Cool Papers — Rendeiro Lab https://rendeiro.group/cool-papers/ Recent interesting papers shared by the Rendeiro Lab team en-us Thu, 15 Oct 2026 20:45:38 -0000 Spatially resolved contrastive analysis of perturbation-driven microenvironmental heterogeneity across tissues and conditions https://www.biorxiv.org/content/10.64898/2025.12.08.693051v2 https://www.biorxiv.org/content/10.64898/2025.12.08.693051v2 Andre Rendeiro Wed, 14 Oct 2026 12:15:21 +0000 [bioRxiv] Accurate and well-powered case–control analysis of spatial molecular data https://www.nature.com/articles/s41592-026-03236-1 https://www.nature.com/articles/s41592-026-03236-1 Andre Rendeiro Wed, 14 Oct 2026 12:13:51 +0000 [Nature Methods] ResolVI: addressing noise and bias in spatial transcriptomics https://www.nature.com/articles/s41592-026-03212-9 https://www.nature.com/articles/s41592-026-03212-9 Andre Rendeiro Wed, 14 Oct 2026 12:12:53 +0000 [Nature Methods] probably a key method/modeling framework for the Xenium data Written in development and lost in ageing: the grammar of cellular identity https://www.nature.com/articles/s41586-026-10955-0?utm_source=substack&utm_medium=email https://www.nature.com/articles/s41586-026-10955-0?utm_source=substack&utm_medium=email Andre Rendeiro Wed, 14 Oct 2026 12:11:09 +0000 [Nature] probbaly a good review for everyone to read on some of the basics of aging but also in light of the latest research Prevalent mesenchymal drift in aging and disease is reversed by partial reprogramming https://www.cell.com/cell/fulltext/S0092-8674(25)00853-0 https://www.cell.com/cell/fulltext/S0092-8674(25)00853-0 Andre Rendeiro Wed, 14 Oct 2026 12:10:00 +0000 [Cell] probably an important paper formalizing what we and many others see in tissue: most tissues will drift towards a mesenchymal (fibroblast) identity with age Systematic comparison of affinity plasma proteomic technologies across multiple cohorts reveals generalizability of proteomic prediction https://www.nature.com/articles/s41467-026-78443-7 https://www.nature.com/articles/s41467-026-78443-7 Andre Rendeiro Wed, 14 Oct 2026 12:03:41 +0000 [Nature Communications] maybe an interesting technical comparison GRASS-MIL: graph-based representation and discovery of phenotype-associated spatial structures with multiple instance learning https://www.biorxiv.org/content/10.64898/2026.10.08.757722v1?ct= https://www.biorxiv.org/content/10.64898/2026.10.08.757722v1?ct= Andre Rendeiro Wed, 14 Oct 2026 12:01:14 +0000 [bioRxiv] let's have a close look, especially Shrestha and Tamas TechBio 3.0 closes the drug discovery loop with multimodal AI and generative chemistry https://www.nature.com/articles/s44386-026-00078-x https://www.nature.com/articles/s44386-026-00078-x Andre Rendeiro Wed, 14 Oct 2026 11:58:52 +0000 [npj Drug Discovery] maybe an interesting perspective to dig into Population-scale reconstruction of menopause dynamics reveals a physiological cliff at the final menstrual period https://www.nature.com/articles/s41591-026-04614-0 https://www.nature.com/articles/s41591-026-04614-0 Andre Rendeiro Wed, 14 Oct 2026 11:57:33 +0000 [Nature Medicine] Histology-aware Inference of Cell-cell Communication in Spatial Transcriptomics https://www.biorxiv.org/content/10.64898/2026.01.22.701166v3?ct= https://www.biorxiv.org/content/10.64898/2026.01.22.701166v3?ct= Andre Rendeiro Tue, 13 Oct 2026 12:37:23 +0000 [bioRxiv] REZCUE: Rescuing 3D spatial omics from archived FFPE tissue https://www.biorxiv.org/content/10.64898/2026.10.06.757132v1 https://www.biorxiv.org/content/10.64898/2026.10.06.757132v1 Ernesto Abila Tue, 13 Oct 2026 12:25:55 +0000 [bioRxiv] Single-fiber morphometry and spatial transcriptomics reveal selective oxidative muscle fiber atrophy in non-metastatic breast cancer https://www.medrxiv.org/content/10.64898/2026.05.11.26351978 https://www.medrxiv.org/content/10.64898/2026.05.11.26351978 Andre Rendeiro Thu, 08 Oct 2026 12:24:09 +0000 [medRxiv] Deep learning perturbation models can outperform baselines on calibrated metrics https://doi.org/10.1038/s41587-026-03307-w https://doi.org/10.1038/s41587-026-03307-w Ariadna Villanueva Marijuan Wed, 07 Oct 2026 13:08:49 +0000 [Nature Biotechnology] this article is in response to the paper published last year that showed that deep learning models do not outperform linear baselines for gene perturbation prediction (https://doi.org/10.1038/s41592-025-02772-6) Global and regional reference curves for pain across the lifespan in 6.1 million individuals in 118 countries https://www.nature.com/articles/s41591-026-04696-w https://www.nature.com/articles/s41591-026-04696-w Andre Rendeiro Tue, 06 Oct 2026 06:53:55 +0000 [Nature Medicine] Inferring organ aging, hallmark of aging and senescence scores from blood and facial photographs https://www.biorxiv.org/content/10.64898/2026.09.23.753830v1 https://www.biorxiv.org/content/10.64898/2026.09.23.753830v1 Andre Rendeiro Fri, 02 Oct 2026 11:07:08 +0000 [bioRxiv] mc-ASTRA maps population-level variation to interpretable multicellular tissue organization processes https://www.biorxiv.org/content/10.64898/2026.09.18.752722v1 https://www.biorxiv.org/content/10.64898/2026.09.18.752722v1 Andre Rendeiro Mon, 28 Sep 2026 11:23:41 +0000 [bioRxiv] SpaCEy links spatial tissue patterns to clinical outcomes using explainable graph neural networks https://www.nature.com/articles/s41467-026-77924-z https://www.nature.com/articles/s41467-026-77924-z Andre Rendeiro Mon, 28 Sep 2026 07:34:34 +0000 [Nature Communications] a prototypical simple blueprint for a methods paper, so if interested in computational methods have a look; further https://zenodo.org/records/17710588 has datasets that could be useful for topocyte @Simon Single-cell analysis of chromatin accessibility in the human intestine identifies regulatory programs and clarifies genetic associations in Crohn’s disease https://www.nature.com/articles/s41588-026-02755-z https://www.nature.com/articles/s41588-026-02755-z Andre Rendeiro Sun, 27 Sep 2026 14:40:12 +0000 [Nature Genetics] Clinical Uses of Common Genetic Variants Associated with Common Diseases https://www.nejm.org/doi/full/10.1056/NEJMra2413201 https://www.nejm.org/doi/full/10.1056/NEJMra2413201 Andre Rendeiro Fri, 25 Sep 2026 16:46:28 +0000 https://bsky.app/profile/mikeinouye.bsky.social/post/3mwb4owzbq22e IMILIA: interpretable multiple instance learning for inflammation prediction in IBD from H&E whole slide images https://arxiv.org/abs/2512.13440 https://arxiv.org/abs/2512.13440 Andre Rendeiro Thu, 24 Sep 2026 16:52:54 +0000 [arXiv] https://lnkd.in/p/dRTF4Eb9 Blood proteomics of menopause map to brain aging and dementia risk https://www.nature.com/articles/s41591-026-04648-4 https://www.nature.com/articles/s41591-026-04648-4 Ernesto Abila Tue, 22 Sep 2026 20:38:11 +0000 [Nature Medicine] Pretrained gene representations transfer mean expression more broadly than spatial patterns in virtual spatial transcriptomics https://www.biorxiv.org/content/10.64898/2026.09.15.751768 https://www.biorxiv.org/content/10.64898/2026.09.15.751768 Andre Rendeiro Tue, 22 Sep 2026 12:00:15 +0000 [bioRxiv] didn't see in detail but looks like very pertinent work addressing one well-known limitation of these approaches Multi-organelle signatures map cell-state diversity and metabolic adaptation in tissues https://www.science.org/doi/10.1126/science.ady6372 https://www.science.org/doi/10.1126/science.ady6372 Andre Rendeiro Tue, 22 Sep 2026 11:59:13 +0000 [Science] interesting work on the sub-cellular real - nice to see a fresh take on this and potentially relevant for us and the whole LBI-NetMed A universal visual foundation model for computational cytopathology https://www.nature.com/articles/s43018-026-01240-0 https://www.nature.com/articles/s43018-026-01240-0 Andre Rendeiro Tue, 22 Sep 2026 11:58:20 +0000 [Nature Cancer] a cytopathology foundation model (mostly blood/immune cells spread on glass); strange choice of baselines but looks like good work nonetheless CT-based biological age as a biomarker of aging and age-related disease assessment https://www.nature.com/articles/s41514-026-00523-1 https://www.nature.com/articles/s41514-026-00523-1 Andre Rendeiro Tue, 22 Sep 2026 11:49:38 +0000 [npj Aging] cool paper, unfortunately no data WHO working definition of vitality capacity for healthy longevity monitoring https://www.thelancet.com/journals/lanhl/article/PIIS2666-7568(22)00200-8/fulltext https://www.thelancet.com/journals/lanhl/article/PIIS2666-7568(22)00200-8/fulltext Andre Rendeiro Thu, 17 Sep 2026 11:17:52 +0200 [The Lancet] a nice concept which may be useful when referring to overal physiological capacity which includes more - a good reference for introductions, etc Modelling interpretable patient-level representations from structured and simple multimodal data https://www.biorxiv.org/content/10.64898/2026.08.31.748244v1 https://www.biorxiv.org/content/10.64898/2026.08.31.748244v1 Andre Rendeiro Tue, 08 Sep 2026 22:06:44 +0200 [bioRxiv] Integration of proteomic aging clocks in a phase 2a clinical trial supports simultaneous geroprotective assessment https://www.nature.com/articles/s41587-026-03286-y https://www.nature.com/articles/s41587-026-03286-y arendeiro Tue, 08 Sep 2026 13:28:45 +0200 [Nature Biotechnology] worth noting as a AI-designed drug (for a supposedly AI discovered target) proceeds at breackneck pace (comparatively) through clinical phases: Phase 1: https://www.nature.com/articles/s41587-024-02143-0; [1] Phase 2a: https://www.nature.com/articles/s41591-025-03743-2 (2025); but also because aging clocks were used as a primary readout (why those I'm not sure) [1] https://www.nature.com/articles/s41587-024-02143-0; https://www.nature.com/articles/s41587-024-02143-0 Declines in mRNA synthesis set the rate of organismal aging https://www.biorxiv.org/content/10.64898/2026.07.02.733740v2.full https://www.biorxiv.org/content/10.64898/2026.07.02.733740v2.full arendeiro Sun, 06 Sep 2026 10:13:04 +0200 [bioRxiv] interesting fundamental work from Nick Stroustrup who visited last year A comprehensive atlas of somatic mutation rates and mutational signatures in normal human cells https://www.biorxiv.org/content/10.64898/2026.08.28.747772 https://www.biorxiv.org/content/10.64898/2026.08.28.747772 arendeiro Fri, 04 Sep 2026 11:31:57 +0200 [bioRxiv] a relevant reference for somatic mutation (and their rates) with age https://www.biorxiv.org/content/10.64898/2026.08.28.747772v1 SlideChat is a multimodal generative artificial intelligence assistant for whole-slide computational pathology across cancer types https://www.nature.com/articles/s43018-026-01220-4 https://www.nature.com/articles/s43018-026-01220-4 YZheng Thu, 03 Sep 2026 15:07:07 +0200 [Nature Cancer] If it works as it claim, it could be a nice resource for improving explainability for many of our models. CONCH -> LongNet (Gigapath slide encoder) -> Qwen2.5-7B-Instruct Code: https://github.com/uni-medical/SlideChat Weight: https://huggingface.co/General-Medical-AI/SlideChat_Weight DistillPath: An Efficient 22M Distilled Pathology Encoder Approaching Large Foundation Model Performance https://arxiv.org/pdf/2608.17872 https://arxiv.org/pdf/2608.17872 Ernesto Abila Thu, 03 Sep 2026 10:35:39 +0200 [arXiv] MechanoMaST – a multimodal pipeline for spatially registering mechanical and transcriptomic tissue data https://www.biorxiv.org/content/10.64898/2026.08.29.747727v1 https://www.biorxiv.org/content/10.64898/2026.08.29.747727v1 arendeiro Thu, 03 Sep 2026 00:22:35 +0200 [bioRxiv] maybe interesting JCI - Markers of compromised gut epithelial barrier integrity increase during the menopause transition https://jci.org/articles/view/205059 https://jci.org/articles/view/205059 arendeiro Wed, 02 Sep 2026 11:40:22 +0200 see also https://jci.org/articles/view/209807 and https://lnkd.in/p/eUX9AMMP Virtual Aging Cell — Insilico Medicine https://virtualcell.insilico.com/ https://virtualcell.insilico.com/ arendeiro Tue, 01 Sep 2026 21:22:42 +0200 nothing quite actionable at least for now or for us, but just FYI Mapping structural aging across human tissues reveals tissue-specific trajectories and coordinated deterioration https://www.nature.com/articles/s43587-026-01200-4 https://www.nature.com/articles/s43587-026-01200-4 arendeiro Tue, 01 Sep 2026 09:01:32 +0200 [Nature Aging] https://www.nature.com/articles/s43587-026-01200-4#MOESM1 The Biobank Rare Variant consortium powers the discovery of rare genetic associations through global collaboration https://www.medrxiv.org/content/10.64898/2026.05.21.26353759 https://www.medrxiv.org/content/10.64898/2026.05.21.26353759 arendeiro Wed, 19 Aug 2026 00:25:41 +0200 [medRxiv] maybe useful resource P3CA: Encoder-Agnostic Interpretation of Vision Foundation Model Embeddings via Spatial Probing https://arxiv.org/abs/2608.10131 https://arxiv.org/abs/2608.10131 arendeiro Wed, 19 Aug 2026 00:09:47 +0200 [arXiv] interesting, perhaps worth a read Three-dimensional mapping of intact ovaries reveals the aging dynamics of the ovarian reserve https://www.nature.com/articles/s43587-026-01178-z https://www.nature.com/articles/s43587-026-01178-z arendeiro Thu, 13 Aug 2026 10:06:27 +0200 [Nature Aging] super interesting, let's have a close look. Commentary here: https://lnkd.in/p/dJMY-y47 Deep-learning triage of three-dimensional pathology datasets for comprehensive and efficient pathologist assessments https://www.nature.com/articles/s41551-026-01760-1 https://www.nature.com/articles/s41551-026-01760-1 arendeiro Wed, 12 Aug 2026 21:36:00 +0200 [Nature Biomedical Engineering] a dataset to check out: https://zenodo.org/records/20052262 A Bayesian framework for longitudinal EHR and genetic discovery https://doi.org/10.1038/s41586-026-10780-5 https://doi.org/10.1038/s41586-026-10780-5 Ariadna Villanueva Marijuan Tue, 11 Aug 2026 11:48:41 +0200 [Nature] Genetic decoding reveals druggable biology implicitly learned by a medical-history foundation model https://doi.org/10.64898/2026.07.28.26359117 https://doi.org/10.64898/2026.07.28.26359117 Ariadna Villanueva Marijuan Tue, 11 Aug 2026 11:47:57 +0200 [medRxiv] The Virtual Tissues foundation model resolves spatial proteomics across scales https://www.nature.com/articles/s41586-026-10884-y https://www.nature.com/articles/s41586-026-10884-y Andre Rendeiro Tue, 11 Aug 2026 09:41:00 +0200 [Nature] Why studying females reveals more about aging: The reproductive resilience hypothesis for the evolution of sex-specific aging https://www.cell.com/cell/fulltext/S0092-8674(26)00811-1 https://www.cell.com/cell/fulltext/S0092-8674(26)00811-1 Ernesto Abila Mon, 10 Aug 2026 13:57:38 +0200 [Cell] An interesting perspective, highlighting that females should be prioritized in studies of aging. On Fermi Problems in Human Genetics https://jkpritchard.substack.com/p/on-fermi-problems-in-human-genetics https://jkpritchard.substack.com/p/on-fermi-problems-in-human-genetics arendeiro Mon, 10 Aug 2026 13:51:06 +0200 [Substack] nice post on something I often insist on: having good ballpark answers/estimates for problems Multi-modal foundation model with whole-slide attention enables transferrable digital pathology at single-cell resolution https://www.biorxiv.org/content/10.64898/2026.07.31.741265 https://www.biorxiv.org/content/10.64898/2026.07.31.741265 arendeiro Mon, 10 Aug 2026 10:34:22 +0200 [bioRxiv] Topology Inference for Immune System Networks by Using Cell Amount Data https://arxiv.org/abs/2608.07403 https://arxiv.org/abs/2608.07403 arendeiro Mon, 10 Aug 2026 10:30:05 +0200 [arXiv] quite far from our ideas, but maybe useful A compendium of next-generation patient-derived models for diverse cancers https://www.nature.com/articles/s41586-026-10806-y https://www.nature.com/articles/s41586-026-10806-y Ernesto Abila Thu, 06 Aug 2026 22:24:43 +0200 [Nature] quite impressive resource from the 'Human Cancer Models Initiative'. " The resource provides 522 models with comprehensive clinical data, 153 models of rare cancers". multimodal molecular profiling and clinical information are available. Spatial remodeling of the thymic stroma with age disrupts niches for T cell selection and tolerance https://www.biorxiv.org/content/10.64898/2026.07.29.741472v2?ct= https://www.biorxiv.org/content/10.64898/2026.07.29.741472v2?ct= Andre Rendeiro Thu, 06 Aug 2026 15:28:47 +0200 [bioRxiv] from the abstract it seems they also say something like loss of epithelial cells alone doesn't explain the global architectural changes. Have a close look and see if it makes sense to cite e.g. in the discussion XunZi, an AI biologist, reveals disease-modifying targets https://www.nature.com/articles/s41551-026-01769-6 https://www.nature.com/articles/s41551-026-01769-6 arendeiro Thu, 06 Aug 2026 12:18:44 +0200 [Nature Biomedical Engineering] maybe worth bringing the BioMistral-7B based LLM to life locally and test it out on biology mechanistic reasoning https://github.com/biocuckooHXH/XunZi Multi-scale modeling of human tissues from spatial transcriptomics with TERRA https://www.biorxiv.org/content/10.64898/2026.07.29.741565 https://www.biorxiv.org/content/10.64898/2026.07.29.741565 arendeiro Thu, 06 Aug 2026 10:15:08 +0200 [bioRxiv] Tissue-resident immune cells drive genetic risk in autoimmune and lung diseases https://doi.org/10.1038/s41590-026-02596-2 https://doi.org/10.1038/s41590-026-02596-2 Ariadna Villanueva Marijuan Wed, 05 Aug 2026 09:05:14 +0000 [Nature Immunology] they derive eQTLs from single cell data of immune cells, and then colocalize the signal with GWAS of diseases related to the lung Unified Sample Difficulty Estimation in Pathology Foundation Models https://openreview.net/forum?id=LLlOJs4o2N https://openreview.net/forum?id=LLlOJs4o2N Ernesto Abila Sun, 02 Aug 2026 11:22:18 +0200 [OpenReview] Pubertal maturation and chemotherapy-associated disruption of the pediatric ovary revealed by multimodal single-cell profiling https://www.biorxiv.org/content/10.64898/2026.06.03.729786v1 https://www.biorxiv.org/content/10.64898/2026.06.03.729786v1 Andre Rendeiro Sat, 01 Aug 2026 11:38:03 +0200 [bioRxiv] please have a close look. We should reach out to them and ask whether they would be interested in collaborating Local and global patterns support medical imaging as a biomarker of ageing https://www.nature.com/articles/s43856-026-01722-3 https://www.nature.com/articles/s43856-026-01722-3 arendeiro Wed, 29 Jul 2026 17:58:51 +0200 [Communications Medicine] maybe useful code to look at: https://github.com/tamaramueller/age_biomarkers/blob/main/source/analysis/perform_phewas.py Imaging-based organ-specific aging clock predicts human diseases and mortality https://www.nature.com/articles/s41746-026-02488-7 https://www.nature.com/articles/s41746-026-02488-7 arendeiro Wed, 29 Jul 2026 17:37:39 +0200 [npj Digital Medicine] Is the staggeringly profitable business of scientific publishing bad for science? | The Guardian https://www.theguardian.com/science/2017/jun/27/profitable-business-scientific-publishing-bad-for-science https://www.theguardian.com/science/2017/jun/27/profitable-business-scientific-publishing-bad-for-science Andre Rendeiro Wed, 29 Jul 2026 12:42:42 +0200 an older article but worth as a deep dive into the roots of the current publishing system Pathology-CoT: learning visual chain-of-thought agents from expert whole-slide image diagnosis behaviour https://www.nature.com/articles/s41551-026-01739-y https://www.nature.com/articles/s41551-026-01739-y YZheng Mon, 27 Jul 2026 09:00:00 +0200 [Nature Biomedical Engineering] Encode the pathologists slide viewing behaviors as language tokens and viewing ROI as visual tokens to train a VLM. A spatial multi-omics atlas of immunosenescence reveals germinal-center B cell alteration in human lymph nodes https://www.cell.com/cell-press-blue/fulltext/S3051-3839(26)00051-4 https://www.cell.com/cell-press-blue/fulltext/S3051-3839(26)00051-4 arendeiro Mon, 27 Jul 2026 08:29:29 +0200 [Cell Press] Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data https://www.nature.com/articles/s41592-026-03155-1 https://www.nature.com/articles/s41592-026-03155-1 arendeiro Sun, 26 Jul 2026 09:22:49 +0200 [Nature Methods] Integrating LLM-Assisted Vibe Coding into the Classroom https://jean.fan/2026/03/15/vibe-coding-in-class.html https://jean.fan/2026/03/15/vibe-coding-in-class.html arendeiro Fri, 24 Jul 2026 16:04:42 +0200 interesting attempt and relevant to our bioinfo course Ten simple rules for computational biologists collaborating with wet lab researchers https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012174 https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012174 arendeiro Fri, 24 Jul 2026 14:44:07 +0200 [PLOS Computational Biology] don't think I had shared this one before A multimodal and temporal foundation model for virtual patient representations at healthcare system scale https://arxiv.org/abs/2604.18570 https://arxiv.org/abs/2604.18570 arendeiro Thu, 23 Jul 2026 11:59:54 +0200 [arXiv] Faisal Mahmood lab goes electronic health record (EHR); 7.2M patients, 25B records Tree of Attributes Prompt Learning for Vision-Language Models https://proceedings.iclr.cc/paper_files/paper/2025/hash/7e57131fdeb815764434b65162c88895-Abstract-Conference.html https://proceedings.iclr.cc/paper_files/paper/2025/hash/7e57131fdeb815764434b65162c88895-Abstract-Conference.html arendeiro Thu, 23 Jul 2026 11:53:24 +0200 worth having a look. https://github.com/HHenryD/TAP Genetic trade-offs in fertility and longevity explain the maintenance of disease-associated alleles in humans https://www.nature.com/articles/s41559-026-03140-z https://www.nature.com/articles/s41559-026-03140-z arendeiro Thu, 23 Jul 2026 11:17:58 +0200 [Nature Ecology & Evolution] quite interesting paper, but also potentially useful to use the PGSs it uses Leveraging multiplicity in biologically informed neural networks to uncover disease heterogeneity https://doi.org/10.64898/2026.07.15.738681 https://doi.org/10.64898/2026.07.15.738681 Ariadna Villanueva Marijuan Thu, 23 Jul 2026 08:30:15 +0000 [bioRxiv] graph neural network that predicts polygenic scores and uses integrated gradients to map trait-specific predictive signals to genes, biological processes or cellular components Small-cohort GWAS discovery with AI over massive functional genomics knowledge graph https://www.medrxiv.org/content/10.1101/2024.12.03.24318375v1 https://www.medrxiv.org/content/10.1101/2024.12.03.24318375v1 arendeiro Wed, 22 Jul 2026 16:28:13 +0200 [medRxiv] did you ever have a proper look at this? it seems one can just plug in summary statistics from classical GWAS analysis... may be we are missing a nice opportunity where it may not be as hard to use this GigaPath-Flash and GigaTIME-Flash: Efficient Pathology Foundation Models for Whole-Slide and Tumor Microenvironment Analysis https://arxiv.org/abs/2607.18218 https://arxiv.org/abs/2607.18218 arendeiro Tue, 21 Jul 2026 22:00:20 +0200 [arXiv] Multi-modal atlas of lifestyle interventions reveals malleability of ageing-linked molecular features https://www.biorxiv.org/content/10.1101/2025.08.30.673115v2 https://www.biorxiv.org/content/10.1101/2025.08.30.673115v2 arendeiro Tue, 21 Jul 2026 21:34:24 +0200 [bioRxiv] AI-CURA, an automated LLM workflow for high-accuracy genetic variant classification https://www.science.org/doi/10.1126/scitranslmed.adz4172 https://www.science.org/doi/10.1126/scitranslmed.adz4172 Lisa Kleissl Mon, 20 Jul 2026 08:47:45 +0200 [Science Translational Medicine] ALICE: Learning a General-Purpose Pathology Founda- tion Model from Vision, Vision-Language, and Slide-Level Experts https://arxiv.org/pdf/2607.09526 https://arxiv.org/pdf/2607.09526 SSchindler Sat, 18 Jul 2026 11:09:44 +0200 [arXiv] TLDR Knowledge distillation from all the major foundation models into a single new general purpose model. Seems to be very versatile. Health system learning enables generalist neuroimaging models https://www.nature.com/articles/s41591-026-04497-1 https://www.nature.com/articles/s41591-026-04497-1 arendeiro Fri, 17 Jul 2026 12:56:26 +0200 [Nature Medicine] the latest in models for the radiology field Network-driven discovery of repurposable drugs targeting hallmarks of aging https://doi.org/10.1038/s43587-026-01161-8 https://doi.org/10.1038/s43587-026-01161-8 Ariadna Villanueva Marijuan Fri, 17 Jul 2026 10:59:25 +0200 [Nature Aging] Towards a decentralized future for open-science databases https://www.nature.com/articles/s41588-026-02606-x https://www.nature.com/articles/s41588-026-02606-x arendeiro Tue, 14 Jul 2026 10:15:56 +0200 [Nature Genetics] maybe relevant in light of SlideHub TopoCellGen: Generating Histopathology Cell Topology with a Diffusion Model https://arxiv.org/pdf/2412.06011 https://arxiv.org/pdf/2412.06011 SSchindler Mon, 13 Jul 2026 10:10:44 +0200 [arXiv] TLDR: Very similar to Samirs idea of generating simplified versions (sketches) of a tissue in the first pass. In the case they generated the cell positions in a slide using a diffusion model and regularized the training using a topology derived loss term. Caveat: This will not scale to whole slide images due to computational constraints. Another note: They do not work with point clouds but with pixel grids (images). Staining normalization in histopathology: Method benchmarking using multicenter dataset https://www.nature.com/articles/s41598-026-40943-3 https://www.nature.com/articles/s41598-026-40943-3 Ernesto Abila Fri, 10 Jul 2026 20:32:36 +0200 [Scientific Reports] STAG: Biologically guided spatial transcriptomics prediction via hypergraph learning https://www.sciencedirect.com/science/article/pii/S1361841526002756?via%3Dihub https://www.sciencedirect.com/science/article/pii/S1361841526002756?via%3Dihub Clemens Kohl Fri, 10 Jul 2026 17:21:02 +0200 [Cell Press] hypergraph-based framework for spatial gene expression prediction from histology images. Works for 2D and pseudo-3D histology and incorporates structure/topology as well as long ranging relationships into the model. Multimodal clocks of human aging https://www.cell.com/cell/fulltext/S0092-8674(26)00460-5 https://www.cell.com/cell/fulltext/S0092-8674(26)00460-5 arendeiro Fri, 10 Jul 2026 14:26:11 +0200 [Cell] looks like a great resource: https://cbb.cncb.ac.cn/abb/ Modeling patient tissues at molecular resolution with Eva https://www.biorxiv.org/content/10.64898/2025.12.10.693553 https://www.biorxiv.org/content/10.64898/2025.12.10.693553 arendeiro Wed, 08 Jul 2026 21:52:16 +0200 [bioRxiv] Generalized cell phenotyping for spatial proteomics with language-informed vision models https://www.biorxiv.org/content/10.1101/2024.11.02.621624 https://www.biorxiv.org/content/10.1101/2024.11.02.621624 arendeiro Tue, 07 Jul 2026 15:37:20 +0200 [bioRxiv] An Integrated Skin Cell Atlas Decodes the Pilosebaceous Unit https://www.sciencedirect.com/science/article/pii/S0022202X2602662X?via%3Dihub https://www.sciencedirect.com/science/article/pii/S0022202X2602662X?via%3Dihub Ernesto Abila Mon, 06 Jul 2026 14:36:55 +0200 [Cell Press] Might be useful for the skin projects, ~820,000 cells from 34 public datasets together with visium HD data. A deep learning framework for efficient pathology image analysis https://www.nature.com/articles/s41467-026-74918-9 https://www.nature.com/articles/s41467-026-74918-9 YZheng Mon, 06 Jul 2026 10:49:12 +0200 [Nature Communications] Select only useful patches for the model, significantly reducing computational workload. Organ aging signatures in the plasma proteome track health and disease https://www.nature.com/articles/s41586-023-06802-1 https://www.nature.com/articles/s41586-023-06802-1 arendeiro Thu, 02 Jul 2026 12:42:53 +0200 [Nature] the paper I mentioned. And more recently: https://www.nature.com/articles/s41591-026-04446-y Biological aging and generational shifts in early-onset cancer risk https://www.nature.com/articles/s41591-026-04448-w https://www.nature.com/articles/s41591-026-04448-w arendeiro Wed, 01 Jul 2026 17:28:53 +0200 [Nature Medicine] interesting case of age gaps across populations of different generations/decades TopoMIL: Topology Improves Multiple Instance Learning in Diagnostic Microscopic Images https://www.biorxiv.org/content/10.64898/2026.06.10.731443v1.full.pdf https://www.biorxiv.org/content/10.64898/2026.06.10.731443v1.full.pdf SSchindler Tue, 30 Jun 2026 10:24:49 +0200 [bioRxiv] After embedding tiles into some latent space with a foundation model they not only use the embeddings for downstream classification but also different topological descriptors of the points in the embedding space. Improves downstream performance for every dataset tested. Abstract Microscopic images of cells and tissues are central to disease diagnosis. In computational pathology, multiple instance learning (MIL) has emerged as a key paradigm for analyzing numerous images within a single patient s Perceived age as clinically useful biomarker of ageing: cohort study https://www.bmj.com/content/339/bmj.b5262 https://www.bmj.com/content/339/bmj.b5262 arendeiro Mon, 29 Jun 2026 09:55:51 +0200 an older study but one we should all be aware of Disparate privacy risks from medical AI https://www.nature.com/articles/s41586-026-10688-0 https://www.nature.com/articles/s41586-026-10688-0 arendeiro Mon, 29 Jun 2026 09:41:56 +0200 [Nature] A Single-Cell Bioprinting Method to Reconstruct Native Cellular Microenvironments with Subcellular Resolution https://www.biorxiv.org/content/10.1101/2024.02.01.578499v3 https://www.biorxiv.org/content/10.1101/2024.02.01.578499v3 arendeiro Mon, 29 Jun 2026 09:07:03 +0200 [bioRxiv] looks pretty cool Meta-analysis of DNA methylation aging signatures in 17 human tissues https://www.nature.com/articles/s43587-026-01164-5 https://www.nature.com/articles/s43587-026-01164-5 Lisa Kleissl Mon, 29 Jun 2026 08:39:54 +0200 [Nature Aging] Predicting Immune Biomarkers with MultiModal Mixture-of-Expert Pathology Foundation Models Empowers Precision Oncology https://arxiv.org/abs/2606.18123 https://arxiv.org/abs/2606.18123 Ernesto Abila Thu, 25 Jun 2026 10:01:31 +0200 [arXiv] Aging disrupts spatiotemporal coordination in the cycling murine ovary https://www.nature.com/articles/s43587-026-01140-z https://www.nature.com/articles/s43587-026-01140-z Lisa Kleissl Mon, 22 Jun 2026 16:22:01 +0200 [Nature Aging] maybe helpful for Parijat. They use Slide-seq, a near-cellular spatial transcriptomics method, here we profile 22 mouse ovaries across the reproductive cycle and chronological ages, capturing 610,620 spots across 69 spatial profiles. Single-cell spatial multi-omics molecular pathology enabled by SuperFocus https://www.biorxiv.org/content/10.64898/2025.12.26.696575v2 https://www.biorxiv.org/content/10.64898/2025.12.26.696575v2 arendeiro Fri, 19 Jun 2026 22:12:55 +0200 [bioRxiv] have a look at this paper, in particular on how they train a model across scales/resolutions reusing features An open competition for biomarkers of aging https://www.nature.com/articles/s43587-026-01139-6 https://www.nature.com/articles/s43587-026-01139-6 arendeiro Fri, 19 Jun 2026 22:06:49 +0200 [Nature Aging] Towards autonomous medical artificial intelligence agents https://www.nature.com/articles/s41586-026-10675-5 https://www.nature.com/articles/s41586-026-10675-5 Andre Rendeiro Fri, 19 Jun 2026 18:27:35 +0200 [Nature] Cellular architecture and neighborhood-informed virtual spatial tumor profiling from histopathology https://www.cell.com/cell/fulltext/S0092-8674(26)00590-8 https://www.cell.com/cell/fulltext/S0092-8674(26)00590-8 Ernesto Abila Wed, 17 Jun 2026 12:17:21 +0200 [Cell] qdrant/qdrant at opensourceprojects.dev https://github.com/qdrant/qdrant https://github.com/qdrant/qdrant arendeiro Tue, 16 Jun 2026 15:20:05 +0200 may be worth having a look Cerebellar aging is spatially heterogeneous and supports cognitive resilience in later life https://www.nature.com/articles/s41593-026-02289-x https://www.nature.com/articles/s41593-026-02289-x arendeiro Tue, 16 Jun 2026 08:45:55 +0200 [Nature Neuroscience] very interesting work on brain MRI focused on the cerebelum. Related work: https://www.nature.com/articles/s44220-024-00297-z and https://www.nature.com/articles/s41467-026-72940-5 Plasma proteomic signatures of cellular aging predict human disease https://www.nature.com/articles/s41591-026-04446-y https://www.nature.com/articles/s41591-026-04446-y Lisa Kleissl Mon, 15 Jun 2026 20:32:33 +0200 [Nature Medicine] Last author is the speaker from last years Landsteiner lecture. They developed machine learning models to estimate the biological age of over 40 cell types from plasma proteomics. An integrated multimodal pan-organ atlas of the female reproductive system across the lifespan contextualises gynaecological pathologies https://www.biorxiv.org/content/10.64898/2026.06.10.731198v1 https://www.biorxiv.org/content/10.64898/2026.06.10.731198v1 Ernesto Abila Mon, 15 Jun 2026 19:36:25 +0200 [bioRxiv] Persistent stromal reprogramming defines incomplete mucosal healing and predicts therapeutic response in ulcerative colitis https://www.biorxiv.org/content/10.64898/2026.06.09.730670v1 https://www.biorxiv.org/content/10.64898/2026.06.09.730670v1 Andre Rendeiro Mon, 15 Jun 2026 17:35:54 +0200 [bioRxiv]