Javier E. Fernandez

After the great plasmids evolution session in the morning I followed up on the topic with my poster. Very nice discussions with colleagues that passed by to check it. Enjoyed it very much 🙏

#ESCMIDGlobal #genomics #bioinformatics #AMR #OneHealth

Interested in a snapshot of plasmids phylogeny and AMR? Come get a look at poster P1864 today and let’s chat!

#ESCMIDGlobal #genomics #bioinformatics #plasmids #AMR

Ready for #ESCMID2025, looking forward to meeting colleagues and hearing about recent developments on the field!
#InfectiousDiseases #Microbiology #ESCMID #OneHealth
#GlobalHealth #ESCMIDGlobal

Genetics, ecology and evolution of phage satellites Nature Reviews Microbiology - In this Review, Penadés et al. explore the genetics, potential origins and life cycle of phage satellites, and they discuss the impact of these elements on the...

If you are interested in phage satellites, we hope you'll enjoy this. Fun collaboration with the Rocha, Seed, Bikard, and Chen labs! rdcu.be/efkvG

JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale Transmission reconstruction--the inference of who infects whom in disease outbreaks--offers critical insights into how pathogens spread and provides opportunities for targeted control measures. We dev...

We present JUNIPER, our outbreak reconstruction tool that incorporates within-host variants, models missing data, and scales to large, sparsely sampled datasets to achieve state-of-the-art performance. Led by @ivan_specht et al. @sabeti_lab. www.medrxiv.org/content/10.1... 1/12 🧵

Diversification of bla OXA-48-harbouring plasmids among carbapenemase-producing Enterobacterales, 11 years after a large outbreak in a general hospital in the Netherlands Introduction. Genes encoding OXA-48-like carbapenem-hydrolyzing enzymes are often located on plasmids and are abundant among carbapenemase-producing Enterobacterales (CPE) worldwide. After a large bla...

Diversification of blaOXA-48-harbouring plasmids among carbapenemase-producing Enterobacterales, 11 years after a large outbreak in a general hospital in the Netherlands www.microbiologyresearch.org/content/jour...

Global phylogenomic analysis of Staphylococcus pseudintermedius reveals genomic and prophage diversity in multidrug-resistant lineages Staphylococcus pseudintermedius is the foremost cause of opportunistic canine skin and mucosal infections worldwide. Multidrug-resistant (MDR) and methicillin-resistant Staphylococcus pseudintermedius...

www.microbiologyresearch.org/content/jour...
We got a new paper out on Staphylococcus pseudintermedius genomics, led by @jaimehat.bsky.social from @uniofsurrey.bsky.social with Fitzpatrick referrals.

We've released our lecture notes for the course Probabilistic AI at ETH Zurich, covering uncertainty in ML and its importance for sequential decision making. Thanks a lot to @jonhue.bsky.social for his amazing effort and to everyone who contributed! We hope this resource is useful to you!

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...

🦘✂️ 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...

As we can expect PubMed dysfunction more and more or to be swamped with fake journals I suggest you get acquainted to this nice alternative: europepmc.org

Enjoying and learning a lot from this piece! I don’t know if the best reading choice for a week of holiday 🤣🤯 but 100% recommended if you are like me still getting your head around TDL/GDL.
@mathildepapillon.bsky.social and co-authors 🙌👏

arxiv.org/pdf/2407.09468

Our paper describing mettannotator, a new prokaryotic annotation pipeline, is out: academic.oup.com/bioinformati...
📝 Mettannotator generates comprehensive structural & functional annotations
⚙️ Built with #Nextflow — scalable, no installation needed

Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy Plasmids are a ubiquitous feature of bacterial genomes, but the evolutionary forces driving genes to become associated with plasmids are poorly understood. To address this problem, we compared the fit...

New pre-print!!! What types of genes end up on plasmids and why? The take home message of this paper is that beneficial genes move from plasmids to chromosome, causing the ecological value of plasmids to decay over time.
www.biorxiv.org/content/10.1...

🤯 learning so much from this piece!
Highly recommended!!
#GDL

maurice-weiler.gitlab.io#cnn_book

getphylo: rapid and automatic generation of multi-locus phylogenetic trees - BMC Bioinformatics Background The increasing amount of genomic data calls for tools that can create genome-scale phylogenies quickly and efficiently. Existing tools rely on large reference databases or require lengthy d...

getphylo is finally official! Build phylogenetic trees directly from genbank files - at breakneck speed! I'd like to thank everyone who provided feedback and encourage you to continue. Improving getphylo doesn't stop now the paper is out!
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🧪
bmcbioinformatics.biomedcentral.com/articles/10....

Nice to read this today! I had to decide if going for a softer core or not, and luckily I made the right choice 😅👌 #mustread

High-throughput method characterizes hundreds of previously unknown antibiotic resistance mutations - Nature Communications Resistance mutations are challenging to characterize because their effects are highly context dependent. Here, authors present a quantitative mutant screening technique that deconstructs how factors l...

Very excited that my 1st first-author paper has just been published!! We present a novel mutant screening technique that can rapidly identify 100s of antibiotic resistance mutations, while evaluating how likely they are in different genetic backgrounds.

www.nature.com/articles/s41...

Graph Transformers (GTs) can handle long-range dependencies and resolve information bottlenecks, but they’re computationally expensive. Our new model, Spexphormer, helps scale them to much larger graphs – check it out at NeurIPS next week, or the preview here!
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#NeurIPS2024

Two deadlines coming up in the next few weeks!

Pre-print alert:
Extracellular Vesicles of Minimalistic Mollicutes as Mediators of Immune Modulation and Horizontal Gene Transfer

www.researchsquare.com/article/rs-5...

I have received my copy 😍📖
#GNN #deeplearning #genomics #bioinformatics

Home A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
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Ten months ago I posted this comic on LinkedIn. It has received over 300 likes in different forms. With humor, but as a critique of those who don't value our work. Let's keep making our demands in 2025! #Bioinformatics

Re-reading these wonderful pieces preparing for what comes in 2025 😉
#GNNs #deeplearning #genomics #bioinformatics

Very much enjoying the pre-print. I hope Santa brings me the actual book 📖. 🎄 @cambridgeup.bsky.social

Unicore enables scalable and accurate phylogenetic reconstruction with structural core genes https://www.biorxiv.org/content/10.1101/2024.12.22.629535v1 🧬🖥️🧪 https://github.com/steineggerlab/unicore

Come join the group in Utrecht!  I have a post-doc position to fill to work on using microbial genomics and metagenomics to build machine learning models to better understand the spread of pathogens and dissemination of resistance www.uu.nl/en/organisat...