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Ling-Yi

@lingyi.bsky.social
142 followers 103 following 4 posts

🧬🦠👩🏻‍💻bioinformatics | machine learning | microbiology

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Sultan Nazir @sultannazir.bsky.social · 25/08/2025
Excited to present work from my preprint at #SMBI2025 @uni-jena.de on September 18th. I will be speaking on how spatial structure can explain the association of microbial accessory genes with inducible prophages. asb-conference.hki-jena.de/schedule/
asb-conference.hki-jena.de
Schedule – Applied Systems Biology Symposia
Emmanuel Saliba, University of Würzburg, Germany.
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Reposted by Ling-Yi
Theoretical Biology & Bioinformatics @ UU @binfutrecht.bsky.social · 14/03/2025
📣 New, free webtool by the Snoek lab! Meet SpeSpeNet, an intuitive platform for automated network analysis of microbiomes to uncover complex interactions between microbes and their environments @ismepublications.bsky.social @isme-microbes.bsky.social doi.org/10.1093/isme... #microsky #mevosky
doi.org
SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks
Abstract. Correlation networks are commonly used to explore microbiome data. In these networks, nodes are taxa and edges represent correlations between the
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Reposted by Ling-Yi
Bas E. Dutilh @bedutilh.bsky.social · 27/01/2025
Get a grasp of the chemistry of microbiomes! Check out Pilleriin Peets' preprint: she developed chemical characteristics vectors to reanalyze EMP's untargeted metabolomics data: www.biorxiv.org/content/10.1... with Aris Litos, Daniel Garza, Kai Dührkop, @jjjvanderhooft.bsky.social & Sebastian Böcker
biorxiv.org
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Simon Roux @simrouxvirus.bsky.social · 22/07/2025
We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt
rdcu.be
Viromics approaches for the study of viral diversity and ecology in microbiomes
Nature Reviews Genetics - In this Review, Roux and Coclet outline current viromics approaches and discuss how they have contributed to our growing understanding of viral genomic diversity, focusing...
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Rob Edwards @linsalrob.bsky.social · 22/08/2025
New in @asm.org #MMBR Computational function prediction of bacteria and phage proteins. How to annotate your #phage and #bacteria genomes by @susiegriggo.bsky.social @bedutilh.bsky.social @gbouras13.bsky.social and Bob #phagesky #microsky journals.asm.org/doi/epub/10....
Examples of protein annotations across functional classification schemes. Yellow: hierarchical classification schemes, red: orthologous/homologous groups, and blue: methods using protein domain information. Protein structures were generated using the ColabFold Alphafold MMseqs2 interactive notebook (version 1.5.2) (57) and visualized using ChimeraX (58). (A) Functional labels associated with the glycogen synthase protein in Escherichia coli (UniprotKB P0A6U8). (B) Functional labels associated with Kehishuvirus sp. tikala major capsid protein (NCBI WEU69752.1).
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Ling-Yi @lingyi.bsky.social · 25/04/2024
#Viromics #VirusDiscovery 🦠 by #Metagenomics 🧬! We used real metagenomic data from diverse biomes to #benchmark state-of-the-art #bioinformatics virus identification tools: genomebiology.biomedcentral.com/articles/10.... @goncalopiedade.bsky.social @bedutilh.bsky.social 🧵 (1/4)
genomebiology.biomedcentral.com
Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes - Genome Biology
Background As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinfo...
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