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
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 🧵...
Reposted by Miguel V. Almeida
Thrilled to share our new review in Current Opinion in Genetics & Development on TE driven innovation in gene regulation🤘. I am honored to be part of this with two major TE aficionados @cedricfeschotte.bsky.social and @trono-lab.bsky.social
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
November 15, 2025 at 5:23 PM
Thrilled to share our new review in Current Opinion in Genetics & Development on TE driven innovation in gene regulation🤘. I am honored to be part of this with two major TE aficionados @cedricfeschotte.bsky.social and @trono-lab.bsky.social
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
Reposted by Miguel V. Almeida
I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A
Insertion of an invading retrovirus regulates a novel color trait in swordtail fish
For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable wi...
shorturl.at
November 12, 2025 at 8:34 PM
I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A
Reposted by Miguel V. Almeida
TEs aren’t just genomic parasites, they’re also engines of genomic novelty.
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen - Nature Communications
In this study, the authors analysed a large genomic dataset to trace how jumping genes shaped the global spread of a major wheat pathogen and reveal bursts of activity over decades that drove adaptati...
www.nature.com
November 12, 2025 at 1:17 PM
TEs aren’t just genomic parasites, they’re also engines of genomic novelty.
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Reposted by Miguel V. Almeida
Excited to share our new preprint on BioRxiv!
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons
Background. Paramecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual gene...
www.biorxiv.org
November 10, 2025 at 9:21 AM
Excited to share our new preprint on BioRxiv!
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5
Reposted by Miguel V. Almeida
PhD opportunity in plant developmental biology for UK based students of Black heritage!
How do they know when to grow up? Join us at the University of Bristol to find out.
Application deadline Jan 6th
www.findaphd.com/phds/project...
#PlantSciencePhDs @blackinplantsci.bsky.social
How do they know when to grow up? Join us at the University of Bristol to find out.
Application deadline Jan 6th
www.findaphd.com/phds/project...
#PlantSciencePhDs @blackinplantsci.bsky.social
November 7, 2025 at 10:37 AM
PhD opportunity in plant developmental biology for UK based students of Black heritage!
How do they know when to grow up? Join us at the University of Bristol to find out.
Application deadline Jan 6th
www.findaphd.com/phds/project...
#PlantSciencePhDs @blackinplantsci.bsky.social
How do they know when to grow up? Join us at the University of Bristol to find out.
Application deadline Jan 6th
www.findaphd.com/phds/project...
#PlantSciencePhDs @blackinplantsci.bsky.social
Reposted by Miguel V. Almeida
Having a lot of fun at #EMBOMobileGenome 😃
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Young KRAB-zinc finger gene clusters are highly dynamic incubators of ERV-driven genetic heterogeneity in mice - Nature Communications
KRAB-zinc finger proteins repress retrotransposons and rapidly evolve in mammals. Here, the authors show that ERV insertions drive the emergence and diversification of new KZFP genes in mice, revealin...
www.nature.com
November 6, 2025 at 9:40 AM
Having a lot of fun at #EMBOMobileGenome 😃
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!
…and I’m currently on the job market looking for a new scientific home!
www.nature.com/articles/s41...
Reposted by Miguel V. Almeida
Welcome to Day 1 of 'The mobile genome: genetic and physiological impacts of transposable elements'! 🧬
The opening remarks by Julius Brennecke accompanied by his fellow scientific organisers:
🔹Déborah Bourc'his
🔹Josefa González
🔹Joseph Peters
#EMBOMobileGenome
The opening remarks by Julius Brennecke accompanied by his fellow scientific organisers:
🔹Déborah Bourc'his
🔹Josefa González
🔹Joseph Peters
#EMBOMobileGenome
November 4, 2025 at 1:31 PM
Welcome to Day 1 of 'The mobile genome: genetic and physiological impacts of transposable elements'! 🧬
The opening remarks by Julius Brennecke accompanied by his fellow scientific organisers:
🔹Déborah Bourc'his
🔹Josefa González
🔹Joseph Peters
#EMBOMobileGenome
The opening remarks by Julius Brennecke accompanied by his fellow scientific organisers:
🔹Déborah Bourc'his
🔹Josefa González
🔹Joseph Peters
#EMBOMobileGenome
Reposted by Miguel V. Almeida
1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
October 29, 2025 at 9:02 AM
1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
Reposted by Miguel V. Almeida
New preprint! We unexpectedly discovered that some Caenorhabditis species delete parts of their somatic genome early in development, which fragments their chromosomes and eliminates key germline genes. Multiple lines of evidence suggest this bizarre process was present in the ancestors of C. elegans
October 28, 2025 at 12:11 PM
New preprint! We unexpectedly discovered that some Caenorhabditis species delete parts of their somatic genome early in development, which fragments their chromosomes and eliminates key germline genes. Multiple lines of evidence suggest this bizarre process was present in the ancestors of C. elegans
Reposted by Miguel V. Almeida
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Antiviral reverse transcriptases reveal the evolutionary origin of telomerase
Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...
www.biorxiv.org
October 17, 2025 at 5:22 PM
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Reposted by Miguel V. Almeida
Reposted by Miguel V. Almeida
Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity https://www.biorxiv.org/content/10.1101/2025.10.09.681187v1
October 10, 2025 at 6:31 PM
Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity https://www.biorxiv.org/content/10.1101/2025.10.09.681187v1
Reposted by Miguel V. Almeida
#TEsky The phenotypic variation of widefins medaka is due to the insertion of a giant transposon containing a viral genome within hoxca cluster doi.org/10.1093/gene...
The phenotypic variation of widefins medaka is due to the insertion of a giant transposon containing a viral genome within hoxca cluster
Abstract. Phenotypic variation in species arises from genetic differences and environmental influences on gene expression. Differences in epigenetic modifi
doi.org
October 7, 2025 at 12:08 PM
#TEsky The phenotypic variation of widefins medaka is due to the insertion of a giant transposon containing a viral genome within hoxca cluster doi.org/10.1093/gene...
Reposted by Miguel V. Almeida
Very sad news, John Gurdon has died.
A developmental biologist's developmental biologist, Nobel prize winner
His work is the foundation of much of today's dev & stem cell bio.
An inspiration to many, including me. Always asking questions & wanting the answers
www.magd.cam.ac.uk/news/profess...
A developmental biologist's developmental biologist, Nobel prize winner
His work is the foundation of much of today's dev & stem cell bio.
An inspiration to many, including me. Always asking questions & wanting the answers
www.magd.cam.ac.uk/news/profess...
Professor Sir John Gurdon FRS (1933-2025) | Magdalene College
Magdalene College is deeply saddened to announce the death of Professor Sir John Gurdon FRS, who served as Master of the College from 1995 to 2002.
www.magd.cam.ac.uk
October 7, 2025 at 4:02 PM
Very sad news, John Gurdon has died.
A developmental biologist's developmental biologist, Nobel prize winner
His work is the foundation of much of today's dev & stem cell bio.
An inspiration to many, including me. Always asking questions & wanting the answers
www.magd.cam.ac.uk/news/profess...
A developmental biologist's developmental biologist, Nobel prize winner
His work is the foundation of much of today's dev & stem cell bio.
An inspiration to many, including me. Always asking questions & wanting the answers
www.magd.cam.ac.uk/news/profess...
Reposted by Miguel V. Almeida
We discovered an endogenous retrovirus that's still spreading in natural D. melanogaster populations! It was horizontally transferred from D. erecta in Central Africa, so we named it "Kuruka", which means "jump" in Swahili. Read its cool story here: www.biorxiv.org/content/10.1...
October 4, 2025 at 5:50 AM
We discovered an endogenous retrovirus that's still spreading in natural D. melanogaster populations! It was horizontally transferred from D. erecta in Central Africa, so we named it "Kuruka", which means "jump" in Swahili. Read its cool story here: www.biorxiv.org/content/10.1...
Reposted by Miguel V. Almeida
Preprint Alert! 🦥
We produced complete genomes for 2 Xenarthra and placed them in a mammalian comparative framework. We found that Xenarthra harbour the largest number of retrocopies in mammals! www.biorxiv.org/content/10.1...
We produced complete genomes for 2 Xenarthra and placed them in a mammalian comparative framework. We found that Xenarthra harbour the largest number of retrocopies in mammals! www.biorxiv.org/content/10.1...
Retrocopy formation and domestication shape genome evolution in sloths and other xenarthrans
Xenarthrans, comprising sloths, anteaters, and armadillos, represent one of the most morphologically and physiologically specialised mammalian clades, yet the genomic basis of their adaptations remain...
www.biorxiv.org
October 2, 2025 at 9:16 PM
Preprint Alert! 🦥
We produced complete genomes for 2 Xenarthra and placed them in a mammalian comparative framework. We found that Xenarthra harbour the largest number of retrocopies in mammals! www.biorxiv.org/content/10.1...
We produced complete genomes for 2 Xenarthra and placed them in a mammalian comparative framework. We found that Xenarthra harbour the largest number of retrocopies in mammals! www.biorxiv.org/content/10.1...
Reposted by Miguel V. Almeida
Hi fellow C. elegans scientists, I've made a few videos that may be of use for new trainees working in worm labs. Hoping to add more in the future, but figured I'd share this resource as is in case it's helpful :)
www.youtube.com/@Workingwith...
www.youtube.com/@Workingwith...
Working with C. elegans
This channel provides clear demonstrations of core C. elegans lab skills, including: recognizing life stages and common phenotypes, picking and manipulating worms, and maintaining healthy cultures. De...
www.youtube.com
October 1, 2025 at 7:20 PM
Hi fellow C. elegans scientists, I've made a few videos that may be of use for new trainees working in worm labs. Hoping to add more in the future, but figured I'd share this resource as is in case it's helpful :)
www.youtube.com/@Workingwith...
www.youtube.com/@Workingwith...
Reposted by Miguel V. Almeida
So happy to see my first first-author paper published! 🎈
A short thread on how Ectocarpus and its TE secrets have kept me busy lately:
rdcu.be/eITQH
A short thread on how Ectocarpus and its TE secrets have kept me busy lately:
rdcu.be/eITQH
Characterization of the transposable element landscape shaping the Ectocarpus genome | Genome Biology
rdcu.be
October 1, 2025 at 8:12 AM
So happy to see my first first-author paper published! 🎈
A short thread on how Ectocarpus and its TE secrets have kept me busy lately:
rdcu.be/eITQH
A short thread on how Ectocarpus and its TE secrets have kept me busy lately:
rdcu.be/eITQH