rosanna Wright
www.biorxiv.org/content/10.1...
Professor (full) or Associate Professor (tenure track) in Microbial Genetics of Health (U. Turku Finland). Competitive starting package included! Please share.
duunitori.fi/tyopaikat/ty...
A new ggCaller version is out! v1.4 includes tweaks to improve efficiency, outputs Panaroo-friendly GFFs, and enables iterative gene calling; if you have already called a gene set, you can now add more genomes either one by one or in batches github.com/bacpop/ggCal...
24.09.2025 13:27 — 👍 11 🔁 7 💬 1 📌 0Now peer-reviewed, improved and published in @microbiologysociety.org Microbiology - thanks to editor and reviewers!
www.microbiologyresearch.org/content/jour...
"Suomen Akatemia varoittaa yliopistoja perussuomalaisista
Yliopistoihin lähetetyssä ”varautumisviestissä” annetaan ohjeistusta häirinnän, maalittamisen ja mustamaalauksen kohteeksi joutuneille tutkijoille."
www.is.fi/kotimaa/art-...
Thrilled to share this preprint on Klebsiella pneumoniae plasmids in a One Health setting 🦠 Fantastic work by @twinkler.bsky.social! 🎉 @irenlohr.bsky.social @margaretlam.bsky.social
16.09.2025 09:40 — 👍 16 🔁 10 💬 0 📌 0Don't tell them about fastq
15.09.2025 15:05 — 👍 3 🔁 0 💬 0 📌 0
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Phenotypic heterogeneity of capsule production across opportunistic pathogens | mBio
#microsky #phage #phagesky
journals.asm.org/doi/10.1128/...
Powerful, typically eloquent, and deeply troubling editorial from @berndpulverer.bsky.social ( @embopress.org ) on the ongoing attacks on #academics and #academia itself in the USA. 👇
www.embopress.org/doi/full/10....
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Sequence data from the new Ebola outbreak in DRC suggests it is indeed a new spillover.
And just incredible to see the virus sequenced and the data publicly shared less than 24 hours after confirmation of the outbreak.
#IDsky 🧪
virological.org/t/the-16th-e...
