Theoretical Biology & Bioinformatics @ UU

Our group consists of a Theoretical Biology group (headed by Rob de Boer) and a Bioinformatics group (headed by Berend Snel) @UniUtrecht

[Vivek Bhardwaj @vivekbhr]

We are #hiring!

Come join us at Utrecht University (NL) and help centralize our ongoing #genomics efforts into a new core unit, embedded in our inter-divisional lab. We are looking for a #Postdoc in #molecular biology and a #Bioinformatics engineer. Please apply/forward.

[Petros Skiadas @pskiadas]

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. 😇 https://t.co/j8YzsLGjWX

[Theoretical Biology & Bioinformatics @ UU @BinfUtrecht]

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

[Yasas Wijesekara @RajithaYasas1]

Of course, the Jaeger source code is completely open, we even made it available through BioConda and PyPi https://t.co/ST8dZLw9SK - we look forward to hearing your opinion about it! Many thanks to @LKaderali @BEDutilh @lingyi_owl @Piotr_Rozwalak @EHauptfeld

[Yasas Wijesekara @RajithaYasas1]

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.
https://t.co/xdsCOHvJKV

[Biology+AI Daily @BiologyAIDaily]

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 state-of-the-art methods.

- A significant innovation is Jaeger's speed—it's 20 times faster in CPU mode and up to 140 times faster with GPU acceleration, making it an ideal choice for large-scale virus detection tasks in metagenomic data.

- Jaeger applies a dilated Convolutional Neural Network (CNN) to directly recognize protein-level signatures from six-frame translated nucleotide sequences, outperforming traditional approaches.

- The tool also includes a reliability score system that alerts users when predictions might need human verification, improving decision-making for high-stakes virome studies.

- Jaeger was tested on over 16,000 metagenomic assemblies from the MGnify database, detecting over 5 million putative phage contigs across diverse environmental samples.

- Benchmark results highlight Jaeger's superior performance, particularly its ability to distinguish phages from non-phage sequences, including eukaryotic genomes.

@LKaderali @BEDutilh @SwapnilDoijad @Piotr_Rozwalak
💻Code: https://t.co/qwUICoZs6B
📜Paper: https://t.co/zSF5l9j9Jy

[Daniel Tamarit @DanielTamarit]

Thanks for the high praise, Iñaki!

[Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @Ettema_lab]

To learn about the latest views, disputes and future research directions on the origin of the eukaryotic cell, read our review in @Nature here:
https://t.co/49fPxj23QB
Non-paywalled version here: https://t.co/87oj4ajiwh

[Daniel Tamarit @DanielTamarit]

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!

[Julian Vosseberg @JulianVosseberg]

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: https://t.co/LnGcoz50ot

[Iñaki Ruiz-Trillo @multicellgenome]

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 identify hundreds of new ‘isomorphic’ eukaryotic signature proteins. Great idea! @koestlste @Ettema_lab @JvHooff @kassiani_panag @DanielTamarit @val_deanda @archaeal #Asgard #evolution

[Vivek Bhardwaj @vivekbhr]

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 https://t.co/rcYrZ6VZwA

[Beste-ID.NL @beste-id.bsky.social @Beste_ID]

De functie van de kleuren bij bacteriën: https://t.co/CywNGzrG6u
@BEDutilh @BinfUtrecht @UniUtrecht

[Daniel Tamarit @DanielTamarit]

Glad to have been part of this tremendous effort by @koestlste @JvHooff @Ettema_lab & 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! 👇

[Michael F Seidl @MFSeidl]

Kick-off of the symposium to celebrate the PhD defense of @xin43617988 @BinfUtrecht @_Westerdijk_ looking forward to reflect on her work of the last four years

[Daniel Tamarit @DanielTamarit]

Congrats @fabaiwu 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! 👇

[Anouk van Westerhoven @AvWesterhoven]

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 https://t.co/VjyaP1qUzd

[Daniel Tamarit @DanielTamarit]

Asgardarchaeum abyssi helps validate the Asgardarchaeota phylum name in accordance with the @seq_code. We hope this brings stability to archaeal taxonomy by preserving this taxon name used in 500+ papers!

And indeed, more on this theme soon!

[Thorsten Langner @ThorstenLangner]

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

[Michael F Seidl @MFSeidl]

Always a very special day to receive the final product of a PhD trajectory. Congratulations @xin43617988 really looking forward to your defense! @BinfUtrecht @_Westerdijk_