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Matteo Trovato

@mattetrovato.bsky.social
123 followers 199 following 7 posts

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

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Reposted by Matteo Trovato
Alex Eve @amjeve.uk · 18/06/2026
Journal impact factors were released yesterday. In our latest @dev-journal.bsky.social Editorial, @jamesbriscoe.bsky.social and I discuss how we are all architects of impact, highlighting that measuring the influence and support journals provide goes beyond a single number. doi.org/10.1242/dev....
doi.org
The elephant in the room: impact factor
Summary: This Editorial offers an honest look at impact factor trends in developmental biology, explains how Development serves its community, and makes the case that sustaining developmental biology ...
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Olga Sigalova @olgasigalova.bsky.social · 16/04/2026
Happy to share our new preprint on non-coding genetic variation in the human brain and Parkinson's disease. Great team effort with @alexanrna.bsky.social, @juliedeman.bsky.social, Koen Theunis, and all co-authors, supervised by @steinaerts.bsky.social and @jdemeul.bsky.social. Thread below:
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Matteo Trovato @mattetrovato.bsky.social · 16/04/2026
Check out this computational postdoc position at IEO in Milan (IT), focused on multi-omics data integration to investigate transcriptional programs and cellular heterogeneity in myeloid neoplasms! 📢📢 More details below:
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The Lewis Lab @peterlewislab.bsky.social · 22/03/2026
Happy 30th birthday to this paper published March 22, 1996, one of the studies that moved chromatin biology from correlation toward mechanism. Brownell et al. linked a transcription-associated Tetrahymena HAT to yeast Gcn5p, providing a biochemical link for chromatin modification to gene activation.
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Ivano Legnini @ilegnini.bsky.social · 23/02/2026
Still a few days to apply :)
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Nature Biotechnology @natbiotech.nature.com · 23/02/2026
Transposable elements in the dark genome go.nature.com/4tQ1zTn
go.nature.com
Transposable elements in the dark genome - Nature Biotechnology
Transposable elements (TEs), such as retrotransposons and endogenous retroviruses, are increasingly recognized for their important roles in genome function and impact on disease development. Residing ...
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Danica Milovanović @1995dana.bsky.social · 29/01/2026
It is finally out! If you are interested in TE-derived CREs, and newly described, but evolutionary old KZFP-TE mechanistic modalities, read it at www.cell.com/cell-reports.... Thankful to everyone who took part in this work, namely @orpsf.bsky.social and other @trono-lab.bsky.social members. 🫀🧬✨
cell.com
Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity
Milovanović et al. uncover a mechanism by which KZFPs restrict the activity of transposon-derived cis-regulatory elements to safeguard cardiomyocyte functionality. This work extends the classical TE-K...
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Reposted by Matteo Trovato
FragileNucleosome @fnucleosome.bsky.social · 24/11/2025
Do you have an exciting new chromatin/transcription story that you'd like to share with the #FN community? Fill out this form to be considered for a talk in our Jan-June 2026 schedule! forms.gle/TBi38UgYxPAB... Please repost and share!
forms.gle
Application to speak in the Fragile Nucleosome series
Thank you for your interest in our seminar series! We use a variety of different session formats but, in general, trainees can plan for a ~15 min talk + 5min Q/A and PIs can plan for a ~25min talk +...
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Cedric Feschotte @cedricfeschotte.bsky.social · 18/11/2025
TE x ZFP = Evolution! Writing this with Olga @orpsf.bsky.social & Didier @trono-lab.bsky.social was a major highlight of my 🇨🇭sabbatical. Such a treat! 🍫Hope you enjoy it as much as we enjoy piecing it together.
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Johanna Joyce @johannajoyce.bsky.social · 01/10/2025
Dr. Jane Goodall, 1934-2025 An exceptional scientist, and a singular woman in science #WomeninScience 🐒 www.nytimes.com/2025/10/01/o...
nytimes.com
Jane Goodall, Eminent Primatologist Who Chronicled the Lives of Chimps, Dies at 91
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matthew.bendall @mlbendall.bsky.social · 22/07/2025
🧵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
cell.com
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...
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Matteo Trovato @mattetrovato.bsky.social · 19/07/2025
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! 👏🏼
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Rebecca Berrens @rberrens.bsky.social · 16/07/2025
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...
doi.org
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...
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Axel Visel @axelvisel.bsky.social · 18/06/2025
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
A meme-style comic panel with three parts. Left: A stylized enhancer with a mutation, surrounded by colored blocks representing functional motifs, a neural network diagram, chromatin accessibility signal traces, and a sequence motif. Two cartoon mouse embryos below show different LacZ reporter activity patterns. Top right: A hand hovers anxiously between two red buttons labeled “Experiments” and “AI,” with the caption “HOW DO ENHANCERS REALLY WORK?” Bottom right: A sweating superhero wipes his forehead, looking stressed about the difficult choice.
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Stefan Schoenfelder @stefanschoenfelder.bsky.social · 03/06/2025
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
biorxiv.org
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...
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Matteo Trovato @mattetrovato.bsky.social · 25/05/2025
If you're at #ESHG2025, don't miss the chance to visit the poster and have a chat with my friend @sanchezgaya.bsky.social!!! 👏🏼😎
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Victor Sanchez Gaya @sanchezgaya.bsky.social · 23/05/2025
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 ❤️
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Jamie Hackett @jamiehackett.bsky.social · 15/05/2025
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...
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Transposon and Cancer Epigenetics Group @deniz-lab.bsky.social · 06/05/2025
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...
nature.com
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
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Duncan Sproul @sproullab.bsky.social · 23/04/2025
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
findaphd.com
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...
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Valentina Baderna @valentinabaderna.bsky.social · 08/04/2025
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
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Matteo Trovato @mattetrovato.bsky.social · 22/03/2025
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
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Arnau Sebé-Pedrós @arnausebe.bsky.social · 19/03/2025
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.
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Moritz Mall @moritzmall.bsky.social · 13/02/2025
#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
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Ana Janeva @anajaneva.bsky.social · 06/02/2025
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!
biorxiv.org
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Cristina Viéitez @crisvieitez.bsky.social · 04/02/2025
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!
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Ben Martin @benjaminmartin.bsky.social · 26/01/2025
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...
us06web.zoom.us
Welcome! You are invited to join a webinar: Fragile Nucleosome. After registering, you will receive a confirmation email about joining the webinar.
Welcome! You are invited to join a webinar: Fragile Nucleosome. After registering, you will receive a confirmation email about joining the webinar.
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brumbaugh-lab.bsky.social @brumbaugh-lab.bsky.social · 10/01/2025
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!
rdcu.be
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...
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Kasia Siudeja @ksiudeja.bsky.social · 03/01/2025
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
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...
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Saez-Rodriguez Group @saezlab.bsky.social · 23/12/2024
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
GRETA graphical abstract
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The Lonely Pipette @lonelypipette.bsky.social · 15/11/2024
👋 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
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Giulia Pasquesi @giuliapasquesi.bsky.social · 07/12/2024
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
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
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Ewan Birney @ewanbirney.bsky.social · 27/11/2024
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.
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The Lonely Pipette @lonelypipette.bsky.social · 26/11/2024
[🔴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
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Rong Fan @rongfan8.bsky.social · 12/11/2024
The second preprint presents an experiment workflow and a broadly applicable computional framework to integrate sequencing-based and imaging-based spatial omics data for the SAME tissue slide to construct a single cell spatial omics atlas. www.biorxiv.org/content/10.1...
biorxiv.org
Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus
Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we ...
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