Javier E. Fernandez
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javif86.bsky.social
Javier E. Fernandez
@javif86.bsky.social
780 followers 2.5K following 9 posts
🧬🦠 Postdoc AMR/Microbial Genomics/Bioinformatics. Tracking AMR bacteria and its MGEs from a One-Health perspective. Passionate ➡️ phylogenomics, GDL, TDL, deep learning, graphs, plasmids, phages,... 🇦🇷 in 🇨🇭
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javif86.bsky.social
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
April 14, 2025 at 4:52 PM
javif86.bsky.social
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
April 14, 2025 at 6:58 AM
javif86.bsky.social
Ready for #ESCMID2025, looking forward to meeting colleagues and hearing about recent developments on the field!
#InfectiousDiseases #Microbiology #ESCMID #OneHealth
#GlobalHealth #ESCMIDGlobal
April 11, 2025 at 8:58 AM
Reposted by Javier E. Fernandez
jrpenades.bsky.social
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
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...
rdcu.be
March 27, 2025 at 11:28 AM
Reposted by Javier E. Fernandez
pardissabeti.bsky.social
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 🧵
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...
www.medrxiv.org
March 6, 2025 at 3:13 PM
Reposted by Javier E. Fernandez
aphendrickx.bsky.social
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...
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...
www.microbiologyresearch.org
January 12, 2025 at 6:32 PM
Reposted by Javier E. Fernandez
dutchscientist.bsky.social
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.
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
March 11, 2025 at 6:56 PM
Reposted by Javier E. Fernandez
arkrause.bsky.social
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!
jonhue.bsky.social Jonas Hübotter @jonhue.bsky.social · Feb 11
I'm very excited to share notes on Probabilistic AI that I have been writing with @arkrause.bsky.social 🥳

arxiv.org/pdf/2502.05244

These notes aim to give a graduate-level introduction to probabilistic ML + sequential decision-making.
I'm super glad to be able to share them with all of you now!
February 17, 2025 at 7:20 AM
Reposted by Javier E. Fernandez
torstenseemann.bsky.social
🦘✂️ 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...
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...
forms.gle
March 4, 2025 at 9:04 AM
Reposted by Javier E. Fernandez
plantepigenetics.ch
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
Europe PMCHome - Europe PMC
Europe PMC is an archive of life sciences journal literature.
europepmc.org
March 2, 2025 at 7:54 AM
javif86.bsky.social
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
February 6, 2025 at 2:32 PM
Reposted by Javier E. Fernandez
tgurbich.bsky.social
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
January 28, 2025 at 4:03 PM
Reposted by Javier E. Fernandez
craigmaclean.bsky.social
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...
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...
www.biorxiv.org
January 24, 2025 at 11:10 PM
javif86.bsky.social
🤯 learning so much from this piece!
Highly recommended!!
#GDL

maurice-weiler.gitlab.io#cnn_book
January 24, 2025 at 9:46 AM
Reposted by Javier E. Fernandez
thombooth.bsky.social
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!
1/5
🧪
bmcbioinformatics.biomedcentral.com/articles/10....
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...
bmcbioinformatics.biomedcentral.com
January 22, 2025 at 11:31 AM
javif86.bsky.social
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
January 21, 2025 at 10:02 AM
Reposted by Javier E. Fernandez
mattjago.bsky.social
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...
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...
www.nature.com
January 18, 2025 at 12:00 PM
Reposted by Javier E. Fernandez
hamedshirzad.bsky.social
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!
[1/13]
#NeurIPS2024
December 5, 2024 at 7:58 PM
Reposted by Javier E. Fernandez
rachelmwheatley.bsky.social
Two deadlines coming up in the next few weeks!
rachelmwheatley.bsky.social Rachel M. Wheatley @rachelmwheatley.bsky.social · Dec 30
Sharing three fully funded PhD opportunities to join my lab at Queen’s to work on topics spanning bacterial pathogens, antibiotic resistance, microbial interactions, & mobile genetic elements 🦠. Closing dates in January and February, and open to international candidates 🌍 Projects detailed below ⬇️
January 15, 2025 at 4:17 PM
Reposted by Javier E. Fernandez
resawagner.bsky.social
Pre-print alert:
Extracellular Vesicles of Minimalistic Mollicutes as Mediators of Immune Modulation and Horizontal Gene Transfer

www.researchsquare.com/article/rs-5...
January 14, 2025 at 2:48 PM
javif86.bsky.social
I have received my copy 😍📖
#GNN #deeplearning #genomics #bioinformatics
January 10, 2025 at 6:33 AM
Reposted by Javier E. Fernandez
rrwick.bsky.social
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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Home
A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler
github.com
December 31, 2024 at 11:43 PM
Reposted by Javier E. Fernandez
misssalmonella.bsky.social
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
January 1, 2025 at 11:45 AM
javif86.bsky.social
Re-reading these wonderful pieces preparing for what comes in 2025 😉
#GNNs #deeplearning #genomics #bioinformatics
December 30, 2024 at 12:53 PM
javif86.bsky.social
Very much enjoying the pre-print. I hope Santa brings me the actual book 📖. 🎄 @cambridgeup.bsky.social
December 28, 2024 at 1:13 PM