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here comes WebAtlas: our "Google Maps" for tissue atlases with integrated single cell and spatial transcriptomics so anyone & anywhere can access/explore atlas datasets on a web browser. Fantastic collab with Muzlifah Haniffa, led by Tong LI 李彤 Dave Horsfall & Daniela. Links 👇

53,035 Aufrufe • vor 3 Jahren •via X (Twitter)

17 Kommentare

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

Paper: Portal where you can access datasets:

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

The integration of single cell + spatial transcriptomics can build awesome tissue atlases but it is hard to share these datasets in a globally accessible & usable format without technical burden on the users. We aimed to solve this problem with WebAtlas

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

WebAtlas addresses 2 key challenges in this area: 1) how to deal with myriad technologies and data types in sc/spatial omics? and 2) how to freely browse integrated datasets?

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

The core of WebAtlas is a data ingestion pipeline that unifies data types from nearly all commonly used atlassing technologies (works on sc/snRNAseq, Visium, Xenium, MERSCOPE, In Situ Sequencing, seqFISH) into the cloud-optimised & scalable Zarr format @zarr_dev

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

We put special care into image components of spatial data i.e. raw images and cell segmentation masks are handled as OME-Zarr for multi-scale visualisation. This was a parallel effort with SpatialData & we are keen to support their format in the future

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

We then re-used the awesome Vitessce web visualisation framework from @ngehlenborg that allows fully interactive exploration of sc + ST data. We customised it for coordinated browsing of cell types & gene expression in integrated sc and ST datasets

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

We showcased WebAtlas on a "triple" modality atlas of the developing human hindlimb from @teichlab that combines scRNAseq, Visium spatial RNA-Seq and In Situ Sequencing (ISS done by @krobertssci in my lab). You can explore it on & few more tweets below.

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

We harmonised cell types & gene expression across 3X modalities with computational integration: our Cell2location tool to integrate scRNAseq + Visium and StabMap from @shazanfar to transfer cell types & impute gene expression from scRNA-seq to ISS (

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

The result is stunning WebAtlas (the video on top) where you can cross-query cell types & genes across all modalities in one place, where you can browse the ISS spatial cell map to explore the beautiful structure of the developing bone, muscle and skin across the embryonic limb.

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

Many fun things to do on the integrated atlas. For example, the scRNAseq -> ISS imputation allowed us to identify a novel spatial gene expression gradient in chondroprogenitors that give rise to the cartilage anlage! On WebAtlas, you can cross-validate this on Visium data!

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

WebAtlas is tech agnostic and supports many technologies as listed above e.g. see a Xenium dataset of a human breast tumour on WebAtlas here

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

...and an integrated scRNA-seq + seqFISH atlas of mouse embryogenesis from @MarioniLab ( - webAtlas link here:

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

Finally, WebAtlas is scalable: to date it has handled scRNAseq with 900k cells and MERSCOPE with 700k cells Currently works best with <10 Million RNA molecules

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

Try WebAtlas! Our landing page with all datasets tweeted above & shown in paper: Repo: Tutorials:

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

I am excited about sharing our upcoming @humancellatlas datasets with the community on WebAtlas and a future where we can build "Next-Gen" multi-modal tissue atlases on the cloud. If you are interested, please reach out!

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

This was a wonderful collab with @Muzz_Haniffa @BioinfoTongLI @Dave_Horsfall @krobertssci @PengHeCam @shazanfar @teichlab. Special thx to @notjustmoore who aligned us with SpatialData from @fabian_theis and @OliverStegle...

Profilbild von Omer Ali Bayraktar
Omer Ali Bayraktarvor 3 Jahren

..., @zarr_dev & Vitessce @ngehlenborg & @openmicroscopy teams for our technical foundations, and @wellcometrust @sangerinstitute for supporting our work!

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Qiusheng Wu

14,793 Aufrufe • vor 18 Tagen

Excited to share our new work. Over the past decade, single-cell genomics has transformed our ability to map cellular systems. But a major question remains: Can we predict how perturbations reshape cellular trajectories over time? In 2018, we first showed that it is possible to predict cellular responses to perturbations — ranging from disease signals to chemical treatments — even in unseen contexts. In 2022, we introduced CPA (MSB 2022; NeurIPS 2022), extending this idea to predict responses to unseen chemical and genetic perturbations, including their combinations. Since then, the field of perturbation modeling has grown enormously. The community has pushed the space forward with many creative ideas and powerful models. It’s exciting to see how fast things are moving — even though many fundamental challenges remain. One of the biggest is that cells are not static. They move through trajectories during development, immune responses, and disease. Yet most current models still predict perturbation effects within a single state, rather than how early perturbations propagate across future states and reshape downstream outcomes. To address this, we developed PerturbGen, a trajectory-aware generative AI model that predicts how genetic perturbations reshape downstream cellular states. Huge credit to the people who made this work possible. Thanks to co-first authors Kevin Ly, Adib Miraki, Tomoya Isobe, AmirHoss3in Vahidi, Delshad Vaghari & Anthony Rostron. Special recognition to Kevin Ly and Adib Miraki for driving this work over the finish line. Grateful for our outstanding collaborators from Haniffa Lab, Bertie Gottgens lab Gosia Trynka and many others — a true cross-institute effort across Cambridge Stem Cell Institute, Open Targets ,Wellcome Sanger Institute and Cambridge University.🎉 PerturbGen learns transcriptional dynamics across cellular trajectories. By introducing perturbations at an early source state, it can simulate how these effects propagate into future states along differentiation trajectories. Scaling this across genes enables the creation of dynamic in silico perturbation atlases — maps of how perturbations reshape biological trajectories over time. We explored this idea across three biological questions. First, in a human in vivo LPS immune challenge, PerturbGen predicted that perturbing a transient IL1B signal dampens downstream inflammatory programs in myeloid cells, with pathway changes reversing signatures observed in an independent IL-1β stimulation experiment. Second, in human hematopoiesis, PerturbGen predicted transcriptional responses to CRISPR transcription factor knockouts and enabled construction of perturbation atlases revealing lineage- and age-specific regulatory programs. These programs could also be linked to human genetics and blood diseases, including recapitulation of signatures associated with ETV6-related thrombocytopenia. Finally, we asked whether perturbation modeling could help improve complex tissue models. We built a dynamic perturbation atlas of human skin organoids to identify perturbations that could guideorganoid cells towardhuman fetal skin states. PerturbGen prioritized activation of Wnt signaling via GSK3β inhibition. Experimental validation confirmed the prediction: treatment with CHIR99021 induced stromal gene programs and shifted organoid fibroblasts toward transcriptional states observed in fetal skin stroma. Together, these results show how trajectory-aware perturbation modeling can connect gene perturbations to developmental programs, human genetics, disease mechanisms, and experimental interventions. More broadly, we think these point toward a future where single-cell atlases become predictive systems. As atlases expand across tissues, developmental windows, and modalities, models like PerturbGen could enable dynamic, virtual perturbation atlases— allowing us to simulate interventions, generate hypotheses, and design experiments before stepping into the lab. Preprint Code Excited to see how the community builds on this work.

Mo Lotfollahi

17,165 Aufrufe • vor 6 Monaten

Spectre AI Soars and Secures Google Scale Tier Membership with $200,000 in Development Resources We're thrilled to announce a significant milestone for Spectre AI! After a lot of networking, and a rigorous selection process, we've been accepted into the prestigious Google Scale Tier program. We had Start Tier, now we have Scale Tier! This membership signifies Google's recognition of Spectre AI's potential to become a potential game-changer in the blockchain space, and it grants us access to a wealth of resources to fuel our growth – $200,000 in development funding from GoogleStartups to use their advanced tools. What is the Google Scale Tier? The Google Scale Tier is a highly selective program designed to nurture high-growth startups with exceptional potential. Going beyond simple funding, this program grants a comprehensive suite of benefits to empower us to scale our technology and achieve new heights. Unlocking Cutting-Edge Tech and Expertise Our Google Scale Tier membership unlocks a treasure trove of resources to accelerate our development journey: $200,000 in Google Development Resources: This crucial boost will allow us to leverage Google Cloud and cutting-edge tools, along with collaboration with top Google engineers. These experts will work closely with our team to integrate these powerful resources seamlessly into our entire suite of products, including AI Predictions, Sentiment Analysis, and Technical Analysis. Imagine the possibilities for enhanced accuracy, efficiency, and deeper market insights leveraged by Google's technology! Collaboration with Google Engineering Experts: As mentioned earlier, the $200,000 in development resources includes access to Google engineers – the masterminds behind cutting-edge technologies like Long Short-Term Memory (LSTM) models, Machine Learning (ML), and advanced graphing models. These experts will collaborate with our team to integrate these powerful tools into our products. Dedicated Google Representative: A dedicated Google representative from their Irish headquarters has become our go-to person, ensuring seamless collaboration and ongoing support throughout our journey. Thank you GoogleStartupUK The Future of Spectre AI: Enhanced All-in-One Products This partnership extends far beyond individual features. Here's what you can expect across our entire product suite: Next-Level Functionality: We'll leverage Google's advanced algorithms and massive datasets to refine all our tools, including AI Predictions, Sentiment Analysis, and Technical Analysis. This means more reliable and insightful information to guide your investment strategies. Expanded Capabilities: We're exploring groundbreaking new features for our entire product suite, like real-time analysis, multi-factor modeling, and even deeper market insights. Enhanced User Experience: Navigating through all our tools will be smoother than ever. We'll work with Google to refine the user interface across the board, making it easier to understand and leverage the power of AI in your crypto journey. The Data Visualization Revolution: Buckle up, X Bubblemaps users! Google's advanced graphing models are poised to transform how you visualize and explore data within Spectre AI. We can't wait to unveil a whole new level of visualization that will take your on-chain analysis to the next level. This is just the beginning! We're incredibly grateful for this opportunity to partner with Google and revolutionize the future of our all-in-one blockchain analysis suite. Stay tuned for exciting updates as we develop groundbreaking new features together. Thank you for being a part of the Spectre AI community! #google #googlecloud #spectre #ai #tech #innovation $spect

SPECTRE AI

46,737 Aufrufe • vor 2 Jahren