iiinova — where your digital self keeps evolving

Javier E. Fernandez @javif86.bsky.social · 02/01/2026

After 7 years, I’m saying goodbye to the lab that shaped a big part of my scientific journey. I earned here my PhD in Genomics & Bioinformatics, publishing research and building the lab’s bioinformatics pipelines from the ground up. A challenging and very rewarding experience.

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Javier E. Fernandez @javif86.bsky.social · 14/04/2025

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

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Javier E. Fernandez @javif86.bsky.social · 14/04/2025

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

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Javier E. Fernandez @javif86.bsky.social · 11/04/2025

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

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pardissabeti.bsky.social @pardissabeti.bsky.social · 06/03/2025

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 🧵

medrxiv.org

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...

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Andreas Krause @arkrause.bsky.social · 17/02/2025

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!

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Torsten Seemann @torstenseemann.bsky.social · 04/03/2025

🦘✂️ 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...

forms.gle

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...

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Etienne Bucher 🌾🧬🇪🇺 @plantepigenetics.ch · 02/03/2025

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

europepmc.org

Europe PMCHome - Europe PMC

Europe PMC is an archive of life sciences journal literature.

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Javier E. Fernandez @javif86.bsky.social · 06/02/2025

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

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Tatiana Gurbich @tgurbich.bsky.social · 28/01/2025

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

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Craig MacLean @craigmaclean.bsky.social · 24/01/2025

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...

biorxiv.org

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...

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Javier E. Fernandez @javif86.bsky.social · 24/01/2025

🤯 learning so much from this piece! Highly recommended!! #GDL maurice-weiler.gitlab.io#cnn_book

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Reposted by Javier E. Fernandez

Thom Booth @thombooth.bsky.social · 22/01/2025

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....

bmcbioinformatics.biomedcentral.com

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...

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Javier E. Fernandez @javif86.bsky.social · 21/01/2025

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

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Reposted by Javier E. Fernandez

Matt Jago @mattjago.bsky.social · 18/01/2025

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...

nature.com

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...

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Hamed Shirzad @hamedshirzad.bsky.social · 05/12/2024

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

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Rachel M. Wheatley @rachelmwheatley.bsky.social · 15/01/2025

Two deadlines coming up in the next few weeks!

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Theresa Wagner @resawagner.bsky.social · 14/01/2025

Pre-print alert: Extracellular Vesicles of Minimalistic Mollicutes as Mediators of Immune Modulation and Horizontal Gene Transfer www.researchsquare.com/article/rs-5...

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Ryan Wick @rrwick.bsky.social · 31/12/2024

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... (1/5)

github.com

Home

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

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Miss Salmonella @misssalmonella.bsky.social · 01/01/2025

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

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Javier E. Fernandez @javif86.bsky.social · 30/12/2024

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

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Javier E. Fernandez @javif86.bsky.social · 28/12/2024

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

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Stephen Turner @stephenturner.us · 24/12/2024

Unicore enables scalable and accurate phylogenetic reconstruction with structural core genes www.biorxiv.org/content/10.1101/202… 🧬🖥️🧪 github.com/steineggerlab/unicore

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Tim Dallman @tdallman.bsky.social · 29/02/2024

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...

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