· #AcademicSky · The European Research Council is launching €7m Plus Grants for ambitious, long‑term research — open to researchers at any career stage but limited to about 30 awards; current ERC grantees and applicants are ineligible, reports @clanicholson.bsky.social.

Defining models and modelling tasks in ways that avoid “the model knows something that cells don’t” should be the guiding principle for making models.

Strongly recommend taking a look!

How many hours per week do you talk to ChatGPT? I generally do 2-5h in total and several times per day - across coding, science, career, life, health. It’s becoming quite integral. Hard to believe I would say this given what I thought before.

First week in @jamesbriscoe.bsky.social lab at @crick.ac.uk! 1/n

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...

Good to see this study from Ribes & co in print: PAX3/PAX7 transcription factors control neural tube patterning by simultaneously repressing ventral fates via H3K27me3 deposition at silencers & activating dorsal fates as pioneer factors at enhancers @ribes journals.plos.org/plosbiology/...

Very exciting work. Reshaping understanding.

I am wondering what people think about building an AI system to coordinate research. It would be an agent similar to ChatGPT 5. You can talk to it about your research with persistent memory across chats. All chats are used for training without opt-out option. 1/n

Hot take. Excessive benchmarking demands on computational method papers slow down progress. Benchmarks in the paper need to show that your solution works well enough for your goals - not that it is the best solution ever proposed or how exactly it differs from all other existing solutions.

@biorxivpreprint.bsky.social Scalable transcription factor mapping uncovers the regulatory dynamics of natural and synthetic transcription factors in human T cell states www.biorxiv.org/content/10.1...

🚨 new glioblastoma preprint alert! we present the first spatially resolved single cell atlas comparing radionecrotic changes (RN) and recurrent IDH-wildtype glioblastoma (GB) –– shedding light on a long-standing diagnostic challenge. 🧵 1/

How many papers are truly irreproducible and how many show a possible causal path which often isn’t the limiting factor and is conditional on important context (eg mutations, genetics, environment of the experiment)? Thinking about omnigenic model, “mechanistic bias” in medicine, personalised PRS.

Hepatic acetyl-CoA metabolism modulates neuroinflammation and depression susceptibility via acetate @cp-cellmetabolism.bsky.social www.cell.com/cell-metabol...

Very impressive work and interesting modelling ideas 💡:

By training GPN-Star on vertebrate, mammal, and primate alignments, we reveal task-dependent advantages of modeling deeper versus more recent evolution. These findings offer new biological insights and practical guidance for developing future gLMs and evolutionary models. (6/n)

This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/

If you feel like you need noise canceling headphones 🎧 - you probably actually need to buy them right now. Don’t delay this decision and loose time trying to operate without them. Noise cancelling headphones are like your work email+slack - you may be able to work without them but it’s pretty hard.

Has anyone ever seen a house/flat in the UK/Cambridge that had an HRV or ERV system? If you can’t have windows open at night due to security concerns how are you supposed to ventilate? I tried closing windows and even with the fan on max CO2 levels never got below 850ppm (bad for sleep quality).

With unprecedented 38× coverage, our atlas resolves single neuron clusters and shows that separate waves of neurogenesis use different modes of molecular identity encoding: discrete in early born and continuous in late born. 3/8

Neuronal diversity is written in transcriptional codes 🧬. But what is the logic of these codes that define cell types and wiring patterns? To find out we built a #scRNAseq developmental atlas of the Drosophila nerve cord and linked it to the #connectome 🪰🧠 #preprint thread ⬇️1/8

And he made it again!...tour the force from JIa-Wei´s Wang lab using comparative sc-transcriptomes, and developing new analytical tools, to tackle evolutionary trajectories of plant cell types!. Amazing work as usual! www.cell.com/cell/abstrac...

Ended up coming back to these points to articulate state of the GRN field in the paper/fellowship introduction. Introductions need to be specific about the task specification and model-task mismatch in existing work. Task specification need to match biology terms at the right level of abstraction.

👀 we are involved in projects 1 & 6 on the list: 1️⃣ Multicellular molecular characterisation of inflammatory bowel disease 6️⃣ Designing Efficient Single-Cell Perturbation Experiments with Lab-in-the-Loop AI Agents 📅 Application deadline is 30th September ❗

Welcome @timcoorens.bsky.social ‪ ‬🇳🇱, our new Research Group Leader. Find out how Tim’s group is exploring using large-scale single-cell and spatial data to trace cell lineages, understand cancer origins, and uncover how mutations drive disease. www.ebi.ac.uk/about/news/p... 🖥️🧬

Looks like this platform became almost as unusable as Twitter/X. I rarely open it. If you want to reach out - you can use slack or email or maybe LinkedIn or for code issues - GitHub Issues. Please don’t email about the code issues - GitHub Issues is much more useful for managing them.

Biologist folk (especially in evolutionary biology and/or ecology, but it don’t matter): Can you give me your favorite examples of trade offs in biology? Organism or system don’t matter. Primary literature or reviews preferred.

I think small focused fully remote research conferences should exist. You can ask participants to record 1, 5, 20 & 60 min talks that others can watch in advance, then provide a structure for scheduling meetings with the authors for questions. You can even just email the authors to ask for a call.

How do enhancer-gene contacts relate to transcription activation? In mouse embryonic stem cells, a combo of STED, oligoFISH & RNA FISH shows that 3% of Dppa3 alleles transcribe. For these, enhancers and promoters come closer (panel E). Stumberger ... Leonhardt & Harz www.biorxiv.org/content/10.1...

If you are interested in peptide-based protein binders, check out this new @biorxivpreprint.bsky.social by the group of @sebastianpomplun.bsky.social of our @led3hub.bsky.social on their computer-based design.

Unpopular opinion. You can’t expect scientists to spend time on code engineering before seeing any results that illustrate why spending 6 months in human hours on engineering is warranted. Same re coming up with optimal ways to work. Those things in academia need to be supported by dedicated teams.

Are world models necessary to achieve human-level agents, or is there a model-free short-cut? Our new #ICML2025 paper tackles this question from first principles, and finds a surprising answer, agents _are_ world models… 🧵 arxiv.org/abs/2506.01622

Hakime, as part of @elsa-ai.eu, is organizing a dedicated Health Privacy Session which will feature a keynote talk, a panel discussion, and the recap of the Health Privacy Challenge with contributed presentations from the challenge participants. #CAMDA 📅 July 24 | 🕑 11:20-15:00 | 📍 Room 01C

John will share how to achieve higher throughput and fidelity in screening via flexible, high-accuracy barcode decoding. He presents a principled, information theory-based software solution that unifies diverse, demanding decoding tasks within one robust framework. #HiTSeq 📅 July 23 | 📍 Poster C-192

@elihei.bsky.social is gonna present our new tool segger, developed in collaboration with Moritz Gerstung and @danapeer.bsky.social, for fast and accurate segmentation of spatial transcriptomics using attention-based graph neural networks. #MLCSB 📅 July 22 | 🕑 15:50 | 📍 Room 01A

@thbec.bsky.social is going to share preliminary results on Meta-DeepRVAT, a new approach for deep learning based meta-analysis improving the power of rare variant association studies using population scale external control cohorts. #MLCSB 📅 July 21 |📍 Poster A-312

Excited to present our ongoing work @steglelab.bsky.social @sangerinstitute.bsky.social @bayraktarlab.bsky.social @mhaniffa.bsky.social @teichlab.bsky.social on whole embryo modeling of how TFs interact to drive specific CRE element activation in human organogenesis. #RegSys Wed 23 July, 14:40, 11BC

@vitaliikl.bsky.social will discuss how biophysical deep learning improves understanding of embryogenesis. He applied cell2state, his new method leveraging TF-motif interactions and biophysical constraints, on an unpublished multimodal sc and spatial atlas. #RegSys 📅 July 23 | 🕑 14:40 | 📍 Room 11BC

🚨 Join us tomorrow for this really exciting talk on the interplay between morphogen signalling and tissue organization! 🚨

German food hospitality is pure incompetence. That’s the tweet. I don’t think I ever had a positive experience.

Cambridge busses are useless. Scheduled 2 minutes before trains arrive not after. Drivers stop where they want not on the stops. Taxi or driving is the only way to get around. @stagecoachwales.bsky.social * But what about 🚲 ? Cycling is extremely dangerous for people without advanced experience.

Night science: semi overlapping clouds ⛅️ 🌧️ ☁️ of ideas 💡 Day science: PyTorch computation graph Challenge is going from imprecise cloud ☁️ to precisely connecting all project parts into a process that results in paper figures and intermediate results.

@iscb.bsky.social 2025 morning yoga sessions are a nice touch. I hope I can wake up in time! Looking forward to presenting our work modelling how TFs specify genomic DNA accessibility state in every cell - as cell types develop in organogenesis (cell2state model + multiome of >1000 populations).

New work on dynamics of morphogen signaling: Cells decode BMP gradient via temporal integration of signaling level, not instantaneous thresholds. While GRN gates response to provide additional spatial input Morphogen signalling dynamics + GRN for tissue patterning www.biorxiv.org/content/10.1...

New method for reducing high-dimensional neuronal responses in visual cortex to low-d latents in 🐁 BUT while this works with simple stimuli eg drifting gratings, natural image responses cannot be similarly reduced... 👀🧠 #neuroskyence www.biorxiv.org/content/10.1...

The "rubber hand illusion" in mice... @lucestebanez.bsky.social &co use automated videography to show that mice display quantifiable behavioral markers of the embodiment of an #ArtificialLimb, opening the door to future research into human #BodyOwnership disorders @plosbiology.org 🧪 plos.io/4jHsESn

Fine-tuning improved PromoterAI’s ability to predict the direction of motif effects — a known issue of multitask models. The model often recognized motifs before fine-tuning, but got the direction wrong. After fine-tuning, its predictions aligned better with the data. (8/)

Excited to share my first contribution here at Illumina! We developed PromoterAI, a deep neural network that accurately identifies non-coding promoter variants that disrupt gene expression.🧵 (1/)

Specialised models are a part of science programme of the field - steps on a path to deeper understanding - not software you make & sell. No effort towards understanding -> the models & tasks they solve are not assessed for how well they match the science programme -> recipe for wrong & not useful.