Cedric Laczny 🖥️🦠💡
@claczny.bsky.social
My scientific passions: microbiomes and bioinformatics
Find me also on LinkedIn: https://www.linkedin.com/in/cedric-laczny-02b720150/
or ORCID: https://orcid.org/0000-0002-1100-1282
Find me also on LinkedIn: https://www.linkedin.com/in/cedric-laczny-02b720150/
or ORCID: https://orcid.org/0000-0002-1100-1282
Reposted by Cedric Laczny 🖥️🦠💡
Highly accurate prophage island detection with PIDE genomebiology.biomedcentral.com/articles/10.... #jcampubs
Highly accurate prophage island detection with PIDE - Genome Biology
As important mobile elements in prokaryotes, prophages shape the genomic context of their hosts and regulate the structure of bacterial populations. However, it is challenging to precisely identify pr...
genomebiology.biomedcentral.com
August 21, 2025 at 3:25 PM
Highly accurate prophage island detection with PIDE genomebiology.biomedcentral.com/articles/10.... #jcampubs
Reposted by Cedric Laczny 🖥️🦠💡
🚨New paper 🚨
Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
1/12
Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
1/12
August 17, 2025 at 3:42 AM
🚨New paper 🚨
Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
1/12
Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
1/12
Reposted by Cedric Laczny 🖥️🦠💡
📉Despite the hype, protein language models trained across the “protein universe” are outperformed by even the simplest, site-independent alignment-based model.
5/12
5/12
August 17, 2025 at 3:42 AM
📉Despite the hype, protein language models trained across the “protein universe” are outperformed by even the simplest, site-independent alignment-based model.
5/12
5/12
Reposted by Cedric Laczny 🖥️🦠💡
Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports...
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
August 15, 2025 at 4:33 PM
Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports...
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
Reposted by Cedric Laczny 🖥️🦠💡
This is v cool
My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology:
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
Mathematical modelling for biologists - Modelling concepts in biological research
Mathematical modelling for biologists - Modelling concepts in biological research
www.ebi.ac.uk
August 15, 2025 at 10:43 AM
This is v cool
Reposted by Cedric Laczny 🖥️🦠💡
Archaea are often surrounded by bacteria. But is there ever active conflict between the two? Can archaea kill bacteria? If so, how do they do it?
Work by @romainstrock.bsky.social shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases. journals.plos.org/plosbiology/...
Work by @romainstrock.bsky.social shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases. journals.plos.org/plosbiology/...
Archaea produce peptidoglycan hydrolases that kill bacteria
Archaea regularly interact with bacteria but reports of archaea killing bacteria are very rare. This study shows that many archaea encode peptidoglycan hydrolases, which specifically target bacterial ...
journals.plos.org
August 14, 2025 at 6:50 PM
Archaea are often surrounded by bacteria. But is there ever active conflict between the two? Can archaea kill bacteria? If so, how do they do it?
Work by @romainstrock.bsky.social shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases. journals.plos.org/plosbiology/...
Work by @romainstrock.bsky.social shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases. journals.plos.org/plosbiology/...
Reposted by Cedric Laczny 🖥️🦠💡
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!
See the thread below from @biocs.bsky.social for more info!
August 15, 2025 at 8:11 AM
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!
See the thread below from @biocs.bsky.social for more info!
Reposted by Cedric Laczny 🖥️🦠💡
If you are interested in learning more about Clinical Methods for Nutrition and Obesity Research - I strongly recommend you apply for this course - it's free and they provide a $500 travel stipend to offset costs of attendance.
www.pbrc.edu/training-and...
www.pbrc.edu/training-and...
NIDDK Clinical Methods for Nutrition and Obesity Research Course
www.pbrc.edu
August 12, 2025 at 10:04 PM
If you are interested in learning more about Clinical Methods for Nutrition and Obesity Research - I strongly recommend you apply for this course - it's free and they provide a $500 travel stipend to offset costs of attendance.
www.pbrc.edu/training-and...
www.pbrc.edu/training-and...
Reposted by Cedric Laczny 🖥️🦠💡
We just bumped into something very preliminary… but very exciting:
AF2.3 and AF3.0 distograms may potentially reproduce MD-like behavior.
Until we do further tests, you can reach our early insights at www.biorxiv.org/content/10.1...
AF2.3 and AF3.0 distograms may potentially reproduce MD-like behavior.
Until we do further tests, you can reach our early insights at www.biorxiv.org/content/10.1...
July 29, 2025 at 1:01 PM
We just bumped into something very preliminary… but very exciting:
AF2.3 and AF3.0 distograms may potentially reproduce MD-like behavior.
Until we do further tests, you can reach our early insights at www.biorxiv.org/content/10.1...
AF2.3 and AF3.0 distograms may potentially reproduce MD-like behavior.
Until we do further tests, you can reach our early insights at www.biorxiv.org/content/10.1...
Reposted by Cedric Laczny 🖥️🦠💡
Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...
and GH repo: github.com/refresh-bio/...
FAMSA2 enables accurate multiple sequence alignment at protein-universe scale
We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...
www.biorxiv.org
July 19, 2025 at 9:28 PM
Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...
and GH repo: github.com/refresh-bio/...
Reposted by Cedric Laczny 🖥️🦠💡
The new paper published in @nature.com reveals that 90% of mycorrhizal fungal biodiversity hotspots lie outside protected areas.
Details ➡️ www.avcr.cz/en/media/pre... #SoilHealth #CarbonStorage
Research by @spun.earth, @ethz.ch, @stanford.edu, @biologylu.bsky.social, @mbuavcr.bsky.social et al.
Details ➡️ www.avcr.cz/en/media/pre... #SoilHealth #CarbonStorage
Research by @spun.earth, @ethz.ch, @stanford.edu, @biologylu.bsky.social, @mbuavcr.bsky.social et al.
July 25, 2025 at 8:19 AM
The new paper published in @nature.com reveals that 90% of mycorrhizal fungal biodiversity hotspots lie outside protected areas.
Details ➡️ www.avcr.cz/en/media/pre... #SoilHealth #CarbonStorage
Research by @spun.earth, @ethz.ch, @stanford.edu, @biologylu.bsky.social, @mbuavcr.bsky.social et al.
Details ➡️ www.avcr.cz/en/media/pre... #SoilHealth #CarbonStorage
Research by @spun.earth, @ethz.ch, @stanford.edu, @biologylu.bsky.social, @mbuavcr.bsky.social et al.
Reposted by Cedric Laczny 🖥️🦠💡
New workshop paper out today with 60 of our closest friends, providing guidance on how to design a study attributing health impacts to climate change. Hopefully this helps expand the field and start closing the representation gaps we discuss in our forthcoming work link.springer.com/article/10.1...
The attribution of human health outcomes to climate change: transdisciplinary practical guidance - Climatic Change
For over 30 years, detection and attribution (D&A) studies have informed key conclusions in international and national assessments of climate science, providing compelling evidence for the reality and...
link.springer.com
July 25, 2025 at 2:05 PM
New workshop paper out today with 60 of our closest friends, providing guidance on how to design a study attributing health impacts to climate change. Hopefully this helps expand the field and start closing the representation gaps we discuss in our forthcoming work link.springer.com/article/10.1...
Reposted by Cedric Laczny 🖥️🦠💡
📣 New paper alert!
One of the most exciting projects we've done in recent years is now out on BioRxiv: "An Asgard archaeon from a modern analog of ancient microbial mats".
Glimpse into early complex life! ❄️🦠 🔬🧬
www.biorxiv.org/content/10.1.... A thread...
One of the most exciting projects we've done in recent years is now out on BioRxiv: "An Asgard archaeon from a modern analog of ancient microbial mats".
Glimpse into early complex life! ❄️🦠 🔬🧬
www.biorxiv.org/content/10.1.... A thread...
An Asgard archaeon from a modern analog of ancient microbial mats
It has been proposed that eukaryotic cells evolved via symbiosis between sulfate-reducing bacteria and hydrogen-producing archaea. Here we describe a highly enriched culture of a novel Asgard archaeon...
www.biorxiv.org
July 25, 2025 at 1:29 PM
📣 New paper alert!
One of the most exciting projects we've done in recent years is now out on BioRxiv: "An Asgard archaeon from a modern analog of ancient microbial mats".
Glimpse into early complex life! ❄️🦠 🔬🧬
www.biorxiv.org/content/10.1.... A thread...
One of the most exciting projects we've done in recent years is now out on BioRxiv: "An Asgard archaeon from a modern analog of ancient microbial mats".
Glimpse into early complex life! ❄️🦠 🔬🧬
www.biorxiv.org/content/10.1.... A thread...
Reposted by Cedric Laczny 🖥️🦠💡
Our article showing energy production from air alone is in PNAS today. This paper provides an ultimate biochemical proof that microbes can survive simply by 'making' energy from air (making two ATP per molecule atmospheric H2 consumed) and has biotech applications. www.pnas.org/doi/10.1073/...
ATP synthesis driven by atmospheric hydrogen concentrations | PNAS
All cells require a continuous supply of the universal energy currency, adenosine
triphosphate (ATP), to drive countless cellular reactions. The un...
www.pnas.org
July 25, 2025 at 12:54 AM
Our article showing energy production from air alone is in PNAS today. This paper provides an ultimate biochemical proof that microbes can survive simply by 'making' energy from air (making two ATP per molecule atmospheric H2 consumed) and has biotech applications. www.pnas.org/doi/10.1073/...
Reposted by Cedric Laczny 🖥️🦠💡
🦠🧍♀️From bacterial to human immunity.
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
www.science.org
July 24, 2025 at 6:23 PM
🦠🧍♀️From bacterial to human immunity.
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
Reposted by Cedric Laczny 🖥️🦠💡
🎧 New SciLux episode!
Professor Elisabeth Letellier (@uni.lu) and Dr. Mina Tsenkova (@amgen.bsky.social) discuss how diet and gut microbiome influence colorectal cancer development.
🎙️Listen now.
Powered by @researchluxembourg.org
#ColorectalCancer #GutHealth #SciLux #SciencePodcast
Professor Elisabeth Letellier (@uni.lu) and Dr. Mina Tsenkova (@amgen.bsky.social) discuss how diet and gut microbiome influence colorectal cancer development.
🎙️Listen now.
Powered by @researchluxembourg.org
#ColorectalCancer #GutHealth #SciLux #SciencePodcast
July 8, 2025 at 6:38 AM
🎧 New SciLux episode!
Professor Elisabeth Letellier (@uni.lu) and Dr. Mina Tsenkova (@amgen.bsky.social) discuss how diet and gut microbiome influence colorectal cancer development.
🎙️Listen now.
Powered by @researchluxembourg.org
#ColorectalCancer #GutHealth #SciLux #SciencePodcast
Professor Elisabeth Letellier (@uni.lu) and Dr. Mina Tsenkova (@amgen.bsky.social) discuss how diet and gut microbiome influence colorectal cancer development.
🎙️Listen now.
Powered by @researchluxembourg.org
#ColorectalCancer #GutHealth #SciLux #SciencePodcast
Reposted by Cedric Laczny 🖥️🦠💡
#NatMicroPicks
Tracking the gut microbiome evolution 🦠
A big data analysis of gut microbiome of kids from infancy to 8 years of age.
#MicroSky #MicrobiomeSky
www.nature.com/articles/s41...
Tracking the gut microbiome evolution 🦠
A big data analysis of gut microbiome of kids from infancy to 8 years of age.
#MicroSky #MicrobiomeSky
www.nature.com/articles/s41...
Gut microbiome evolution from infancy to 8 years of age - Nature Medicine
In a unique cohort of twins followed from birth to 8 years of age, shotgun sequencing of stool samples reveals that the transmission, persistence and evolutionary adaptation of bacterial strains are s...
www.nature.com
June 26, 2025 at 3:32 PM
#NatMicroPicks
Tracking the gut microbiome evolution 🦠
A big data analysis of gut microbiome of kids from infancy to 8 years of age.
#MicroSky #MicrobiomeSky
www.nature.com/articles/s41...
Tracking the gut microbiome evolution 🦠
A big data analysis of gut microbiome of kids from infancy to 8 years of age.
#MicroSky #MicrobiomeSky
www.nature.com/articles/s41...
Reposted by Cedric Laczny 🖥️🦠💡
Preprint alert! 🦌
Our new abundance index, REINDEER2, is out!
It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput.
Short thread!
www.biorxiv.org/content/10.1...
github.com/Yohan-Hernan...
Our new abundance index, REINDEER2, is out!
It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput.
Short thread!
www.biorxiv.org/content/10.1...
github.com/Yohan-Hernan...
www.biorxiv.org
June 19, 2025 at 9:13 AM
Preprint alert! 🦌
Our new abundance index, REINDEER2, is out!
It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput.
Short thread!
www.biorxiv.org/content/10.1...
github.com/Yohan-Hernan...
Our new abundance index, REINDEER2, is out!
It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput.
Short thread!
www.biorxiv.org/content/10.1...
github.com/Yohan-Hernan...
Reposted by Cedric Laczny 🖥️🦠💡
🟣 Quantum algorithms aren’t science fiction anymore. They’re shaping the future, right here in #Luxembourg.
At our first #QuantumBreakfast, experts explored how quantum tech could revolutionise AI, medicine, security, and more.
#QuantumAtUniLu
At our first #QuantumBreakfast, experts explored how quantum tech could revolutionise AI, medicine, security, and more.
#QuantumAtUniLu
Quantum algorithms unlock tomorrow's impossible problems
Imagine a world where quantum computing solves problems that even our most powerful supercomputers can't handle today. This technology could help design
www.uni.lu
June 20, 2025 at 9:09 AM
🟣 Quantum algorithms aren’t science fiction anymore. They’re shaping the future, right here in #Luxembourg.
At our first #QuantumBreakfast, experts explored how quantum tech could revolutionise AI, medicine, security, and more.
#QuantumAtUniLu
At our first #QuantumBreakfast, experts explored how quantum tech could revolutionise AI, medicine, security, and more.
#QuantumAtUniLu
Reposted by Cedric Laczny 🖥️🦠💡
For those at the #ASMicrobe @asm.org conference this weekend, my PhD student Alejandro De Santiago (a bioinformatics ninja) is presenting his poster on a new nematode-bacterial symbiosis we’ve recently discovered! TODAY in the poster hall www.abstractsonline.com/pp8/#!/20974...
June 20, 2025 at 4:34 PM
For those at the #ASMicrobe @asm.org conference this weekend, my PhD student Alejandro De Santiago (a bioinformatics ninja) is presenting his poster on a new nematode-bacterial symbiosis we’ve recently discovered! TODAY in the poster hall www.abstractsonline.com/pp8/#!/20974...
Reposted by Cedric Laczny 🖥️🦠💡
A short preprint describing the GlobDB is now on arXiv: arxiv.org/abs/2506.11896
If you find the resource useful, please also check globdb.org for info on how to cite the underlying resources and tools.
If you find the resource useful, please also check globdb.org for info on how to cite the underlying resources and tools.
I'm happy to announce the latest release of the GlobDB, available at globdb.org.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
home | GlobDB
globdb.org
June 16, 2025 at 8:44 PM
A short preprint describing the GlobDB is now on arXiv: arxiv.org/abs/2506.11896
If you find the resource useful, please also check globdb.org for info on how to cite the underlying resources and tools.
If you find the resource useful, please also check globdb.org for info on how to cite the underlying resources and tools.
Reposted by Cedric Laczny 🖥️🦠💡
Klimaschutz trifft Darmgesundheit: Unsere Mikrobiomexpertin Christine Moissl-Eichinger erhält den prestigeträchtigen Advanced Grant (2,5 Mio. €) des für ihre Forschung zu Methanobrevibacter – einem winzigen Mikroorganismus mit großem Potenzial ➡ https://bit.ly/3FDDJpO.
#ERCAdG
#ERCAdG
June 17, 2025 at 10:38 AM
Klimaschutz trifft Darmgesundheit: Unsere Mikrobiomexpertin Christine Moissl-Eichinger erhält den prestigeträchtigen Advanced Grant (2,5 Mio. €) des für ihre Forschung zu Methanobrevibacter – einem winzigen Mikroorganismus mit großem Potenzial ➡ https://bit.ly/3FDDJpO.
#ERCAdG
#ERCAdG
Reposted by Cedric Laczny 🖥️🦠💡
🥳 Important + positive changes to the @erc.europa.eu program:
- PhD age eligibility up to 10 years (starting) and 15 years (consolidator
- Application Part I focuses on the aim + strategy
- Application Part II restricted to 7 pages
- PhD age eligibility up to 10 years (starting) and 15 years (consolidator
- Application Part I focuses on the aim + strategy
- Application Part II restricted to 7 pages
Planning to apply for #research #funding from the ERC?
From the next application rounds, expect changes to the:
• proposal structure
• evaluation process
• extra funding you can request
• eligibility for Starting & Consolidator #Grants (from 2027)
More 👇 europa.eu/!RPHWvv
From the next application rounds, expect changes to the:
• proposal structure
• evaluation process
• extra funding you can request
• eligibility for Starting & Consolidator #Grants (from 2027)
More 👇 europa.eu/!RPHWvv
Changes to the 2026 and 2027 Work Programmes
With the launch of the competitions for grants under ERC Work Programme 2026 in July of this year, several changes to the submission of applications and the evaluation of proposals will apply. The mai...
europa.eu
June 2, 2025 at 3:54 PM
🥳 Important + positive changes to the @erc.europa.eu program:
- PhD age eligibility up to 10 years (starting) and 15 years (consolidator
- Application Part I focuses on the aim + strategy
- Application Part II restricted to 7 pages
- PhD age eligibility up to 10 years (starting) and 15 years (consolidator
- Application Part I focuses on the aim + strategy
- Application Part II restricted to 7 pages
Reposted by Cedric Laczny 🖥️🦠💡
This is cool - bacteria wrap their flagella to propel themselves through narrow passages www.biorxiv.org/content/10.1...
Bacteria break through one-micrometer-square passages by flagellar wrapping
Confined spaces are omnipresent in the micro-environments, including soil aggregates and intestinal crypts, yet little is known about how bacteria behave under such conditions where movement is challe...
www.biorxiv.org
May 21, 2025 at 8:36 PM
This is cool - bacteria wrap their flagella to propel themselves through narrow passages www.biorxiv.org/content/10.1...
Reposted by Cedric Laczny 🖥️🦠💡
Absolutely thrilled to announce the launch of ARTIC2 - a £5.5M 5 year project funded by @wellcometrust.bsky.social to build on the ARTIC approach of low-cost, globally accessible genome sequencing for surveillance of outbreaks, epidemics and endemic diseases: www.birmingham.ac.uk/news/2025/am...
Ambitious project to develop low-cost genome sequencing for pathogens known and unknown - University of Birmingham
Project will build on research that helped diagnostic labs to adopt sequencing capacity for COVID-19 and permit characterisation of future infectious threats
www.birmingham.ac.uk
May 22, 2025 at 10:57 AM
Absolutely thrilled to announce the launch of ARTIC2 - a £5.5M 5 year project funded by @wellcometrust.bsky.social to build on the ARTIC approach of low-cost, globally accessible genome sequencing for surveillance of outbreaks, epidemics and endemic diseases: www.birmingham.ac.uk/news/2025/am...