Miguel V. Almeida
@migueldvalmeida.bsky.social
Postdoc at the University of Cambridge. Interested in transposons, evolution, epigenetics, worms and African cichlid fishes.
Pinned
📢The peer-reviewed version of our work on TEs driving innovation of F-box genes is out now on @molbioevol.bsky.social. 🎉
paper here:
academic.oup.com/mbe/article/...
Check my previous, but still up-to-date 🧵 to read the highlights. #TEsky #evosky #Celegans
paper here:
academic.oup.com/mbe/article/...
Check my previous, but still up-to-date 🧵 to read the highlights. #TEsky #evosky #Celegans
Reposted by Miguel V. Almeida
New preprint from the lab! We dig into the regulatory roles of TEs in the mouse placenta, with some surprising findings. Led by the awesome @smamante.bsky.social. Particular kudos to him for navigating the many twists and turns of the project.
www.biorxiv.org
February 2, 2026 at 10:25 AM
New preprint from the lab! We dig into the regulatory roles of TEs in the mouse placenta, with some surprising findings. Led by the awesome @smamante.bsky.social. Particular kudos to him for navigating the many twists and turns of the project.
Reposted by Miguel V. Almeida
Today, we're sharing an open letter from our Chief Executive, Professor Sir Ian Chapman, outlining changes to UKRI investment approach, and addressing concerns about research funding and the financial position of STFC. Read his letter here: www.ukri.org/news/open-le...
Open letter from Ian Chapman to research and innovation community
UKRI Chief Executive outlines changes to UKRI investment approach, addressing concerns about research funding and the financial position of STFC.
www.ukri.org
February 1, 2026 at 5:16 PM
Today, we're sharing an open letter from our Chief Executive, Professor Sir Ian Chapman, outlining changes to UKRI investment approach, and addressing concerns about research funding and the financial position of STFC. Read his letter here: www.ukri.org/news/open-le...
Reposted by Miguel V. Almeida
Huge congratulations to @juancruedas.bsky.social for successfully passing his PhD viva with minor corrections yesterday! 🧬We’re incredibly proud of you! And even more exciting, the manuscript is on the way. Stay tuned! 👏🥳
@cambiochem.bsky.social
@cambiochem.bsky.social
January 29, 2026 at 10:09 PM
Huge congratulations to @juancruedas.bsky.social for successfully passing his PhD viva with minor corrections yesterday! 🧬We’re incredibly proud of you! And even more exciting, the manuscript is on the way. Stay tuned! 👏🥳
@cambiochem.bsky.social
@cambiochem.bsky.social
Reposted by Miguel V. Almeida
One protein. One pathway. A whole germline fate.
New paper from my postdoc @mpi-bio-fml.bsky.social out in PNAS:
Germline fate determination by a single ARGONAUTE protein in Ectocarpus www.pnas.org/doi/10.1073/...
New paper from my postdoc @mpi-bio-fml.bsky.social out in PNAS:
Germline fate determination by a single ARGONAUTE protein in Ectocarpus www.pnas.org/doi/10.1073/...
Germline fate determination by a single ARGONAUTE protein in Ectocarpus | PNAS
ARGONAUTE (AGO) proteins are a highly conserved family of RNA-binding proteins that
play central roles in gene regulation and developmental process...
www.pnas.org
January 30, 2026 at 9:14 AM
One protein. One pathway. A whole germline fate.
New paper from my postdoc @mpi-bio-fml.bsky.social out in PNAS:
Germline fate determination by a single ARGONAUTE protein in Ectocarpus www.pnas.org/doi/10.1073/...
New paper from my postdoc @mpi-bio-fml.bsky.social out in PNAS:
Germline fate determination by a single ARGONAUTE protein in Ectocarpus www.pnas.org/doi/10.1073/...
Reposted by Miguel V. Almeida
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. 🫀🧬✨
Thankful to everyone who took part in this work, namely @orpsf.bsky.social and other @trono-lab.bsky.social members. 🫀🧬✨
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...
www.cell.com
January 29, 2026 at 2:20 PM
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. 🫀🧬✨
Thankful to everyone who took part in this work, namely @orpsf.bsky.social and other @trono-lab.bsky.social members. 🫀🧬✨
Reposted by Miguel V. Almeida
Crushed to hear of Mark Batzer’s passing. He was the Boyd Professor at Louisiana State University. His influential research revealed how mobile elements shape the genomes of humans & other mammals. Mark’s personality, generosity & positivity were larger than life. He lifted everyone up. HUGE loss 💔
January 22, 2026 at 5:38 PM
Crushed to hear of Mark Batzer’s passing. He was the Boyd Professor at Louisiana State University. His influential research revealed how mobile elements shape the genomes of humans & other mammals. Mark’s personality, generosity & positivity were larger than life. He lifted everyone up. HUGE loss 💔
Reposted by Miguel V. Almeida
We had a great time at the @cambiochem.bsky.social Away Days, learning about the exciting research across the Department! It was a pleasure to share some of our group’s projects thanks to @migueldvalmeida.bsky.social and @ecwalsh.bsky.social . All set for a year full of science! Stay tuned!
January 15, 2026 at 5:05 PM
We had a great time at the @cambiochem.bsky.social Away Days, learning about the exciting research across the Department! It was a pleasure to share some of our group’s projects thanks to @migueldvalmeida.bsky.social and @ecwalsh.bsky.social . All set for a year full of science! Stay tuned!
Reposted by Miguel V. Almeida
Interested in the unexpected? How about a link between piRNAs and maternal histone mRNAs … Great collab with @sebastianfalk.bsky.social, @koenig-lab.bsky.social and Florian Steiner.
#piRNA #histone #mRNA #maternal #RNAbiology #RNASky
www.biorxiv.org/content/10.6...
#piRNA #histone #mRNA #maternal #RNAbiology #RNASky
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 8, 2026 at 8:51 AM
Interested in the unexpected? How about a link between piRNAs and maternal histone mRNAs … Great collab with @sebastianfalk.bsky.social, @koenig-lab.bsky.social and Florian Steiner.
#piRNA #histone #mRNA #maternal #RNAbiology #RNASky
www.biorxiv.org/content/10.6...
#piRNA #histone #mRNA #maternal #RNAbiology #RNASky
www.biorxiv.org/content/10.6...
Reposted by Miguel V. Almeida
New Year, New Paper!🎊
Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system
www.biorxiv.org/content/10.6...
Centerpiece of Jason Chobirko's PhD, talented PhD student co-mentored by Andrew Grimson & me. Really excited about it!🧵
Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system
www.biorxiv.org/content/10.6...
Centerpiece of Jason Chobirko's PhD, talented PhD student co-mentored by Andrew Grimson & me. Really excited about it!🧵
Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system
Transposable elements (TEs) make up about half of the human and mouse genomes and play important regulatory roles in immune responses. However, the cis -regulatory contribution of TEs to immune cell d...
www.biorxiv.org
January 7, 2026 at 7:45 PM
New Year, New Paper!🎊
Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system
www.biorxiv.org/content/10.6...
Centerpiece of Jason Chobirko's PhD, talented PhD student co-mentored by Andrew Grimson & me. Really excited about it!🧵
Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system
www.biorxiv.org/content/10.6...
Centerpiece of Jason Chobirko's PhD, talented PhD student co-mentored by Andrew Grimson & me. Really excited about it!🧵
Reposted by Miguel V. Almeida
Need a bit of escapism? Not exactly Lord of the Rings, but in similar vein:
doi.org/10.1038/s443...
doi.org/10.1038/s443...
Epimutations: raw material for evolution? - The EMBO Journal
Epigenetics is fundamental to cell differentiation as it enables cells with identical genomes to adopt distinct fates. Some epigenetic information can also be transmitted between generations, in a pro...
link.springer.com
January 6, 2026 at 6:33 PM
Need a bit of escapism? Not exactly Lord of the Rings, but in similar vein:
doi.org/10.1038/s443...
doi.org/10.1038/s443...
Very happy to see this preprint out! 🎉 This was the last project I started during my time in the Ketting lab, which was later picked up by Shamitha, who did an amazing job extending our initial observations on C. elegans GTSF-1 to other nematodes + further insights into RdRP interaction.
What a way to start the new year with one more submission to BioRxiv. This one is on how GTSF-1 enable RdRP activity in nematodes (for Piwi aficionados: correct, it does not affect Piwi😊)
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
An Evolutionarily Conserved N-terminal Domain of RRF-3 Governs GTSF-1 Binding in Nematodes
GTSF1 is an essential activating cofactor for PIWI proteins in many metazoans. In the nematode Caenorhabditis elegans, however, GTSF-1 does not bind PIWI, but associates with the RNA-dependent RNA pol...
www.biorxiv.org
January 6, 2026 at 2:33 PM
Very happy to see this preprint out! 🎉 This was the last project I started during my time in the Ketting lab, which was later picked up by Shamitha, who did an amazing job extending our initial observations on C. elegans GTSF-1 to other nematodes + further insights into RdRP interaction.
Reposted by Miguel V. Almeida
Happy to share two BioRxiv manuscripts from our lab. One on genetic Argonaute interaction and unexpected non-correlation between small RNAs and their targets:
doi.org/10.64898/202...
The second on IDR processing and IDR-mediated Argonaute loading control:
doi.org/10.64898/202...
Merry Xmas😊
doi.org/10.64898/202...
The second on IDR processing and IDR-mediated Argonaute loading control:
doi.org/10.64898/202...
Merry Xmas😊
December 22, 2025 at 2:06 PM
Happy to share two BioRxiv manuscripts from our lab. One on genetic Argonaute interaction and unexpected non-correlation between small RNAs and their targets:
doi.org/10.64898/202...
The second on IDR processing and IDR-mediated Argonaute loading control:
doi.org/10.64898/202...
Merry Xmas😊
doi.org/10.64898/202...
The second on IDR processing and IDR-mediated Argonaute loading control:
doi.org/10.64898/202...
Merry Xmas😊
Reposted by Miguel V. Almeida
☕Earl Grey v7.0.0 brewed fresh☕
Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.
Happy new year to the TE folks! 🧬
github.com/TobyBaril/Ea...
Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.
Happy new year to the TE folks! 🧬
github.com/TobyBaril/Ea...
GitHub - TobyBaril/EarlGrey: Earl Grey: A fully automated TE curation and annotation pipeline
Earl Grey: A fully automated TE curation and annotation pipeline - TobyBaril/EarlGrey
github.com
January 5, 2026 at 3:10 PM
☕Earl Grey v7.0.0 brewed fresh☕
Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.
Happy new year to the TE folks! 🧬
github.com/TobyBaril/Ea...
Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.
Happy new year to the TE folks! 🧬
github.com/TobyBaril/Ea...
Reposted by Miguel V. Almeida
Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway.
And found a hidden RNA-decay axis from Piwi to the RNA exosome.
And found a hidden RNA-decay axis from Piwi to the RNA exosome.
RNA decay via the nuclear exosome is essential for piwi-mediated transposon silencing https://www.biorxiv.org/content/10.64898/2025.12.16.694471v1
December 22, 2025 at 6:14 PM
Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway.
And found a hidden RNA-decay axis from Piwi to the RNA exosome.
And found a hidden RNA-decay axis from Piwi to the RNA exosome.
Reposted by Miguel V. Almeida
Very happy to share that I have been awarded an ERC CoG to build predictive and mechanistic models of pigment pattern development and evolution across cichlids!! 🐠🎨 I've been dreaming about this for a long time, and I’m incredibly excited that we can now pursue it in full. #ERCCoG @erc.europa.eu 1/3
December 9, 2025 at 8:56 PM
Very happy to share that I have been awarded an ERC CoG to build predictive and mechanistic models of pigment pattern development and evolution across cichlids!! 🐠🎨 I've been dreaming about this for a long time, and I’m incredibly excited that we can now pursue it in full. #ERCCoG @erc.europa.eu 1/3
Reposted by Miguel V. Almeida
WormTagDB: A Systematic Survey of Endogenously Tagged Proteins in C. elegans and Roadmap Towards the Tagged Proteome https://www.biorxiv.org/content/10.64898/2025.12.02.691955v1
December 5, 2025 at 9:32 PM
WormTagDB: A Systematic Survey of Endogenously Tagged Proteins in C. elegans and Roadmap Towards the Tagged Proteome https://www.biorxiv.org/content/10.64898/2025.12.02.691955v1
Reposted by Miguel V. Almeida
High-quality mouse reference genomes [PacBio Long Read genomes of 17 strains] reveal the structural complexity of the murine protein-coding landscape, Cell Genomics. www.cell.com/cell-genomic... Genomes and annotations here: projects.ensembl.org/mouse_genomes/
High-quality mouse reference genomes reveal the structural complexity of the murine protein-coding landscape
Helmy et al. provide a collection of high-quality mouse reference genomes. They were
able to resolve some of the most complex regions among mouse genomes that are involved
in immune defense. These fin...
www.cell.com
December 2, 2025 at 4:30 AM
High-quality mouse reference genomes [PacBio Long Read genomes of 17 strains] reveal the structural complexity of the murine protein-coding landscape, Cell Genomics. www.cell.com/cell-genomic... Genomes and annotations here: projects.ensembl.org/mouse_genomes/
Reposted by Miguel V. Almeida
Rapid compensatory evolution within a multiprotein complex preserves telomere integrity www.science.org/doi/10.1126/... @levine-lab.bsky.social very cool work
Rapid compensatory evolution within a multiprotein complex preserves telomere integrity
Intragenomic conflict with selfish genetic elements spurs adaptive changes in subunits of essential multiprotein complexes. Whether and how these adaptive changes disrupt interactions within such comp...
www.science.org
November 27, 2025 at 8:43 PM
Rapid compensatory evolution within a multiprotein complex preserves telomere integrity www.science.org/doi/10.1126/... @levine-lab.bsky.social very cool work
Reposted by Miguel V. Almeida
All hail Caenorhabditis elegans, one of the most researched organisms on Earth. Collaborative data sharing in the nematode research community led to four Nobel Prize-winning discoveries about human development and disease. In PNAS: https://ow.ly/uNqU50Xyj4e
November 26, 2025 at 7:01 PM
All hail Caenorhabditis elegans, one of the most researched organisms on Earth. Collaborative data sharing in the nematode research community led to four Nobel Prize-winning discoveries about human development and disease. In PNAS: https://ow.ly/uNqU50Xyj4e
Reposted by Miguel V. Almeida
Happy to share that my PhD project is finally published!🪱✨
Selfish genes are found across the tree of life. They can disrupt inheritance patterns and at the same time act as units for molecular innovation. Here we tried to answer one big question: how do selfish genes emerge in the first place?
Selfish genes are found across the tree of life. They can disrupt inheritance patterns and at the same time act as units for molecular innovation. Here we tried to answer one big question: how do selfish genes emerge in the first place?
Recurrent evolution of selfishness from an essential tRNA synthetase in Caenorhabditis tropicalis 🧪
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Recurrent evolution of selfishness from an essential tRNA synthetase in Caenorhabditis tropicalis - Nature Ecology & Evolution
In Caenorhabditis tropicalis, three toxin–antidote elements arose via gene duplication from the essential tRNA-synthetase subunit FARS-3. The ancestral antidote probably acquired affinity for FARS-3, ...
www.nature.com
November 24, 2025 at 9:10 PM
Happy to share that my PhD project is finally published!🪱✨
Selfish genes are found across the tree of life. They can disrupt inheritance patterns and at the same time act as units for molecular innovation. Here we tried to answer one big question: how do selfish genes emerge in the first place?
Selfish genes are found across the tree of life. They can disrupt inheritance patterns and at the same time act as units for molecular innovation. Here we tried to answer one big question: how do selfish genes emerge in the first place?
Reposted by Miguel V. Almeida
Roussel, Suh, @fjruizruano.bsky.social & @amdioncote.bsky.social characterized TE content in naturally occurring killifish hybrids, finding higher TE load and accumulation of Neptune subfamilies in hybrids.
🔗 doi.org/10.1093/molbev/msaf266
#evobio #molbio #TEsky
🔗 doi.org/10.1093/molbev/msaf266
#evobio #molbio #TEsky
Accumulation of a Biparentally Inherited Neptune Transposable Element in Natural Killifish Hybrids (Fundulus diaphanus × F. heteroclitus)
Abstract. Transposable elements (TEs) are abundant selfish genetic elements that can mobilize in their host genome, causing DNA damage, mutations, and chro
doi.org
November 20, 2025 at 2:45 PM
Roussel, Suh, @fjruizruano.bsky.social & @amdioncote.bsky.social characterized TE content in naturally occurring killifish hybrids, finding higher TE load and accumulation of Neptune subfamilies in hybrids.
🔗 doi.org/10.1093/molbev/msaf266
#evobio #molbio #TEsky
🔗 doi.org/10.1093/molbev/msaf266
#evobio #molbio #TEsky
Reposted by Miguel V. Almeida
Looking for a PhD in RNA biology? The deadline is approaching fast! This is a great opportunity to do a PhD together with an industry partner fully funded by @nrpdtp.bsky.social BBSRC Case studentship.
New BBSRC funded PhD opportunity in my group with Inspiralis Ltd and @conradn.bsky.social. If you are interested in RNA - protein interactions and RNA modifications check the details below for how to apply. @nrpdtp.bsky.social @biouea.bsky.social @earlhaminst.bsky.social tinyurl.com/bdzvn4dr
How do RNA molecules shape genome regulation in the nervous system? (AKAY_U26CASE) | Doctoral Training Partnership
This PhD project will investigate how RNA modifications influence the activity of topoisomerase I (TOP1), a crucial enzyme that regulates DNA supercoiling during replication and transcription. Using C...
biodtp.norwichresearchpark.ac.uk
November 20, 2025 at 8:05 AM
Looking for a PhD in RNA biology? The deadline is approaching fast! This is a great opportunity to do a PhD together with an industry partner fully funded by @nrpdtp.bsky.social BBSRC Case studentship.
Reposted by Miguel V. Almeida
piRNA-directed DNA methylation may not be a mammalian invention, but can already be found in the germline of axolotl salamanders
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
November 13, 2025 at 11:54 AM
piRNA-directed DNA methylation may not be a mammalian invention, but can already be found in the germline of axolotl salamanders
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
Reposted by Miguel V. Almeida
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics
Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.
www.nature.com
November 18, 2025 at 12:00 PM
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Reposted by Miguel V. Almeida
🚨 New preprint alert!
Our latest work from @immler.bsky.social lab 🐟🧬
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
#TESky #TE #piRNA #miRNA #zebrafish #DanioDigest
🔗 Read here www.biorxiv.org/content/10.1...
A thread 🧵...
Our latest work from @immler.bsky.social lab 🐟🧬
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
#TESky #TE #piRNA #miRNA #zebrafish #DanioDigest
🔗 Read here www.biorxiv.org/content/10.1...
A thread 🧵...
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
Environmental fluctuations influence heritable phenotypes through complex molecular mechanisms. In zebrafish (Danio rerio), the interplay between temperature variation, transposable element (TE) activ...
www.biorxiv.org
November 16, 2025 at 10:18 AM
🚨 New preprint alert!
Our latest work from @immler.bsky.social lab 🐟🧬
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
#TESky #TE #piRNA #miRNA #zebrafish #DanioDigest
🔗 Read here www.biorxiv.org/content/10.1...
A thread 🧵...
Our latest work from @immler.bsky.social lab 🐟🧬
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
#TESky #TE #piRNA #miRNA #zebrafish #DanioDigest
🔗 Read here www.biorxiv.org/content/10.1...
A thread 🧵...