Alex de Mendoza
@alexdemendoza.bsky.social
Evolutionary epigenomics ( eukaryotes / Transcription Factors / Transposable Elements / DNA methylation ) @ QMUL (London).
Lab website: https://www.demendozalab.com/
Lab website: https://www.demendozalab.com/
Pinned
Thrilled to share that the lab has been awarded a @wellcometrust.bsky.social Discovery Award to keep exploring the evolution of 6-methyladenine #6mA in Eukaryotes. We'll open postdoc (3️⃣) and tech (1️⃣) positions to start in 2026, please share with candidates or reach out if you’d like to join us.
Reposted by Alex de Mendoza
🚨 We're hiring! 🚨 Our lab at the University of Málaga, Spain🇪🇸 is looking for a bioinformatician researcher for a postdoc position (1+1 years). Check the ad, and if you're interested, get in touch!
📅 Starting date early 2026, with some flexibility.
🙏Please, RT!
📅 Starting date early 2026, with some flexibility.
🙏Please, RT!
October 30, 2025 at 5:50 PM
🚨 We're hiring! 🚨 Our lab at the University of Málaga, Spain🇪🇸 is looking for a bioinformatician researcher for a postdoc position (1+1 years). Check the ad, and if you're interested, get in touch!
📅 Starting date early 2026, with some flexibility.
🙏Please, RT!
📅 Starting date early 2026, with some flexibility.
🙏Please, RT!
Reposted by Alex de Mendoza
I am delighted to share our latest work on memory gene circuits for plants. This work was led by the phenomenal PhD student @patrickgong.bsky.social
A lot of debugging & highlights how even simple components in synthetic biology can have unexpected properties.
www.biorxiv.org/content/10.1...
A lot of debugging & highlights how even simple components in synthetic biology can have unexpected properties.
www.biorxiv.org/content/10.1...
CREation of an expanded plant memory gene circuit toolkit
Genetic circuits rely on modular, well-characterized genetic parts to achieve predictable cellular behaviour. Despite their widespread adoption, biological parts are complex and when used in a new mol...
www.biorxiv.org
October 31, 2025 at 9:24 AM
I am delighted to share our latest work on memory gene circuits for plants. This work was led by the phenomenal PhD student @patrickgong.bsky.social
A lot of debugging & highlights how even simple components in synthetic biology can have unexpected properties.
www.biorxiv.org/content/10.1...
A lot of debugging & highlights how even simple components in synthetic biology can have unexpected properties.
www.biorxiv.org/content/10.1...
Reposted by Alex de Mendoza
🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
October 31, 2025 at 2:42 PM
🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
Reposted by Alex de Mendoza
Very happy to see our paper published online natcomms.nature.com. Thank you to @wellcometrust.bsky.social for funding this work during my time with @robklose.bsky.social and David Booth! Thanks also to collaborators @garcialabms.bsky.social @alexdemendoza.bsky.social and the other authors!
Chromatin profiling identifies putative dual roles for H3K27me3 in regulating cell type-specific genes and transposable elements in choanoflagellates
Nature Communications - Here, the authors investigate chromatin-based gene regulation in the closest relative of animal, choanoflagellates. They uncover a putative dual role for the histone...
rdcu.be
October 29, 2025 at 1:40 PM
Very happy to see our paper published online natcomms.nature.com. Thank you to @wellcometrust.bsky.social for funding this work during my time with @robklose.bsky.social and David Booth! Thanks also to collaborators @garcialabms.bsky.social @alexdemendoza.bsky.social and the other authors!
Come join the #LondonEvoDevo network half day meeting, hosted at @ucl.ac.uk on Friday November 7th, 2025. Submit your abstract by Oct 27th (or your interest in joining) here: forms.gle/TRbdrCkQTcY2.... Friendly vibes and free registration. More info here: londonevodevo.co.uk.
LondonEvoDevo
meeting's website
londonevodevo.co.uk
October 20, 2025 at 1:42 PM
Come join the #LondonEvoDevo network half day meeting, hosted at @ucl.ac.uk on Friday November 7th, 2025. Submit your abstract by Oct 27th (or your interest in joining) here: forms.gle/TRbdrCkQTcY2.... Friendly vibes and free registration. More info here: londonevodevo.co.uk.
Reposted by Alex de Mendoza
Did transposable elements shape brain evolution — and if so, which ones, and in which cell states and lineages? Led by @tyamadat.bsky.social, we explored this question in cerebellum development using sequence-based deep learning models!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 16, 2025 at 10:01 PM
Did transposable elements shape brain evolution — and if so, which ones, and in which cell states and lineages? Led by @tyamadat.bsky.social, we explored this question in cerebellum development using sequence-based deep learning models!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Alex de Mendoza
We are happy to share our latest work in @nature.com . We study the genomic and cellular basis of facultative symbiosis in Oculina patagonica - a Mediterranean coral remarkable for its ability to survive long periods without algal symbionts. Led by Shani Levy and @xgrau.bsky.social
rdcu.be/eLbaZ
rdcu.be/eLbaZ
October 15, 2025 at 7:58 PM
We are happy to share our latest work in @nature.com . We study the genomic and cellular basis of facultative symbiosis in Oculina patagonica - a Mediterranean coral remarkable for its ability to survive long periods without algal symbionts. Led by Shani Levy and @xgrau.bsky.social
rdcu.be/eLbaZ
rdcu.be/eLbaZ
As a Transposable Element aficionado and a birder, this paper is just the best. Oenanthes are such beautiful birds.
1/9 New in @science.org www.science.org/doi/10.1126/science.ado8005
How does genetic architecture constrain evolutionary trajectories? To address this question, we inferred the genetic architecture of convergent plumage coloration and its evolutionary history in wheatears.
How does genetic architecture constrain evolutionary trajectories? To address this question, we inferred the genetic architecture of convergent plumage coloration and its evolutionary history in wheatears.
A mosaic of modular variation at a single gene underpins convergent plumage coloration
The reshuffling of genomic variation from multiple origins is an important contributor to phenotypic diversification, yet insights into the evolutionary trajectories of this combinatorial process and ...
www.science.org
October 17, 2025 at 2:08 PM
As a Transposable Element aficionado and a birder, this paper is just the best. Oenanthes are such beautiful birds.
Reposted by Alex de Mendoza
Our latest paper on a histone methyltransferase-independent function of PRC2 controlling small RNA dynamics during programmed DNA elimination in Paramecium is now published in #NAR.
#RNAbiology #TEsky #smallRNAs #PRC2 #DNAelimination
1/5
academic.oup.com/nar/article-...
#RNAbiology #TEsky #smallRNAs #PRC2 #DNAelimination
1/5
academic.oup.com/nar/article-...
A histone methyltransferase-independent function of PRC2 controls small RNA dynamics during programmed DNA elimination in Paramecium
Abstract. To limit transposable element (TE) mobilization, most eukaryotes have evolved small RNAs to silence TE activity via homology-dependent mechanisms
academic.oup.com
October 17, 2025 at 11:58 AM
Our latest paper on a histone methyltransferase-independent function of PRC2 controlling small RNA dynamics during programmed DNA elimination in Paramecium is now published in #NAR.
#RNAbiology #TEsky #smallRNAs #PRC2 #DNAelimination
1/5
academic.oup.com/nar/article-...
#RNAbiology #TEsky #smallRNAs #PRC2 #DNAelimination
1/5
academic.oup.com/nar/article-...
Reposted by Alex de Mendoza
Reposted by Alex de Mendoza
Latest from ours: www.cell.com/cell-reports...
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
October 5, 2025 at 10:35 AM
Latest from ours: www.cell.com/cell-reports...
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
Reposted by Alex de Mendoza
"(...) an extremely large transposon, Teratorn, containing a herpesvirus genome, was inserted into the hoxc12a 3' UTR. This insertion decreased hoxc12a expression & (...) also affected neighboring hox genes, resulting in variations in fin size and the presence or absence of dorsal fins."
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
academic.oup.com
October 9, 2025 at 8:30 AM
"(...) an extremely large transposon, Teratorn, containing a herpesvirus genome, was inserted into the hoxc12a 3' UTR. This insertion decreased hoxc12a expression & (...) also affected neighboring hox genes, resulting in variations in fin size and the presence or absence of dorsal fins."
Reposted by Alex de Mendoza
It was fantastic welcoming back Chema Martin @chemamd.bsky.social from @qmulsbbs.bsky.social at the Centre today 👏 He shared with us his latest work on spiralian larvae evolution, with fascinating insights on the timing of gene expression during development. Thank you for visiting us!
October 10, 2025 at 2:28 PM
It was fantastic welcoming back Chema Martin @chemamd.bsky.social from @qmulsbbs.bsky.social at the Centre today 👏 He shared with us his latest work on spiralian larvae evolution, with fascinating insights on the timing of gene expression during development. Thank you for visiting us!
Reposted by Alex de Mendoza
Connecting different “neighborhoods” of a genome has many benefits. For one, it can allow a gene to be regulated by multiple sources, increasing the possibility for more complexity.
Loops of DNA Equipped Ancient Life To Become Complex | Quanta Magazine
New work shows that physical folding of the genome to control genes located far away may have been an early evolutionary development.
www.quantamagazine.org
October 10, 2025 at 8:04 PM
Connecting different “neighborhoods” of a genome has many benefits. For one, it can allow a gene to be regulated by multiple sources, increasing the possibility for more complexity.
Reposted by Alex de Mendoza
A Nobel-winning scientist of great modesty and humour, John Gurdon died on 7 Oct. Not only did he make a discovery that laid the foundations for stem cell research, he also created one of the best environments for research at the Wellcome/CRUK Gurdon Institute wellcome.org/news/sir-joh...
Sir John Gurdon, 1933-2025 | Wellcome
A Nobel-winning scientist of great modesty and humour, John Gurdon died on 7 October. He made a discovery that opened up the field of cloning research, and created one of the best environments for res...
wellcome.org
October 9, 2025 at 1:39 PM
A Nobel-winning scientist of great modesty and humour, John Gurdon died on 7 Oct. Not only did he make a discovery that laid the foundations for stem cell research, he also created one of the best environments for research at the Wellcome/CRUK Gurdon Institute wellcome.org/news/sir-joh...
Reposted by Alex de Mendoza
Our latest: combining single-cell RNA-seq from 16 species and HCR validation, we show that monoaminergic neurons share a conserved transcriptional identity across Bilateria. In contrast, we find no evidence for this program in non-bilaterian metazoans. www.biorxiv.org/content/10.1...
Monoaminergic neurons share transcriptional identity across Bilaterian animals
The evolutionary conservation of cell types over deep time has long been theorised but remains difficult to demonstrate. Monoaminergic neurons, which produce molecules such as serotonin and dopamine, ...
www.biorxiv.org
October 10, 2025 at 9:43 PM
Our latest: combining single-cell RNA-seq from 16 species and HCR validation, we show that monoaminergic neurons share a conserved transcriptional identity across Bilateria. In contrast, we find no evidence for this program in non-bilaterian metazoans. www.biorxiv.org/content/10.1...
Reposted by Alex de Mendoza
🚨 My lab is hiring at all levels!
Interested in animal origins & evolutionary cell biology?
I'm recruiting a postdoc, PhD students & a research assistant to study the molecular evolution of cell adhesion using marine invertebrates + comparative genomics.
🔗: clarkelab.com/join/
Please repost!
Interested in animal origins & evolutionary cell biology?
I'm recruiting a postdoc, PhD students & a research assistant to study the molecular evolution of cell adhesion using marine invertebrates + comparative genomics.
🔗: clarkelab.com/join/
Please repost!
October 8, 2025 at 5:49 PM
🚨 My lab is hiring at all levels!
Interested in animal origins & evolutionary cell biology?
I'm recruiting a postdoc, PhD students & a research assistant to study the molecular evolution of cell adhesion using marine invertebrates + comparative genomics.
🔗: clarkelab.com/join/
Please repost!
Interested in animal origins & evolutionary cell biology?
I'm recruiting a postdoc, PhD students & a research assistant to study the molecular evolution of cell adhesion using marine invertebrates + comparative genomics.
🔗: clarkelab.com/join/
Please repost!
Thrilled to share that the lab has been awarded a @wellcometrust.bsky.social Discovery Award to keep exploring the evolution of 6-methyladenine #6mA in Eukaryotes. We'll open postdoc (3️⃣) and tech (1️⃣) positions to start in 2026, please share with candidates or reach out if you’d like to join us.
October 8, 2025 at 12:17 PM
Thrilled to share that the lab has been awarded a @wellcometrust.bsky.social Discovery Award to keep exploring the evolution of 6-methyladenine #6mA in Eukaryotes. We'll open postdoc (3️⃣) and tech (1️⃣) positions to start in 2026, please share with candidates or reach out if you’d like to join us.
Reposted by Alex de Mendoza
Our latest #preprint led by Yumary M. Vasquez & Frederik Schulz @jgi.doe.gov
The largest database of giant #virus MAGs (GVMAGs V2) with >18,000 genomes from #marine, freshwater, anthropogenic and terrestrial environments.
www.biorxiv.org/content/10.1...
The largest database of giant #virus MAGs (GVMAGs V2) with >18,000 genomes from #marine, freshwater, anthropogenic and terrestrial environments.
www.biorxiv.org/content/10.1...
October 2, 2025 at 9:10 AM
Our latest #preprint led by Yumary M. Vasquez & Frederik Schulz @jgi.doe.gov
The largest database of giant #virus MAGs (GVMAGs V2) with >18,000 genomes from #marine, freshwater, anthropogenic and terrestrial environments.
www.biorxiv.org/content/10.1...
The largest database of giant #virus MAGs (GVMAGs V2) with >18,000 genomes from #marine, freshwater, anthropogenic and terrestrial environments.
www.biorxiv.org/content/10.1...
Reposted by Alex de Mendoza
Today in @nature.com, we present our work leveraging functional genomics and human blastoids to uncover a human-specific mechanism in preimplantation development driven by the endogenous retrovirus HERVK.
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
A human-specific regulatory mechanism revealed in a pre-implantation model
Nature - Genetic manipulation of blastoids reveals the role of recently emerged transposable elements and genes in human development.
rdcu.be
October 1, 2025 at 6:08 PM
Today in @nature.com, we present our work leveraging functional genomics and human blastoids to uncover a human-specific mechanism in preimplantation development driven by the endogenous retrovirus HERVK.
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
Reposted by Alex de Mendoza
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
Reposted by Alex de Mendoza
Historically, viruses were thought to primarily use host cell's translational machinery. New work from @harvardcellbio.bsky.social faculty Amy Lee reveals that a giant DNA virus encodes its own IF4F initiation complex, suggesting an unexpected evolutionary innovation. www.biorxiv.org/content/10.1...
Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life
In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral transcripts. Here, we discover that giant DNA virus...
www.biorxiv.org
October 2, 2025 at 6:10 PM
Historically, viruses were thought to primarily use host cell's translational machinery. New work from @harvardcellbio.bsky.social faculty Amy Lee reveals that a giant DNA virus encodes its own IF4F initiation complex, suggesting an unexpected evolutionary innovation. www.biorxiv.org/content/10.1...
Reposted by Alex de Mendoza
Check out our latest work on the discovery and engineering of PiggyBac transposases! 🧵
Discovery and protein language model-guided design of hyperactive transposases - @marcguellc.bsky.social @upf.edu @icreacommunity.bsky.social @crg.eu go.nature.com/4gXLGEw
Discovery and protein language model-guided design of hyperactive transposases - Nature Biotechnology
Phylogenetic mining and protein language models uncover improved PiggyBac transposase sequences.
go.nature.com
October 2, 2025 at 6:09 PM
Check out our latest work on the discovery and engineering of PiggyBac transposases! 🧵
Reposted by Alex de Mendoza
We have a new PhD studentship in the lab on the immunogenic roles of transposable elements in paediatric acute myeloid leukaemia! Come and work with us! www.colcc.ac.uk/2026-cyp-phd...
October 2, 2025 at 6:51 PM
We have a new PhD studentship in the lab on the immunogenic roles of transposable elements in paediatric acute myeloid leukaemia! Come and work with us! www.colcc.ac.uk/2026-cyp-phd...
Reposted by Alex de Mendoza
Registration deadline for @embo.org workshop EvoChromo extended until September 30.
meetings.embo.org/event/24-evo...
meetings.embo.org/event/24-evo...
September 14, 2025 at 5:00 PM
Registration deadline for @embo.org workshop EvoChromo extended until September 30.
meetings.embo.org/event/24-evo...
meetings.embo.org/event/24-evo...