Tara Bartolec
@tarabartolec.bsky.social
EIPOD-LinC postdoc fellow in the Savitski and Typas labs at EMBL, Heidelberg. Proteomics, phages, PTMs, XLMS 🇦🇺🦠🧑🔬
Pinned
Tara Bartolec
@tarabartolec.bsky.social
· Dec 23
1/11 - With Karin Mitosch and Clément Potel + colleagues in Savitski lab and @typaslab.bsky.social @embl.org, I’m very happy to share our discovery of a hyper-promiscuous phage protein kinase (T7K) which broadly deactivates bacterial defenses! 🦠
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Tara Bartolec
Happy to see our HT-PELSA paper now published in @natsmb.nature.com 🎊 Big thanks for the constructive review process! 📖Read the manuscript here (www.nature.com/articles/s41...) & check the thread for additional information ⬇️
November 5, 2025 at 10:15 AM
Happy to see our HT-PELSA paper now published in @natsmb.nature.com 🎊 Big thanks for the constructive review process! 📖Read the manuscript here (www.nature.com/articles/s41...) & check the thread for additional information ⬇️
Reposted by Tara Bartolec
Finally out! 🤩 Check out our HT- PELSA for high throughput screening！
Happy to see our HT-PELSA paper now published in @natsmb.nature.com 🎊 Big thanks for the constructive review process! 📖Read the manuscript here (www.nature.com/articles/s41...) & check the thread for additional information ⬇️
November 5, 2025 at 4:28 PM
Finally out! 🤩 Check out our HT- PELSA for high throughput screening！
Reposted by Tara Bartolec
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 Tara Bartolec
Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️
www.biorxiv.org/content/10.1...
#teamtomo
www.biorxiv.org/content/10.1...
#teamtomo
October 15, 2025 at 6:26 AM
Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️
www.biorxiv.org/content/10.1...
#teamtomo
www.biorxiv.org/content/10.1...
#teamtomo
Reposted by Tara Bartolec
Excited to share our preprint led by Carlos Voogdt et al
We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...
We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...
October 13, 2025 at 7:48 AM
Excited to share our preprint led by Carlos Voogdt et al
We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...
We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...
Reposted by Tara Bartolec
New Preprint from Voogdt et al 👇
Establishes efficient genome-wide transposon mutagenesis & barcode mutant libraries for three Bacteroidales gut bacteria, identifying shared & species-specific essential genes, non-coding elements, & toxin pathways, advancing gut microbiome functional genomics
Establishes efficient genome-wide transposon mutagenesis & barcode mutant libraries for three Bacteroidales gut bacteria, identifying shared & species-specific essential genes, non-coding elements, & toxin pathways, advancing gut microbiome functional genomics
October 11, 2025 at 5:43 PM
New Preprint from Voogdt et al 👇
Establishes efficient genome-wide transposon mutagenesis & barcode mutant libraries for three Bacteroidales gut bacteria, identifying shared & species-specific essential genes, non-coding elements, & toxin pathways, advancing gut microbiome functional genomics
Establishes efficient genome-wide transposon mutagenesis & barcode mutant libraries for three Bacteroidales gut bacteria, identifying shared & species-specific essential genes, non-coding elements, & toxin pathways, advancing gut microbiome functional genomics
Reposted by Tara Bartolec
new preprint: Ubiquitin is a protein modification linked with degradation but known to regulate other functions. Over 100k ubiquitination sites have been discovered and here we (@julianvangerwen.bsky.social + others) try to prioritize those most critical to the cell www.biorxiv.org/content/10.1...
The functional landscape of the human ubiquitinome
Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme...
www.biorxiv.org
October 9, 2025 at 7:07 AM
new preprint: Ubiquitin is a protein modification linked with degradation but known to regulate other functions. Over 100k ubiquitination sites have been discovered and here we (@julianvangerwen.bsky.social + others) try to prioritize those most critical to the cell www.biorxiv.org/content/10.1...
Reposted by Tara Bartolec
Happy to see that Spacedust is now published on Nature Methods!
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6🧵
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6🧵
Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data.
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
De novo discovery of conserved gene clusters in microbial genomes with Spacedust - Nature Methods
This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.
www.nature.com
September 16, 2025 at 8:26 PM
Happy to see that Spacedust is now published on Nature Methods!
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6🧵
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6🧵
Reposted by Tara Bartolec
New impact case study outlines the impressive economic & scientific value of UniProt - the world-leading open data resource for protein sequence & functional information.
Users save up to 219 hours per year, equivalent to net benefits of up to €5,475 per user.
www.ebi.ac.uk/about/news/a...
Users save up to 219 hours per year, equivalent to net benefits of up to €5,475 per user.
www.ebi.ac.uk/about/news/a...
Measuring the value and impact of UniProt
Case study shows the economic value and impact of UniProt, showing estimated annual gains of up to €5,475 per user.
www.ebi.ac.uk
June 25, 2025 at 3:24 PM
New impact case study outlines the impressive economic & scientific value of UniProt - the world-leading open data resource for protein sequence & functional information.
Users save up to 219 hours per year, equivalent to net benefits of up to €5,475 per user.
www.ebi.ac.uk/about/news/a...
Users save up to 219 hours per year, equivalent to net benefits of up to €5,475 per user.
www.ebi.ac.uk/about/news/a...
Reposted by Tara Bartolec
Excited for New Approaches and Concepts in Microbiology 2025 with sessions on Bacterial systems biology, Bacterial cell biology & protein machines, Microbiomes, Environment & evolution, Pathogenesis & phage, Antibiotic discovery, mechanisms, and resistance. #EESMicrobiology
June 23, 2025 at 7:23 PM
Excited for New Approaches and Concepts in Microbiology 2025 with sessions on Bacterial systems biology, Bacterial cell biology & protein machines, Microbiomes, Environment & evolution, Pathogenesis & phage, Antibiotic discovery, mechanisms, and resistance. #EESMicrobiology
Reposted by Tara Bartolec
Very excited to share our preprint on a new resource: the Encyclopaedia of Viral Anti-Defence Systems (EVADES)! This is the main result of my PhD at EMBL-EBI (@ebi.embl.org)
and the University of Cambridge (@cam.ac.uk)! 🔗 www.biorxiv.org/content/10.1... 🧵1/n"
and the University of Cambridge (@cam.ac.uk)! 🔗 www.biorxiv.org/content/10.1... 🧵1/n"
Elucidating the mechanisms of action and evolutionary history of phage anti-defence proteins
Phages and bacteria are locked in a molecular arms race, with phage anti-defence proteins (ADPs) enabling them to evade bacterial immune systems. To streamline access to information on ADPs, we develo...
www.biorxiv.org
June 8, 2025 at 11:08 AM
Very excited to share our preprint on a new resource: the Encyclopaedia of Viral Anti-Defence Systems (EVADES)! This is the main result of my PhD at EMBL-EBI (@ebi.embl.org)
and the University of Cambridge (@cam.ac.uk)! 🔗 www.biorxiv.org/content/10.1... 🧵1/n"
and the University of Cambridge (@cam.ac.uk)! 🔗 www.biorxiv.org/content/10.1... 🧵1/n"
Reposted by Tara Bartolec
Want to know how the ligands interact with proteins beyond model cell lines, e.g., in tissues or bacteria? Interested in membrane targets? Check out our High-Throughput PELSA method which allows you do all these cool screenings for dozens of ligands within two hours! www.biorxiv.org/content/10.1...
High-throughput peptide-centric local stability assay extends protein-ligand identification to membrane proteins, tissues, and bacteria
Systematic mapping of protein-ligand interactions is essential for understanding biological processes and drug mechanisms. Peptide-centric local stability assay (PELSA) is a powerful tool for detectin...
www.biorxiv.org
April 29, 2025 at 6:13 PM
Want to know how the ligands interact with proteins beyond model cell lines, e.g., in tissues or bacteria? Interested in membrane targets? Check out our High-Throughput PELSA method which allows you do all these cool screenings for dozens of ligands within two hours! www.biorxiv.org/content/10.1...
Reposted by Tara Bartolec
And here it is, the completed BASEL collection finally published as early access in @plosbiology.org - see the thread for more details. 🤗🧬🎣
April 8, 2025 at 4:59 AM
And here it is, the completed BASEL collection finally published as early access in @plosbiology.org - see the thread for more details. 🤗🧬🎣
Reposted by Tara Bartolec
Now online! Jumbo phage killer immune system targets early infection of nucleus-forming phages
Jumbo phage killer immune system targets early infection of nucleus-forming phages
Jumbo phage killer (Juk) system, a common bacterial immune system in Proteobacteria, recognizes and targets the early phage infection vesicle specific to ϕKZ-like jumbo phages, terminates phage infection, and saves the bacterial cell.
dlvr.it
March 19, 2025 at 6:51 PM
Now online! Jumbo phage killer immune system targets early infection of nucleus-forming phages
Reposted by Tara Bartolec
Join our favorite microbiology meeting! Fantastic talks, poster sessions, new technologies, and all the hot areas of microbiology in a great environment - experts in cell & systems biology, microbiomes, environment & evolution, pathogenesis, phage & antibiotics
DON’T MISS abstract deadline, April 1
DON’T MISS abstract deadline, April 1
March 26, 2025 at 9:23 AM
Join our favorite microbiology meeting! Fantastic talks, poster sessions, new technologies, and all the hot areas of microbiology in a great environment - experts in cell & systems biology, microbiomes, environment & evolution, pathogenesis, phage & antibiotics
DON’T MISS abstract deadline, April 1
DON’T MISS abstract deadline, April 1
Reposted by Tara Bartolec
Updated validation reports are now available for structures determined using integrative & hybrid methods (IHM) that extends to structures derived from Crosslinking-MS data, along with previously supported Small Angle Scattering (SAS) data!
⬇️ Read more⬇️
www.wwpdb.org/news/news
⬇️ Read more⬇️
www.wwpdb.org/news/news
March 11, 2025 at 3:54 PM
Updated validation reports are now available for structures determined using integrative & hybrid methods (IHM) that extends to structures derived from Crosslinking-MS data, along with previously supported Small Angle Scattering (SAS) data!
⬇️ Read more⬇️
www.wwpdb.org/news/news
⬇️ Read more⬇️
www.wwpdb.org/news/news
Reposted by Tara Bartolec
🚀 #AlphaFold Database update
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
March 3, 2025 at 4:33 PM
🚀 #AlphaFold Database update
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
Reposted by Tara Bartolec
It is finally out!
Muntathar Al-Shimary, @doudna-lab.bsky.social , @cresslab.bsky.social and I present a gene knockdown tool that works in diverse bacteriophages: CRISPRi through antisense RNA Targeting (CRISPRi-ART)!
Check it out @naturemicrobiol.bsky.social
www.nature.com/articles/s41...
Muntathar Al-Shimary, @doudna-lab.bsky.social , @cresslab.bsky.social and I present a gene knockdown tool that works in diverse bacteriophages: CRISPRi through antisense RNA Targeting (CRISPRi-ART)!
Check it out @naturemicrobiol.bsky.social
www.nature.com/articles/s41...
CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d - Nature Microbiology
Leveraging RNA-targeting dCas13d enables selective interference with phage protein translation and facilitates measurement of phage gene fitness at a transcriptome-wide scale.
www.nature.com
February 26, 2025 at 4:43 PM
It is finally out!
Muntathar Al-Shimary, @doudna-lab.bsky.social , @cresslab.bsky.social and I present a gene knockdown tool that works in diverse bacteriophages: CRISPRi through antisense RNA Targeting (CRISPRi-ART)!
Check it out @naturemicrobiol.bsky.social
www.nature.com/articles/s41...
Muntathar Al-Shimary, @doudna-lab.bsky.social , @cresslab.bsky.social and I present a gene knockdown tool that works in diverse bacteriophages: CRISPRi through antisense RNA Targeting (CRISPRi-ART)!
Check it out @naturemicrobiol.bsky.social
www.nature.com/articles/s41...
Reposted by Tara Bartolec
In our latest review, we explore 12 deep-learning tools for metagenomic analysis, covering their strengths, limitations, and key applications. We hope it serves as both a resource and inspiration for new ways to analyze metagenomic data. Great work by Eli Levy Karin!
📄 doi.org/10.1093/nsr/...
📄 doi.org/10.1093/nsr/...
February 22, 2025 at 5:47 AM
In our latest review, we explore 12 deep-learning tools for metagenomic analysis, covering their strengths, limitations, and key applications. We hope it serves as both a resource and inspiration for new ways to analyze metagenomic data. Great work by Eli Levy Karin!
📄 doi.org/10.1093/nsr/...
📄 doi.org/10.1093/nsr/...
Reposted by Tara Bartolec
New version of DefenseFinder available defensefinder.mdmlab.fr (& cli)
Now encompassing 263 systems (+111 this year..!).
Thanks @ftesson.bsky.social, DefenseFinder grandmaster. Full list of systems here: defense-finder-models/List_system_article.md at master · mdmparis/defense-finder-models
Now encompassing 263 systems (+111 this year..!).
Thanks @ftesson.bsky.social, DefenseFinder grandmaster. Full list of systems here: defense-finder-models/List_system_article.md at master · mdmparis/defense-finder-models
Webservice | DefenseFinder webservice and knowledge base
On this site, you can freely use (without any login) the DefenseFinder webservice (see below) and get help to navigate the ever expanding world of defense systems.There is a collaborative knowledge ba...
defensefinder.mdmlab.fr
February 19, 2025 at 4:28 AM
New version of DefenseFinder available defensefinder.mdmlab.fr (& cli)
Now encompassing 263 systems (+111 this year..!).
Thanks @ftesson.bsky.social, DefenseFinder grandmaster. Full list of systems here: defense-finder-models/List_system_article.md at master · mdmparis/defense-finder-models
Now encompassing 263 systems (+111 this year..!).
Thanks @ftesson.bsky.social, DefenseFinder grandmaster. Full list of systems here: defense-finder-models/List_system_article.md at master · mdmparis/defense-finder-models
Reposted by Tara Bartolec
Excited to see this huge piece of work out 🎉 Congrats to everyone involved! If you ever wanted to read a 8in1 paper grab a cup of tea and enjoy 📖
We are very happy to present our work on N-glycoproteomics!🍬 Our method enables the selective enrichment and precise quantification of intact N-glycopeptides to explore the dynamics of glycosylation microheterogeneity.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
February 10, 2025 at 10:32 AM
Excited to see this huge piece of work out 🎉 Congrats to everyone involved! If you ever wanted to read a 8in1 paper grab a cup of tea and enjoy 📖
Reposted by Tara Bartolec
We are very happy to present our work on N-glycoproteomics!🍬 Our method enables the selective enrichment and precise quantification of intact N-glycopeptides to explore the dynamics of glycosylation microheterogeneity.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
February 10, 2025 at 10:20 AM
We are very happy to present our work on N-glycoproteomics!🍬 Our method enables the selective enrichment and precise quantification of intact N-glycopeptides to explore the dynamics of glycosylation microheterogeneity.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Tara Bartolec
🚨 🧬 Updated preprint on the completed BASEL collection - what's new? Some fun with bacterial immunity and a new P22 relative infecting E. coli K-12. A thread 🧵
February 6, 2025 at 6:05 AM
🚨 🧬 Updated preprint on the completed BASEL collection - what's new? Some fun with bacterial immunity and a new P22 relative infecting E. coli K-12. A thread 🧵
Reposted by Tara Bartolec
Excited to share our preprint with @savitski_lab led by @tarabartolec.bsky.social, @KMitosch & Clément Potel! We uncovered a mechanism by which the T7 phage broadly counteracts DNA-targeting bacterial defenses by deploying a loose cannon kinase in its genome @embl.org www.biorxiv.org/content/10.1...
Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses
Bacteria and bacteriophages are in a constant arms race to develop bacterial defense and phage counter-defense systems. Currently known phage counter-defense systems are specific to (the activity of) ...
www.biorxiv.org
December 23, 2024 at 7:29 AM
Excited to share our preprint with @savitski_lab led by @tarabartolec.bsky.social, @KMitosch & Clément Potel! We uncovered a mechanism by which the T7 phage broadly counteracts DNA-targeting bacterial defenses by deploying a loose cannon kinase in its genome @embl.org www.biorxiv.org/content/10.1...
1/11 - With Karin Mitosch and Clément Potel + colleagues in Savitski lab and @typaslab.bsky.social @embl.org, I’m very happy to share our discovery of a hyper-promiscuous phage protein kinase (T7K) which broadly deactivates bacterial defenses! 🦠
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 23, 2024 at 7:29 AM
1/11 - With Karin Mitosch and Clément Potel + colleagues in Savitski lab and @typaslab.bsky.social @embl.org, I’m very happy to share our discovery of a hyper-promiscuous phage protein kinase (T7K) which broadly deactivates bacterial defenses! 🦠
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...