3 days full of evolution, divergent orthomyxos/chuviruses and mosquitoes - thank you @evogytis.bsky.social for an invite to Puvociai retreat & discussions with his team & polycipi-ally Serafín Gutiérrez! ☀️ eclipse + meteorite showers 🌠 - perfect for late-night scientific (and life) talks.

A mandatory “I attended a conference where I presented my super cool research” post. Overall, European Cystic Fibrosis Conference was a unique experience because clinicians, industry representatives, researchers, and people with #CF all met in one space.

François Blanquart et al. dive into the genetic basis of HIV virulence with very cool statistical methods. They show that viral load is shaped by host-dependent HLA escape variants with large effects, alongside many additional variants whose effects are too subtle to reach genome-wide significance.

The genetic architecture of HIV-1 virulence

Abstract. The virulence of HIV-1 is partly determined by viral genetic variation. Finding individual genetic variants affecting virulence is important for

academic.oup.com

Unbelievable, Bakta reached its 1,000th citation! A huge shout out and thank you to all Bakta users, bug reporters, those sharing ideas and suggesting features... ...just the entire incredibly supporting binfie community! Without you, Bakta wouldn't be the same. Thank you!

Dr. Jane Goodall filmed an interview with Netflix in March 2025 that she understood would only be released after her death.

Very interesting!

EMBL-EBI@ebi.embl.org · 11mo ago

Antimicrobial resistance (AMR) causes over a million deaths each year, and is rising. Scientists analysed 40,000 bacterial plasmids across 100 years and six continents, to reveal that a few plasmids evolved after antibiotic use to drive most multi-drug resistance. www.ebi.ac.uk/about/news/r... 🧬💻

Even though talks at a conference are always cool, the most exciting part of #EYSF2025 is the @nightsciencepod.bsky.social workshop by @itaiyanai.bsky.social and @martinlercher.bsky.social . They are a great resource for scientific creativity and they even have a podcast!

Next, at #EYSF2025 @reviewcommons.org is presented by @saramonaco-rc.bsky.social. It’s journal-agnostic, concentrates on science only and can save time as the peer-reviewed preprints can easily be resubmitted. How great would it be if we could ditch publishing and switch to reviewed preprints?

Continuing #EYSF2025 on CRISPR-Cas, Stephan Rieserberg is presenting how they developed cool tools to efficiently break complicated dsDNA targets and where conventional methods barely work. Also, there are cool CRISPR-Cas based methods to get rid of everything where initial DNA editing didn’t work.

As the conference season continues, it’s time for EMBO Young Scientists’ Forum in Vilnius. The day starts with a talk by Prof. Virginijus Šikšnys about bacteria antiviral defense systems, and how his lab was among the first to show that Cas9 can be used for programmable DNA cleavage. #EYSF2025

I can't believe that only now I found out about BakRep by @oschwengers.bsky.social. There you can search and interactively explore all the genomes from AllTheBacteria that includes >2.4 million genomes assembled by @zaminiqbal.bsky.social group.

Now that #IMMEMXIV has ended, I can say that it was one of the best conferences I have ever attended. Fantastic and diverse (!) speakers, incredibly good posters, good food and enough wine to make the experience truly unforgettable. Happy to have met so many inspiring scientists!

Third day of #IMMEMXIV starts with a session on environmental surveillance and its importance for infectious diseases and AMR control. Before starting the day, together with the shark I got to explore truly stunning Porto.

Matthijs S. Berends continues #IMMEMXIV bioinformatics session with the presentation of AMRgen that combines genotype and phenotype data and interpretation. It definitely should save hours of manual labor (at least for bacteria with known resistance mechanisms).

The most anticipated session at #IMMEMXIV is, of course, about bioinformatics. It starts with presentation of the hackathon that took place prior to the conference. All the code is on GitHub (link in the pictures).

Continuing #IMMEMXIV with Benjamin Howden and genomic surveillance and how it can help control and prevent outbreaks and make informed decisions. However, for it to work we need to ensure that not only the infrastructure is there but also that the insights can be used for decision making.

Not so related to #immemxiv but I am still unsure how I feel about Delphi-2M even though the authors try to make the model explainable. Also, I’m curious how the model performs in real life situations, not only in high income countries and mostly white people. www.nature.com/articles/s41...

Which diseases will you have in 20 years? This AI accurately predicts your risks

A modified large language model called Delphi-2M analyses a person’s medical records and lifestyle to provide risk estimates for more than 1,000 diseases.

nature.com

Taxonomy matters and if we call the same strain different names in different countries, we quickly run into problems not knowing what’s happening around us. @sylvainbrisse.bsky.social is defining the main requirements and offers a solution using cgMLST and LIN codes.

The second day of #immemxiv in Porto starts with GTDB taxonomy by Maria Chuvochina. NCBI often lacks species assignments and, from my personal experience, can be incorrect often than expected. Also, ~2% of all species are fuzzy/hard to discriminate by ANI.

Last week we had a 3-day lab retreat at Vilnius University's base in Puvočiai with Lander de Coninck & @ingrida.bsky.social joining us as visitors. These retreats keep getting better & more productive thanks to the students & especially fellow PI @mgabrielaite.bsky.social. I'm super proud!

Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports... PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.

Intraspecies associations from strain-rich metagenome samples

Qu et al. present PHLAME, a method to analyze strain composition in metagenomic samples where many strains of the same species coexist. Using PHLAME, they show relationships between strain abundances ...

cell.com

Evan Qu@quevan.bsky.social · 2y ago

Excited to share my preprint describing a new microbiome analysis method, PHLAME, for detecting strain-level associations in difficult sample types. 🧵 www.biorxiv.org/content/10.1... This work was done with my great coauthors and my amazing advisor @contaminatedsci.bsky.social

nf-core/proteinfamilies: A scalable [Nextflow] pipeline for the generation of protein families www.biorxiv.org/content/10.1... 🧬🖥️🧪 Code (MIT): github.com/nf-core/prot... Docs/launch: nf-co.re/proteinfamil...

Authors publish an article with some isolates with wrong species. I reach out to them to point that out. They publish yet another preprint with the same wrong species and some crazy findings because of that. What else can I do besides contacting them again?

This is quite late but our lab has a preprint out about a SARS-CoV-2 situation we had in mink in Lithuania back in 2021. It's a doozy with re-emergence of extinct lineages, a country-wide test of all mink farms in Lithuania & some interesting dynamics in mink. www.medrxiv.org/content/10.1... 1/5🧵

medRxivpreprint@medrxivpreprint.bsky.social · last yr.

Anthropozoonotic spillovers reveal sustained long-term cryptic circulation of SARS-CoV-2 within and between Lithuanian mink farms https://www.medrxiv.org/content/10.1101/2025.07.15.25331253v1

Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...

Intraspecies warfare restricts strain coexistence in human skin microbiomes - Nature Microbiology

About 15,000 pairwise interactions within S. epidermidis from 18 people in 6 families reveal the antagonism and molecular trade-offs that shape the skin microbiota.

nature.com

Chris Mancuso@mancusosci.bsky.social · 2y ago

Why don’t people who live together have the same strains of microbes? Tami Lieberman (@contaminatedsci.bsky.social) and I put forward one underexplored reason in our new preprint: Intraspecies warfare restricts strain coexistence in human skin microbiomes

The new version of MetaPhlAn v4.2.2 released! 📌taxonomic profiling of long-read metagenomes for the first time 📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs Try it out & @hutlab.bsky.social and we are looking forward to your feedback! forum.biobakery.org/t/metaphlan-...

MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update)

Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhl...

forum.biobakery.org

1. When did AI become so good with figures and text?! 2. I am really looking for a PhD student (deadline in June)

I spent a week in Georgia 🇬🇪 talking about genomic epidemiology: from the very basics to case studies and false information as a part of the EU funded TWINNING project. It was a week full of beautiful Tbilisi 🏔, incredible food 🥘 and insightful discussions about the power of genomic epidemiology 🧬.

There are so many situations when using #LLM and #AI is just wrong. However, there are also ways to use it in everyday life to help save the time and make our lives a bit easier. Here is the ultimate guide to AI for research: www.nature.com/articles/d41...

AI for research: the ultimate guide to choosing the right tool

Curious about using artificial intelligence to boost your research? Here are the programs you shouldn’t miss.

nature.com

Ecology, global diversity and evolutionary mechanisms in the #Mycobacterium tuberculosis complex rdcu.be/ee47G

Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex - Nature Reviews Microbiology

In this Review, Gagneux and colleagues discuss ecological and evolutionary concepts related to the biology and epidemiology of the Mycobacterium tuberculosis complex, including new phylogenetic lineag...

nature.com