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Please share! We are recruiting a PhD student to join us in the CropXR consortium to research the evolution of stress response networks in plants. More information, and application link, here: uu.nl/en/organisatio…

Always a very special day to receive the final product of a PhD trajectory. Congratulations xin really looking forward to your defense! Theoretical Biology & Bioinformatics @ UU Westerdijk Institute

It is my great pleasure to host Michael Seidl Michael F Seidl from Theoretical Biology & Bioinformatics @ UU for our @MPI_Bio seminar series! Beautiful plant pathogen genomics from primary sequence analysis to the 3D organisation of the genome 🤩🧬

Asgardarchaeum abyssi helps validate the Asgardarchaeota phylum name in accordance with the SeqCode. We hope this brings stability to archaeal taxonomy by preserving this taxon name used in 500+ papers! And indeed, more on this theme soon!

Happy to share our work on the pan-mitogenome of Fusarium oxysporum. Pangenome graphs work great for large-scale comparison of mitogenomes! Frequent genetic exchange shapes the pan-mitogenome of the fungal plant pathogen Fusarium oxysporum biorxiv.org/content/10.110…

Congrats Fabai Wu Lab and all main authors! Glad to have been able to participate on this interesting project. Make sure to read Fabai's thread for a nice summary of the main findings! 👇

Kick-off of the symposium to celebrate the PhD defense of xin Theoretical Biology & Bioinformatics @ UU Westerdijk Institute looking forward to reflect on her work of the last four years

Glad to have been part of this tremendous effort by Stephan Köstlbacher @JvHooff Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 & others! Read Stephan's thread to find out how he used protein structural predictions to discover 'isomorphic' eukaryotic signature proteins beyond what sequence similarity searches can find! 👇

De functie van de kleuren bij bacteriën: beste-id.nl/nieuws/de-func… @BEDutilh Theoretical Biology & Bioinformatics @ UU Utrecht University

Due to their unique exploration challenges, the data from emerging #singlecell #epigenomics protocols can be difficult to work with. We present sincei, a toolkit for exploring sc(epi)genomics data directly from BAM files, using bash one-liners or #python biorxiv.org/content/10.110…

Once more, it seems the #archaeal ancestor of eukaryotes was more complex than previously thought! 😀 (reminds me of the unicellular ancestor of animals). In this occasion, it is the use of de novo protein structure modeling & sensitive sequence similarity algorithms that helped

Many novel Asgard genomes, cultivated Lokiarchaeia, new phylogenetic analyses: what insights do these and other recent studies provide into the enigmatic origin of eukaryotes? In this review in nature , we discuss the latest findings and open questions: nature.com/articles/s4158…

To learn about the latest views, disputes and future research directions on the origin of the eukaryotic cell, read our review in nature here: nature.com/articles/s4158… Non-paywalled version here: rdcu.be/dTFrR

An unbroken thread links us to the first cells. But understanding our ancestry still requires studying the most impactful and mysterious evolutionary transition: the origin of the eukaryotic cell Here we summarise current views in light of the latest advances. Exciting times!

Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences - Jaeger is a new deep-learning tool that excels in detecting bacteriophage genome fragments with high accuracy, achieving sensitivity (0.87) and precision (0.92) in benchmarks against

Thanks for the high praise, Iñaki!

After three years of hard work, I’m thrilled to share the brainchild of my PhD project. Jaeger: a deep learning tool for identifying bacteriophage sequences in metagenomes! 🧬🦠 Empowering exploration of the viral world with greater accuracy and insight. biorxiv.org/content/10.110…

Of course, the Jaeger source code is completely open, we even made it available through BioConda and PyPi github.com/MGXlab/Jaeger - we look forward to hearing your opinion about it! Many thanks to Lars Kaderali @BEDutilh Ling-Yi Wu Piotr E. Hauptfeld

Prof Berend Snel gave the first keynote at the Utrecht Bioinformatics Center 10th annual symposium Bioinformatics, remembering his talk on the year of inauguration. Bioinformatics has moved forward in and out of Utrecht, but plenty of data-driven opportunities remain!

We compared genomes at every level, from the nucleotide to the chromosome, and from the single gene or TE to the whole proteome. The findings were almost too many for a single publication... almost. 😇 doi.org/10.1371/journa…