Migle Gabrielaite
@mgabrielaite.bsky.social
Marie Sklodowska Curie Actions Postdoc at Vilnius University 🇱🇹 | Previously Rigshospitalet & University of Copenhagen 🇩🇰 | Bioinformatician 🧑💻 | Exploring bacterial evolution & transmission 🦠 | Toddler mom 🧒
Pinned
Hi, I'm Migle, a postdoc at Vilnius University 🇱🇹, trying to better understand Achromobacter genomics, its transmission and spread with an emphasis on antibiotic resistance and host adaptation. I am back after a few year break from science social media (and academia).
Reposted by Migle Gabrielaite
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!
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!
October 6, 2025 at 8:11 AM
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!
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!
Reposted by Migle Gabrielaite
Dr. Jane Goodall filmed an interview with Netflix in March 2025 that she understood would only be released after her death.
October 5, 2025 at 9:08 AM
Dr. Jane Goodall filmed an interview with Netflix in March 2025 that she understood would only be released after her death.
Reposted by Migle Gabrielaite
Very interesting!
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...
🧬💻
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...
🧬💻
September 26, 2025 at 12:13 PM
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!
September 25, 2025 at 11:39 AM
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?
September 24, 2025 at 12:27 PM
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.
September 24, 2025 at 12:21 PM
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
#EYSF2025
September 24, 2025 at 7:06 AM
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
#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.
BakRep
bakrep.computational.bio
September 22, 2025 at 9:24 AM
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!
September 20, 2025 at 4:27 PM
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.
September 19, 2025 at 8:23 AM
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).
September 18, 2025 at 4:16 PM
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).
September 18, 2025 at 3:09 PM
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.
September 18, 2025 at 10:16 AM
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...
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.
www.nature.com
September 18, 2025 at 10:08 AM
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...
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.
September 18, 2025 at 8:21 AM
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.
September 18, 2025 at 8:03 AM
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.
Reposted by Migle Gabrielaite
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!
August 28, 2025 at 8:38 AM
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!
Reposted by Migle Gabrielaite
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.
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
August 15, 2025 at 4:33 PM
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.
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
Reposted by Migle Gabrielaite
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...
Code (MIT): github.com/nf-core/prot...
Docs/launch: nf-co.re/proteinfamil...
August 17, 2025 at 10:10 AM
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...
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?
August 7, 2025 at 12:37 PM
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 Gabrielaite
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🧵
July 17, 2025 at 8:44 AM
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🧵
Reposted by Migle Gabrielaite
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...
June 30, 2025 at 12:26 PM
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...
Reposted by Migle Gabrielaite
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-...
📌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
June 11, 2025 at 6:15 AM
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-...
📌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)
2. I am really looking for a PhD student (deadline in June)
April 15, 2025 at 7:33 AM
1. When did AI become so good with figures and text?!
2. I am really looking for a PhD student (deadline in June)
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 🧬.
April 14, 2025 at 8:57 AM
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 🧬.