Enea Maffei
@phagemuffin.bsky.social
Post-doc at D-HEST, ETH Zurich. PhD in microbiology at Biozentrum, Basel. Phagehunter. Hiker. Scout. Music and food enthusiast. Per aspera ad astra
https://orcid.org/0000-0002-0751-9572
https://orcid.org/0000-0002-0751-9572
Reposted by Enea Maffei
🚨NEW paper: Benchmarking Hi-C for virus–host inference
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking
Virus discovery has accelerated but linking viruses to hosts remains challenging. This study uses synthetic microbiomes to optimize and benchmark Hi-C for virus-host linkage inference, and applies thi...
journals.plos.org
November 21, 2025 at 7:31 PM
🚨NEW paper: Benchmarking Hi-C for virus–host inference
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
Reposted by Enea Maffei
In bacteria, TnSeq revolutionized genetics by linking genes to phenotypes at scale. But for phages nothing equivalent exists. So we built HIDEN-SEQ, the first TnSeq approach for phages, enabled by a hide-and-seek interplay between the host CRISPR-Cas13a and a phage anti-CRISPR protein.
November 20, 2025 at 6:52 PM
In bacteria, TnSeq revolutionized genetics by linking genes to phenotypes at scale. But for phages nothing equivalent exists. So we built HIDEN-SEQ, the first TnSeq approach for phages, enabled by a hide-and-seek interplay between the host CRISPR-Cas13a and a phage anti-CRISPR protein.
Reposted by Enea Maffei
🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
November 20, 2025 at 8:40 PM
🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
Reposted by Enea Maffei
🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
November 20, 2025 at 6:52 PM
🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
Reposted by Enea Maffei
Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...
Strain displacement in microbiomes via ecological competition - Nature Microbiology
Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.
www.nature.com
November 7, 2025 at 10:34 PM
Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...
Reposted by Enea Maffei
Genome-scale CRISPRi profiling reveals metabolic vulnerabilities of uropathogenic Escherichia coli in human urine https://www.biorxiv.org/content/10.1101/2025.10.31.685768v1
November 1, 2025 at 2:17 AM
Genome-scale CRISPRi profiling reveals metabolic vulnerabilities of uropathogenic Escherichia coli in human urine https://www.biorxiv.org/content/10.1101/2025.10.31.685768v1
Reposted by Enea Maffei
Thinking only of Rosalind Franklin today, and what was stolen from her (and so many other female scientists alongside her).
Rosalind Franklin and the damage of gender harassment
Spurred by a recent report on sexual harassment in academia, our columnist revisits a historical case and reflects on what has changed—and what hasn’t
www.science.org
November 7, 2025 at 7:58 PM
Thinking only of Rosalind Franklin today, and what was stolen from her (and so many other female scientists alongside her).
Reposted by Enea Maffei
🚨 Excited to share our new paper is out! 🎉
We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut.
Now published in @natcomms.nature.com rdcu.be/eOf63
We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut.
Now published in @natcomms.nature.com rdcu.be/eOf63
Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes
Nature Communications - The role of ecological factors in modulating the spread of antibiotic-resistance bacteria in the gut remains unclear. Here, the authors use anaerobic microcosms to study the...
rdcu.be
November 7, 2025 at 9:15 AM
🚨 Excited to share our new paper is out! 🎉
We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut.
Now published in @natcomms.nature.com rdcu.be/eOf63
We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut.
Now published in @natcomms.nature.com rdcu.be/eOf63
Reposted by Enea Maffei
Bacterial Halloween mask crafted by uniquely talented MSc student Dominic Spichtig - the team of Enea @phagemuffin.bsky.social is setting new standards in the lab! 🎃🔥🧬
November 5, 2025 at 6:35 PM
Bacterial Halloween mask crafted by uniquely talented MSc student Dominic Spichtig - the team of Enea @phagemuffin.bsky.social is setting new standards in the lab! 🎃🔥🧬
Happy to see this hit the public! A story worth checking out that started back during my days as master student 🧑🔬🧬🦠
Coenzyme A depletion causes antibiotic tolerance in Pseudomonas aeruginosa https://www.biorxiv.org/content/10.1101/2025.10.24.684135v1
October 27, 2025 at 8:27 AM
Happy to see this hit the public! A story worth checking out that started back during my days as master student 🧑🔬🧬🦠
Reposted by Enea Maffei
Day 22, GOAT. The most iconic (if not the greatest phage of all time) in terms of looks are myovirus like phages. They look like a lunar lander and are instantly recognisable as a virus. #Drawtober #SciArt #PhageSky
October 22, 2025 at 10:39 PM
Day 22, GOAT. The most iconic (if not the greatest phage of all time) in terms of looks are myovirus like phages. They look like a lunar lander and are instantly recognisable as a virus. #Drawtober #SciArt #PhageSky
Reposted by Enea Maffei
Very excited to share the latest work from our lab, which was published today in Nature!
nature.com/articles/s41...
PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
nature.com/articles/s41...
PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
Isolation, engineering and ecology of temperate phages from the human gut - Nature
Human host-associated cellular products may act as induction agents for bacteriophages.
nature.com
October 15, 2025 at 9:41 PM
Very excited to share the latest work from our lab, which was published today in Nature!
nature.com/articles/s41...
PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
nature.com/articles/s41...
PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
Reposted by Enea Maffei
For those of you working on tailed #phages, this is the virus realm for you!
#Duplodnaviria #virus #taxonomy
The Profile in #JGenVirol provides the citable reference. More details in the chapter on the ICTV website: ictv.global/report/chapt...
#Duplodnaviria #virus #taxonomy
The Profile in #JGenVirol provides the citable reference. More details in the chapter on the ICTV website: ictv.global/report/chapt...
October 10, 2025 at 8:07 AM
For those of you working on tailed #phages, this is the virus realm for you!
#Duplodnaviria #virus #taxonomy
The Profile in #JGenVirol provides the citable reference. More details in the chapter on the ICTV website: ictv.global/report/chapt...
#Duplodnaviria #virus #taxonomy
The Profile in #JGenVirol provides the citable reference. More details in the chapter on the ICTV website: ictv.global/report/chapt...
Reposted by Enea Maffei
Day 4, Claw. Phages don't really have claws, but they do have tail fibres that recognise receptors on host cells and clamp on, allowing phage particles to infect their hosts. #drawtober #SciArt #Phagesky
October 4, 2025 at 9:04 PM
Day 4, Claw. Phages don't really have claws, but they do have tail fibres that recognise receptors on host cells and clamp on, allowing phage particles to infect their hosts. #drawtober #SciArt #Phagesky
Reposted by Enea Maffei
📢 OUR 2025 FELLOWSHIP CALLS ARE NOW OPEN 📢
🎓PhD Fellowship 👉 nccr-antiresist.ch/join-us/
👩⚕️Research Fellowship in Infection and Treatment for clinicians 👉 nccr-antiresist.ch/join-us/
#TransformingAntimicrobialResearch #AMR
@biozentrum.unibas.ch @unibas.ch
🎓PhD Fellowship 👉 nccr-antiresist.ch/join-us/
👩⚕️Research Fellowship in Infection and Treatment for clinicians 👉 nccr-antiresist.ch/join-us/
#TransformingAntimicrobialResearch #AMR
@biozentrum.unibas.ch @unibas.ch
October 6, 2025 at 9:38 AM
📢 OUR 2025 FELLOWSHIP CALLS ARE NOW OPEN 📢
🎓PhD Fellowship 👉 nccr-antiresist.ch/join-us/
👩⚕️Research Fellowship in Infection and Treatment for clinicians 👉 nccr-antiresist.ch/join-us/
#TransformingAntimicrobialResearch #AMR
@biozentrum.unibas.ch @unibas.ch
🎓PhD Fellowship 👉 nccr-antiresist.ch/join-us/
👩⚕️Research Fellowship in Infection and Treatment for clinicians 👉 nccr-antiresist.ch/join-us/
#TransformingAntimicrobialResearch #AMR
@biozentrum.unibas.ch @unibas.ch
Reposted by Enea Maffei
Viral AlphaFold Database (VAD) is live in Science Advances
~27,000 predicted viral protein monomers & homodimers
Conserved folds across bacteria, archaea & eukaryotic viruses
New toxin–antitoxin system KreTA uncovered
Vast “functional darkness” remains uncharted
www.science.org/doi/10.1126/...
~27,000 predicted viral protein monomers & homodimers
Conserved folds across bacteria, archaea & eukaryotic viruses
New toxin–antitoxin system KreTA uncovered
Vast “functional darkness” remains uncharted
www.science.org/doi/10.1126/...
The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes
VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.
www.science.org
October 2, 2025 at 8:48 AM
Viral AlphaFold Database (VAD) is live in Science Advances
~27,000 predicted viral protein monomers & homodimers
Conserved folds across bacteria, archaea & eukaryotic viruses
New toxin–antitoxin system KreTA uncovered
Vast “functional darkness” remains uncharted
www.science.org/doi/10.1126/...
~27,000 predicted viral protein monomers & homodimers
Conserved folds across bacteria, archaea & eukaryotic viruses
New toxin–antitoxin system KreTA uncovered
Vast “functional darkness” remains uncharted
www.science.org/doi/10.1126/...
Reposted by Enea Maffei
That’s really cool. Every lab should have it!
I made a sign for the lab with our informal lab motto, inspired by this convo between @itaiyanai.bsky.social and Martin Lercher: nightscience.buzzsprout.com/1744020/epis.... A good reminder that talking is among the best forms of thinking!
September 30, 2025 at 5:41 PM
That’s really cool. Every lab should have it!
Reposted by Enea Maffei
Reposted by Enea Maffei
It is not only antibiotics but also certain viruses – known as bacteriophages – that can kill off pathogenic bacteria. However, Switzerland lacks the legal framework for the use of these viruses in therapy. What would need to change? Researcher Alexander Harms explains.
ethz.ch/en/news-and-...
ethz.ch/en/news-and-...
“Treatment with bacteriophages can combat antibiotic-resistant infections, but Swiss patients lack access”
It is not only antibiotics but also certain viruses – known as bacteriophages – that can kill off pathogenic bacteria. However, Switzerland lacks the legal framework for the use of these viruses in th...
ethz.ch
September 26, 2025 at 6:42 AM
It is not only antibiotics but also certain viruses – known as bacteriophages – that can kill off pathogenic bacteria. However, Switzerland lacks the legal framework for the use of these viruses in therapy. What would need to change? Researcher Alexander Harms explains.
ethz.ch/en/news-and-...
ethz.ch/en/news-and-...
Reposted by Enea Maffei
Had a short but sweet visit to Zürich to speak at @ethz.ch. Many thanks to @phagemuffin.bsky.social and @aharms485.bsky.social!
September 22, 2025 at 8:47 AM
Had a short but sweet visit to Zürich to speak at @ethz.ch. Many thanks to @phagemuffin.bsky.social and @aharms485.bsky.social!
I can confirm this applies to postdocs too 😇😁
Did anyone else start running during their phds?
If so, I would love to follow/connect with you all on Strava :)
If so, I would love to follow/connect with you all on Strava :)
September 18, 2025 at 5:03 PM
I can confirm this applies to postdocs too 😇😁
Reposted by Enea Maffei
One technician position (80-100%)
Group Médéric Diard
Start date: 1 November 2025 or as per agreement
@biozentrum.unibas.ch
@unibas.ch s.ch
www.biozentrum.unibas.ch/open-positio...
#job #research #Hiwi #biology #science #basel #recruiting #career
Group Médéric Diard
Start date: 1 November 2025 or as per agreement
@biozentrum.unibas.ch
@unibas.ch s.ch
www.biozentrum.unibas.ch/open-positio...
#job #research #Hiwi #biology #science #basel #recruiting #career
September 16, 2025 at 7:21 AM
One technician position (80-100%)
Group Médéric Diard
Start date: 1 November 2025 or as per agreement
@biozentrum.unibas.ch
@unibas.ch s.ch
www.biozentrum.unibas.ch/open-positio...
#job #research #Hiwi #biology #science #basel #recruiting #career
Group Médéric Diard
Start date: 1 November 2025 or as per agreement
@biozentrum.unibas.ch
@unibas.ch s.ch
www.biozentrum.unibas.ch/open-positio...
#job #research #Hiwi #biology #science #basel #recruiting #career
Reposted by Enea Maffei
Writing a recommendation letter for yourself
September 12, 2025 at 4:13 AM
Writing a recommendation letter for yourself
Reposted by Enea Maffei
Thrilled to share our two latest papers with the @tcostalab.bsky.social
lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species.
@imperialcollegeldn.bsky.social
www.cell.com/cell/fulltex...
lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species.
@imperialcollegeldn.bsky.social
www.cell.com/cell/fulltex...
Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization
Capsid-forming PICIs (cf-PICIs) produce their own capsids and exploit phage tails
from unrelated species to transfer their DNA across bacterial hosts. This tail piracy
enables broad dissemination and ...
www.cell.com
September 9, 2025 at 5:05 PM
Thrilled to share our two latest papers with the @tcostalab.bsky.social
lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species.
@imperialcollegeldn.bsky.social
www.cell.com/cell/fulltex...
lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species.
@imperialcollegeldn.bsky.social
www.cell.com/cell/fulltex...