| Homepage | https://www.bork.embl.de/ |
| GitHub | https://github.com/grp-bork/ |
| BlueSky | https://bsky.app/profile/borklab.bsky.social |
Peer did pioneering work in so many research fields, and we aim that our research on the microbiome within the human gut and across environments will continue in his spirit. We have many ongoing projects, papers under review, and some coming out soon.
Thank you to everyone who reached out or shared what he meant to them and how he inspired them! We will keep working together, striving to fulfill Peer's scientific legacy. We hope you'll follow along!
It has been two weeks since the unexpected death of Peer Bork, and all of us in his research group are deeply missing him. His scientific vision brought us together as a team, and we are immensely grateful for the time we spent together. ๐งต
https://www.embl.org/news/people-perspectives/remembering-peer-bork-obituary/
Dear #Microbiology community ๐งซ
2025 was a highly successful year for #nfdi4microbiota: mid-term evaluation passed with flying colors, renewal proposal submitted & defended, widely used FAIR services launched, expanded training & outreach, and strengthened collaborations across #NFDI life sciences consortia. A highlight: our Annual Conference in Cologne, bringing the community together for exchange & networking.
We wish you peaceful holidays and a great start to a healthy and successful 2026! ๐โจ
During my PhD @borklab.bsky.social, we extracted drug side effect data from package inserts and used the dataset to predict new drug targets (https://doi.org/10.1126/science.1158140) and pinpoint proteins that mediate the side effects (https://doi.org/10.1038/msb.2013.10). We also published the underlying database, but life intervened and funding changed, so SIDER http://sideeffects.embl.de/ is unfortunately gathering dust since its last update in 2015.
But there's good news: ChEMBL and OpenTargets are starting a new effort to mine the available data and produce a high-quality databases! Text-mining tools have progressed a lot in the last two decades, and I'm excited to see what can be done now.
More info https://chembl.blogspot.com/2025/12/new-position-nlp-data.html
Apply here: https://embl.wd103.myworkdayjobs.com/EMBL/job/Hinxton-Cambridgeshire/NLP-Data-Scientist-Scientific-Data-Engineer_JR2866 The position is at EBI.
Targets for drugs have so far been predicted on the basis of molecular or cellular features, for example, by exploiting similarity in chemical structure or in activity across cell lines. We used phenotypic side-effect similarities to infer whether ...
metaTraits: https://metatraits.embl.de/ ๐ฆ Interactively explore 140+ ๐บ๐ถ๐ฐ๐ฟ๐ผ๐ฏ๐ถ๐ฎ๐น ๐ฝ๐ต๐ฒ๐ป๐ผ๐๐๐ฝ๐ถ๐ฐ ๐๐ฟ๐ฎ๐ถ๐๐, harmonized & integrated from culture-derived collections ๐ฌ & genome-based predictions ๐งฌ for >2M MAGs & genomes.
See the publication at NAR: https://doi.org/10.1093/nar/gkaf1241 and the BlueSky thread by @dpodlesny https://bsky.app/profile/podlesny.bsky.social/post/3m6zj2zoptc2y
Even more resource papers from the group in the NAR Database Issue!
VIRE is a planetary-scale database of >1.7M viral genomes reconstructed from 100k+ metagenomes across diverse environments https://doi.org/10.1093/nar/gkaf1225 , led by Suguru Nishijima. Website: https://vire.embl.de/
The paper by @biocs has been published in the NAR Database Issue! https://doi.org/10.1093/nar/gkaf1118
Visit the database itself on https://metalog.embl.de/ to access manually annotated contextual data for #microbiome samples around the globe. We're up to 1000 included studies as of today!
New preprint from lab: https://www.biorxiv.org/content/10.1101/2025.08.14.670324v1 describing the Metalog database of manually annotated contextual data for >110k metagenomics samples around the globe https://metalog.embl.de/
See Bluesky thread for more info: https://bsky.app/profile/biocs.bsky.social/post/3lwgfkpthjs2d
At the ISMB conference, Anastasia @agrekova.bsky.social will present her recent work on detecting mobile genetic elements in both reference and metagenome-assembled genomes in the Microbiome track on Thursday at 3 pm. Come for a sneak peek of the content in https://promge.embl.de/ version 2 (to be released in ~1 month)!
NFDI4Microbiota
Michael Kuhn
