Ling-Yi
@lingyi.bsky.social
🧬🦠👩🏻💻bioinformatics | machine learning | microbiology
Pinned
Ling-Yi
@lingyi.bsky.social
· Apr 25
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...
genomebiology.biomedcentral.com
#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)
Reposted by Ling-Yi
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/
Schedule – Applied Systems Biology Symposia
Emmanuel Saliba, University of Würzburg, Germany.
asb-conference.hki-jena.de
August 25, 2025 at 6:17 PM
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/
Reposted by Ling-Yi
📣 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
@ismepublications.bsky.social @isme-microbes.bsky.social
doi.org/10.1093/isme...
#microsky #mevosky
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
doi.org
March 14, 2025 at 2:15 PM
📣 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
@ismepublications.bsky.social @isme-microbes.bsky.social
doi.org/10.1093/isme...
#microsky #mevosky
Reposted by Ling-Yi
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
www.biorxiv.org
January 27, 2025 at 1:25 PM
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
Reposted by Ling-Yi
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
July 22, 2025 at 3:06 PM
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
Reposted by Ling-Yi
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....
by @susiegriggo.bsky.social @bedutilh.bsky.social @gbouras13.bsky.social and Bob
#phagesky #microsky
journals.asm.org/doi/epub/10....
August 22, 2025 at 4:00 AM
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....
by @susiegriggo.bsky.social @bedutilh.bsky.social @gbouras13.bsky.social and Bob
#phagesky #microsky
journals.asm.org/doi/epub/10....
#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)
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...
genomebiology.biomedcentral.com
April 25, 2024 at 8:29 AM
#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)