Matteo Trovato
@mattetrovato.bsky.social
Passionate about (epi)genomics and chromatin biology.
Postdoc at @ifomresearch.bsky.social (Milan 🇮🇹) @LabPagani //
@AIRC_it & @MSCActions Fellow //
Alumnus @embl.org (Heidelberg 🇩🇪)
🔬🧬🦕
📣 Latest: tinyurl.com/H33K9AK27A
Postdoc at @ifomresearch.bsky.social (Milan 🇮🇹) @LabPagani //
@AIRC_it & @MSCActions Fellow //
Alumnus @embl.org (Heidelberg 🇩🇪)
🔬🧬🦕
📣 Latest: tinyurl.com/H33K9AK27A
Reposted by Matteo Trovato
Dr. Jane Goodall, 1934-2025
An exceptional scientist, and a singular woman in science
#WomeninScience 🐒
www.nytimes.com/2025/10/01/o...
An exceptional scientist, and a singular woman in science
#WomeninScience 🐒
www.nytimes.com/2025/10/01/o...
Jane Goodall, Eminent Primatologist Who Chronicled the Lives of Chimps, Dies at 91
www.nytimes.com
October 1, 2025 at 7:23 PM
Dr. Jane Goodall, 1934-2025
An exceptional scientist, and a singular woman in science
#WomeninScience 🐒
www.nytimes.com/2025/10/01/o...
An exceptional scientist, and a singular woman in science
#WomeninScience 🐒
www.nytimes.com/2025/10/01/o...
Reposted by Matteo Trovato
🧵1/ Introducing Stellarscope: an EM-based tool for quantifying locus-specific transposable element expression in single cells.
A single-cell transposable element atlas of human cell identity: Cell Reports Methods www.cell.com/cell-reports...
@hamarillo.bsky.social #TEHub #singlecell #genomics
A single-cell transposable element atlas of human cell identity: Cell Reports Methods www.cell.com/cell-reports...
@hamarillo.bsky.social #TEHub #singlecell #genomics
A single-cell transposable element atlas of human cell identity
Reyes-Gopar et al. introduce Stellarscope, a computational approach for quantifying
locus-specific transposable element expression in single-cell RNA sequencing data.
The authors profile human PBMCs a...
www.cell.com
July 22, 2025 at 2:47 PM
🧵1/ Introducing Stellarscope: an EM-based tool for quantifying locus-specific transposable element expression in single cells.
A single-cell transposable element atlas of human cell identity: Cell Reports Methods www.cell.com/cell-reports...
@hamarillo.bsky.social #TEHub #singlecell #genomics
A single-cell transposable element atlas of human cell identity: Cell Reports Methods www.cell.com/cell-reports...
@hamarillo.bsky.social #TEHub #singlecell #genomics
What a great week at @earlhaminst.bsky.social, spent together with the awesome @longtrec.bsky.social folks! Learned a lot and had some great discussions about long-reads sequencing analysis! 🙌🏻💡
Big thanks to @anaconesa.bsky.social and everyone who made it happen! 👏🏼
Big thanks to @anaconesa.bsky.social and everyone who made it happen! 👏🏼
Thank you for hosting us!!! The LongTREC summer school has been a great success and the amazing
@earlhaminst.bsky.social facilities ensured a smooth and enjoyable week for all involved. #LongTREC #SummerSchool
@earlhaminst.bsky.social facilities ensured a smooth and enjoyable week for all involved. #LongTREC #SummerSchool
A great week-long summer school on #longread #bioinformatics with the @longtrec.bsky.social Doctoral Network!
LongTREC brings together scientists from across Europe to train the next generation of #computationalbiologists to develop novel applications from #transcriptomic data. 🖥️🧬
longtrec.eu
LongTREC brings together scientists from across Europe to train the next generation of #computationalbiologists to develop novel applications from #transcriptomic data. 🖥️🧬
longtrec.eu
July 19, 2025 at 8:38 AM
What a great week at @earlhaminst.bsky.social, spent together with the awesome @longtrec.bsky.social folks! Learned a lot and had some great discussions about long-reads sequencing analysis! 🙌🏻💡
Big thanks to @anaconesa.bsky.social and everyone who made it happen! 👏🏼
Big thanks to @anaconesa.bsky.social and everyone who made it happen! 👏🏼
Reposted by Matteo Trovato
Very happy to share our protocols paper for CELLO-seq. This will make single cell long read RNA-seq more accessible and provides analysis guidelines. We hope this helps the #transposon #TEsky community and folks working on #singleCell isoform and allelic #gene expression. doi.org/10.1038/s415...
Long-read RNA sequencing of transposable elements from single cells using CELLO-seq - Nature Protocols
Single-cell long-read RNA sequencing enables the high-fidelity mapping of single-cell expression data from highly sequence-similar transposable elements to unique genomic loci by correcting errors fro...
doi.org
July 16, 2025 at 4:55 PM
Very happy to share our protocols paper for CELLO-seq. This will make single cell long read RNA-seq more accessible and provides analysis guidelines. We hope this helps the #transposon #TEsky community and folks working on #singleCell isoform and allelic #gene expression. doi.org/10.1038/s415...
Reposted by Matteo Trovato
Textbooks: “Enhancers are just a bunch of TFBSs”
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
June 18, 2025 at 5:56 PM
Textbooks: “Enhancers are just a bunch of TFBSs”
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
Reposted by Matteo Trovato
Delighted & excited to share our latest preprint on non-canonical enhancers in human pluripotent stem cells, the result of a fantastic and fun collaboration with @guenesdoganlab.bsky.social:
www.biorxiv.org/content/10.1...
🧵 below
www.biorxiv.org/content/10.1...
🧵 below
Non-canonical enhancers control gene expression and cell fate in human pluripotent stem cells
Enhancers are key gene regulatory elements that ensure the precise spatiotemporal execution of developmental gene expression programmes. However recent findings indicate that approaches to identify en...
www.biorxiv.org
June 2, 2025 at 11:26 PM
Delighted & excited to share our latest preprint on non-canonical enhancers in human pluripotent stem cells, the result of a fantastic and fun collaboration with @guenesdoganlab.bsky.social:
www.biorxiv.org/content/10.1...
🧵 below
www.biorxiv.org/content/10.1...
🧵 below
If you're at #ESHG2025, don't miss the chance to visit the poster and have a chat with my friend @sanchezgaya.bsky.social!!! 👏🏼😎
Ready and excited to start with #ESHG2025. If you want to hear about how developmental genes can contribute to the insulation of their own TADs, and the consequences for SV interpretation, find me on P22.020.A poster on Sunday 13:00-14:00. Special thanks to the best host @mattetrovato.bsky.social ❤️
May 25, 2025 at 12:47 PM
If you're at #ESHG2025, don't miss the chance to visit the poster and have a chat with my friend @sanchezgaya.bsky.social!!! 👏🏼😎
Reposted by Matteo Trovato
Ready and excited to start with #ESHG2025. If you want to hear about how developmental genes can contribute to the insulation of their own TADs, and the consequences for SV interpretation, find me on P22.020.A poster on Sunday 13:00-14:00. Special thanks to the best host @mattetrovato.bsky.social ❤️
May 23, 2025 at 10:09 PM
Ready and excited to start with #ESHG2025. If you want to hear about how developmental genes can contribute to the insulation of their own TADs, and the consequences for SV interpretation, find me on P22.020.A poster on Sunday 13:00-14:00. Special thanks to the best host @mattetrovato.bsky.social ❤️
Reposted by Matteo Trovato
We are looking to take on an intern at EMBL Rome, for anyone interested in CRISPR and Epigenetics training.
The traineeship is 3-12-months, in Rome (Italy), should start by July, and is supervised by the outstanding @steliostsagkris.bsky.social.
#job #internship; see info below...
The traineeship is 3-12-months, in Rome (Italy), should start by July, and is supervised by the outstanding @steliostsagkris.bsky.social.
#job #internship; see info below...
May 15, 2025 at 7:38 AM
We are looking to take on an intern at EMBL Rome, for anyone interested in CRISPR and Epigenetics training.
The traineeship is 3-12-months, in Rome (Italy), should start by July, and is supervised by the outstanding @steliostsagkris.bsky.social.
#job #internship; see info below...
The traineeship is 3-12-months, in Rome (Italy), should start by July, and is supervised by the outstanding @steliostsagkris.bsky.social.
#job #internship; see info below...
Reposted by Matteo Trovato
I am excited to share our lab's first review out with in Blood Cancer Journal. We discuss the impact of transposable elements on genome regulation and variation in both normal
haematopoietic processes and haematological cancers. www.nature.com/articles/s41...
haematopoietic processes and haematological cancers. www.nature.com/articles/s41...
Transposable elements as genome regulators in normal and malignant haematopoiesis - Blood Cancer Journal
Blood Cancer Journal - Transposable elements as genome regulators in normal and malignant haematopoiesis
www.nature.com
May 6, 2025 at 4:31 PM
I am excited to share our lab's first review out with in Blood Cancer Journal. We discuss the impact of transposable elements on genome regulation and variation in both normal
haematopoietic processes and haematological cancers. www.nature.com/articles/s41...
haematopoietic processes and haematological cancers. www.nature.com/articles/s41...
Reposted by Matteo Trovato
Want to work with us on DNA methylation and rare genetic disease? Fully funded PhD project with deadline 16th May:
www.findaphd.com/phds/project...
Excited to collaborate with @hannahlong.bsky.social and Daria Bunina (@uoe-igc.bsky.social/@mdc-berlin.bsky.social).
Please share 🙏
#epigenetics
www.findaphd.com/phds/project...
Excited to collaborate with @hannahlong.bsky.social and Daria Bunina (@uoe-igc.bsky.social/@mdc-berlin.bsky.social).
Please share 🙏
#epigenetics
Fully Funded PhD Studentship in Human Genetics, Genomics and Disease: Dissecting DNMT3B functions in Immunodeficiency-centromeric instability facial anomalies syndrome at University of Edinburgh on Fi...
PhD Project - Fully Funded PhD Studentship in Human Genetics, Genomics and Disease: Dissecting DNMT3B functions in Immunodeficiency-centromeric instability facial anomalies syndrome at University of E...
www.findaphd.com
April 23, 2025 at 9:49 AM
Want to work with us on DNA methylation and rare genetic disease? Fully funded PhD project with deadline 16th May:
www.findaphd.com/phds/project...
Excited to collaborate with @hannahlong.bsky.social and Daria Bunina (@uoe-igc.bsky.social/@mdc-berlin.bsky.social).
Please share 🙏
#epigenetics
www.findaphd.com/phds/project...
Excited to collaborate with @hannahlong.bsky.social and Daria Bunina (@uoe-igc.bsky.social/@mdc-berlin.bsky.social).
Please share 🙏
#epigenetics
Reposted by Matteo Trovato
Happy to share the latest story from @arnaudkr.bsky.social's lab @embl.org! With @guidobarzaghi.bsky.social, we used Single Molecule Footprinting to quantify how often chromatin is accessible at enhancers after TF and chromatin environment changes! Check our preprint bit.ly/3XQMFxN + thread ⬇️ 1/11
April 8, 2025 at 1:52 PM
Happy to share the latest story from @arnaudkr.bsky.social's lab @embl.org! With @guidobarzaghi.bsky.social, we used Single Molecule Footprinting to quantify how often chromatin is accessible at enhancers after TF and chromatin environment changes! Check our preprint bit.ly/3XQMFxN + thread ⬇️ 1/11
And then, one day before heading to the lab, you stop by uni to hear Shinya Yamanaka sharing the latest on iPSCs research!! Not a bad way to start a Friday...! 😄
#MLS
#MilanLongevitySummit
#MLS
#MilanLongevitySummit
March 22, 2025 at 11:45 AM
And then, one day before heading to the lab, you stop by uni to hear Shinya Yamanaka sharing the latest on iPSCs research!! Not a bad way to start a Friday...! 😄
#MLS
#MilanLongevitySummit
#MLS
#MilanLongevitySummit
Reposted by Matteo Trovato
Check out our latest work on chromatin evolution by @crisnava.bsky.social and @seanamontgomery.bsky.social. Building on our study of histone mark conservation (www.nature.com/articles/s41...), we now explore whether these same marks define similar chromatin states across eukaryotes.
Excited to share this story from the “Chromatin Dream Team” in the @arnausebe.bsky.social lab on chromatin evo across eukaryotes! 12 histone mark profiles from 12 species, including rhizarians, discobans, and cryptomonads. Read on to see what we found! www.biorxiv.org/content/10.1... 1/n
Diversity and evolution of chromatin regulatory states across eukaryotes
Histone post-translational modifications (hPTMs) are key regulators of chromatin states, influencing gene expression, epigenetic memory, and transposable element repression across eukaryotic genomes. ...
www.biorxiv.org
March 19, 2025 at 12:09 PM
Check out our latest work on chromatin evolution by @crisnava.bsky.social and @seanamontgomery.bsky.social. Building on our study of histone mark conservation (www.nature.com/articles/s41...), we now explore whether these same marks define similar chromatin states across eukaryotes.
Reposted by Matteo Trovato
#CellPlasticity—the ability of cells to change their identity—is vital for tissue growth and repair. But when it goes unchecked, it can fuel #cancer. Our latest study examines how to block #LiverCancer by actively suppressing plasticity. www.nature.com/articles/s41... #CancerBiology
February 13, 2025 at 12:16 PM
#CellPlasticity—the ability of cells to change their identity—is vital for tissue growth and repair. But when it goes unchecked, it can fuel #cancer. Our latest study examines how to block #LiverCancer by actively suppressing plasticity. www.nature.com/articles/s41... #CancerBiology
Reposted by Matteo Trovato
Next Wed 12.02. at 6pm CET I will be speaking about our latest preprint: www.biorxiv.org/content/10.1... and present our findings on how we developed a machine learning model that identified new reprogramming barriers, such as H3K27ac, and our in vivo experiments to test it. See you there!
February 6, 2025 at 12:23 PM
Next Wed 12.02. at 6pm CET I will be speaking about our latest preprint: www.biorxiv.org/content/10.1... and present our findings on how we developed a machine learning model that identified new reprogramming barriers, such as H3K27ac, and our in vivo experiments to test it. See you there!
Reposted by Matteo Trovato
I am looking for postdocs to work across the fields of #CellSignalling and Chromatin. Background in #Bioinformatics #PTMbiology
#ERC-funded positions - Reach out if you want to discuss.
Please share among potential candidates!
#ERC-funded positions - Reach out if you want to discuss.
Please share among potential candidates!
Our lab is recruiting Postdocs with strong background in Epigenetics, PTM biology and/or Cell Signalling along with experience with bioinformatics 👩💻👨💻
📢 Apply through the IBFG Postdoc Call 2025!
🔗 Check all the positions here 👇
drive.google.com/file/d/1JxNd...
📢 Apply through the IBFG Postdoc Call 2025!
🔗 Check all the positions here 👇
drive.google.com/file/d/1JxNd...
February 4, 2025 at 4:04 PM
I am looking for postdocs to work across the fields of #CellSignalling and Chromatin. Background in #Bioinformatics #PTMbiology
#ERC-funded positions - Reach out if you want to discuss.
Please share among potential candidates!
#ERC-funded positions - Reach out if you want to discuss.
Please share among potential candidates!
Reposted by Matteo Trovato
2025 Fragile Nucleosome talks kick off this Wednesday with two great speakers! We'll hear about everything from tardigrades and cryo-EM of nucleosome bound factors to SWI/SNF, LTRs, and ovarian tumors.
You won't want to miss this one, register here! us06web.zoom.us/webinar/regi...
You won't want to miss this one, register here! us06web.zoom.us/webinar/regi...
January 26, 2025 at 10:50 PM
2025 Fragile Nucleosome talks kick off this Wednesday with two great speakers! We'll hear about everything from tardigrades and cryo-EM of nucleosome bound factors to SWI/SNF, LTRs, and ovarian tumors.
You won't want to miss this one, register here! us06web.zoom.us/webinar/regi...
You won't want to miss this one, register here! us06web.zoom.us/webinar/regi...
Reposted by Matteo Trovato
Our new paper defining the role of H3K36 methylation in regulating cell fate and plasticity is available online: rdcu.be/d5AEc
Thanks to our entire team for their tireless work and to the editors at @naturecellbiology.bsky.social for the opportunity!
Thanks to our entire team for their tireless work and to the editors at @naturecellbiology.bsky.social for the opportunity!
H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium
Nature Cell Biology - Pashos et al. show that H3K36 methylation maintains intestinal epithelial fate commitment, whereas its suppression, which is also observed upon injury, induces a plastic state...
rdcu.be
January 10, 2025 at 5:22 AM
Our new paper defining the role of H3K36 methylation in regulating cell fate and plasticity is available online: rdcu.be/d5AEc
Thanks to our entire team for their tireless work and to the editors at @naturecellbiology.bsky.social for the opportunity!
Thanks to our entire team for their tireless work and to the editors at @naturecellbiology.bsky.social for the opportunity!
Reposted by Matteo Trovato
To kick start the New Year, I'm delighted to share the lab's first preprint - now online:
biorxiv.org/cgi/content/...
See below for a couple of highlights👇
Any feedback is welcome!
"TEsky"
HAPPY NEW YEAR to everyone! 🥂
biorxiv.org/cgi/content/...
See below for a couple of highlights👇
Any feedback is welcome!
"TEsky"
HAPPY NEW YEAR to everyone! 🥂
An endogenous retroviral element co-opts an upstream regulatory sequence to achieve somatic expression and mobility
Retrotransposons, multi-copy sequences that propagate via copy-and-paste mechanisms involving an RNA intermediate, occupy large portions of all eukaryotic genomes. A great majority of their manifold c...
biorxiv.org
January 3, 2025 at 11:15 AM
To kick start the New Year, I'm delighted to share the lab's first preprint - now online:
biorxiv.org/cgi/content/...
See below for a couple of highlights👇
Any feedback is welcome!
"TEsky"
HAPPY NEW YEAR to everyone! 🥂
biorxiv.org/cgi/content/...
See below for a couple of highlights👇
Any feedback is welcome!
"TEsky"
HAPPY NEW YEAR to everyone! 🥂
Reposted by Matteo Trovato
We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
December 23, 2024 at 8:43 AM
We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
Reposted by Matteo Trovato
👋 Hi there ! We are The Lonely Pipette podcast. We are back here to connect with academics. #academicsky
We help scientists do better science by sharing conversations with scientists all around the world, tips to improve the academic ecosystem 🫂
🎧 You can check us here ➡️ bit.ly/TLPtree
We help scientists do better science by sharing conversations with scientists all around the world, tips to improve the academic ecosystem 🫂
🎧 You can check us here ➡️ bit.ly/TLPtree
November 15, 2024 at 7:31 AM
👋 Hi there ! We are The Lonely Pipette podcast. We are back here to connect with academics. #academicsky
We help scientists do better science by sharing conversations with scientists all around the world, tips to improve the academic ecosystem 🫂
🎧 You can check us here ➡️ bit.ly/TLPtree
We help scientists do better science by sharing conversations with scientists all around the world, tips to improve the academic ecosystem 🫂
🎧 You can check us here ➡️ bit.ly/TLPtree
Reposted by Matteo Trovato
Following up on Nat. Commun. 2018, we analyzed the relationship between TE transcription and expression levels of genes involved in TE silencing in somatic and germline tissues across vertebrates.
doi.org/10.1093/gbe/...
doi.org/10.1093/gbe/...
Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues
Abstract. Transposable elements (TEs) comprise a major fraction of vertebrate genomes, yet little is known about their expression and regulation across tis
doi.org
December 7, 2024 at 2:28 AM
Following up on Nat. Commun. 2018, we analyzed the relationship between TE transcription and expression levels of genes involved in TE silencing in somatic and germline tissues across vertebrates.
doi.org/10.1093/gbe/...
doi.org/10.1093/gbe/...
Reposted by Matteo Trovato
Very nice combinatorics experiment on chromatin IP (ChIP) (one of those like - of course one can do this, why didn't I think of this? - no doubt it is fiddly and complex to get all right) - being able to do ~150 way parallel chip. Gets me thinking about other combinatorics one can do here.
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
www.nature.com
November 27, 2024 at 5:39 PM
Very nice combinatorics experiment on chromatin IP (ChIP) (one of those like - of course one can do this, why didn't I think of this? - no doubt it is fiddly and complex to get all right) - being able to do ~150 way parallel chip. Gets me thinking about other combinatorics one can do here.
Reposted by Matteo Trovato
[🔴New episode] What's the ideal recipe to go from 🔲 to ✅?
🎙️ Ana Boskovic, group leader @embl.org shares with us what we might call the “First lab manifesto”
LISTEN NOW 🎧 ► www.buzzsprout.com/1356877/epis...
💌 ► Receive Season 3 in your mailbox : bit.ly/NLTLP
🎙️ Ana Boskovic, group leader @embl.org shares with us what we might call the “First lab manifesto”
LISTEN NOW 🎧 ► www.buzzsprout.com/1356877/epis...
💌 ► Receive Season 3 in your mailbox : bit.ly/NLTLP
November 26, 2024 at 10:41 AM
[🔴New episode] What's the ideal recipe to go from 🔲 to ✅?
🎙️ Ana Boskovic, group leader @embl.org shares with us what we might call the “First lab manifesto”
LISTEN NOW 🎧 ► www.buzzsprout.com/1356877/epis...
💌 ► Receive Season 3 in your mailbox : bit.ly/NLTLP
🎙️ Ana Boskovic, group leader @embl.org shares with us what we might call the “First lab manifesto”
LISTEN NOW 🎧 ► www.buzzsprout.com/1356877/epis...
💌 ► Receive Season 3 in your mailbox : bit.ly/NLTLP