Matthias Flotho
@mflot.bsky.social
PhD candidate at Helmholtz Institute for Pharmaceutical Research Saarland
Pinned
Reposted by Matthias Flotho
We are excited that our paper "Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index" is now published at Bioinformatics (doi.org/10.1093/bioi...).
You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.
You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.
Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index
AbstractMotivation. The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many co
doi.org
November 27, 2025 at 11:27 AM
We are excited that our paper "Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index" is now published at Bioinformatics (doi.org/10.1093/bioi...).
You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.
You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.
Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index
doi.org/10.1093/bioi...
#metagenomics #openscience
doi.org/10.1093/bioi...
#metagenomics #openscience
Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index
AbstractMotivation. The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many co
doi.org
November 27, 2025 at 11:50 AM
Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index
doi.org/10.1093/bioi...
#metagenomics #openscience
doi.org/10.1093/bioi...
#metagenomics #openscience
Just out:
PBMCpedia: a harmonized PBMC scRNA-seq database with unified mapping and enhanced celltype annotation
doi.org/10.1093/nar/...
#openscience #scRNAseq
PBMCpedia: a harmonized PBMC scRNA-seq database with unified mapping and enhanced celltype annotation
doi.org/10.1093/nar/...
#openscience #scRNAseq
PBMCpedia: a harmonized PBMC scRNA-seq database with unified mapping and enhanced celltype annotation
Abstract. Single-cell transcriptomic studies of peripheral blood mononuclear cells (PBMCs) offer valuable insights into immune states across diverse biolog
doi.org
November 24, 2025 at 2:10 PM
Just out:
PBMCpedia: a harmonized PBMC scRNA-seq database with unified mapping and enhanced celltype annotation
doi.org/10.1093/nar/...
#openscience #scRNAseq
PBMCpedia: a harmonized PBMC scRNA-seq database with unified mapping and enhanced celltype annotation
doi.org/10.1093/nar/...
#openscience #scRNAseq
Reposted by Matthias Flotho
💥 Fewer than 3,000 scientists worldwide are working on antibiotic discovery, and progress is slowing.
We need bold action to develop new antibiotics that are both innovative and accessible to everyone, everywhere.
That’s what drives GARDP’s DER programme.
This is BIG.
#WAAW2025 #AMR #ThisIsBig
We need bold action to develop new antibiotics that are both innovative and accessible to everyone, everywhere.
That’s what drives GARDP’s DER programme.
This is BIG.
#WAAW2025 #AMR #ThisIsBig
November 23, 2025 at 12:59 PM
💥 Fewer than 3,000 scientists worldwide are working on antibiotic discovery, and progress is slowing.
We need bold action to develop new antibiotics that are both innovative and accessible to everyone, everywhere.
That’s what drives GARDP’s DER programme.
This is BIG.
#WAAW2025 #AMR #ThisIsBig
We need bold action to develop new antibiotics that are both innovative and accessible to everyone, everywhere.
That’s what drives GARDP’s DER programme.
This is BIG.
#WAAW2025 #AMR #ThisIsBig
Reposted by Matthias Flotho
⏰ tomorrow, Nov 18, 5pm Berlin/4pm London
“Data Vis for Cancer Patient Education“ - a #DataVis #BioVis talk
Link & Abstract: alt-text and also:
biovis.net/2025/meetup/ (right under picture)
“Data Vis for Cancer Patient Education“ - a #DataVis #BioVis talk
Link & Abstract: alt-text and also:
biovis.net/2025/meetup/ (right under picture)
November 18, 2025 at 9:53 AM
⏰ tomorrow, Nov 18, 5pm Berlin/4pm London
“Data Vis for Cancer Patient Education“ - a #DataVis #BioVis talk
Link & Abstract: alt-text and also:
biovis.net/2025/meetup/ (right under picture)
“Data Vis for Cancer Patient Education“ - a #DataVis #BioVis talk
Link & Abstract: alt-text and also:
biovis.net/2025/meetup/ (right under picture)
Reposted by Matthias Flotho
The Hektoria Glacier on the Antarctic Peninsula retreated by at least 8 km in two months, a rate nearly 10 times faster than previously measured for a grounded glacier, according to a study in Nature Geoscience. go.nature.com/4nETBYJ ⚒️ 🧪
November 13, 2025 at 2:29 AM
The Hektoria Glacier on the Antarctic Peninsula retreated by at least 8 km in two months, a rate nearly 10 times faster than previously measured for a grounded glacier, according to a study in Nature Geoscience. go.nature.com/4nETBYJ ⚒️ 🧪
Reposted by Matthias Flotho
Chaos is coming for scholarly publishing
#AcademicPublishing #WCRI2026 #WCRI
www.researchprofessionalnews.com/rr-news-uk-v...
#AcademicPublishing #WCRI2026 #WCRI
www.researchprofessionalnews.com/rr-news-uk-v...
Chaos is coming for scholarly publishing - Research Professional News
Buckling of commercial models alongside maturing of community-led efforts promises major shifts, says Caroline Edwards
www.researchprofessionalnews.com
November 13, 2025 at 3:37 AM
Chaos is coming for scholarly publishing
#AcademicPublishing #WCRI2026 #WCRI
www.researchprofessionalnews.com/rr-news-uk-v...
#AcademicPublishing #WCRI2026 #WCRI
www.researchprofessionalnews.com/rr-news-uk-v...
Reposted by Matthias Flotho
piRNA-directed DNA methylation may not be a mammalian invention, but can already be found in the germline of axolotl salamanders
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
November 13, 2025 at 11:54 AM
piRNA-directed DNA methylation may not be a mammalian invention, but can already be found in the germline of axolotl salamanders
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
Reposted by Matthias Flotho
Here is our Exxon study in Science, with @naomioreskes.bsky.social and @geoffreysupran.bsky.social !
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Assessing ExxonMobil’s global warming projections
ExxonMobil’s own climate models showed that fossil fuel use would cause climate warming.
www.science.org
November 3, 2025 at 3:34 PM
Here is our Exxon study in Science, with @naomioreskes.bsky.social and @geoffreysupran.bsky.social !
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
November 3, 2025 at 4:22 PM
October 27, 2025 at 2:18 PM
Reposted by Matthias Flotho
See how the U.S. got hooked on ultraprocessed foods, one of the greatest health threats of our time.
How America Got Hooked on Ultraprocessed Foods
They promised convenience and cheap nutrition. But they became one of the greatest health threats of our time.
nyti.ms
October 25, 2025 at 8:57 PM
See how the U.S. got hooked on ultraprocessed foods, one of the greatest health threats of our time.
Reposted by Matthias Flotho
Droht durch die Einigung im Zollstreit der EU mit den USA eine Schwächung von EU-Fahrzeugstandards? 😟🚗🌍
Das befürchten zahlreiche europäische Städte und zivile Organisationen in einem Brief an die EU!
Das befürchten zahlreiche europäische Städte und zivile Organisationen in einem Brief an die EU!
Accepting US car standards would risk European lives, warn cities and civil society
Opening the EU market to vehicles certified under US standards would weaken the protections that save lives in Europe, say more than 80 civil society organisations and the administrations of…
etsc.eu
October 22, 2025 at 5:01 PM
Droht durch die Einigung im Zollstreit der EU mit den USA eine Schwächung von EU-Fahrzeugstandards? 😟🚗🌍
Das befürchten zahlreiche europäische Städte und zivile Organisationen in einem Brief an die EU!
Das befürchten zahlreiche europäische Städte und zivile Organisationen in einem Brief an die EU!
Reposted by Matthias Flotho
MCPmed is live🎉 Make biomedical APIs, and databases LLM-ready via the Model Context Protocol (MCP)!
- MCPmed Templates: wrap APIs fast
- Breadcrumbs: drop LLM-readable tags in your web service
More projects online now. Star & follow: github.com/MCPmed #LLM #Bioinformatics #OpenScience
- MCPmed Templates: wrap APIs fast
- Breadcrumbs: drop LLM-readable tags in your web service
More projects online now. Star & follow: github.com/MCPmed #LLM #Bioinformatics #OpenScience
MCPmed
MCPmed has 6 repositories available. Follow their code on GitHub.
github.com
July 14, 2025 at 6:26 PM
MCPmed is live🎉 Make biomedical APIs, and databases LLM-ready via the Model Context Protocol (MCP)!
- MCPmed Templates: wrap APIs fast
- Breadcrumbs: drop LLM-readable tags in your web service
More projects online now. Star & follow: github.com/MCPmed #LLM #Bioinformatics #OpenScience
- MCPmed Templates: wrap APIs fast
- Breadcrumbs: drop LLM-readable tags in your web service
More projects online now. Star & follow: github.com/MCPmed #LLM #Bioinformatics #OpenScience
Reposted by Matthias Flotho
A few more #SingleCell and #SpatialBiology methods have been published recently, making it a total of 362 in the table I compiled over the years. lookerstudio.google.com/reporting/c3...
September 9, 2025 at 7:30 AM
A few more #SingleCell and #SpatialBiology methods have been published recently, making it a total of 362 in the table I compiled over the years. lookerstudio.google.com/reporting/c3...
Reposted by Matthias Flotho
😱 “A researcher recalled wondering about the level of 6 LIN tanks used to maintain samples “going back to the 80s” and checked on them to find that “all of them were bone dry. Then they checked with their business office and learned that “our lab hadn’t purchased any liquid nitrogen since 2016.”
Exclusive: How a researcher faked data and gaslit a labmate for years
Ryan Evanoff Sometime in early 2019, a postdoc in a veterinary microbiology lab at Washington State University (WSU) in Pullman came to suspect that a research assistant in her lab was fabricating …
retractionwatch.com
September 6, 2025 at 10:58 AM
😱 “A researcher recalled wondering about the level of 6 LIN tanks used to maintain samples “going back to the 80s” and checked on them to find that “all of them were bone dry. Then they checked with their business office and learned that “our lab hadn’t purchased any liquid nitrogen since 2016.”
Reposted by Matthias Flotho
www.ingentaconnect.com/content/wfbi...
In our new paper we have described several new species of Hypoxylaceae and found that the genus Rostrohypoxylon is obsolete because it is nested in Annulohypoxylon in the multi-locus phylogeny. Secondary metabolite profiles of all taxa are also reported.
In our new paper we have described several new species of Hypoxylaceae and found that the genus Rostrohypoxylon is obsolete because it is nested in Annulohypoxylon in the multi-locus phylogeny. Secondary metabolite profiles of all taxa are also reported.
September 6, 2025 at 6:01 AM
www.ingentaconnect.com/content/wfbi...
In our new paper we have described several new species of Hypoxylaceae and found that the genus Rostrohypoxylon is obsolete because it is nested in Annulohypoxylon in the multi-locus phylogeny. Secondary metabolite profiles of all taxa are also reported.
In our new paper we have described several new species of Hypoxylaceae and found that the genus Rostrohypoxylon is obsolete because it is nested in Annulohypoxylon in the multi-locus phylogeny. Secondary metabolite profiles of all taxa are also reported.
Reposted by Matthias Flotho
Angiopoietin signalling is a central axis of amyloid-driven vascular dysfunction in Alzheimer's disease https://www.biorxiv.org/content/10.1101/2025.08.25.672093v1
August 29, 2025 at 2:15 PM
Angiopoietin signalling is a central axis of amyloid-driven vascular dysfunction in Alzheimer's disease https://www.biorxiv.org/content/10.1101/2025.08.25.672093v1
Reposted by Matthias Flotho
Angiopoietin signalling is a central axis of amyloid-driven vascular dysfunction in Alzheimer's disease https://www.biorxiv.org/content/10.1101/2025.08.25.672093v1
August 29, 2025 at 2:15 PM
Angiopoietin signalling is a central axis of amyloid-driven vascular dysfunction in Alzheimer's disease https://www.biorxiv.org/content/10.1101/2025.08.25.672093v1
Reposted by Matthias Flotho
Making Your Research Free May Cost You
* With federal funding exceptionally unreliable, scientists say they are stressed about spending thousands of grant dollars on unexpected and questionable open-access charges.
By @stephaniemlee.bsky.social for @chronicle.com
www.chronicle.com/article/maki...
* With federal funding exceptionally unreliable, scientists say they are stressed about spending thousands of grant dollars on unexpected and questionable open-access charges.
By @stephaniemlee.bsky.social for @chronicle.com
www.chronicle.com/article/maki...
Making Your Research Free May Cost You
Under a new requirement that NIH-funded research be freely, immediately available, some journals are forcing researchers to pay to publish.
www.chronicle.com
August 29, 2025 at 4:54 PM
Making Your Research Free May Cost You
* With federal funding exceptionally unreliable, scientists say they are stressed about spending thousands of grant dollars on unexpected and questionable open-access charges.
By @stephaniemlee.bsky.social for @chronicle.com
www.chronicle.com/article/maki...
* With federal funding exceptionally unreliable, scientists say they are stressed about spending thousands of grant dollars on unexpected and questionable open-access charges.
By @stephaniemlee.bsky.social for @chronicle.com
www.chronicle.com/article/maki...
Reposted by Matthias Flotho
Exercise can reduce pain, but you don’t have to work out harder to feel the benefit.
New research suggests that fitness level and sex may play a bigger role than exercise intensity in how we experience exercise-induced pain relief.
New research suggests that fitness level and sex may play a bigger role than exercise intensity in how we experience exercise-induced pain relief.
Painkiller exercise
High-intensity exercise relieves pain more than low-intensity activity – but only in males with high fitness levels.
buff.ly
August 29, 2025 at 8:02 PM
Exercise can reduce pain, but you don’t have to work out harder to feel the benefit.
New research suggests that fitness level and sex may play a bigger role than exercise intensity in how we experience exercise-induced pain relief.
New research suggests that fitness level and sex may play a bigger role than exercise intensity in how we experience exercise-induced pain relief.