computational and systems biology
Boston
Joined May 2019
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1/8 The Human Gut Cell Atlas (HGCA) v1.0 is out on bioRxiv! doi.org/10.64898/2026.10.09.…
Built by the gut community, for the gut community. For this HCA resource, we aimed for high-resolution healthy cell subtypes and robustness for downstream tasks like label transfer.
ALT HGCA Figure 1a-b. A workflow links global data contributions and public review to integration benchmarking, expert annotation jamborees, evidence review and consensus cell identities. The resulting atlas includes 944,390 cells from 24 datasets and 265 donors aged 0-89. A gut diagram and bar charts show coverage across intestinal regions and donor ages. The atlas combines healthy and disease-adjacent tissue.
7/8 Do organoid cells made from ileal biopsies resemble ileum cells? Some types retain regional identity, others don't. Longer cultures often approach in vivo states, but the effect varies by cell type. HGCA lets us quantify both regional fidelity and maturation.
ALT HGCA Figure 5c-f. A dot plot compares organoid cell subtypes with their declared intestinal region across adult, fetal and pluripotent stem-cell sources. Three circular treemaps show changing cell composition and similarity to adult HGCA cells over culture time. A scatterplot across 41 samples from 9 publications shows decreasing distance to the adult reference with maturation. Cell-type-specific estimates show that this trend is not uniform across identities. Adult-like maturation and regional specification are distinct dimensions.
8/8 HGCA v1 will grow through community use, critique, and contributions. Explore the data, map your cells and help fill gaps in populations, ages and tissues. Thank you to everyone who built this! Want to build the next versions with us? Reach out! data.humancellatlas.org/hca-…
Kyle.kimler retweeted
The integrated HCA v1 Human Gut Cell Atlas is now available on the HCA Data Portal! Integrating nearly 1 million single cells from 265 donors, the #Gut Atlas is a reference map to understand gut health and diseases like Crohn’s.
Explore here buff.ly/X0Rfj39
#Genomics
Kyle.kimler retweeted
What can we learn from all cytokines in the human genome? For most, we have limited info on what they do and when to target them
Meet TAPAS & EPICURE: tools to synthesize all human cytokines➡️scRNA data of primary human immune responses➡️🖥️methods to use them in your work (1/n)
Kyle.kimler retweeted
Our new publication from the @ordovas_phd and von Andrian lab in this month's issue of @ImmunityCP sniffs out what there is to know about nasal immunity and memory to viral infections cell.com/immunity/abstract/S… 1/8
Kyle.kimler retweeted
What a pleasure collaborating with the Craneo team on this podcast (en Español!) on the digestive system (el sistema digestivo)! Such amazing questions from young kids. Stay curious! open.spotify.com/episode/0Fi… #Science #podcast
Kyle.kimler retweeted
The peer-reviewed version of our study on the evolution of tissue-specific expression across vertebrates and insects is finally published in @NatureEcoEvo ! @FedeMantica @CRGenomica @UPFbiomed
nature.com/articles/s41559-0…
🚨Exciting pre-print from the lab!👉"Pervasive evolution of tissue-specificity of ancestral genes differentially shaped vertebrates and insects". Deep comparative #transcriptomics across #bilateria by @FedeMantica et al @CRGenomica. 👀biorxiv.org/content/10.1101/…. Summary👇
Translating scRNAseq results to the clinic is difficult... could comparing to clinical trials data be key to bridging the gap? @teichlab shows scRNAseq data supports many successful drug targets by bringing in ct data!
medrxiv.org/content/10.1101/…
Kyle.kimler retweeted
Multicellular Factor Analysis is now fully available in @eLife's website, including the editor's evaluation and our updated revision.
Estimate multicellular programs and perform unsupervised analysis of samples from cross-condition single cell atlases
elifesciences.org/articles/9…
Kyle.kimler retweeted
AI is catalyzing scientific discovery into health and disease.
To accelerate progress, we’re building one of the world’s largest computing systems dedicated to non-profit life science research that we’ll leverage to create predictive models of whole cells
Kyle.kimler retweeted
We are sharing our pre-print which seeks to ask how a viral infection in the nose sets up effective local memory biorxiv.org/content/10.1101/…
Kyle.kimler retweeted
1/9 CPAis finally published. It can predict single-cell responses to combinatorial perturbation (drugs, CRISPR). This is a joint collab between @meta and @fabian_theis @HelmholtzMunich. Read the thread to understand the LEGO analogy! embopress.org/doi/full/10.15…
Kyle.kimler retweeted
Our latest! Philosophical and practical arguments for a tree-based nomenclature for defining, naming, and organizing cell types (a "consensus ontogeny"), from Silvia Domcke (@sdomcke) and me.
authors.elsevier.com/a/1glnf…
Kyle.kimler retweeted
Thanks @Sara_Busatto for organizing additional peer-review by some amazing kids for our original study on SARS-CoV-2 nasal infection! Our manuscript here led by Faith and @JaclynMLong kids.frontiersin.org/article… based on work by @carlygailz sciencedirect.com/science/ar… @FrontYoungMinds
