Dynamics of Living Systems (https://www.frohlichlab.com) group leader @thecrick.bsky.social Understanding signalling & cell state dynamics through mathematical modelling and machine learning.
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I like how the QWERTY keyboard mirrors evolution. Proteins and pathways adapted to a situation persist, even when the situation changes. So we end up with mysteriously complex Rube Goldberg machines across biology that only make sense if you know about clashing type bars in Victorian machines.
Exciting day for @crick.ac.uk today: Edith Heard takes over as Director We're looking forward to this new chapter in the story www.crick.ac.uk/about-us/lea...
Latest pre-print from our lab is out. Great work by @alexbendel.bsky.social and team. Full deep mutational scan of an entire human protein interaction domain family 2M quantitative measurement of protein-protein interaction -> deep learning model to predict PPI from sequence More details 👇
Our latest research is out today on @medrxivpreprint.bsky.social: www.medrxiv.org/content/10.1... Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk. Led by the amazing Phoebe Dace. This one’s packed full of data, so check out the paper. Quick highlights… 🧵 1/n
Open postdoc positions in the lab: Come work with us if you're interested in computational modelling of neural dynamics in the brain. www.kcl.ac.uk/jobs/121068-...
Out now! Our very first paper@crick.ac.uk, an impressive feat by @tobyandrews.bsky.social where we show how a developing heart grows and scales up its morphological complexity to keep beating...an excellent summary below ⬇️ www.cell.com/developmenta...
Yes, fully agreed that we should keep (investing in) public transport. But I think the issue with Desmonds opinion is that he is making straw man arguments against the metro, not that he is overstating the impact of AI on personal vehicles.
But self driving cars are a reality in some (small) parts of the US. Given the track record of AI in vision and the amount of training data, it’s not too far fetched that they could replace public transport in a decade or so. Isn’t the issue that we probably do not want to replace it?
An analysis shows that current deep learning models do not beat linear baselines in predicting gene perturbation effects, thus emphasizing the importance of further method development and evaluation. @const-ae.bsky.social @wkhuber.bsky.social @s-anders.bsky.social www.nature.com/articles/s41...
What a fantastic accomplishment -- and what a fantastic story! www.quantamagazine.org/at-17-hannah...
www.dbreunig.com/2025/06/22/h...
Excited to share our latest work published in #ScienceSignaling! 🚀 www.science.org/doi/10.1126/... (1/4)
This project has been in the making for quite some time. CORNETO not only integrates key concepts and methodologies in biological network inference, but also introduces a novel framework for multi-condition analysis. Congrats to the team, and especially to @pablormier.bsky.social for leading this.
How can we reform science? I have some ideas. But I am not sure you’ll like them, because they don’t promise much. elevanth.org/blog/2025/07...
revealjs.com
www.science.org/doi/10.1126/...
I do not think you could invent Quantum Mechanics solely from 1900 data. And it could be very much architecture dependent : LLMs are not able to even infer Newton's laws from a massive number simulations arxiv.org/abs/2507.06952
Schmidt Fellowships for #AI in #cancer research 2025 round is now open. These are pathway to independence fellowships between @icr.ac.uk & @imperialcollegeldn.bsky.social that support fellows to be competitive for faculty jobs at the end of the 2 year funding. www.imperial.ac.uk/jobs/search-...
join us at ISMB iscb.bsky.social & @dreamchallenges.bsky.social - benchmarking foundation models w. @anshulkundaje.bsky.social @oldbap.bsky.social G. Stolovitzky @bowang87.bsky.social @mariabrbic.bsky.social K. Kalantar, J. Guinney supported by @ebi.embl.org @cziscience.bsky.social Tempus AI
But it also eliminates of the business model for search engine optimisation and web search ads, which are the primary reasons why we already have such an enormous amount of low-quality content on the internet.
Oh the LLMs have already started usin en dashes
🚨Job alert in theory/math devbio 🚨 I’m currently advertising postdoc positions to join my group. We’re building reaction-diffusion models to understand some of the crazy things embryos can do. We are based in a beautiful part of Scotland :). Please share! www.abdnjobs.co.uk/vacancy/rese...
Good news for all em-dash enthusiasts: ChatGPT now uses en dashes – with spaces, of course.
I remain sceptical about AI’s role in other aspects of science, but this strongly reinforces the idea that without an AI-first coding strategy (including appropriate training), one risks being left far behind in the coming years. www.microsoft.com/en-us/resear...
Novel Research in Biological Artificial Intelligence: Expressions of interest and nominations for a Max Planck Director to lead research in the field of Biological Artificial Intelligence @mpi-cbg.de and @csbdresden.bsky.social. More information: www.mpi-cbg.de/news-outreac...
In yeast, the CDK and cyclin proteins that drive cell division activate first in the nucleus — a different location in the cell from where was previously thought https://go.nature.com/3GdXuEz
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
Ah interesting points, wasn‘t aware about the bit with math formulas. As a probably below average writer l’m okay with average writing. It‘s also worthwhile to read up on the connection between essays and class/socioeconomic background and consider implications for inclusivity.
Audio recording + openai.com/index/whisper/ + any LLM you fancy?
More convinced of writing but still not on board with ubiquity of essay/paper writing. Very asymmetric communication and easily biased/masked by language. And I don't want to outsource the decision-finding on whom to employ to the applicant.
I’m not disagreeing with you, my point is that both models are suited to their respective fields, and there’s value in each learning from the other. What I often see in biology, though, is that ideas are communicated with a lot of flair but little underlying logic ;)
After having spent some time in the world of biology, I have to say that most maths/ml papers are pretty awful in terms of their english language. But that's fine for the field because everything is in the equations.
For me what ChatGPT is most helpful with is turning my thoughts into text that is comprehensible by others. It appears that those two processes are less entangled for me than for you, which is probably the result of our education and part the reason for our different levels of AI skepticism.
In the soft sciences, and biology hard and soft components, thinking is more fuzzy and cannot be assessed and or trained in the same way and doesn't just rely on logic but has other components.
I think this is very much a disconnect between soft and hard sciences as well as semantics what we mean by "thinking". In maths you can define problems that require logic (and thats what the hard sciences mean by thinking) with unique solutions that you can test and thereby also train idependently.
Why do you intentionally confound your evaluation of understanding/analysis/thinking with ability to communicate? Why not test/train both seperately?
The thing with code is that you have really fast feedback loops, so I‘m substantially less worried about using AI for code than for text. Also coding still involved debugging and testing, which AI can only help with.
I have not taught in the UK or US. I‘ve given some lectures, graded and did training in DE in a STEM setting, and maybe I‘m missing something but the reliance on assays in the UK system just does not align with how I was taught to teach.
We use AI for coding on a daily basis and have been for a while. It does not and won‘t replace coding skills completely but massively lowers the entry barrier and, in my experience, really helps people build coding skills. Moreover, everyone knows how much stuff it gets wrong.
Yes, I just fundamentally disagree with that. They are studying bioscience, not language/writing.
Every student I with whom I talked about essays in UK higher education has told me they are mostly nonsense. And I don‘t get why lectureres would put themselves through the misery of grading them. It just seems like a loss-loss for everyone.
The way I was taucht teaching is that you want constructive alignment between learning goals and exams and with essays, unless you are in writing class I don‘t see how you could possible do a good job at that.
Yes and no. Math exam directly test students thinking abilities. The fact that AI can fudge essays, without any critical thinking, means that students were probably able to do so too. I think its a net positive when they are eliminated from the classroom, but students should still learn to write.
It sounds like you are a fan of deductive learning while I favor inductive learning. Bit paradoxical for me since I think knowledge in biology is less hierarchical than maths and therefore more amenable to an inductive approach, but I guess deductive learning is more established in academia.
Yes, I agree. But the issue isn’t the ready meals, but that the student is tested for things that make them think they’re acceptable in the bigger challenge. Test him on flavour pairing, meat preparation, and sauce tasting. If they decide to use ready meals in their dish, fine.
right, so why don't we figure out how to teach them how to think while still allowing them to use the chat bots. My point is those two things don't have to mutually exclusive, but it probably implies to not let them write essays for teaching/examining.
But the answer can't be that we therefore stick with hunting, but that we rather find better ways of training and testing agility skills.
I think the thing that you want to complain about is that while exercising those old skills, you were still learning other things and that's the stuff that is lost and that is a problem. When we stop hunting we will naturally train agility less.
With a similar analogy I would argue that it would be a bad idea to test hunting skills in exams at culinary school and that's a problem with the exam, not with the fact that fridges or hobs exist.
Every single tech that I know creates a dependence. You tend to only notice the dependence for new tech because you probably never learned the skills (hunting) that the tech you grew up with (fridge, hob, ...) replaced. Your argument about not wanting to depend on tech also applied to those.
To what extent is that a limitation of ChatGPT, and to what extent is it a flaw in the exam itself?
Well, by that logic, we might as well retreat to the woods and become hunter-gatherers, since all technology is evil and using it only breeds dependence.
I don't think we disagree on how to teach but what to teach. For example if GenAI can synthesize text incredibly well, I think it's less important to teach that. But there are other skills (abstraction) that we now need to find better ways to test and new skills that are important (AI evaluation).
Yes I write papers, but that mostly thought me writing skills, not critical thinking/abstraction. Most of my peers at uni seemed pretty good if not better at those things as well. If I had to design a test for critical thinking it would probably be multiple choice.
And yes technology changes how we think, but often in unexpected ways (e.g. en.wikipedia.org/wiki/Qwerty_...). So maybe it's better to embrace change and adapt rather than indulging in nostalgia and resentment?
I wrote one, maybe two, assays throughout my whole studies and I think my critical thinking is okay. I don't think we should ask students to understand ring algebras before allowing them to multiply/add on calculators.
Congratulations to the Crick’s Samra Turajlić on her new appointment as Director of the @cruk-mi.bsky.social 🥂
Organoids in a dish are next to one another. Treatment stops some of them from growing but their neighbours just keep going. What’s the difference? Hint: it’s not genetic doi.org/10.1101/2025...
When do girls fall behind in maths? Gigantic study pinpoints the moment www.nature.com/articles/d41...
Our latest "Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data" A rigorous mathematical foundation for Waddington's landscape to study cell fate decision making Applied to ventral neural tube development www.biorxiv.org/content/10.1...
We are recruiting! We're searching for a postdoctoral research fellow to study patient-specific regulators of plasticity in primary and metastatic CRC. Please reach out if you have any questions! www.ucl.ac.uk/work-at-ucl/...
Contrary to popular belief among some AI enthusiasts, biology is about more than just proteins - so I appreciate that you used proteinML at least some of the time 😉
TBA, of course that stands for Treatments, Biomarkers and Analytics
Apparently, transcriptomics is not the only field struggling with overly optimistic results from new deep learning techniques. www.understandingai.org/p/i-got-fool...
You are a scientist or an engineer (with a PhD) and you want to upskill to learn about delivering scientific infrastructure for the lifesciences (experimental or computational)? You want to work in Europe, in an internationally excellent service delivery team? ARISE2 is for you!
New Faraday Fellowships for international applicants moving to the UK Up to £4 million per researcher over 5-10 years Fast-track option for mid-career researchers looking to relocate to the UK
I would actually like to see a benchmark that there solving multiple linear systems can be efficiently parallelized. And I don’t think it’s numpys fault that notation for tensor operations is hard.
Crick researchers have developed a new stem cell model of the mature amniotic sac development. The team is now exploring the potential for using these new 3D models in clinical applications, such as cornea reconstruction and treating ulcers. www.crick.ac.uk/news/2025-05...
Join us in London (12-13 November) for the 10th anniversary of SynBio UK, the premier conference for synthetic and engineering biology. Organised this year by @biochemsoc.bsky.social and colleagues at @ucl.ac.uk. www.eventsforce.net/biochemsoc/s... #synbio
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...
The next session is focused on our @uclspeccoll.bsky.social team and their recent experiences of co-production! If you are interested in the practitioner view, the lessons they have learned and how they are embedding this into future practice, come and join us! buff.ly/4NIzRhq
Can using synthetic approaches to build biology help teach us the design principles of how embryos build themselves? 👷♀️🔧 If this is a question that interests you, come and share your thoughts at this Royal Society Workshop on Generative Biology www.royalsoc.ac.uk/science-even...
If you’re interested in GI organoids please join us for the first LION meeting at The Crick 09/06! 🦁
🔊 Pls repost: we (Membership/Elections & #OpenScience Implementation) are looking for a trainee with expertise in #datascience, #machinelearning, data visualization You can contact me or @tlemberger.bsky.social if you know anyone who is interested More info on project ➡️ www.embo.org/vacancy/ai-a...
Stoked to present our latest, superbly led by Chris et al & @torres-sanchez.bsky.social We tackled a fundamental problem – how tissues are patterned during development – found that geometry-constrained ECM fractures pattern the myocardium in the vertebrate heart 1/n www.biorxiv.org/content/10.1...
Congratulations to Crick group leader @jamesbriscoe.bsky.social and the @uni-of-warwick.bsky.social’s David Rand on being awarded £1.3m from the BBSRC. The pair will work on establishing a rulebook defining how cells determine their ‘type’ during development. www.crick.ac.uk/news/2025-04...
I'd like to share a little bit of happy lab news in these chaotic times: a new preprint, driven by the brilliant Qinhao Cao! www.biorxiv.org/content/10.1... We address a big challenge in synbio: If you give me a protein "X", how can I give you a version of X whose activity is controlled by a kinase?
On the value of exploration of nature and "fishing" expeditions. Hypothesis driven research is important but so is simply observing, measuring and looking for cool new unexpected things.
1/ Ever wondered how to best quantify cell-cell neighbor preferences in tissues? We compared 9+ neighbor preference (NEP) methods for analysing spatial omics data and propose a novel approach that combines the most relevant analysis features which we call COZI 🔬✨ Read more: doi.org/10.1101/2025...
Exciting development! New approach shows potential in restoring GTP hydrolysis in mutant RAS affecting 3.4M cancer cases yearly worldwide. PMID:39476862, Nature 2024, @Nature https://doi.org/10.1038/s41586-024-08283-2 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
Last chance to apply!
The writing was on the wall www.npr.org/2025/03/10/n...
Excellent set of guidelines for anyone developing software for life scientists, from @jwpylvanainen.bsky.social, @lankylaste.bsky.social and @guijacquemet.bsky.social journals.biologists.com/jcs/article/...
We're recruiting! ➡️ (Senior) bioinformatician: join a collaborative project with @mhaniffa.bsky.social and Mo Lotfollahi, supporting the analysis of single-cell and spatial transcriptomics studies to train AI-based foundation models Apply by 25 March sanger.wd103.myworkdayjobs.com/en-US/Wellco...
6 days left to apply to the Post-doc opening in our lab @ebi.embl.org to develop&apply #bioinformatics & #machine-learning methods to study intra-/extra cellular networks to extract disease mechanisms from #single-cell and #spatial multiomic data: embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
congratulation Julio!
Stephen Boyd's reaction when a student says they're using Genetic Algorithms for optimization is priceless 😂 youtu.be/kV1ru-Inzl4?...
Beyond Mechanism—Extending Our Concepts of Causation in Neuroscience onlinelibrary.wiley.com/doi/10.1111/... - really pleased that this paper with Henry Potter is now published in the European Journal of Neuroscience 😊
🧪 Pipettes in a neat row. 🧫 Cells responding to a carefully measured symphony of perturbations. 🦾 Liquid handlers whirring softly. 📋 Protocols, pristine. We are seeking a detail-oriented protagonist to bring order to the world of intracellular signalling. crick.wd3.myworkdayjobs.com/External/job...
One week left to apply!
Excited to share my latest work with @joadelas.bsky.social and @jamesbriscoe.bsky.social Predictable Engineering of Signal-Dependent Cis-Regulatory Elements www.biorxiv.org/content/10.1... 1/11
or it's harder to survive in big labs.
xkcd.com/386/
This is why UK gov needs to invest in PhD training & cut visa costs for scientists Long term economic growth depends on skilled people The UK should make the most of life sciences
congrats!
Decoupling.
Still hard to believe but Béla Novák died suddenly on Saturday. We've lost a fantastic colleague, mentor & great friend to many. There was really no-one else like him. Working with him was so much fun & I owe him a lot. All my thoughts are with his family. www.merton.ox.ac.uk/news/remembe...
Here is the slide I didn't have time to present about my experience working across disciplines. Main takeaway: "explain everything (using small words if possible!), ask all the questions, assume nothing, look at the data". #INTERPHACE2025
"Genes are... the easy part" @philipcball.bsky.social argues biologists need to embrace complexity from the start, rather than beginning with oversimplified "one gene, one trait" models +1 www.cell.com/cell-systems...
Only one week left to apply!