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Tom Ellis

@proftomellis.bsky.social
3.3K followers 354 following 363 posts

Synthetic Biology & Synthetic Genomics @ Imperial College London and the Sanger Institute. Bilingual in English and DNA. Views are either my own or my microbes'

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Reposted by Tom Ellis
The Dark Matter Project @darkmatterproject.bsky.social · 22/08/2026
ZATELLITE: a toolkit to visualize and manipulate human centromeres in live cells using synthetic zinc fingers biorxiv.org/content/10.6... Congrats to Nestor Saiz et al. from the Center of Synthetic Regulatory Genomics!
biorxiv.org
ZATELLITE: a toolkit to visualize and manipulate human centromeres in live cells using synthetic zinc fingers
Changes in the number of chromosomes or their spatial organization within the nucleus have critical consequences for cell fate. Yet capturing the karyotype or three-dimensional architecture of chromat...
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Tom Ellis @proftomellis.bsky.social · 08/08/2026
Sorry to hear this terrible news. The cat cuddles sound like exactly the sort of therapy you and most of us need. If only we could bottle it.
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
It was the PhD of the brilliant Anastasiya Malyshava and she benefited from lots of others helping in the lab and in the analysis including Wil Shaw, Klaudia Ciurkot, Lucas Canizares Alonso and Armand Grollemund. 👏
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
This preprint will hopefully soon be a peer-reviewed paper with even more to it - especially on the modelling side. So if anyone reading this has thoughts or feedback it would be great to hear from you. It’s by no means a complete paper but we’re very proud of it.
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
And the minimal sets of genes that can function reasonably well in lots of growth conditions is a much narrower number than in just standard growth media. An unsurprising but cautionary result for future work in genome minimisation.
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
But perhaps the most interesting result is looking at the robustness. Our yeast can grow relatively well in standard conditions when half of the gene content for cell cycle control is removed. But the same yeast fail badly when moved into more stressful conditions.
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
Anastasiya then isolated and sequenced 25 of these ‘minimised sets’ from the experiment and found gene combinations that had lost multiple cyclin and regulator genes but still grew well in several conditions. Excitingly these sets matched predicted minimal models from Matteo.
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
POLAR-seq revealed hundreds of different deletion combinations present in the pool of yeast cells after recombination, but the vast majority of cells that were growing contained a narrower set - presumably the fitter possibilities.
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
And thanks to the power of our powerful POLAR-seq method (biorxiv.org/content/10.1... ) we could also determine the relative abundance of cells with different gene deletion combinations.
biorxiv.org
Combinatorial Design Testing in Genomes with POLAR-seq
Synthetic biology projects increasingly use modular DNA assembly or synthetic in vivo recombination to generate diverse combinatorial libraries of genetic constructs for testing. But as these designs ...
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
Inducing Cre recombinase in a growing population of yeast cells containing this synthetic genome module led to a huge change in the gene content of the synthetic module in the yeast cells, with bulk sequencing showing which genes are happy to be lost and which need to stay.
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
Once we got to healthy yeast with a synthetic genome module with 6 of the 9 cyclins and the 3 regulators in place, we decided to start the combinatorial work. Theoretically 512 different deletion sets can be made from combinatorial deletion from this 9 gene cluster.
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
This was some hardcore genome engineering as we wanted to keep gene sequences identical to wildtype and we were deleting and reinserting genes that are quite important for the cell to be healthy enough to engineer. Anastasiya pushed the boundaries with CRISPR in yeast to do it.
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
So with Matteo Barberis’ guidance, Anastasiya targeted 3 regulators (Sic1 and Forkhead 1 & 2) and as many cyclin genes as possible and relocated these genes and their flanking regulatory DNA into a synthetic cluster - a module with LoxP recombination sites between each gene.
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
If you relocate all the genes in question into a synthetic genome module (SGM) with recombinase sites between the genes then in one tube, in vivo you can theoretically generate all possible gene deletion combinations in one go. - i.e. thousands of different minimal sets
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
If you relocate all the genes in question into a synthetic genome module (SGM) with recombinase sites between the genes then in one tube, in vivo you can theoretically generate all possible gene deletion combinations in one go. - i.e. thousands of different minimal sets
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
The classic way to attack this question has been by model-guided prediction of potential minimal sets, then going to the lab and doing the deletions to check if the hypothesis is right for one or two of the strongest options. But with #synbio you can do things very differently.
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
This is because there are multiple cyclins used for each phase and multiple versions of regulators too. And lots of experimental gene deletion work and theoretical mathematical simulation work has shown that not all of these genes are needed. >>> So what is the minimum set?
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
It’s led to a lot of understanding of cancer, and has been part of Nobel prizes - especially on how it’s regulators and different cyclins interact to control robust and timely oscillations that govern the cell cycle phases. In yeast it’s also a famous system for gene redundancy.
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
In this work we chose to use this superpower to combinatorially explore the minimal set of genes needed by baker’s yeast to control a fundamental mechanism for life - the cell cycle. The yeast cell cycle is a famous system to study with decades of work uncovering its mechanism.
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
The key superpower for bioscience and biotech that synthetic biology unlocks is combinatorial space: making and testing 100s and 1000s of designs is trivial if DNA is in rearrangeable modules and you have good assays. We’re using this to understand how to design future genomes.
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
The preprint is here online and covers the work done by Anastasiya during her PhD in our group at Imperial Bioengineering sponsored by Darwin Trust Of Edinburgh: www.biorxiv.org/content/10.6...
biorxiv.org
Synthetic Combinatorial Minimisation of Cell Cycle Control in Yeast
The eukaryotic cell cycle, with its inherent regulatory redundancy, provides an ideal target for exploring genome modularisation and minimisation through synthetic genomics. Building upon principles e...
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Tom Ellis @proftomellis.bsky.social · 31/07/2026
Our lab’s latest on synthetic genomics “Synthetic Combinatorial Minimisation of Cell Cycle Control” is up now on BioRxiv - covering ambitious yeast #synbio cell cycle work led by Anastasiya Malyshava and co-supervised by Matteo Barberis.
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Tom Ellis @proftomellis.bsky.social · 02/07/2026
Îi i
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Tom Ellis @proftomellis.bsky.social · 01/07/2026
So many biomaterials! I used a video of this walk in my talk about engineered living materials for several years.
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Reposted by Tom Ellis
Victor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · 30/06/2026
Off to @embl.org in Heidelberg for the 6th edition of the hands-on SynBio @embo.org Course share.google/Dg0qMdsNQl55... that I initiated in 2015. Glad to see that many of its earlier students now star senior PI positions in some the best research centers & universities 😀
share.google
Synthetic biology in action: maturing tools and their potential
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Reposted by Tom Ellis
Olivier Borkowski @oborkowski.bsky.social · 29/06/2026
Our paper "Active-learning-guided optimization of cell-free systems for genome-wide transcriptomic profiling reveals progressive layers of regulation" is online in Nature Communications! Congrats Lea Wagner, very proud of this work! www.nature.com/articles/s41... #cellfree #AI #T7Phage #synbio
nature.com
Active-learning-guided optimization of cell-free systems for genome-wide transcriptomic profiling reveals progressive layers of regulation - Nature Communications
Cell-free is a powerful platform to unravel biological complexity. Here, the authors used active learning to optimize buffer composition, boosting mRNA 20-fold, enabling cell-free transcriptomics and ...
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Tom Ellis @proftomellis.bsky.social · 26/06/2026
lactose free milk is often sweeter - that why my kids want it over normal milk. Wish they'd never tasted it!
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Reposted by Tom Ellis
Marco Fumasoni @marcofumasoni.bsky.social · 19/06/2026
Our paper on the evolution of cellular miniaturization is now out in PNAS! www.pnas.org/doi/10.1073/... A short recap 🧵
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Tom Ellis @proftomellis.bsky.social · 11/06/2026
5 days left now to apply for the postdoc opportunity in my lab at Imperial in London 🇬🇧 - there’s a chance that we can hire 2 people into the team on this synthetic biology and materials theme. Application link is here - www.imperial.ac.uk/jobs/search-...
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Simon Bayly @simonbayly.bsky.social · 09/06/2026
LinkedIn founder Reid Hoffman has founded an AI drug discovery company with Siddhartha Mukherjee author of “The Emperor of All Maladies" #biotech thenextweb.com/news/reid-ho...
thenextweb.com
Reid Hoffman leaves Microsoft board to go 'founder mode' with AI drug startup Manus
LinkedIn co-founder Reid Hoffman is stepping down from Microsoft's board after nearly a decade to focus on Manus, his AI drug discovery startup.
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Reposted by Tom Ellis
bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 07/06/2026
Catalytic Bacterial Nanocellulose Composite That Captures and Degrades PET Microplastics www.biorxiv.org/content/10.64898/20…
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Reposted by Tom Ellis
Rahul K @theresearch.bsky.social · 11/11/2024
I’d like to invite everyone working on engineering living materials to share this starter pack. Please drop me a message or leave a comment if you like to join the #ELMs community. go.bsky.app/RinsDZh
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Reposted by Tom Ellis
Victor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · 07/06/2026
Off to Barcelona for the 2nd SynBYSS Conf www.jcvi.org/events/synbyss organized by the one and only @taeseokmoon.bsky.social along with Marc Güell of @upf.edu & other local SynBio colleagues. Ready to take the pulse of the field & learn from many of its luminaries 😀. I will honor Gaudí in my talk 👇
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Tom Ellis @proftomellis.bsky.social · 05/06/2026
CNS humblebrag joke.
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Tom Ellis @proftomellis.bsky.social · 05/06/2026
Because it’s UGGly
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Reposted by Tom Ellis
Jonas Koeppel @jonaskoeppel.bsky.social · 04/06/2026
1/n What fraction of the human genome is essential for cells? Excited to share our preprint that explores this question by combining an unusual CRISPR system, phage promoters, and thousands of deletion launchpads. @sudpinglay.bsky.social @jshendure.bsky.social www.biorxiv.org/content/10.6...
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
How much of the human genome is essential? Two pieces out today from our lab: 1) a method to map essential genomic intervals at gigabase scale, and 2) an argument that it's time to consider synthesizing a minimal human genome. biorxiv.org/content/10.6... nature.com/articles/d41...
nature.com
Why a synthetic human genome is still worth building
A decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch.
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Tom Ellis @proftomellis.bsky.social · 03/06/2026
Where can my international postdocs go to attend good conferences? They don't want to go to USA (v.high prices & horror stories of ICE). Can't easily go to the EU as Schengen visa appointments are super hard to get in the UK right now. East Asia? Flights are $$$$ thanks to dumb wars. Sad times.
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Mo Khalil @mokhalil.bsky.social · 03/06/2026
🚨 An exciting frontier is bringing synthetic biology to MULTIcellular systems. To effectively engineer them, we need design principles. What are the benefits of group formation? What are the costs? See our new preprint led by @heidiklumpe.bsky.social to learn more!👇 www.biorxiv.org/content/10.6...
biorxiv.org
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Reposted by Tom Ellis
Vivek Mutalik @vivekmutalik.bsky.social · 03/06/2026
www.nature.com/articles/s41... #microsky
nature.com
Engineered Bacteroides thetaiotaomicron sense gut inflammation and deliver therapeutic molecules to alleviate colitis in mice - Nature Microbiology
Engineered Bacteroides thetaiotaomicron, Btbots, use a genetic AND circuit to sense nitric oxide and deoxycholic acid as inflammatory signal in the gut to release therapeutic molecules, TFF3 and IL-35...
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Tom Ellis @proftomellis.bsky.social · 01/06/2026
sure sounds like AI is well-placed to replace the PI but not the PhD student.
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Reposted by Tom Ellis
Richard Sever @richardsever.bsky.social · 30/05/2026
"Hypothesis generation: pretty good...data analysis: a super power...executing experiments: not so much" AI can help at every stage of the research cycle. Jonah Cool from @anthropic.com discuss the benefits of integrating frontier models and potential concerns youtu.be/sz1vQyBzSgw?...
youtu.be
Interview with: Jonah Cool
YouTube video by CSHL Leading Strand
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Reposted by Tom Ellis
Mar Hicks @histoftech.bsky.social · 03/05/2026
Chinese researchers have created a bamboo-based plastic as strong as petroleum-based plastics, which can fully biodegrade in soil in just 2 months phys.org/news/2025-10...
phys.org
Bamboo-based plastic can be made to biodegrade quickly, but still holds up in tough conditions
A new method to produce strong, biodegradable plastic from bamboo is reported in Nature Communications this week. The bioplastic resembles oil-based plastics in strength, shapability, and thermal stab...
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Victor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · 01/05/2026
1/2 The regulatory labyrinth for commercialisation of GE bacteria for deliberate env release eg bioremediation, biofertilization or disease control in the EU. Note that each of the 27 member states must emit an opinion & a vote 😱. No wonder the field is altogether stagnant at this side of the pond ☹️
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Tom Ellis @proftomellis.bsky.social · 01/05/2026
Even if you get EU wide approval then some countries will have further rules. Eg. Cultured meat is banned in Italy. And Norway (not EU but aligned) requires any new technology to also submit evidence to demonstrate it’s better for the environment than an existing technology. So much extra work!
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Tom Ellis @proftomellis.bsky.social · 01/05/2026
In particular, the stage when all 27 countries get a say takes years to actually happen as they are given months to ask questions and then months to reply to answers - can drag on for years.
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Tom Ellis @proftomellis.bsky.social · 01/05/2026
It’s crazy. I couldn’t believe some of the stuff I was hearing via the Webex of the meeting yesterday that you were at. Made me want to give up ever trying to sell biotech in the EU.
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Tom Ellis @proftomellis.bsky.social · 01/05/2026
This is really impressive. Congrats to everyone involved. We are just getting started on testing Bridge Recombinases in yeast and what you can do in bacteria gives us inspiration.
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Reposted by Tom Ellis
Elisa Franco @francolab.bsky.social · 29/04/2026
RNA is more than genetic information: it can be a tool for cellular architects. In our new paper, we engineer RNA motifs to physically reorganize intracellular space in living mammalian cells. www.nature.com/articles/s41...
nature.com
Programmable artificial RNA condensates in mammalian cells - Nature Nanotechnology
Modular RNA nanostar motifs spontaneously assemble into programmable synthetic condensates in the nucleus and cytoplasm, with RNA design controlling localization, sequence-specific target recruitment ...
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Tom Ellis @proftomellis.bsky.social · 09/04/2026
Sadly there was no A.L.E. in the proposal so we can’t claim credit for anything in this movie.
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