Marisa I. Keller
@maelschermarisa.bsky.social
Postdoc | she/her | University Copenhagen
Scientist decoding the Human and Microbiome Relationship via Computational Biology 👩💻
A lover of music 🎶🎷 and the call of the wild 🌿🏔️
Scientist decoding the Human and Microbiome Relationship via Computational Biology 👩💻
A lover of music 🎶🎷 and the call of the wild 🌿🏔️
Reposted by Marisa I. Keller
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-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
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
academic.oup.com
October 31, 2025 at 3:16 PM
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-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Reposted by Marisa I. Keller
Finding microbes in cancer sequencing data has been controversial. Are we seeing real biology… or just contamination + batch effects?
September 3, 2025 at 7:00 PM
Finding microbes in cancer sequencing data has been controversial. Are we seeing real biology… or just contamination + batch effects?
Reposted by Marisa I. Keller
We're still not finding any good evidence for a microbiome in any cancer type: see our new paper in @ScienceTM led by PhD student Yuchen (Peter) Ge www.science.org/doi/10.1126/... and the accompanying news piece, www.science.org/content/arti...
Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project
An analysis of TCGA whole-genome sequencing samples yields a comprehensive resource for investigating the role of microbes in cancer.
www.science.org
September 3, 2025 at 8:45 PM
We're still not finding any good evidence for a microbiome in any cancer type: see our new paper in @ScienceTM led by PhD student Yuchen (Peter) Ge www.science.org/doi/10.1126/... and the accompanying news piece, www.science.org/content/arti...
Reposted by Marisa I. Keller
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
Reposted by Marisa I. Keller
Symbnet PhD Summer School on Host-Microbe Symbioses - Oeiras Portugal. Students from all over the world are eligible, we sponsor selected students. Please Repost!
gimm.idloom.events/phd-summer-s...
gimm.idloom.events/phd-summer-s...
PhD Summer School on Host-Microbe Symbioses 2025
Symbnet PhD Summer School on Host-Microbe Symbioses Gulbenkian Institute for Molecular Medicine (GIMM) & Católica Biomedical Research Centre (CBR) July 06...
gimm.idloom.events
March 16, 2025 at 12:26 PM
Symbnet PhD Summer School on Host-Microbe Symbioses - Oeiras Portugal. Students from all over the world are eligible, we sponsor selected students. Please Repost!
gimm.idloom.events/phd-summer-s...
gimm.idloom.events/phd-summer-s...
Reposted by Marisa I. Keller
🚀 7th GA #Meeting in Cologne, Germany from 27-29 January 2025! A huge thank you to everyone for sharing their latest results and project updates! 👏
And of course, we wrapped it up with some after-work fun, exploring Cologne with a @sciencerallye.bsky.social! 🏙️ ⛲
And of course, we wrapped it up with some after-work fun, exploring Cologne with a @sciencerallye.bsky.social! 🏙️ ⛲
February 17, 2025 at 10:00 AM
🚀 7th GA #Meeting in Cologne, Germany from 27-29 January 2025! A huge thank you to everyone for sharing their latest results and project updates! 👏
And of course, we wrapped it up with some after-work fun, exploring Cologne with a @sciencerallye.bsky.social! 🏙️ ⛲
And of course, we wrapped it up with some after-work fun, exploring Cologne with a @sciencerallye.bsky.social! 🏙️ ⛲
Reposted by Marisa I. Keller
Dear #microsky what is your favorite tool to manage your own strain lab collection (from storage to genomics)? we are looking for open source solution.
November 22, 2024 at 10:32 PM
Dear #microsky what is your favorite tool to manage your own strain lab collection (from storage to genomics)? we are looking for open source solution.
Nice work @fmikus.bsky.social
It's amazing how much the EMBL pond has to offer! Consider adding your images here: maps.app.goo.gl/Jsc1dvQKEtqd...
It's amazing how much the EMBL pond has to offer! Consider adding your images here: maps.app.goo.gl/Jsc1dvQKEtqd...
November 21, 2024 at 7:11 AM
Nice work @fmikus.bsky.social
It's amazing how much the EMBL pond has to offer! Consider adding your images here: maps.app.goo.gl/Jsc1dvQKEtqd...
It's amazing how much the EMBL pond has to offer! Consider adding your images here: maps.app.goo.gl/Jsc1dvQKEtqd...
I am happy to see this paper published. Already a fan of the preprint!
Reading "A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies" from our friends in Berlin and in Leiden
Quotes are from the paper (minor edits for space), non quoted text is me
link.springer.com/article/10.1...
Quotes are from the paper (minor edits for space), non quoted text is me
link.springer.com/article/10.1...
A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies - Genome Biology
Background In microbiome disease association studies, it is a fundamental task to test which microbes differ in their abundance between groups. Yet, consensus on suitable or optimal statistical method...
link.springer.com
November 19, 2024 at 8:55 AM
I am happy to see this paper published. Already a fan of the preprint!
I've been invited to review a paper for the first time! As the Bluesky community continues to grow, I'd love to hear your insights: What are your key do's and don'ts as a reviewer? Any tips for a first-time reviewer like me would be greatly appreciated!
🧪👩🔬 #SciComm
🧪👩🔬 #SciComm
November 18, 2024 at 5:26 PM
I've been invited to review a paper for the first time! As the Bluesky community continues to grow, I'd love to hear your insights: What are your key do's and don'ts as a reviewer? Any tips for a first-time reviewer like me would be greatly appreciated!
🧪👩🔬 #SciComm
🧪👩🔬 #SciComm
Reposted by Marisa I. Keller
Hot off the press: "Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations" www.sciencedirect.com/science/arti...
See below for @suguru-nishijima.bsky.social 's thread on the preprint!
#microsky #microbiome
See below for @suguru-nishijima.bsky.social 's thread on the preprint!
#microsky #microbiome
November 13, 2024 at 4:29 PM
Hot off the press: "Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations" www.sciencedirect.com/science/arti...
See below for @suguru-nishijima.bsky.social 's thread on the preprint!
#microsky #microbiome
See below for @suguru-nishijima.bsky.social 's thread on the preprint!
#microsky #microbiome
🎉 It’s finally official - I am a doctor now! 🎓 I defended my PhD last month and have just received the paperwork from my German university to make it all real. 😊 I am beyond grateful for all the incredible people, especially from the @borklab.bsky.social, who have supported me along the way!
🧫👩💻🧬👩🔬
🧫👩💻🧬👩🔬
November 12, 2024 at 10:32 AM
🎉 It’s finally official - I am a doctor now! 🎓 I defended my PhD last month and have just received the paperwork from my German university to make it all real. 😊 I am beyond grateful for all the incredible people, especially from the @borklab.bsky.social, who have supported me along the way!
🧫👩💻🧬👩🔬
🧫👩💻🧬👩🔬
Reposted by Marisa I. Keller
We're looking for a postdoc on the Computational Analysis of Environmental #Microbiome Data! www.embl.org/jobs/positio...
In the past two years, #EMBL scientists have gathered more than 3000 soil, sediment and water samples from Europe's coastlines within the #TREC expedition. (1/4)
In the past two years, #EMBL scientists have gathered more than 3000 soil, sediment and water samples from Europe's coastlines within the #TREC expedition. (1/4)
EMBL Jobs
We offer a wide range of challenging scientific and non-scientific positions at all of our European locations and encourage applications from international candidates at all career levels.
www.embl.org
November 7, 2024 at 9:24 AM
We're looking for a postdoc on the Computational Analysis of Environmental #Microbiome Data! www.embl.org/jobs/positio...
In the past two years, #EMBL scientists have gathered more than 3000 soil, sediment and water samples from Europe's coastlines within the #TREC expedition. (1/4)
In the past two years, #EMBL scientists have gathered more than 3000 soil, sediment and water samples from Europe's coastlines within the #TREC expedition. (1/4)
Reposted by Marisa I. Keller
The first day of our lab retreat is underway. We didn't venture far from EMBL, just up the hill to Königstuhl overlooking Heidelberg and the Rhine valley. However, we did invite guest from other labs who are working on the microbiome and are enjoying the discussions across the groups!
October 23, 2024 at 9:27 AM
The first day of our lab retreat is underway. We didn't venture far from EMBL, just up the hill to Königstuhl overlooking Heidelberg and the Rhine valley. However, we did invite guest from other labs who are working on the microbiome and are enjoying the discussions across the groups!
Reposted by Marisa I. Keller
Phages to the rescue: in situ editing of the gut microbiota
#TrendsMicrobiol Spotlight by Charlotte Kamm and Chase L Beisel
www.cell.com/trends/micro...
#TrendsMicrobiol Spotlight by Charlotte Kamm and Chase L Beisel
www.cell.com/trends/micro...
Phages to the rescue: in situ editing of the gut microbiota
The gut microbiome contains numerous bacteria tied to our health. However, genetically
modifying this community remains a major challenge. Brödel et al. take a critical
step by engineering bacteriopha...
www.cell.com
September 14, 2024 at 8:06 AM
Phages to the rescue: in situ editing of the gut microbiota
#TrendsMicrobiol Spotlight by Charlotte Kamm and Chase L Beisel
www.cell.com/trends/micro...
#TrendsMicrobiol Spotlight by Charlotte Kamm and Chase L Beisel
www.cell.com/trends/micro...
I am excited to share the first paper of my PhD as a preprint! 🥳
This is a huge milestone and I'm incredibly grateful to everyone who has been involved in this project. ✨ #Science #PhDLife 👩💻
This is a huge milestone and I'm incredibly grateful to everyone who has been involved in this project. ✨ #Science #PhDLife 👩💻
⚡️ Our latest preprint "Refined Enterotyping Reveals Dysbiosis in Global Fecal Metagenomes" led by @maelschermarisa.bsky.social is now available! We’ve revisited the concept of #enterotypes using a massive dataset of 16,772 human fecal #metagenomes from 38 countries! 🌍🧬 doi.org/10.1101/2024... 🧵
August 15, 2024 at 7:04 AM
Reposted by Marisa I. Keller
Interested in analyzing the human #microbiome? We're looking for postdocs! www.embl.org/jobs/positio...
We have lots of data to delve into: metagenomic and metatranscriptomic data from >1000 liver disease patients across disease stages (often w/ multiple timepoints and clinical follow-up data), 1/2
We have lots of data to delve into: metagenomic and metatranscriptomic data from >1000 liver disease patients across disease stages (often w/ multiple timepoints and clinical follow-up data), 1/2
EMBL Jobs
We offer a wide range of challenging scientific and non-scientific positions at all of our European locations and encourage applications from international candidates at all career levels.
www.embl.org
June 11, 2024 at 8:45 AM
Interested in analyzing the human #microbiome? We're looking for postdocs! www.embl.org/jobs/positio...
We have lots of data to delve into: metagenomic and metatranscriptomic data from >1000 liver disease patients across disease stages (often w/ multiple timepoints and clinical follow-up data), 1/2
We have lots of data to delve into: metagenomic and metatranscriptomic data from >1000 liver disease patients across disease stages (often w/ multiple timepoints and clinical follow-up data), 1/2
Reposted by Marisa I. Keller
Congratulations to Askarbek Orakov, who successfully defended his PhD at the University of Würzburg today!
Peer is dressed in a Kazakh traditional “Shapan”, which is given to honorable people – a gift from Askarbek's and his wife's families. Thank you very much for this!
Peer is dressed in a Kazakh traditional “Shapan”, which is given to honorable people – a gift from Askarbek's and his wife's families. Thank you very much for this!
April 30, 2024 at 4:39 PM
Congratulations to Askarbek Orakov, who successfully defended his PhD at the University of Würzburg today!
Peer is dressed in a Kazakh traditional “Shapan”, which is given to honorable people – a gift from Askarbek's and his wife's families. Thank you very much for this!
Peer is dressed in a Kazakh traditional “Shapan”, which is given to honorable people – a gift from Askarbek's and his wife's families. Thank you very much for this!
Reposted by Marisa I. Keller
Excited to share our latest preprint on a novel computational tool to predict fecal microbial load solely from relative species profiles! Our study revealed that fecal microbial load is a substantial confounder in microbiome-disease association studies.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
March 19, 2024 at 11:41 AM
Excited to share our latest preprint on a novel computational tool to predict fecal microbial load solely from relative species profiles! Our study revealed that fecal microbial load is a substantial confounder in microbiome-disease association studies.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Our latest publication highlights the importance of studying antimicrobial resistance! We found an increase in bacterial antibiotic inactivation genes and infections with multi drug-resistant bacteria in patients with decompensated cirrhosis treated with terlipressin (a non-antibiotic drug).
🧫🧪🧬👩🔬
🧫🧪🧬👩🔬
Terlipressin therapy is associated with increased risk of colonisation with multidrug‐resistant bacteria in patients with decompensated cirrhosis
Alimentary Pharmacology & Therapeutics is a global pharmacology journal concerned with the effects of drugs on the human gastrointestinal and hepato-biliary systems
onlinelibrary.wiley.com
March 12, 2024 at 6:56 PM
Our latest publication highlights the importance of studying antimicrobial resistance! We found an increase in bacterial antibiotic inactivation genes and infections with multi drug-resistant bacteria in patients with decompensated cirrhosis treated with terlipressin (a non-antibiotic drug).
🧫🧪🧬👩🔬
🧫🧪🧬👩🔬
Reposted by Marisa I. Keller
Posted the same on X - show me that the blue skies are better! Any ideas on how to quantify sulfite in a(n aqueous or culture) sample? Thanks!
December 5, 2023 at 10:09 PM
Posted the same on X - show me that the blue skies are better! Any ideas on how to quantify sulfite in a(n aqueous or culture) sample? Thanks!
At the end of a busy year, we are on a retreat in Strasbourg for a few days of brainstorming, team-building fun, scientific discussions across the many topics we're working on, and of course to enjoy the Christmas market and the sights
November 30, 2023 at 10:40 AM
Reposted by Marisa I. Keller
🧪 Scientist?
🟦 New to BlueSky?
👀 Wanna find posts by other people in your area and use the right hashtags in your own posts?
📃 Here’s a list of over 170 science-related feeds and their hashtags.
#AcademicSky #PhDSky
🟦 New to BlueSky?
👀 Wanna find posts by other people in your area and use the right hashtags in your own posts?
📃 Here’s a list of over 170 science-related feeds and their hashtags.
#AcademicSky #PhDSky
BlueSky Science-Related Feeds
Sheet1
Likes,Name (Click to visit feed),Tags,Contact to ask to be added to contributor list
11,<a href="https://bsky.app/profile/did:plc:ftnzzw4cnon2pzpw7i5m2xu7/feed/aaaiqnkwsgsz6">#AI&HCI</a>,#HCI,...
docs.google.com
November 2, 2023 at 11:34 AM
🧪 Scientist?
🟦 New to BlueSky?
👀 Wanna find posts by other people in your area and use the right hashtags in your own posts?
📃 Here’s a list of over 170 science-related feeds and their hashtags.
#AcademicSky #PhDSky
🟦 New to BlueSky?
👀 Wanna find posts by other people in your area and use the right hashtags in your own posts?
📃 Here’s a list of over 170 science-related feeds and their hashtags.
#AcademicSky #PhDSky
Reposted by Marisa I. Keller
**SAVE THE DATE**
NOV 14 & 15/16
Remember to check the date and time in your region!
FREE registration hopin.com/events/micro...
We will have the pleasure to host 🇩🇪 @merenbey.bsky.social ey.bsky.social as a keynote & amazing speakers with their short talks and highlights (see below)
1/2
NOV 14 & 15/16
Remember to check the date and time in your region!
FREE registration hopin.com/events/micro...
We will have the pleasure to host 🇩🇪 @merenbey.bsky.social ey.bsky.social as a keynote & amazing speakers with their short talks and highlights (see below)
1/2
October 31, 2023 at 11:05 AM
**SAVE THE DATE**
NOV 14 & 15/16
Remember to check the date and time in your region!
FREE registration hopin.com/events/micro...
We will have the pleasure to host 🇩🇪 @merenbey.bsky.social ey.bsky.social as a keynote & amazing speakers with their short talks and highlights (see below)
1/2
NOV 14 & 15/16
Remember to check the date and time in your region!
FREE registration hopin.com/events/micro...
We will have the pleasure to host 🇩🇪 @merenbey.bsky.social ey.bsky.social as a keynote & amazing speakers with their short talks and highlights (see below)
1/2