Daniel Mende
@pangenomics.bsky.social
PI at Bio2Q - Keio University in Tokyo
https://bio2q.keio.ac.jp/
Microbiome, Computational Biology, Evolution
https://bio2q.keio.ac.jp/
Microbiome, Computational Biology, Evolution
Reposted by Daniel Mende
Last day to apply to come work with me on developing AI approaches to understanding pangenome evolution www.jobs.ac.uk/job/DOU184/p...
Postdoctoral Research Associate - Grade 7 at University of Liverpool
An opportunity for an academic position as a Postdoctoral Research Associate - Grade 7 is available, as advertised on jobs.ac.uk. Apply now and explore other academic job openings.
www.jobs.ac.uk
October 14, 2025 at 11:09 AM
Last day to apply to come work with me on developing AI approaches to understanding pangenome evolution www.jobs.ac.uk/job/DOU184/p...
Looking forward to a few great days of science at the 2025 EMBO/EMBL Human Microbiome conference #EESMicrobiome
September 16, 2025 at 7:38 AM
Looking forward to a few great days of science at the 2025 EMBO/EMBL Human Microbiome conference #EESMicrobiome
Reposted by Daniel Mende
We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7
#microsky
#microsky
Metalog
Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.
metalog.embl.de
August 15, 2025 at 8:07 AM
We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7
#microsky
#microsky
Spending some time in Germany at my parents' place after moving to Bio2Q / Keio University in Tokyo at the beginning of the year. Feels good to contemplate and find that's it was an awesome move.
We have a few open positions at Postdoc level with lots of freedom and resources. DM if interested
We have a few open positions at Postdoc level with lots of freedom and resources. DM if interested
July 19, 2025 at 1:44 PM
Spending some time in Germany at my parents' place after moving to Bio2Q / Keio University in Tokyo at the beginning of the year. Feels good to contemplate and find that's it was an awesome move.
We have a few open positions at Postdoc level with lots of freedom and resources. DM if interested
We have a few open positions at Postdoc level with lots of freedom and resources. DM if interested
Reposted by Daniel Mende
The rare microbial biosphere harbors many chemosensitive microorganisms undetectable by regular shotgun metagenomics. We can now explore them using our custom target-capture sequencing approach. Impressive work by
Claudia Sanchis, part of her PhD thesis!
www.biorxiv.org/content/10.1...
Claudia Sanchis, part of her PhD thesis!
www.biorxiv.org/content/10.1...
June 25, 2025 at 7:25 PM
The rare microbial biosphere harbors many chemosensitive microorganisms undetectable by regular shotgun metagenomics. We can now explore them using our custom target-capture sequencing approach. Impressive work by
Claudia Sanchis, part of her PhD thesis!
www.biorxiv.org/content/10.1...
Claudia Sanchis, part of her PhD thesis!
www.biorxiv.org/content/10.1...
Reposted by Daniel Mende
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
myloasm-docs.github.io
myloasm - metagenomic assembly with (noisy) long reads
myloasm-docs.github.io
May 28, 2025 at 5:54 PM
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
myloasm-docs.github.io
Reposted by Daniel Mende
New #MicrobiomeDigest is OUT microbiomedigest.com/2025/02/13/1...
- infant gut / @pangenomics.bsky.social
- gut-brain / @johannajoyce.bsky.social
- PHLAME / @quevan.bsky.social
- invitation for the next week @microbiomevif.bsky.social
- Outreachy open call
& more.
Happy Friday!
- infant gut / @pangenomics.bsky.social
- gut-brain / @johannajoyce.bsky.social
- PHLAME / @quevan.bsky.social
- invitation for the next week @microbiomevif.bsky.social
- Outreachy open call
& more.
Happy Friday!
February 14, 2025
Check out my list of selected latest microbiome studies and see you next week at #MVIF! Gut microbiome Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy response…
microbiomedigest.com
February 14, 2025 at 7:24 AM
New #MicrobiomeDigest is OUT microbiomedigest.com/2025/02/13/1...
- infant gut / @pangenomics.bsky.social
- gut-brain / @johannajoyce.bsky.social
- PHLAME / @quevan.bsky.social
- invitation for the next week @microbiomevif.bsky.social
- Outreachy open call
& more.
Happy Friday!
- infant gut / @pangenomics.bsky.social
- gut-brain / @johannajoyce.bsky.social
- PHLAME / @quevan.bsky.social
- invitation for the next week @microbiomevif.bsky.social
- Outreachy open call
& more.
Happy Friday!
Though it's already a weeks ago, the newest paper from the (old) lab came out.
We explored the drivers of Bifidobacterium longum subspecies dynamics in the infant gut in detail. Still fascinated by the interplay of ecology, metabolic capacity and diet
peerj.com/articles/186...
We explored the drivers of Bifidobacterium longum subspecies dynamics in the infant gut in detail. Still fascinated by the interplay of ecology, metabolic capacity and diet
peerj.com/articles/186...
Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome
Background The initial colonization of the infant gut is a complex process that defines the foundation for a healthy microbiome development. Bifidobacterium longum is one of the first colonizers of ne...
peerj.com
February 12, 2025 at 6:54 AM
Though it's already a weeks ago, the newest paper from the (old) lab came out.
We explored the drivers of Bifidobacterium longum subspecies dynamics in the infant gut in detail. Still fascinated by the interplay of ecology, metabolic capacity and diet
peerj.com/articles/186...
We explored the drivers of Bifidobacterium longum subspecies dynamics in the infant gut in detail. Still fascinated by the interplay of ecology, metabolic capacity and diet
peerj.com/articles/186...
In the beginning of the year, I moved to the Bio2Q Institute at Keio University in Tokyo (bio2q.keio.ac.jp). Really happy to be here and it's an amazing place to do microbiome research. We are looking for postdocs, so if you're interested please DM or email
Bio2Q : Keio University Human Biology-Microbiome-Quantum Research Center
Bio2Q will develop novel research techniques to understand the interactions between multiple organs and the microbiome, and develop methods to apply quantum computing to human biology.
bio2q.keio.ac.jp
January 30, 2025 at 7:51 AM
In the beginning of the year, I moved to the Bio2Q Institute at Keio University in Tokyo (bio2q.keio.ac.jp). Really happy to be here and it's an amazing place to do microbiome research. We are looking for postdocs, so if you're interested please DM or email
Another year, another attempt to fix my affiliation for that clarivate list everyone is posting about. Let's see if my postdoc institution ask for a quick interview with me again
November 21, 2024 at 9:21 PM
Another year, another attempt to fix my affiliation for that clarivate list everyone is posting about. Let's see if my postdoc institution ask for a quick interview with me again
Today in how to destroy a social Network: Partner with a despised entity.
What will be the next episode in this ongoing series?
What will be the next episode in this ongoing series?
November 19, 2023 at 11:55 AM
Today in how to destroy a social Network: Partner with a despised entity.
What will be the next episode in this ongoing series?
What will be the next episode in this ongoing series?
I'm at #EESMicrobiome this week, will try to post about some highlights
September 20, 2023 at 12:07 PM
I'm at #EESMicrobiome this week, will try to post about some highlights
New site, and a new attempt at being more active online!
September 20, 2023 at 12:05 PM
New site, and a new attempt at being more active online!