iiinova — where your digital self keeps evolving

Reposted by Migle Gabrielaite

Ingrida Olendraite @ingrida.bsky.social · 28/08/2026

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.

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Migle Gabrielaite @mgabrielaite.bsky.social · 09/06/2026

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.

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Migle Gabrielaite @mgabrielaite.bsky.social · 08/12/2025

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.

academic.oup.com

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

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Oliver Schwengers @oschwengers.bsky.social · 06/10/2025

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!

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KOJAMF🤘🖤🤘 @kojamf.bsky.social · 05/10/2025

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

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Samuel Lampa @smllmp.bsky.social · 26/09/2025

Very interesting!

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Migle Gabrielaite @mgabrielaite.bsky.social · 25/09/2025

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!

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Migle Gabrielaite @mgabrielaite.bsky.social · 24/09/2025

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?

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Migle Gabrielaite @mgabrielaite.bsky.social · 24/09/2025

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.

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Migle Gabrielaite @mgabrielaite.bsky.social · 24/09/2025

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

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Migle Gabrielaite @mgabrielaite.bsky.social · 22/09/2025

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.

bakrep.computational.bio

BakRep

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Migle Gabrielaite @mgabrielaite.bsky.social · 20/09/2025

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!

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Migle Gabrielaite @mgabrielaite.bsky.social · 19/09/2025

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.

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Migle Gabrielaite @mgabrielaite.bsky.social · 18/09/2025

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).

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Migle Gabrielaite @mgabrielaite.bsky.social · 18/09/2025

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).

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Migle Gabrielaite @mgabrielaite.bsky.social · 18/09/2025

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.

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Migle Gabrielaite @mgabrielaite.bsky.social · 18/09/2025

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...

nature.com

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.

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Migle Gabrielaite @mgabrielaite.bsky.social · 18/09/2025

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.

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Migle Gabrielaite @mgabrielaite.bsky.social · 18/09/2025

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.

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Gytis Dudas @evogytis.bsky.social · 28/08/2025

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!

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Reposted by Migle Gabrielaite

Tami Lieberman @contaminatedsci.bsky.social · 15/08/2025

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.

cell.com

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 ...

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Reposted by Migle Gabrielaite

Stephen Turner @stephenturner.us · 17/08/2025

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...

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Migle Gabrielaite @mgabrielaite.bsky.social · 07/08/2025

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?

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Reposted by Migle Gabrielaite

Gytis Dudas @evogytis.bsky.social · 17/07/2025

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🧵

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Segata Lab @cibiocm.bsky.social · 11/06/2025

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-...

forum.biobakery.org

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...

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Migle Gabrielaite @mgabrielaite.bsky.social · 15/04/2025

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

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Migle Gabrielaite @mgabrielaite.bsky.social · 14/04/2025

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 🧬.

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Migle Gabrielaite @mgabrielaite.bsky.social · 14/04/2025

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...

nature.com

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.

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PessoaBrain @pessoabrain.bsky.social · 25/03/2025

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

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Reposted by Migle Gabrielaite

Paul Hoskisson 🧫 🦠🐸 @paulhoskisson.bsky.social · 23/03/2025

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...

nature.com

Long-term studies provide unique insights into evolution - Nature

Long-term studies provide insights into the complex interplay between evolutionary process and pattern across multiple systems and timescales.

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Migle Gabrielaite @mgabrielaite.bsky.social · 19/03/2025

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.

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Migle Gabrielaite @mgabrielaite.bsky.social · 18/03/2025

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.

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Migle Gabrielaite @mgabrielaite.bsky.social · 17/03/2025

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

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European Research Council (ERC) @erc.europa.eu · 11/03/2025

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 🧵👇

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Torsten Seemann @torstenseemann.bsky.social · 04/03/2025

🦘✂️ 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...

forms.gle

Snippy: Microbial Variant Calling Community Survey

Help us drive the next wave of innovation in Single-Nucleotide Polymorphism (SNP) discovery and genome analysis by sharing your valuable experiences and insights. This in-depth survey aims at understa...

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Randall Munroe @xkcd.com · 26/02/2025

RNA xkcd.com/3056

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Migle Gabrielaite @mgabrielaite.bsky.social · 26/02/2025

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.

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Guillaume Méric @gmeric.bsky.social · 17/02/2025

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....

microbiomejournal.biomedcentral.com

Antibiotic-associated changes in Akkermansia muciniphila alter its effects on host metabolic health - Microbiome

Background Altered gut microbiota has emerged as a major contributing factor to the etiology of chronic conditions in humans. Antibiotic exposure, historically dating back to the mass production of pe...

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Ran Blekhman @blekhman.bsky.social · 27/01/2025

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...

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Migle Gabrielaite @mgabrielaite.bsky.social · 22/01/2025

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.

science.org

War-torn Ukraine has become a breeding ground for lethal drug-resistant bacteria

Urgent action underway to prevent dangerous microbes from spreading beyond country's borders

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European Virus Bioinformatics Center @evbc.bsky.social · 19/01/2025

🚨 🌟 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...

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Fabien Burki @fburki.bsky.social · 19/01/2025

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...

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Nick Brown @steamtraen.eu · 18/01/2025

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.

statmodeling.stat.columbia.edu

7 steps to junk science that can achieve worldly success | Statistical Modeling, Causal Inference, and Social Science

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PLOS Biology @plosbiology.org · 09/01/2025

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

Success of switching to a second antibiotic is contingent on temporally dynamic collateral effects. Top: Twenty replicate populations of E. faecalis V583 were exposed to increasing concentrations of the antibiotic ceftriaxone over the course of 14 days via serial passage. At the end of each day, a sample of the population was isolated and cultured in a range of doxycycline concentrations for 24 h. Middle: Density (OD) after 24 h versus drug (DOX) concentration for all 20 populations (light gray), and the mean over the 20 populations (dark black) at different days of the evolution experiment. Bottom left: Average sensitivity over 20 populations (error bar standard error of the mean) at different time points. Bottom right: Collateral effects; dashed region highlights a transient six-day window where collateral sensitivity is more pronounced.

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Richard Sever @richardsever.bsky.social · 10/01/2025

"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...

statnews.com

Want to start a fight among virus experts? Ask about HIV’s new name

HIV is now "Lentivirus humimdef1" by another name. Virus researchers are not happy.

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Migle Gabrielaite @mgabrielaite.bsky.social · 02/01/2025

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

nature.com

A new antibiotic traps lipopolysaccharide in its intermembrane transporter - Nature

A mechanism of lipid transport inhibition has been identified for a class of peptide antibiotics effective against resistant Acinetobacter strains, which may have applications in the inhibition of oth...

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