Lightnews — Scholar-powered news

Migle Gabrielaite

@mgabrielaite.bsky.social

330 followers 630 following 51 posts

Marie Sklodowska Curie Actions Postdoc at Vilnius University 🇱🇹 | Previously Rigshospitalet & University of Copenhagen 🇩🇰 | Bioinformatician 🧑‍💻 | Exploring bacterial evolution & transmission 🦠 | Toddler mom 🧒

Posts Media Videos Starter Packs

Pinned

Migle Gabrielaite @mgabrielaite.bsky.social · Oct 23

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).

2 8

Reposted by Migle Gabrielaite

Oliver Schwengers @oschwengers.bsky.social · 2d

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!

1 10 45

Reposted by Migle Gabrielaite

KOJAMF🤘🖤🤘 @kojamf.bsky.social · 3d

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

800 17K 37K

Reposted by Migle Gabrielaite

Samuel Lampa @smllmp.bsky.social · 12d

Very interesting!

EMBL-EBI @ebi.embl.org · 12d

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...
🧬💻

1 1

Migle Gabrielaite @mgabrielaite.bsky.social · 13d

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!

1 3

Migle Gabrielaite @mgabrielaite.bsky.social · 14d

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?

4 2

Migle Gabrielaite @mgabrielaite.bsky.social · 14d

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

Migle Gabrielaite @mgabrielaite.bsky.social · 14d

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.

2 1

Migle Gabrielaite @mgabrielaite.bsky.social · 14d

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.

Migle Gabrielaite @mgabrielaite.bsky.social · 14d

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

2 3

Migle Gabrielaite @mgabrielaite.bsky.social · 16d

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

3 2 8

Migle Gabrielaite @mgabrielaite.bsky.social · 18d

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!

Migle Gabrielaite @mgabrielaite.bsky.social · 19d

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.

Migle Gabrielaite @mgabrielaite.bsky.social · 20d

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.

Migle Gabrielaite @mgabrielaite.bsky.social · 20d

Next, Verónica Mixão is presenting ReporTree for linking pathogen genetic clusters with epidemiological dat and how it can implement wgMLST data for extra resolution.

1 1

Migle Gabrielaite @mgabrielaite.bsky.social · 20d

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).

2 1 4

Migle Gabrielaite @mgabrielaite.bsky.social · 20d

It’s incredible how much a great team of scientists can do in just a fee days!

Migle Gabrielaite @mgabrielaite.bsky.social · 20d

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.

Migle Gabrielaite @mgabrielaite.bsky.social · 20d

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).

1 1 3

Migle Gabrielaite @mgabrielaite.bsky.social · 20d

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.

Migle Gabrielaite @mgabrielaite.bsky.social · 20d

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.

www.nature.com

Migle Gabrielaite @mgabrielaite.bsky.social · 20d

So it’s even higher than I thought! Achromobacter is a mess and >10% have wrong species metadata but I hoped that it’s a more isolated problem.

Migle Gabrielaite @mgabrielaite.bsky.social · 20d

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.

1 3

Migle Gabrielaite @mgabrielaite.bsky.social · 20d

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.

1 3

Migle Gabrielaite @mgabrielaite.bsky.social · 20d

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.

1 1

Migle Gabrielaite @mgabrielaite.bsky.social · 20d

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.

1 1 2