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.

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!

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...

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.

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🧵

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...

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-...

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...

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

𝗖𝗮𝗻 𝘄𝗲 𝗽𝗿𝗲𝗱𝗶𝗰𝘁 𝗲𝘃𝗼𝗹𝘂𝘁𝗶𝗼𝗻? Some aspects are well predicted, others are extremely difficult. doi.org/10.1038/s415...

Really great review from @wcratcliff.bsky.social and @jameststroud.bsky.social Long-term studies provide unique insights into #evolution - a really great read witj some great examples from across biology - including all my favourite systems www.nature.com/articles/s41...

Human microbiome acquisition and transmission www.nature.com/articles/s41... #jcampubs

Day 3 of #TheCOINS with an amazing keynote Kees Moeliker, an Ig Nobel Prize winner. Ig Nobel is awarded to discoveries that make people laugh and then think. Picture shows the detailed notes of an observation of homosexual duck necrophilia case.

Second day of #TheCOINS conference with a fascinating talk by Kirsten Bos on ancient DNA and how it can be used to understand how #diseases evolved and #spread throughout the world. Interestingly, some of the key samples for these analyses are actually from (~15 century) grave sites in Vilnius.

The COINS conference is kicking off with very strong and inspiring talks by @marienordstrom.bsky.social about ecology and food webs and @kellykrause.bsky.social about scientific visualizations

Good news on this 35th anniversary of the #Restoration of #Independence in #Lithuania! A new ERC project from a Lithuanian researcher can now go ahead, as they were able to secure alternative EU funding for her ERC Consolidator Grant. How did this happen? Find out in the thread 🧵👇

🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again! forms.gle/YJP6WQjsk8KK...

RNA xkcd.com/3056

I'm looking for multi-omics articles that wouldn't be behind the paywall and would have public raw data so the students could redo the analyses during my course. The amount of articles in which it is falsely stated that all the data is public (even with database IDs) is absolutely mindblowing.

In this study, 18 940 clinical isolates from 7 760 patients were WGSed. >27% of the patients are suspected for between-patient transmission of bacterial isolates. Almost 70% had direct or indirect epidemiological links. 1/3

This interesting work identifies globally prevalent A. muciniphila variants with specific mutations following penicillin exposure, which show in vivo reduced capacity to mitigate diet-induced obesity in C57BL/6N mice compared to WT strain. 🔗 microbiomejournal.biomedcentral.com/articles/10....

Out now, a comprehensive guide to metagenomics -- from sample collection to data analysis. This primer covers best practices, challenges, and applications in health, agriculture & environment. A roadmap for studying microbial communities 👇 www.nature.com/articles/s43...

www.science.org/content/arti... We'll see more and more stories like this in the future. And it's just a matter of time when it spreads to other countries as bacteria doesn't really accept borders.

🚨 🌟 Submissions & Registrations Open for #ViBioM2025! 🌟 🚨 Join us 13–15 May 2025 in Lisbon, Portugal! 🦠💻 Present your research, connect with global experts, and shape the future of #Virology & #Bioinformatics. 📅 Details & links: evbc.uni-jena.de/events/vibio...

Stoked about this manuscript, many years in the making. We present an original resource of ~700 highly curated plastid MAGs of marine pelagic algae. Among these we found a novel deep branching group of plastid genomes; we informally call them leptophytes www.biorxiv.org/content/10.1...

Excellent† blog post by Andrew Gelman: 7 steps to junk science that can achieve worldly success statmodeling.stat.columbia.edu/2025/01/17/7... † Disclosure: Mentions me.

Evolution of antibiotic resistance #AMR can lead to collateral resistance/sensitivity to other drugs; @jeffmaltas.bsky.social &co show that these effects can fluctuate over time, needing precise timing & stochastic control models to optimize treatment strategies 🧪 @plosbiology.org plos.io/3C2Ao1y

"it’s impossible to separate viruses into species, a clumsy attempt to impose human categories on a viral world that's pure blur" Many arguments over definitions in biology where we must remember what's debated is just a human concept not some fundamental thing www.statnews.com/2025/01/09/v...

I was invited to a podcast to discuss the most important life sciences achievements in #2024. Here is my shortlist (obviously, it's highly influenced by my research interests): 5. New antibiotics targeting LPS: www.nature.com/articles/s41... 4. AlphaFold3: www.nature.com/articles/s41... 1/2

🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips. 🏔️ logan-search.org 🏔️ #Genomics #Bioinformatics #OpenScience

Science takes time - a lot of time. Time that is more and more difficult to make available because of increased workloads. Time that exceeds the temporary contracts of postdocs and PhDs. I'll illustrate this using our paper published in Nature yesterday. 🧵 (1/x) www.nature.com/articles/s41...