Migle Gabrielaite
Marie Sklodowska Curie Actions Postdoc at Vilnius University 🇱🇹 | Previously Rigshospitalet & University of Copenhagen 🇩🇰 | Bioinformatician 🧑💻 | Exploring bacterial evolution & transmission 🦠 | Toddler mom 🧒
- 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.
- I am also happy to have had the opportunity and priviledge to join the study and contribute together with @marvig.bsky.social. It's always exciting working on HIV.
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- Reposted by Migle GabrielaiteDr. Jane Goodall filmed an interview with Netflix in March 2025 that she understood would only be released after her death.
- Reposted by Migle GabrielaiteVery 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.
- Next is Maido Remm presenting how DNA sequencing can be used for typing and diagnostics: StrainSeeker works similarly as Kraken. I wonder if it has the same issues as Kraken does? It’s cool to hear something new even after 4 days spent on this topic at IMMEM XIV. #EYSF2025
- 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
- Even though Cas9 technology is promising in many fields, including gene therapy, it still has many limitations to overcome before its’ full potential can be used. For example, different Cas nucleases require different PAM sequences for cleavage to happen which Šikšnys lab is now working on solving.
- 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).
- Next, Verónica Mixão is presenting ReporTree for linking pathogen genetic clusters with epidemiological dat and how it can implement wgMLST data for extra resolution.
- The last presentation is by Val Fernandez Lanza about BacTaxID - genome-based, scalable, hierarchical, heuristic bacterial typing method. Similar to LIN and EC codes. The shark is very excited for the upcoming poster session.
- 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).
- It covered QC guidelines, assembly graph interpretation, metagenomics, microbial typing specifications, AllTheBacteria workflow implementation on nextflow and interactive and easy-to-use AMR exploration of AllTheBacteria, and plasmid outbreak reporting.
- It’s incredible how much a great team of scientists can do in just a fee days!
- 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.
- GTDB sometimes assigns suffixes for non monophyletic taxa where historically the classification is misleading or ambiguous. And we should all do better when submitting our genomes to public databases and naming species.
- Also, I am attending the conference with the little shark given by my son so I wouldn’t be bored. Today we managed to get to the ocean before the start of the day and enjoy the beauty of Porto.
- Reposted by Migle GabrielaiteLast 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!
- Reposted by Migle GabrielaiteOur 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.
- 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
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- 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?
- Reposted by Migle GabrielaiteThis 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🧵
Anthropozoonotic spillovers reveal sustained long-term cryptic circulation of SARS-CoV-2 within and between Lithuanian mink farms medrxiv.org/content/10.1101/202…
- Reposted by Migle GabrielaiteOur paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...
- 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
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- 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 🧬.
- The project is funded by EU (Enhance National Disease Surveillance System in Georgia through Improvement of the Epidemiological and Molecular (Genomic) Surveillance GE 21 NDICI HE 01 23)
- 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...
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- 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.
- Apart from many of these prizes being awarded to quite funny discoveries, they do indeed have another layer to think about and they highlight the most important thing about science: curiosity about the world around us. It's great to be reminded that science doesn't always have to be serious.
- Next, Nobel Prize Winner Victor Ambros showcased how with the tools available in 1980s, miRNAs were discovered in a long and a very exciting journey. It's remarkable that something what would have taken years to execute 50 years ago can be done in a few weeks nowadays.
- #TheCOINS is a conference organised exclusively by students. The level of it all: the talks, organisation, communication is mind blowing. I am extremely happy to have had the opportunity to take part in it and I'm sure that many of the organisers I already have or will soon have as my colleagues.
- 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
- Key take-home messages: Ocean food webs are not constant and have different robustness to changes Food webs are understudied, while their influence is tremendous - the future is vegan and car-free There are success stories in ocean preservation. We just tend to forget them.
- - When visualising data, less is more, simplify (then simplify again), and know your audience - Animations are more exciting than figures - Start summary figures with pen and paper to enable creativity - There is no need to add ALL the results to one figure, prioritise and decide what really matters
- Reposted by Migle GabrielaiteGood 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 🧵👇
- Reposted by Migle Gabrielaite🦘✂️ 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...
- Reposted by Migle GabrielaiteRNA 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
- E. coli was often genetically related between patients with no epidemiological links suggesting an unknown source outside of hospital. Even though genomic epidemiology can be costly, it has high potential to reduce costs and make informed decisions preventing in-hospital transmissions. 2/3
- I am lucky enough to have had the opportunity to work with several people who made this study a reality, including @marvig.bsky.social 3/3
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- Reposted by Migle GabrielaiteOut 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.
- Reposted by Migle Gabrielaite🚨 🌟 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...
- Reposted by Migle GabrielaiteStoked 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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- Reposted by Migle GabrielaiteEvolution 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
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- 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
- 3. CRISPR-Cas gene therapy approval (technically last days of 2023): www.casgevy.com 2.Alzheimer's disease diagnostics from blood: pubmed.ncbi.nlm.nih.gov/39068545/ 1. Twice-yearly injectable HIV prevention: www.nejm.org/doi/10.1056/... What other achievements should be added to the list? 2/2
- Reposted by Migle Gabrielaite🧬🔍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
- Reposted by Migle GabrielaiteScience 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...
- This is a truly incredible resource for anyone working on bacterial genomics. I'm struggling to assemble and organise 1,000 bacterial genomes, and I can’t even begin to fathom handling 2.4 million 🤯
- Latest data from AllTheBacteria described in our updated preprint. All illumina WGS bacterial+archaeal sequence data to Aug 2024 consistently assembled, QC, and now AMR profiling. That's 2.4 million genomes. Gene annotations almost done , coming next. Please use! www.biorxiv.org/content/10.1...
- AI and LLMs are great for a lot of things and can make our life easier and more efficient. AI nanny and guide for sleep-deprived, tired and desperate parents, however, is dangerous.
