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Bork Group at EMBL Heidelberg

@borklab.bsky.social
2.6K followers 221 following 87 posts

Computational biology lab focusing on microbiomes in the human gut and the environment Homepage: www.bork.embl.de Mastodon: mstdn.science/@BorkLab

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Reposted by Bork Group at EMBL Heidelberg
EMBL Events @events.embl.org · 28/09/2026
Thanks to additional funding, the registration fees for #EMBLBorkMemorial have been set at a reduced rate. This symposium will reflect on Peer Bork's past achievements and explore future directions of fields such as protein biology and more. Submit your abstract by 10 Nov: s.embl.org/pbs27-01-bl
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Reposted by Bork Group at EMBL Heidelberg
EMBL Events @events.embl.org · 07/09/2026
At the start of 2026, EMBL lost long-serving colleague and Interim Director General Peer Bork. Join us in commemorating Peer and his legacy at the #EMBLBorkMemorial. Submit your abstract by 10 November: s.embl.org/pbs27-01-bl
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 03/09/2026
We revived one of our longest-running services, PAL2NAL: www.bork.embl.de/pal2nal/ -- converting a protein sequence alignment and the corresponding DNA sequences into a codon alignment. Even after 20 years, it is still being cited hundreds of times a year! scholar.google.com/scholar?cite...
bork.embl.de
PAL2NAL
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 01/09/2026
We've been very moved by the tributes paid to Peer at conferences around the world: e.g. at ISME by Jeroen Raes, at ECCB by Christian von Mering, and at the Tara conference by Chris Bowler. Thank you! @isme-microbes.bsky.social @eccb-europe.bsky.social @taraoceans-science.bsky.social @raeslab.org
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Reposted by Bork Group at EMBL Heidelberg
European Conference on Computational Biology @eccb-europe.bsky.social · 01/09/2026
This morning we remembered four computational biology pioneers, who the world sadly lost over the past year. Thank you to all speakers for your moving tributes at ECCB. #ECCB2026 #Bioinformatics
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EMBL Events @events.embl.org · 01/09/2026
What a way to start #EMBLPlanktonDiscoveries! ⛵️🌊 We’re live from EMBL Heidelberg, where scientific organiser Chris Bowler has opened the first edition of the meeting, followed by a keynote lecture from Éric Karsenti. We’re excited for what’s ahead this week!
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Jaime Huerta-Cepas @jhcepas.bsky.social · 05/08/2026
The CGMLab is seeking an experienced postdoctoral researcher to work on an EU project focusing on the bioprospecting of novel microbial enzymes and pathways through metagenomics. Further information and application form can be found at: jobs.cgmlab.org/o/postdoc-po...
jobs.cgmlab.org
Postdoc position - Metagenomic mining & Bioprospecting of novel …
The Comparative Genomics & Metagenomics Lab (CGMLab, https://cgmlab.org) at the Centre for Plant Biotechnology and Genomics (CBGP, Madrid) is seeking a postdoc…
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Reposted by Bork Group at EMBL Heidelberg
Jaime Huerta-Cepas @jhcepas.bsky.social · 05/08/2026
The CGMLab is seeking an experienced postdoctoral researcher to work on an international project focusing on the clinical associations of the microbiome of the female reproductive tract and heavy menstrual bleeding disorder. Applications and info at jobs.cgmlab.org/o/postdoc-po...
jobs.cgmlab.org
Postdoc position - Microbiome Signatures of Heavy Menstrual Blee…
The Comparative Genomics & Metagenomics Lab (CGMLab, https://cgmlab.org) at the Centre for Plant Biotechnology and Genomics (CBGP, Madrid) is seeking a postdoc…
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EMBL Events @events.embl.org · 31/07/2026
Get your calendars, because the new 2027 EMBL Annual Poster has arrived: s.embl.org/2027-poster Whether you'd like to enhance your skills in a practical course or engage with the latest research at one of our conferences, we've got you covered. See you at EMBL in 2027! 🙌 #LifeSciences #EMBL
The image depicts the 2027 EMBL Annual Poster featuring the new events programme for 2027. On the left side is a colorful banner, on the right is the list of events sorted by month
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Reposted by Bork Group at EMBL Heidelberg
EMBL @embl.org · 29/07/2026
EMBL researchers are helping improve how satellites interpret tropical forests. EMBL researchers and collaborators are combining microbial DNA and RNA sequencing with airborne and satellite observations to give satellites a ’microbial sense’ of forests. More info 👉 www.embl.org/news/science...
embl.org
Understanding tropical forest health from above and below | EMBL
EMBL, NASA, and partner institutions are combining genomics with remote sensing to give satellites a microbial sense of tropical forests.
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 29/07/2026
New preprint from the lab! "Planetary structure and drivers of diazotroph communities reveal key reservoirs of nitrogen-fixation potential" Nitrogen fixation is scattered right across the prokaryotic tree — but it's heterotrophs, not cyanobacteria, that dominate the potential. 🧵
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Reposted by Bork Group at EMBL Heidelberg
Lisa Maier Lab | Tübingen @lisamaierlab.bsky.social · 29/06/2026
Don‘t forget to register for what promises to be an end-of-the-year highlight in functional microbiome research 👇🏻 !
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Reposted by Bork Group at EMBL Heidelberg
EMBL @embl.org · 11/06/2026
EMBL and partners carried out a new pilot project in Luxembourg to study how freshwater microbiomes respond to environmental change. By sampling rivers and soils along the Moselle and Rhine, researchers aim to provide a way to track ecosystem stress and pollution. www.embl.org/news/connect...
embl.org
Tracing environmental change through river microbiomes in Luxembourg  | EMBL
EMBL and partners carried out a new TREC pilot project in Luxembourg to study how freshwater microbiomes respond to environmental change.
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Reposted by Bork Group at EMBL Heidelberg
Jonas Schiller @jonas-bio.bsky.social · 10/06/2026
Our new paper „Variations in the latitudinal diversity gradients of the ocean microbiome“ was just published in @cp-cellhostmicrobe.bsky.social 🥳 We present a global analysis of prokaryotic #biodiversity in the surface and mesopelagic layers of the ocean 🦠🌊 www.cell.com/cell-host-mi...
cell.com
Variations in the latitudinal diversity gradients of the ocean microbiome
Eriksson et al. conduct a global marine microbiome diversity analysis and demonstrate how the surface ocean latitudinal diversity gradient is disproportionately shaped by a few species-rich taxa. Mask...
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 01/06/2026
New in @natgenet.nature.com: a moving obituary for Peer. Francesca Ciccarelli, Jan Korbel & Christian von Mering reflect on his scientific vision, from protein domains and genome evolution to metagenomics, and on his generosity as a mentor and friend to so many. www.nature.com/articles/s41...
nature.com
Peer Bork (1963–2026) - Nature Genetics
Nature Genetics - Peer Bork (1963–2026)
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Reposted by Bork Group at EMBL Heidelberg
Marisa Isabell Keller @maelschermarisa.bsky.social · 01/06/2026
Our work exploring host-microbial co-metabolism of bile acids in patients with alcohol-related liver disease (ALD) has been published in the JHEP Reports: www.sciencedirect.com/science/arti... 🪐 A big thank you to everyone involved, to the GALAXY and MicrobLiver consortia who made this possible! 🙌
sciencedirect.com
Alcohol-related liver disease disrupts bile acid homeostasis and gut microbial bile acid metabolism
Alcohol overuse disrupts liver function and alters gut microbial communities, with alcohol-related liver disease (ALD) causing half of all liver-relat…
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Reposted by Bork Group at EMBL Heidelberg
Sebastian Schmidt @tsbschm.bsky.social · 28/05/2026
Our study describing `microntology` and annotations for >300k metagenomes is now online in Bioinformatics @academic.oup.com : academic.oup.com/bioinformati... Congratulations to @fullam.bsky.social @vishnuprasoodanan.bsky.social & @biocs.bsky.social ! See the thread below for more details.
academic.oup.com
microntology: a lightweight, data-driven controlled vocabulary to describe Earth’s microbial habitats
AbstractMotivation. Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and
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Reposted by Bork Group at EMBL Heidelberg
MICROB-PREDICT @microb-predict.bsky.social · 16/04/2026
🚨Take this 15 min survey to shape the future of #Hepatology: 👉 survey.alchemer.eu/s3/91085482/... 🦠 #Microbiome-based mechanisms & biomarkers for improved patient stratification + prediction of therapeutic response in decompensated #Cirrhosis / #ACLF ⏳Survey closes on 17 May @easlnews.bsky.social
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 16/04/2026
Due to some IT problems, the Bork group homepage and various services such as SPIRE and Metalog are unfortunately going to be unavailable for a couple of days. We're sorry for that and hope that the outage can soon be resolved!
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Reposted by Bork Group at EMBL Heidelberg
Sebastian Schmidt @tsbschm.bsky.social · 13/03/2026
@fullam.bsky.social has pushed a new #GUNC release, v1.1.0: github.com/grp-bork/gun... It fixes some bugs, updates some underlying databases and brings new features (e.g. you can now BYODB – bring your own database). GUNC v1.1.0 is also live on #bioconda .
github.com
Release v1.1.0 · grp-bork/gunc
Summary ^^^^^^^ This release adds support for two new reference databases (ProGenomes 3, GTDB r214) and a custom database option. A new gunc check subcommand validates your environment before submi...
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Reposted by Bork Group at EMBL Heidelberg
Michael Zimmermann Lab @zimmermannlab.bsky.social · 16/03/2026
Excited to share the upcoming EMBO | EMBL Symposium “Metabolic interactions shape ecosystems” 🧬🌍 📍 Heidelberg & online 📅 21–24 July 2026 Abstract deadline: 14 April! More info & registration: www.embl.org/about/info/c... #Metabolism #Microbiome #SystemsBiology #Ecology #EMBL #EMBO
embl.org
Metabolic interactions shape ecosystems
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Thiago Carvalho @cyrilpedia.bsky.social · 10/03/2026
'Phil was also the founding Editor-in-Chief of PLOS Computational Biology, where he created the beloved Ten Simple Rules series. He was so prolific in the series that the meta-article “Ten Simple Rules for Writing a PLOS Ten Simple Rules Article” literally includes, as Rule 4: “Be Philip E. Bourne.”
blog.stephenturner.us
Remembering Phil Bourne
Personal reflections on a legendary scientist, leader, builder, and mentor
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Reposted by Bork Group at EMBL Heidelberg
EMBL-EBI @ebi.embl.org · 10/02/2026
We’re hiring: Research Group Leader in computational biology. Are you generating more research ideas than you can explore? Lead cutting-edge AI & biology research at EMBL-EBI. Apply by 11 April 2026: embl.wd103.myworkdayjobs.com/en-US/EMBL/j... #ScienceCareers @ewaldlab.org @embl.org
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 09/02/2026
Just published: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" by @podlesny.bsky.social @chanyeong-kim.bsky.social and @jonas-bio.bsky.social www.cell.com/cell/fulltex... See the quoted post below for a thread on the preprint!
cell.com
Planetary microbiome structure and generalist-driven gene flow across disparate habitats
A planetary-scale analysis of over 85,000 metagenomes establishes a framework for exploring the structure and drivers of global microbial habitats, revealing that generalist species bridge ecological ...
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Reposted by Bork Group at EMBL Heidelberg
EMBL @embl.org · 09/02/2026
In the largest study of its kind, scientists in the Bork Group at EMBL have found that a small subset of microbes can carry and transfer genes across disparate habitats, creating a planet-wide, interconnected network of microbiomes 🌍 🦠 🔗 Read more here: www.embl.org/news/science...
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Elisabetta Cacace @elisca.bsky.social · 06/02/2026
Excited to announce my upcoming @snsf.ch Ambizione research group at EPFL on bacteria-host interactions, combining systems approaches and microphysiological models. 🚨 We have an open PhD position! More info on projects and how to apply here: elisabettacacace.github.io/BHI-Lab/ 🧪
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 30/01/2026
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. 🧵
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EMBL @embl.org · 22/01/2026
EMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond. We extend our deepest condolences to his family, friends, and colleagues. www.embl.org/news/people-...
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Sebastian Schmidt @tsbschm.bsky.social · 13/01/2026
We just released a @biorxivpreprint.bsky.social describing the *microntology*, a lightweight controlled vocabulary that we have been using for a while to tag metagenomes with contextual data. Study by @fullam.bsky.social @vishnuprasoodanan.bsky.social et al: 1/ www.biorxiv.org/content/10.6...
biorxiv.org
microntology: a lightweight, data-driven controlled vocabulary to describe Earth's microbial habitats
Summary. We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k m...
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Reposted by Bork Group at EMBL Heidelberg
Lisa Maier Lab | Tübingen @lisamaierlab.bsky.social · 22/12/2025
We’re hiring 2 Postdocs (f/m/d) in Drug–Microbiome–Host Interactions 🦠💊 Focus: how non-antibiotic drugs shape the gut microbiome, drug efficacy & side effects. #PostdocJobs #Microbiome #AcademicJobs Full job ad: lisamaierlab.com/wp-content/u...
lisamaierlab.com
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Michael Kuhn @biocs.bsky.social · 11/12/2025
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 chembl.blogspot.com/2025/12/new-... Apply here: embl.wd103.myworkdayjobs.com/EMBL/job/Hin... The position is at @ebi.embl.org #ScienceJobs #AcademicSky #ChemSky #BioSky [3/3]
chembl.blogspot.com
New position: NLP Data Scientist/Scientific Data Engineer
As part of a funded collaboration with Open Targets, there are two open positions as part of a team to develop a drug side effect resource:...
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Reposted by Bork Group at EMBL Heidelberg
Michael Kuhn @biocs.bsky.social · 11/12/2025
...but life intervened and funding changed, so SIDER sideeffects.embl.de is unfortunately gathering dust since its last update in 2015. But there's good news: @chembl.bsky.social and @opentargets.org are starting a new effort to mine the available data and produce a high-quality databases! [2/3]
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Michael Kuhn @biocs.bsky.social · 11/12/2025
During my PhD @borklab.bsky.social, we extracted drug side effect data from package inserts and used the dataset to predict new drug targets (doi.org/10.1126/scie...) and pinpoint proteins that mediate the side effects (doi.org/10.1038/msb....). We also published the underlying database... [1/3]
doi.org
Drug Target Identification Using Side-Effect Similarity
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 pheno...
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EMBL @embl.org · 11/12/2025
Congratulations, Julia Mahamid! Julia Mahamid receives the @dfg.de Leibniz Prize for her work on structural cell biology! #LeibnizPreis
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BF Francis Ouellette @bffo.bsky.social · 09/12/2025
From @jhcepas.bsky.social and colleagues in the @narjournal.bsky.social #NARDatabaseIssue | eggNOG v7: phylogeny-based orthology predictions and functional annotations | #Bioinformatics #ProteinCentric #Database #OpenScience 🧬 🖥️🧪🇨🇭🇪🇸🇩🇪🔓 ⬇️ academic.oup.com/nar/advance-...
academic.oup.com
eggNOG v7: phylogeny-based orthology predictions and functional annotations
Abstract. The eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) database is a phylogenomic resource for orthology inference, evol
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Reposted by Bork Group at EMBL Heidelberg
Daniel Podlesny @podlesny.bsky.social · 02/12/2025
We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes. Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
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Suguru Nishijima @suguru-nishijima.bsky.social · 01/12/2025
Happy to announce VIRE, a planetary-scale database of >1.7M viral genomes reconstructed from 100k+ metagenomes across diverse environments! In collaboration with @fullam.bsky.social, @tsbschm.bsky.social, and @borklab.bsky.social. academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1225/8356007
academic.oup.com
VIRE: a metagenome-derived, planetary-scale virome resource with environmental context
Abstract. Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a compr
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Reposted by Bork Group at EMBL Heidelberg
Sebastian Schmidt @tsbschm.bsky.social · 20/11/2025
Congrats @fullam.bsky.social @pangenomics.bsky.social @borklab.bsky.social & team(s). Great to see this published! proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...
academic.oup.com
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes
Abstract. The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands rob
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Reposted by Bork Group at EMBL Heidelberg
Michael Kuhn @biocs.bsky.social · 06/11/2025
We're up to 1000 studies in metalog.embl.de ! For the past year the focus was on finding inconsistencies in the data and creating the website, but now I have more time to go through the backlog of annotated issues to do QC and load them into the database.
Metalog statistics, showing 1000 included studies
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Sebastian Schmidt @tsbschm.bsky.social · 31/10/2025
Great to see this finally published! Metalog: curated and harmonised contextual data for global metagenomics samples now out in @narjournal.bsky.social academic.oup.com/nar/advance-...
academic.oup.com
Metalog: curated and harmonised contextual data for global metagenomics samples
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 15/10/2025
Our newest preprint is the work of two talented PhD students: Dominic Eriksson (working in the labs of Meike Vogt, Nicolas Gruber & Shinichi Sunagawa @ethz.ch) and @jonas-bio.bsky.social from our group @embl.org, investigating latitudinal diversity gradients of the ocean microbiome (🧵 linked below)
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Jonas Schiller @jonas-bio.bsky.social · 15/10/2025
Latitudinal diversity gradients (LDGs) are found across 🌱🐨🦠 but their underlying mechanisms remain unclear. In this study, we highlight that LDGs are not universal in marine microbiomes but reflect lineage-specific ecological strategies and environmental responses. doi.org/10.1101/2025...
doi.org
Variations in the latitudinal diversity gradients of the ocean microbiome
Latitudinal diversity gradients (LDGs), typically declining from the equator to the poles, are among the most pervasive macroecological patterns, yet their generality and underlying drivers in the oce...
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Erick Ratamero @erickratamero.com · 08/10/2025
The Data Science team at EMBL is hiring for two open positions! First, for a Scientific Community Manager, focusing on community aspects and training on data science. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
embl.wd103.myworkdayjobs.com
Scientific Community Manager
EMBL is Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation with more than 110 independent research groups and teams performing scientific research in disci...
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Anna Mankowski @oceanna.bsky.social · 30/09/2025
Had a great time yesterday presenting my efforts to use large-scale computational analyses to better understand marine microbes and their impact on carbon cycling. Thanks #SAME18 for the opportunity!
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EMBL Events @events.embl.org · 16/09/2025
Our scientific organisers opened ‘The human microbiome’ symposium by giving us a brief update on their most recent work 🦠 #EESMicrobiome 🔹Mani Arumugam, University of Copenhagen 🔹Ami Bhatt, Stanford University School of Medicine 🔹Peer Bork, EMBL Heidelberg 🔹Nicola Segata, University of Trento
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 15/08/2025
New preprint from lab: www.biorxiv.org/content/10.1... describing the Metalog database of manually annotated contextual data for >110k metagenomics samples around the globe metalog.embl.de See the thread below from @biocs.bsky.social for more info!
biorxiv.org
Metalog: curated and harmonised contextual data for global metagenomics samples
Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals and the environment. While sequencing data is deposited in public databases, the associated context...
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EMBL @embl.org · 07/08/2025
We’re looking for curious, innovative science leaders at EMBL Heidelberg! 🔬🧬🦠 Join a vibrant, interdisciplinary community where collaboration and innovation are nurtured at all levels. Take a look at these four open positions 👇
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Typas Lab @typaslab.bsky.social · 30/07/2025
Ready to lead pioneering research that bridges systems-level investigations of biological systems to molecular mechanism? The EMBL Molecular Systems Biology Unit in Heidelberg is hiring a Group Leader!
embl.wd103.myworkdayjobs.com
Group Leader – Molecular Systems Biology Unit
Are you ready to lead groundbreaking research in Molecular Systems Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group, addressing original biological ...
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Raes Lab @raeslab.org · 23/07/2025
We're hiring a postdoc!🚨 Study human-associated microbial communities in health & disease. 🔬Requirements: - PhD in bioinformatics, microbiology, or related field - Expertise in omics data analysis - Micro & molecular bio techniques are a plus! Apply now!🌟 jobs.vib.be/j/119682/pos...
jobs.vib.be
Postdoctoral position in human gut microbiome and bioinformatics - VIB
About the Lab Thelab of JeroenRaes(VIB, KU Leuven) is home to a vibrant, dynamic and international group of researchers in the field of gut microbial ecology and its
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 22/07/2025
At #ISMBECCB2025, @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 promge.embl.de version 2 (to be released in ~1 month)!
promge.embl.de
proMGE
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