Alex Donovan
@apadonovan.bsky.social
Biologist at the LMB, Cambridge, interested in human brain evolution and how stem cells behave and misbehave 🧠🧬🏳️🌈
Cool work on how male pregnancy works in seahorses and other Syngnathids - brood pouch formation is androgen responsive. Interesting comparison of cell types to mammalian parallels at the end too!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Cellular and molecular mechanisms of seahorse male pregnancy - Nature Ecology & Evolution
Seahorses have a unique sex role reversal with male pregnancy involving the brood pouch, an evolutionarily novel organ. This study uses single-cell genomics and in vivo experiments to reveal the cellu...
www.nature.com
November 18, 2025 at 10:17 AM
Cool work on how male pregnancy works in seahorses and other Syngnathids - brood pouch formation is androgen responsive. Interesting comparison of cell types to mammalian parallels at the end too!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
I haven’t enjoyed reading a review so much as this in a long time - an in depth and beautifully composed overview of metazoan evolution through the lens of transcription factors and transcriptional regulation 🧬
www.nature.com/articles/s41...
www.nature.com/articles/s41...
www.nature.com
November 15, 2025 at 4:31 PM
I haven’t enjoyed reading a review so much as this in a long time - an in depth and beautifully composed overview of metazoan evolution through the lens of transcription factors and transcriptional regulation 🧬
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Alex Donovan
Really great to see more studies like this, exploring how tiny changes in enhancer sequences over evolution can have tangible effects on developmental processes! journals.biologists.com/dev/article/...
Neanderthal-derived variants increase SOX9 enhancer activity in craniofacial progenitors that shape jaw development
Highlighted Article: Neanderthal-specific non-coding variants increase the activity of a human disease-associated craniofacial enhancer proposed to impact SOX9 expression in a pool of progenitor cells...
journals.biologists.com
November 10, 2025 at 12:05 PM
Really great to see more studies like this, exploring how tiny changes in enhancer sequences over evolution can have tangible effects on developmental processes! journals.biologists.com/dev/article/...
Reposted by Alex Donovan
Domesticated animals have pulled our heavy carts and turned our large mills for centuries. But what about the opposite end of the spectrum—what if the wheel you want to turn is so small you can’t see it?
Turns out we can harness the power of bacteria to power the world’s smallest machines.
1/7 ⚛️🧪
Turns out we can harness the power of bacteria to power the world’s smallest machines.
1/7 ⚛️🧪
October 26, 2025 at 2:01 AM
Domesticated animals have pulled our heavy carts and turned our large mills for centuries. But what about the opposite end of the spectrum—what if the wheel you want to turn is so small you can’t see it?
Turns out we can harness the power of bacteria to power the world’s smallest machines.
1/7 ⚛️🧪
Turns out we can harness the power of bacteria to power the world’s smallest machines.
1/7 ⚛️🧪
Reposted by Alex Donovan
What is a promoter? And how does it work?
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
Enhancer-promoter compatibility is mediated by the promoter-proximal region
Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...
www.biorxiv.org
October 16, 2025 at 3:06 PM
What is a promoter? And how does it work?
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
Reposted by Alex Donovan
I am thrilled to share our latest story led by the incredibly talented Brooke D’Arcy and Camila Musso. We discover a rich world of local gene expression in radial glia, essential neural and glial precursors, and develop a new method for sub-cellular mRNA manipulation. www.biorxiv.org/content/10.1...
October 10, 2025 at 10:28 PM
I am thrilled to share our latest story led by the incredibly talented Brooke D’Arcy and Camila Musso. We discover a rich world of local gene expression in radial glia, essential neural and glial precursors, and develop a new method for sub-cellular mRNA manipulation. www.biorxiv.org/content/10.1...
Reposted by Alex Donovan
Delighted that Ziqi Dong's PhD paper is out for all to read! Hypoxia is fundamental to normal development, and fascinating! Thanks to all of our co-authors including @jamesnathanlab.bsky.social @jellevda.bsky.social authors.elsevier.com/sd/article/S...
October 11, 2025 at 8:22 AM
Delighted that Ziqi Dong's PhD paper is out for all to read! Hypoxia is fundamental to normal development, and fascinating! Thanks to all of our co-authors including @jamesnathanlab.bsky.social @jellevda.bsky.social authors.elsevier.com/sd/article/S...
Reposted by Alex Donovan
New online: Computational design of sequence-specific DNA-binding proteins
Computational design of sequence-specific DNA-binding proteins
Nature Structural & Molecular Biology, Published online: 12 September 2025; doi:10.1038/s41594-025-01669-4The authors develop a computational method to design small DNA-binding proteins (DBPs) that target specific sequences. Designed DBPs show structural accuracy and function in both bacterial and mammalian cells for transcriptional regulation.
go.nature.com
September 12, 2025 at 10:29 AM
New online: Computational design of sequence-specific DNA-binding proteins
Very cool paper providing mechanism to how sea slugs can retain photosynthetically active chloroplasts (also love the term kleptosomes) - www.cell.com/cell/fulltex...
A host organelle integrates stolen chloroplasts for animal photosynthesis
Sea slugs steal foreign chloroplasts and store them in specialized organelles that
facilitate photosynthesis and eventual digestion to mediate starvation resistance.
www.cell.com
June 26, 2025 at 3:22 PM
Very cool paper providing mechanism to how sea slugs can retain photosynthetically active chloroplasts (also love the term kleptosomes) - www.cell.com/cell/fulltex...
Reposted by Alex Donovan
Today in relatable science: Gulls making a mysterious daily trip that turned out to be to a potato chip factory
November 15, 2024 at 8:15 PM
Today in relatable science: Gulls making a mysterious daily trip that turned out to be to a potato chip factory
My Cyclops (type of freshwater copepod) culture is teeming with life 🧫
June 5, 2025 at 7:32 PM
My Cyclops (type of freshwater copepod) culture is teeming with life 🧫
Reposted by Alex Donovan
Is there anything more unsettling and beautiful than the eyelids of a red eyed tree frog? They're so ornate and bizarre. I can't think of anything else like them.
June 1, 2025 at 3:05 AM
Is there anything more unsettling and beautiful than the eyelids of a red eyed tree frog? They're so ornate and bizarre. I can't think of anything else like them.
Looking at some water from an algal culture for fun and came across these bizarre creatures, does anyone know what they might be? This looks like it might be part of their development where they initially emerge within this hairy chamber then hatch as they grow (?) more pics to follow 🧫
May 28, 2025 at 3:43 PM
Looking at some water from an algal culture for fun and came across these bizarre creatures, does anyone know what they might be? This looks like it might be part of their development where they initially emerge within this hairy chamber then hatch as they grow (?) more pics to follow 🧫
If you are interested in neural stem cells, epigenetics or both (or neither honestly) you should read Anna’s preprint! Beautiful work characterising histone modification dynamics across neural stem cell quiescence and reactivation, in truly excruciating detail and at great breadth 🤯🪰🧬
Happy to share a preprint of my PhD work! We created a chromatin state model for quiescent and proliferating neural stem cells in Drosophila and found that quiescent cells gain active chromatin to support stem cell functions.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Neural stem cell quiescence is actively maintained by the epigenome
Homeostasis and repair of the nervous system is maintained by a population of resident neural stem cells (NSCs) retained in a state of reversible cell cycle arrest called quiescence. quiescent NSCs ca...
www.biorxiv.org
May 26, 2025 at 9:03 PM
If you are interested in neural stem cells, epigenetics or both (or neither honestly) you should read Anna’s preprint! Beautiful work characterising histone modification dynamics across neural stem cell quiescence and reactivation, in truly excruciating detail and at great breadth 🤯🪰🧬
Reposted by Alex Donovan
I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. www.nature.com/articles/s41...
Chromatin loops are an ancestral hallmark of the animal regulatory genome - Nature
The physical organization of the genome in non-bilaterian animals and their closest unicellular relatives is characterized; comparative analysis shows chromatin looping is a conserved feature of ...
www.nature.com
May 7, 2025 at 3:23 PM
I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. www.nature.com/articles/s41...
New telomere to telomere ape genomes - www.nature.com/articles/s41...
Complete sequencing of ape genomes - Nature
Complete sequences of chromosomes telomere-to-telomere from chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang provide a comprehensive and valuable resource for future evol...
www.nature.com
May 9, 2025 at 4:00 PM
New telomere to telomere ape genomes - www.nature.com/articles/s41...
Reposted by Alex Donovan
In an unprecedented move, the US National Institutes of Health has begun mass terminations of research grants that fund active scientific projects because they no longer meet “agency priorities”.
https://go.nature.com/4bpG2It
https://go.nature.com/4bpG2It
Exclusive: NIH to terminate hundreds of active research grants
Studies that touch on LGBT+ health, gender identity and DEI in the biomedical workforce could be terminated, according to documents obtained by Nature.
go.nature.com
March 6, 2025 at 2:25 AM
In an unprecedented move, the US National Institutes of Health has begun mass terminations of research grants that fund active scientific projects because they no longer meet “agency priorities”.
https://go.nature.com/4bpG2It
https://go.nature.com/4bpG2It
Can’t say that Gilead sciences sponsoring drag race was on my bingo card 😂
January 18, 2025 at 2:02 PM
Can’t say that Gilead sciences sponsoring drag race was on my bingo card 😂
Reposted by Alex Donovan
I have read few papers as immediately useful and important as this one on Cacio e Pepe phase behavior.
Tl;dr: the starchy pasta water is absolutely critical to avoiding “mozzarella phase”
arxiv.org/abs/2501.00536
Tl;dr: the starchy pasta water is absolutely critical to avoiding “mozzarella phase”
arxiv.org/abs/2501.00536
January 4, 2025 at 4:14 AM
I have read few papers as immediately useful and important as this one on Cacio e Pepe phase behavior.
Tl;dr: the starchy pasta water is absolutely critical to avoiding “mozzarella phase”
arxiv.org/abs/2501.00536
Tl;dr: the starchy pasta water is absolutely critical to avoiding “mozzarella phase”
arxiv.org/abs/2501.00536
Reposted by Alex Donovan
Why is human brain development, and particularly neuron morphogenesis, so slow and how is this linked to evolution? doi.org/10.1101/2024.12.28.630576
We developed mouse brain organoid methods capturing differences to human and used these to address this. doi.org/10.1101/2024.12.21.629881
🧵 (1/n)
We developed mouse brain organoid methods capturing differences to human and used these to address this. doi.org/10.1101/2024.12.21.629881
🧵 (1/n)
Calcium dynamics tune developmental tempo to generate evolutionarily divergent axon tract lengths
The considerably slow pace of human brain development correlates with an evolutionary increase in brain size, cell numbers, and expansion of neuronal structures, with axon tracts undergoing an even gr...
doi.org
December 30, 2024 at 7:45 PM
Why is human brain development, and particularly neuron morphogenesis, so slow and how is this linked to evolution? doi.org/10.1101/2024.12.28.630576
We developed mouse brain organoid methods capturing differences to human and used these to address this. doi.org/10.1101/2024.12.21.629881
🧵 (1/n)
We developed mouse brain organoid methods capturing differences to human and used these to address this. doi.org/10.1101/2024.12.21.629881
🧵 (1/n)
Reposted by Alex Donovan
40 years ago all of Genbank was published in print form by NAR. The same format today would require over 4 light seconds of shelf space. To a year of progress in 2025.
December 29, 2024 at 9:50 AM
40 years ago all of Genbank was published in print form by NAR. The same format today would require over 4 light seconds of shelf space. To a year of progress in 2025.
Reposted by Alex Donovan
How proximal is proximity labeling❓ Using DNA nanorulers we found that TurboID/BioID are largely contact labeling, while APEX2 also bears a major contact labeling pathway in parallel with diffusive labeling.
www.biorxiv.org/content/10.1...
Special thanks to @aliceyting.bsky.social for discussions
www.biorxiv.org/content/10.1...
Special thanks to @aliceyting.bsky.social for discussions
December 19, 2024 at 2:22 AM
How proximal is proximity labeling❓ Using DNA nanorulers we found that TurboID/BioID are largely contact labeling, while APEX2 also bears a major contact labeling pathway in parallel with diffusive labeling.
www.biorxiv.org/content/10.1...
Special thanks to @aliceyting.bsky.social for discussions
www.biorxiv.org/content/10.1...
Special thanks to @aliceyting.bsky.social for discussions
A nice (and very random) gift from my local coffee place, Hot Numbers! 🥳
December 24, 2024 at 12:39 PM
A nice (and very random) gift from my local coffee place, Hot Numbers! 🥳
Reposted by Alex Donovan
1/🚀 Excited to share RegVelo, our new cell model combining RNA velocity with gene regulatory network (GRN) dynamics to model cellular changes and predict in silico perturbations. Here's how it works and why it matters! 🧵👇
biorxiv.org/content/10.1101/2024.12.11.627935v1
biorxiv.org/content/10.1101/2024.12.11.627935v1
December 12, 2024 at 2:48 PM
1/🚀 Excited to share RegVelo, our new cell model combining RNA velocity with gene regulatory network (GRN) dynamics to model cellular changes and predict in silico perturbations. Here's how it works and why it matters! 🧵👇
biorxiv.org/content/10.1101/2024.12.11.627935v1
biorxiv.org/content/10.1101/2024.12.11.627935v1