Aren't we all just having AI rewrite the original perl implementations in rust these days?

Unfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism Study The myth of open data, reproducibility, responsibility, and accountability in science, and your role in it

How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism:

merenlab.org/2026/04/15/u...

The correct link: lh3.github.io/2026/04/17/t...

Requested change: Please reduce the scope to match the normal level of free time.
Review: Impressive commitment to a bit nobody asked to be taken this far.
Comment: Implementation exceeds expected effort in ways that raise questions about available bandwidth.

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

Excited to share our new paper out today in @science.org 🎉

We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩

Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/
#microsky #phagesky
www.science.org/doi/10.1126/...

The awesome virome logo of a phage above a strand of DNA

Have you developed a new #bioinformatics tool to understand #phage or #virus? Make sure you add it to #awesome-virome

github.com/shandley/awe...

Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here

📣Huge preprint 🔔
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.

www.biorxiv.org/content/10.6...

There is so much to explore in this data that one can spend life time going through. To make it easier to go through the data, @miloj.bsky.social
put together this beautiful “Phage Datasheet”🤩

iseq.lbl.gov/PhageDataShe...

Postdoctoral Associate - Blacksburg, Virginia, United States Job Description A full-time postdoctoral researcher position is available in the Scharf lab in the Department of Biological Sciences at Virginia Tech to study motility and chemotaxis in the symbioti...

Pls share: A postdoctoral researcher position is available in the Scharf lab in the Department of Biological Sciences at Virginia Tech to study motility and chemotaxis in the symbiotic soil bacterium Sinorhizobium meliloti.

jobs.apply.vt.edu/jobs/postdoc...

Our perspective on measuring individual virus traits, led by staff scientist @antanij.bsky.social
#phagesky #microsky

Want to annotate a bacterial genome with structures?

@oschwengers.bsky.social bakta and @gbouras13.bsky.social phold got together, and the result is Baktfold: protein annotation across the microbial tree of life using structures

www.biorxiv.org/content/10.6...

#phagesky #microsky #microbiomesky

Stop Reducing Us into Simplistic Numbers: An Academic Outcry!

Please reject simplistic metrics and evaluate academics with nuance, integrity, and real impact!

stnjournal.com/stop-reducin...

So good to hang out with @lucyleef.bsky.social and @laurabonofiglio.bsky.social in Perth

Taking over the @abacbs.bsky.social Meetup to talk #phage

The pre-print for Slorado and openfish is out. biorxiv.org/content/10.6...

You can do @nanoporetech.com basecalling with not just NVIDIA GPU, but also using a range of AMD GPU.

Would be useful since popular GPUs are now 💸💸💸💸(& hard to buy),

Work by @bonson-wong.bsky.social

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social

Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.

rdcu.be/famFj

Microbial Ecological Signatures Predict Pathogen Emergence and Multidrug Resistance in Cystic Fibrosis Airways up to a Year in Advance Chronic infections in cystic fibrosis (CF) emerge from gradual ecological transitions in the airway microbiome, yet early predictive markers remain poorly defined. We developed a new autoencoder-based...

Check out our preprint on airway microbiome CF

www.medrxiv.org/content/10.6...

Q: Can we predict clinical outcomes before the clinic?
A: Yes!

🦠 Microbiome predicts Pseudomonas colonisation & AMR early
🦠 Resistance mechanisms mirror those seen in lab!

#Microbiome #CysticFibrosis #Metagenomics

Hello, Bluesky.

We fund research that helps shape Australia’s future.

Follow us for updates on funding, research and outcomes.

AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions
📄 research.nvidia.com/labs/dbr/ass...
🌐 alphafold.ebi.ac.uk

Check out some of the great work by @cynthiasilveira.bsky.social e.g. looking at Hi-C in marine environments pubmed.ncbi.nlm.nih.gov/39657233/

In our latest work, we characterise the Tmn defence system. We reveal plasmolysis as a new way to block phage infection, dramatically reducing secondary infections.

I've been using FigTree for ~18 years. Very excited for this new iteration of the best phylogenetic visualisation tool there is.

A virus hiding inside bacteria may help explain colorectal cancer Scientists found an unexpected viral hitchhiker lurking inside a common gut bacterium – and it was twice as prevalent in people with colorectal cancer.

Really enjoyed writing a piece for @uk.theconversation.com - trying to write for a general audience, you suddenly realise how much jargon is deeply embedded in your brain #Phages #Microbiome #SciComm

theconversation.com/a-virus-hidi...

Hey #Microsky, time to celebrate your amazing female colleagues, students and mentors for #IWD2026! Nominate an inspiring woman whose research, teaching, innovation, or community leadership deserves recognition! @femsmicro.org crm.fems-microbiology.org/ssp/internat...

In case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! 🚨

Let me hit you with some highlights on why spatial structure matters. (and why you should care!)

Sharing is appreciated 🙏 🧵👇

doi.org/10.1093/fems...

Deciphering the etiology of the 2024 outbreak of undiagnosed febrile illness in Panzi, Democratic Republic of the Congo - Nature Medicine This multidisciplinary response to investigate the large outbreak of unknown febrile illness in the Panzi Health Zone in the Democratic Republic of the Congo in late 2024 suggests that the outbreak wa...

What happened during a febrile illness outbreak in Panzi, Democratic Republic of the Congo?

Was it something new or something we knew?

Check out the amazing collaboration (inc. @pathogenomenick.bsky.social & @arambaut.bsky.social ) that came together:

www.nature.com/articles/s41...

The @isvm-society.bsky.social is organising monthly #virus of #microbes (including #phage). Nominate a speaker and register for the upcoming events at isvm.org/ivom/

Binning genomes from metagenomes? Try @vijinim.bsky.social new graph visualisation tool to understand where your bins go bad!

metagentools.github.io/graphbin-vis...

#Lithium doesn’t act directly on the brain. Instead, it signals via the gut–brain axis, acts on EC cells, engages TRPM2 and vagal pathways. Our team found a mechanism with major implications for #psychiatry and #bipolar disorder

@flindersuniversity.bsky.social

www.biorxiv.org/content/10.6...

Registration form for iVoM4 After submitting this form, you will receive the instructions to join our webinars at the email address you provide.

New 2026 iVoM series coming up!

Each session includes SCR and 3 ECRs, & plenty of opportunities to interact with the speakers and ask questions.

Sign up for links/updates: docs.google.com/forms/d/1hAB...

First up: Viral Biotechnologies Wed, 28 th January at 17:00 CET / 11:00 EST / 08:00 PST