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Judit Burgaya

@jburgaya.bsky.social
59 followers 192 following 4 posts

Postdoctoral researcher @ Uni Bern

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Reposted by Judit Burgaya
Thomas Ipoutcha @tomipou.bsky.social · 16/09/2026
Finally out! 🎉 After 3 years of postdoc in London, here is my main work, now published in Nature Comm. (and as co-corresponding author!) Using a combination of bioinformatic and experimental approaches, we propose a model of plasmid evolution in Staphylococcus. www.nature.com/articles/s41... ⬇️ 1/4
nature.com
Mobile genetic elements drive a plasmid fusion and deletion lifecycle shaping evolution and antimicrobial resistance - Nature Communications
Plasmids drive bacterial adaptation, but how their diversity arises has remained unclear. Here, they show that in Staphylococcus aureus, mobile genetic elements repeatedly fuse and delete plasmids, re...
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Reposted by Judit Burgaya
Marco Galardini @mgalactus.bsky.social · 12/08/2026
It took us two (2!) years to get our manuscript on resistance determinants to asobiotics published, and of course that had to happen during my summer vacation 🏝️🇪🇺 Thanks to @mulkern.bsky.social , @vuthuhien176.bsky.social and the other co-authors! www.nature.com/articles/s41...
nature.com
A systematic identification of resistance determinants to antisense antibiotics suggests adaptation strategies dependent on the delivery peptide - Nature Communications
In this study, authors investigate the evolution of bacterial resistance to antisense peptide nucleic acid (PNA) antibiotics. They observe that this typically occurs mainly by reducing drug uptake via...
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Reposted by Judit Burgaya
Arvid Ågren @arvidagren.bsky.social · 04/06/2026
Much has been written about The Selfish Gene, and few books have been both as influential and as persistently contested. To commemorate its 50th anniversary, here are some brief thoughts in the latest issue of @science.org. www.science.org/doi/10.1126/...
science.org
A provocative view of evolution turns 50
The Selfish Gene continues to challenge readers half a century later
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Judit Burgaya @jburgaya.bsky.social · 21/05/2026
I am absolutely thrilled to have received a Robert Austrian Research Award at this year’s ISPPD meeting. Seeing all the great science being done, but especially the community around it, has been amazing and very inspiring. See you all soon👋🏽 #ISPPD14 #ISPPD2026 #pneumonia #pneumococcalresearch
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Reposted by Judit Burgaya
Marco Galardini @mgalactus.bsky.social · 04/05/2026
Our lab's website has a summary of what we have done: www.microbial-pangenomes-lab.org/2026/05/04/T...
microbial-pangenomes-lab.org
Time is relative (in genomic epidemiology)
This is the official web page for the Microbial Pangenomes Lab at Twincore.
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Reposted by Judit Burgaya
Marco Galardini @mgalactus.bsky.social · 04/05/2026
Are you frustrated by how arbitrary fixed SNPs thresholds "feel"? Are you wondering if there are genetic differences between "promiscuous" and "shy" pathogens? If yes, then read our latest preprint to see what @jburgaya.bsky.social has been up to! www.medrxiv.org/content/10.6...
medrxiv.org
Coupling time-aware SNP thresholds with genetic markers to define bacterial transmission chains in hospital surveillance
Hospital settings can act as reservoirs for pathogens, with many nosocomial bacteria surviving for extended periods of time and spreading via contaminated environments, healthcare workers, or medical ...
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Reposted by Judit Burgaya
Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.
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Sam Horsfield @samuelhorsfield.bsky.social · 13/04/2026
ggCallaroo v0.1.0 is now out! This snakemake pipeline predicts, clusters and annotates bacterial genes using ggCaller, Panaroo and Bakta. It generates Panaroo files with functional annotations already integrated, which can then be used with the usual downstream tools. github.com/samhorsfield...
github.com
GitHub - samhorsfield96/ggCallaroo: A snakelike pipeline combining ggCaller and Panaroo.
A snakelike pipeline combining ggCaller and Panaroo. - samhorsfield96/ggCallaroo
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Reposted by Judit Burgaya
Yunha Hwang @microyunha.bsky.social · 03/03/2026
Protein–protein interactions (PPIs) are key to discovering and interpreting new biological functions. We’re excited to introduce 𝑭𝒍𝒂𝒔𝒉𝑷𝑷𝑰: a new application of gLM2 that uses genomic language modeling to predict proteome-wide PPIs in microbial genomes in minutes.
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Torsten Seemann @torstenseemann.bsky.social · 13/12/2025
💾 Shovill 1.4.1 has been released! The best way to de novo assemble microbial genomes from Illumina FASTQ. Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking. #bioinformatiocs #genomics #microbiology github.com/tseemann/sho...
github.com
Releases · tseemann/shovill
⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads - tseemann/shovill
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Judit Burgaya @jburgaya.bsky.social · 03/10/2025
On Wednesday I started my postdoc at the Institut für Infektionskrankheiten (IFIK) @unibe.ch 🧬💻 Excited to get started on my project exploring Streptococcus pneumoniae virulence and all the science ahead!
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Reposted by Judit Burgaya
Zamin Iqbal @zaminiqbal.bsky.social · 25/09/2025
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n
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Kate Baker @ksbakes.bsky.social · 27/08/2025
Awesome to see the transparent, systematic, and evidence-based approach behind the WHO Bacterial Priority Pathogens List 2024 out in the Lancet Infectious Diseases www.thelancet.com/journals/lan...
thelancet.com
The WHO Bacterial Priority Pathogens List 2024: a prioritisation study to guide research, development, and public health strategies against antimicrobial resistance
The 2024 WHO BPPL is a key tool for prioritising research and development investments and informing global public health policies to combat AMR. Gram-negative bacteria and rifampicin-resistant M tuber...
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Judit Burgaya @jburgaya.bsky.social · 03/07/2025
Truly honored to receive the Infection Biology PhD Prize. Grateful for the support @resist-cluster.bsky.social
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Judit Burgaya @jburgaya.bsky.social · 01/07/2025
PhD, done 🥹🥂 Massive thanks to my brilliant supervisor @mgalactus.bsky.social and amazing colleagues!
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Reposted by Judit Burgaya
Marco Galardini @mgalactus.bsky.social · 11/06/2025
Are you interested what proportion of differentially expressed genes in bacteria can be explained by cis non-coding variants? Then head over to our latest preprint, in which Bamu used her dry- and wet-lab skills to answer this and other related questions! www.biorxiv.org/content/10.1...
biorxiv.org
Cis non-coding genetic variation drives gene expression changes in the E. coli and P. aeruginosa pangenomes
Bacteria use gene regulation to dynamically adapt to changes in their environment, including resistance to stress and the occupation of new niches. Gene expression is known to vary within a species pa...
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Marco Galardini @mgalactus.bsky.social · 21/05/2025
We are very happy to report that the 3rd and 4th PhD theses from the lab have been submitted! This time we had a “tale of two theses”: @jburgaya.bsky.social had her thesis 99% ready more than a week before the deadline (!), while Hannes preferred to wait until just before it was due ☕ Congrats!
A double photo of Judit and Hannes and their submitted PhD thesis. Both are smiling
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Reposted by Judit Burgaya
Alvaro San Millan @sanmillan.bsky.social · 15/05/2025
New opinion paper from the lab! www.cell.com/trends/micro...
cell.com
Plasmid–bacteria associations in the clinical context
Antimicrobial resistance (AMR) is one of the most pressing global health problems, with plasmids playing a central role in its evolution and dissemination. Over the past decades, many studies have inv...
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Reposted by Judit Burgaya
Jörg Vogel @jorg-vogel-lab.bsky.social · 05/05/2025
And this only the beginning! I’m glad we did that collaboration with the Maric lab. ASOs for the people!
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Reposted by Judit Burgaya
Tami Lieberman @contaminatedsci.bsky.social · 01/05/2025
Do people in the same household share strains when they have the same species? How many cells transmit when a strain is shared? Can strain composition be dynamic when species composition is stable? We answer these and related questions for the facial skin microbiome in our latest paper. 🧵[1/10]
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Willem van Schaik @wvschaik.bsky.social · 29/04/2025
This is fascinating, but also terrible news regarding antimicrobial resistance in multidrug-resistant Gram-positives 'Emergence of transferable daptomycin resistance in Gram-positive bacteria' www.nature.com/articles/s44...
nature.com
Emergence of transferable daptomycin resistance in Gram-positive bacteria - npj Antimicrobials and Resistance
npj Antimicrobials and Resistance - Emergence of transferable daptomycin resistance in Gram-positive bacteria
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Sonja Lehtinen @sonjalehtinen.bsky.social · 07/04/2025
New paper: long-term trends in antibiotic resistance show signs of stabilisation (thread). journals.plos.org/plospathogen...
journals.plos.org
The evolution of antibiotic resistance in Europe, 1998–2019
Author summary Antibiotic resistance is an important public health threat: resistant infections are currently associated with 5 million deaths per year globally. This burden may increase further in th...
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Reposted by Judit Burgaya
Exzellenzcluster RESIST @resist-cluster.bsky.social · 12/02/2025
Properties of bacteria are constantly changing. @mgalactus.bsky.social is developing methods to better predict the properties. His team has now developed software that facilitates genome-wide association studies #GWAS Congratulations to all 🧫🦠😊 www.resist-cluster.de/en/better-pr...
resist-cluster.de
Better prediction of bacterial properties
Each bacterial species has not just a single genome, but a diverse ensemble of gene combinations. This means that the properties of bacteria are constantly changing – for example, how ill they can mak...
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Reposted by Judit Burgaya
Marco Galardini @mgalactus.bsky.social · 12/02/2025
We even got the press office to take this lovely photo of the three main authors :) Quite nice that we got it published on the International Day of Women and Girls in Science!
A photo of Judit, Jenny, and Bamu "working" hard on the pipeline
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Reposted by Judit Burgaya
Marco Galardini @mgalactus.bsky.social · 12/02/2025
Our paper describing the microGWAS pipeline was published yesterday in Microbial Genomics. Lots of fixes and additions to the code/documentation since the preprint, including a hard to reproduce bug that only showed up in a specific HPC 🥵 www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
microGWAS: a computational pipeline to perform large-scale bacterial genome-wide association studies
Identifying genetic variants associated with bacterial phenotypes, such as virulence, host preference and antimicrobial resistance, has great potential for a better understanding of the mechanisms inv...
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