Cool Papers
Papers shared by the lab that are relevant to our group and the field.
Spatially resolved contrastive analysis of perturbation-driven microenvironmental heterogeneity across tissues and conditions
2026-10-14 · shared by Andre Rendeiro · bioRxiv
Accurate and well-powered case–control analysis of spatial molecular data
2026-10-14 · shared by Andre Rendeiro · Nature Methods
ResolVI: addressing noise and bias in spatial transcriptomics
2026-10-14 · shared by Andre Rendeiro · Nature Methods
probably a key method/modeling framework for the Xenium data
Written in development and lost in ageing: the grammar of cellular identity
2026-10-14 · shared by Andre Rendeiro · 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
2026-10-14 · shared by Andre Rendeiro · 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
2026-10-14 · shared by Andre Rendeiro · Nature Communications
maybe an interesting technical comparison
GRASS-MIL: graph-based representation and discovery of phenotype-associated spatial structures with multiple instance learning
2026-10-14 · shared by Andre Rendeiro · 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
2026-10-14 · shared by Andre Rendeiro · 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
2026-10-14 · shared by Andre Rendeiro · Nature Medicine
Histology-aware Inference of Cell-cell Communication in Spatial Transcriptomics
2026-10-13 · shared by Andre Rendeiro · bioRxiv
REZCUE: Rescuing 3D spatial omics from archived FFPE tissue
2026-10-13 · shared by Ernesto Abila · bioRxiv
Single-fiber morphometry and spatial transcriptomics reveal selective oxidative muscle fiber atrophy in non-metastatic breast cancer
2026-10-08 · shared by Andre Rendeiro · medRxiv
Deep learning perturbation models can outperform baselines on calibrated metrics
2026-10-07 · shared by Ariadna Villanueva Marijuan · 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
2026-10-06 · shared by Andre Rendeiro · Nature Medicine
Inferring organ aging, hallmark of aging and senescence scores from blood and facial photographs
2026-10-02 · shared by Andre Rendeiro · bioRxiv
mc-ASTRA maps population-level variation to interpretable multicellular tissue organization processes
2026-09-28 · shared by Andre Rendeiro · bioRxiv
SpaCEy links spatial tissue patterns to clinical outcomes using explainable graph neural networks
2026-09-28 · shared by Andre Rendeiro · 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
2026-09-27 · shared by Andre Rendeiro · Nature Genetics
Clinical Uses of Common Genetic Variants Associated with Common Diseases
2026-09-25 · shared by Andre Rendeiro
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
2026-09-24 · shared by Andre Rendeiro · arXiv
https://lnkd.in/p/dRTF4Eb9
Blood proteomics of menopause map to brain aging and dementia risk
2026-09-22 · shared by Ernesto Abila · Nature Medicine
Pretrained gene representations transfer mean expression more broadly than spatial patterns in virtual spatial transcriptomics
2026-09-22 · shared by Andre Rendeiro · 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
2026-09-22 · shared by Andre Rendeiro · 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
2026-09-22 · shared by Andre Rendeiro · 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
2026-09-22 · shared by Andre Rendeiro · npj Aging
cool paper, unfortunately no data
WHO working definition of vitality capacity for healthy longevity monitoring
2026-09-17 · shared by Andre Rendeiro · 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
2026-09-08 · shared by Andre Rendeiro · bioRxiv
Integration of proteomic aging clocks in a phase 2a clinical trial supports simultaneous geroprotective assessment
2026-09-08 · shared by arendeiro · 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…
Declines in mRNA synthesis set the rate of organismal aging
2026-09-06 · shared by arendeiro · 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
2026-09-04 · shared by arendeiro · 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
2026-09-03 · shared by YZheng · 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
2026-09-03 · shared by Ernesto Abila · arXiv
MechanoMaST – a multimodal pipeline for spatially registering mechanical and transcriptomic tissue data
2026-09-03 · shared by arendeiro · bioRxiv
maybe interesting
JCI - Markers of compromised gut epithelial barrier integrity increase during the menopause transition
2026-09-02 · shared by arendeiro
see also https://jci.org/articles/view/209807 and https://lnkd.in/p/eUX9AMMP
Virtual Aging Cell — Insilico Medicine
2026-09-01 · shared by arendeiro
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
2026-09-01 · shared by arendeiro · 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
2026-08-19 · shared by arendeiro · medRxiv
maybe useful resource
P3CA: Encoder-Agnostic Interpretation of Vision Foundation Model Embeddings via Spatial Probing
2026-08-19 · shared by arendeiro · arXiv
interesting, perhaps worth a read
Three-dimensional mapping of intact ovaries reveals the aging dynamics of the ovarian reserve
2026-08-13 · shared by arendeiro · 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
2026-08-12 · shared by arendeiro · Nature Biomedical Engineering
a dataset to check out: https://zenodo.org/records/20052262
A Bayesian framework for longitudinal EHR and genetic discovery
2026-08-11 · shared by Ariadna Villanueva Marijuan · Nature
Genetic decoding reveals druggable biology implicitly learned by a medical-history foundation model
2026-08-11 · shared by Ariadna Villanueva Marijuan · medRxiv
The Virtual Tissues foundation model resolves spatial proteomics across scales
2026-08-11 · shared by Andre Rendeiro · Nature
Why studying females reveals more about aging: The reproductive resilience hypothesis for the evolution of sex-specific aging
2026-08-10 · shared by Ernesto Abila · Cell
An interesting perspective, highlighting that females should be prioritized in studies of aging.
On Fermi Problems in Human Genetics
2026-08-10 · shared by arendeiro · 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
2026-08-10 · shared by arendeiro · bioRxiv
Topology Inference for Immune System Networks by Using Cell Amount Data
2026-08-10 · shared by arendeiro · arXiv
quite far from our ideas, but maybe useful
A compendium of next-generation patient-derived models for diverse cancers
2026-08-06 · shared by Ernesto Abila · 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
2026-08-06 · shared by Andre Rendeiro · 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
2026-08-06 · shared by arendeiro · 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
2026-08-06 · shared by arendeiro · bioRxiv
Tissue-resident immune cells drive genetic risk in autoimmune and lung diseases
2026-08-05 · shared by Ariadna Villanueva Marijuan · 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
2026-08-02 · shared by Ernesto Abila · OpenReview
Pubertal maturation and chemotherapy-associated disruption of the pediatric ovary revealed by multimodal single-cell profiling
2026-08-01 · shared by Andre Rendeiro · 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
2026-07-29 · shared by arendeiro · 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
2026-07-29 · shared by arendeiro · npj Digital Medicine
Is the staggeringly profitable business of scientific publishing bad for science? | The Guardian
2026-07-29 · shared by Andre Rendeiro
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
2026-07-27 · shared by YZheng · 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
2026-07-27 · shared by arendeiro · Cell Press
Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data
2026-07-26 · shared by arendeiro · Nature Methods
Integrating LLM-Assisted Vibe Coding into the Classroom
2026-07-24 · shared by arendeiro
interesting attempt and relevant to our bioinfo course
Ten simple rules for computational biologists collaborating with wet lab researchers
2026-07-24 · shared by arendeiro · 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
2026-07-23 · shared by arendeiro · arXiv
Faisal Mahmood lab goes electronic health record (EHR); 7.2M patients, 25B records
Tree of Attributes Prompt Learning for Vision-Language Models
2026-07-23 · shared by arendeiro
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
2026-07-23 · shared by arendeiro · 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
2026-07-23 · shared by Ariadna Villanueva Marijuan · 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
2026-07-22 · shared by arendeiro · 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
2026-07-21 · shared by arendeiro · arXiv
Multi-modal atlas of lifestyle interventions reveals malleability of ageing-linked molecular features
2026-07-21 · shared by arendeiro · bioRxiv
AI-CURA, an automated LLM workflow for high-accuracy genetic variant classification
2026-07-20 · shared by Lisa Kleissl · Science Translational Medicine
ALICE: Learning a General-Purpose Pathology Founda- tion Model from Vision, Vision-Language, and Slide-Level Experts
2026-07-18 · shared by SSchindler · 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
2026-07-17 · shared by arendeiro · Nature Medicine
the latest in models for the radiology field
Network-driven discovery of repurposable drugs targeting hallmarks of aging
2026-07-17 · shared by Ariadna Villanueva Marijuan · Nature Aging
Towards a decentralized future for open-science databases
2026-07-14 · shared by arendeiro · Nature Genetics
maybe relevant in light of SlideHub
TopoCellGen: Generating Histopathology Cell Topology with a Diffusion Model
2026-07-13 · shared by SSchindler · 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 i…
Staining normalization in histopathology: Method benchmarking using multicenter dataset
2026-07-10 · shared by Ernesto Abila · Scientific Reports
STAG: Biologically guided spatial transcriptomics prediction via hypergraph learning
2026-07-10 · shared by Clemens Kohl · 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
2026-07-10 · shared by arendeiro · Cell
looks like a great resource: https://cbb.cncb.ac.cn/abb/
Modeling patient tissues at molecular resolution with Eva
2026-07-08 · shared by arendeiro · bioRxiv
Generalized cell phenotyping for spatial proteomics with language-informed vision models
2026-07-07 · shared by arendeiro · bioRxiv
An Integrated Skin Cell Atlas Decodes the Pilosebaceous Unit
2026-07-06 · shared by Ernesto Abila · 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
2026-07-06 · shared by YZheng · Nature Communications
Select only useful patches for the model, significantly reducing computational workload.
Organ aging signatures in the plasma proteome track health and disease
2026-07-02 · shared by arendeiro · 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
2026-07-01 · shared by arendeiro · Nature Medicine
interesting case of age gaps across populations of different generations/decades
TopoMIL: Topology Improves Multiple Instance Learning in Diagnostic Microscopic Images
2026-06-30 · shared by SSchindler · 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 o…
Perceived age as clinically useful biomarker of ageing: cohort study
2026-06-29 · shared by arendeiro
an older study but one we should all be aware of
Disparate privacy risks from medical AI
2026-06-29 · shared by arendeiro · Nature
A Single-Cell Bioprinting Method to Reconstruct Native Cellular Microenvironments with Subcellular Resolution
2026-06-29 · shared by arendeiro · bioRxiv
looks pretty cool
Meta-analysis of DNA methylation aging signatures in 17 human tissues
2026-06-29 · shared by Lisa Kleissl · Nature Aging
Predicting Immune Biomarkers with MultiModal Mixture-of-Expert Pathology Foundation Models Empowers Precision Oncology
2026-06-25 · shared by Ernesto Abila · arXiv
Aging disrupts spatiotemporal coordination in the cycling murine ovary
2026-06-22 · shared by Lisa Kleissl · 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
2026-06-19 · shared by arendeiro · 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
2026-06-19 · shared by arendeiro · Nature Aging
Towards autonomous medical artificial intelligence agents
2026-06-19 · shared by Andre Rendeiro · Nature
Cellular architecture and neighborhood-informed virtual spatial tumor profiling from histopathology
2026-06-17 · shared by Ernesto Abila · Cell
Cerebellar aging is spatially heterogeneous and supports cognitive resilience in later life
2026-06-16 · shared by arendeiro · 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
2026-06-15 · shared by Lisa Kleissl · 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
2026-06-15 · shared by Ernesto Abila · bioRxiv
Persistent stromal reprogramming defines incomplete mucosal healing and predicts therapeutic response in ulcerative colitis
2026-06-15 · shared by Andre Rendeiro · bioRxiv
Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis
2026-06-15 · shared by Andre Rendeiro · bioRxiv
Querying Counterfactuals on Tissue Graphs with Supervised Disentanglement
2026-06-15 · shared by Andre Rendeiro · arXiv
maybe worth having a closer look
The Challenge of Cell Segmentation in Spatially Resolved Transcriptomics
2026-06-15 · shared by Andre Rendeiro · arXiv
The molecular asynchrony of single cells
2026-06-15 · shared by Lisa Kleissl · bioRxiv
SeqTag, a single-cell multiomics sequencing method that simultaneously profiles the transcriptome, chromatin accessibility, and histone modifications, supported by an analytical framework to identify asynchronous states across regulatory layers for characterization of single-cell kinetics.
Towards robust foundation models for digital pathology
2026-06-15 · shared by arendeiro · arXiv
nice comparative analysis of models (tl;dr Virchow2 and CONCHv1.5 best), and new strategies for their robustification (Fig.7) with implications for StainX and SlideHub
General-purpose large language models outperform specialized clinical AI tools on medical benchmarks
2026-06-15 · shared by arendeiro · Nature Medicine
Back to basics: Observed statistics are sufficient to predict drug responses
2026-06-15 · shared by arendeiro · bioRxiv
worth looking into this very short paper. Understanding the data is so so more worth than brute force modeling. Also, if you don't know him yet, check out the first author's blog: https://www.nxn.se/
Spatial biomarker discovery via interpretable semantic learning in histopathology
2026-06-12 · shared by Ernesto Abila · Cancer Cell
Plasma signals of lung tumor promotion for molecular cancer prevention
2026-06-09 · shared by arendeiro · Cell
they identified a 14-protein plasma signature predicting lung cancer more than 5 years before diagnosis!
DaX: Learning General Pathology Representations Across Scales
2026-06-08 · shared by Ernesto Abila · arXiv
Alibaba joins the histopathology game with a multi scale DINOv3 framework with cross-scale self-supervision, trained on GTEx, TCGA and HistAi. Apparently, they outperform all the other current models.
A multimodal perturbation atlas defines the phenotypic resolution of cellular morphology
2026-06-05 · shared by Andre Rendeiro · bioRxiv
The Human Pleiotropic Map of GWAS Associations and Therapeutic Implications
2026-06-03 · shared by Ariadna Villanueva Marijuan · bioRxiv
genome-wide target prioritization
Cracks in the Foundation: How Data-Hungry and Sensitive to Domain Shift are Vision Foundation Models for Computational Pathology?
2026-06-02 · shared by Andre Rendeiro · medRxiv
maybe relevant in the context of StainX. Unfortunately I didn't see any statement on data sharing, but maybe I missed it
Thousandfold Expansion Microscopy
2026-06-02 · shared by Ernesto Abila · bioRxiv
Slightly off topic, but maybe we can soon study sub cellular structures by eye or cheap microscopes?
Prioritizing perturbation-responsive gene patterns using interpretable deep learning
2026-06-02 · shared by Andre Rendeiro · Nature Communications
we should cite papers like this, maybe in light of spatial transcriptomics lacking scale
Machine-learning models based on histological images from healthy donors identify imageQTLs and predict chronological age
2026-06-02 · shared by Andre Rendeiro · Proceedings of the National Academy of Sciences
just re-sending as another example, also combining modalities - hits still not particularly striking I'd say
Cophenetic Spatial Topology Embedding reveals multiscale tissue architecture in spatial omics
2026-06-01 · shared by Andre Rendeiro · bioRxiv
Pan-cancer spatial atlas of tertiary lymphoid structures
2026-05-29 · shared by Andre Rendeiro · Science
MORPHE: Bridging Image Generation and Spatial Omics for Tissue Synthesis
2026-05-28 · shared by Andre Rendeiro · bioRxiv
Universal transcriptomic hallmarks of mammalian ageing and mortality
2026-05-28 · shared by Ernesto Abila · Nature
Spatiotemporal transcriptome atlas of human embryos after gastrulation
2026-05-28 · shared by YZheng · Nature
Typically BGI work
TopoSlide: Topologically-Informed Histopathology Whole Slide Image Representation Learning
2026-05-27 · shared by Ernesto Abila · CVF Open Access
Might be useful for Simon & Shrestha
A deep-learning framework reveals whole-body perturbations at cell level
2026-05-20 · shared by Ernesto Abila · Nature
Systematic common and rare variant association testing in 392,030 whole genomes in All of Us
2026-05-19 · shared by Andre Rendeiro · medRxiv
potentially useful to cross-check on age/age-gap variants
Multiplexed magnetic resonance imaging
2026-05-19 · shared by Andre Rendeiro · Nature
the latest in cutting-edge MRI
Differential Analysis of Gene Spatial Organisation with Minkowski Functionals and Tensors
2026-05-19 · shared by Andre Rendeiro · bioRxiv
please have a close look
Integrated multi-omics identifies distinct macrophage alterations during progression of metabolic dysfunction-associated steatohepatitis
2026-05-19 · shared by Andre Rendeiro · Nature Genetics
seems like a cool and potentially useful dataset
A Perturb-seq screen guided by species divergence uncovers pathways for collateral artery formation
2026-05-19 · shared by Andre Rendeiro · bioRxiv
seems like a super cool approach, would love to hear your thoughts
Sleep chart of biological ageing clocks in middle and late life
2026-05-19 · shared by Andre Rendeiro · Nature
sleep clocks! Strange paper but interesting phenotypes and genetics @Ariadna Villanueva Marijuan
HESpotEx: a dual-stream deep learning framework for spot-level gene expression prediction from histological images
2026-05-19 · shared by Andre Rendeiro · Nature Computational Science
one more for the collection
A Spatial Proteomic Atlas of Tertiary Lymphoid Structures in Non-Small Cell Lung Cancer Identifies a Novel Predictive Class of Lymphoid Aggregates
2026-05-19 · shared by Ernesto Abila · bioRxiv
Although from cancer patients (NSCLC and tonsil samples) it could be interesting to understand TLAs better, especially for @Clemens Kohl. Apparently, they also developed digital pathology classifier to identify mature LAs. Code, image data, segmentation data, region masks, single cell feature data, …
Plasma proteomic signature of frailty in 50,506 adults
2026-05-18 · shared by Andre Rendeiro · Cell Press
Hidden immune memory niches in inflammatory skin diseases
2026-05-13 · shared by Lisa Kleissl · bioRxiv
The study links histopathology and atlas-scale genomics to reveal novel insights into inflammatory disease pathogenesis, chronicity, and potentially curative therapeutic avenues, using skin as an exemplar tissue for this approach
sc-ChromAging: A Single-Cell Chromatin Accessibility-based Clock Decodes Cell-Type-Specific Epigenetic Aging Trajectories
2026-05-13 · shared by Lisa Kleissl · npj Aging
sc-ChromAging, a chromatin accessibility-based aging clock, was developed using single-cell ATACseq from 401 Chinese individuals.
Non-invasive profiling of the tumour microenvironment with spatial ecotypes
2026-05-13 · shared by Ernesto Abila · Nature
Quite interesting study where they find conserved spatial ecotypes (spatially dependent cell states and multicellular ecosystems) in spatial transcriptomics data, which are linked to immune therapy response. They can even recover the spatial ecotypes' methylation profiles from plasma cDNA.
SPARC: A mechanism-aware spatial representation from routine histology predicts cancer survival and therapy response
2026-05-13 · shared by Ernesto Abila · medRxiv
IBDome: An integrated molecular, histopathological, and clinical atlas of inflammatory bowel diseases
2026-05-11 · shared by Andre Rendeiro · bioRxiv
in case we didn't talk about it before - this is a great resource that may be of use to you. I know the last author so we could ask for data before it's accepted.
How to design effective scientific figures
2026-05-08 · shared by YZheng · Nature Human Behaviour
A nice little article on Nature human behavior discussing general ideas on how to design scientific figures.
OptimusKG: Unifying biomedical knowledge in a modern multimodal graph
2026-05-06 · shared by Andre Rendeiro · arXiv
finally an easy way to load the Zitnik lab Knowledge-graph! https://github.com/mims-harvard/OptimusKG import optimuskg nodes, edges = optimuskg.load_graph(lcc=True)
Pleiotropy and disease interactors: the dual nature of genes linking ageing and ageing-related diseases
2026-05-06 · shared by Andre Rendeiro · Biogerontology
probably worth a look e.g. https://link.springer.com/article/10.1007/s10522-026-10429-w/figures/4
Linking spatial biology and clinical histology via Haiku
2026-05-05 · shared by Ernesto Abila · arXiv
“A tri-modal contrastive learning model trained on multiplexed immunofluorescence (mIF), H&E and clinical metadata from 11 organs of 1,606 patients. Both code and model weights are available: Github: https://github.com/zhihuanglab/Haiku Model weights: https://huggingface.co/zhihuanglab/Haiku
Pan-cancer virtual spatial transcriptomics from routine histology with Phoenix
2026-05-04 · shared by Andre Rendeiro · bioRxiv
spatial gene expression prediction from H&E via flow matching. Code available now: https://github.com/peng-lab/phoenix Weights not available yet. Full TCGA dataset with inference will be available.
AI framework for multidisease detection via retinal imaging
2026-05-04 · shared by Andre Rendeiro · Nature Medicine
the latest in ocular AI with implications for multi-organ health prediction - note this not OCT but color fundus photography - a much simpler, faster (30sec) and cheaper imaging method
Multimodal data analysis reveals asynchronous aging dynamics across female reproductive organs
2026-04-30 · shared by Andre Rendeiro · Nature Aging
the published version of https://www.biorxiv.org/content/10.1101/2025.05.16.654406 - would be good to have a close look and see what resources we can use
An agentic framework for autonomous scientific discovery in cancer pathology
2026-04-30 · shared by YZheng · Nature Medicine
Discovery of candidate therapeutic targets with Geneformer
2026-04-28 · shared by Andre Rendeiro · Nature Protocols
when you have some time, could you have a look at this an understand the intuition for how do they discover targets? It might be something we want to benchmark against down the line.
VitaminP: cross-modal learning enables whole-cell segmentation from routine histology
2026-04-28 · shared by Ernesto Abila · arXiv
Nuclear and cell segmentation by using a cross-modal framework and transferring molecular boundary information from mIF and detect cytoplasmic contrast in H&E images. They also provide their models, the models seem to be straight forward to use: https://github.com/idso-fa1-pathology/VitaminP
A 3D morphogenetic blueprint for metastatic outgrowth in breast cancer
2026-04-27 · shared by YZheng · Cell
Basically, they found that the metastatic potential of breast cancer is highly correlated with the 3D architecture
Dynamics of genetic and somatic trade-offs in ageing and mortality
2026-04-24 · shared by Andre Rendeiro · Nature
Weighted Genetic Risk Scores and Prediction of Weight Gain in Solid Organ Transplant Populations
2026-04-22 · shared by Ariadna Villanueva Marijuan · PLOS ONE
Here they describe a more or less similar approach to what I proposed when creating a PGS with a very small population. Three GRS were built following a weighted GRS (w-GRS) method as previously described [28] with 32 SNPs (SNP group#1) and 97 SNPs (SNP group#2) both from GWAS, and 19 SNPs (SNP grou…
A spatial atlas of the healthy human liver from live donors
2026-04-17 · shared by Andre Rendeiro · Nature
95% of Experimental Life-Science Papers in Three Months of Nature Used Hypothesis Testing Without Justifying Sample Sizes
2026-04-17 · shared by Andre Rendeiro
a so(m)ber assessment of statistical testing use in life sciences. To me the idea that life science research is largely designed to discover the hypothesis, not test pre-specified ones and its implications is the take-home message here.
Tissue morphology predicts telomere shortening in human tissues
2026-04-16 · shared by YZheng · Cell Reports Methods
Instead of predicting chronological age, they just predict telomere length, an interesting study.
Whole organism 3D mapping reveals universal branching topology and biophysical optimization governs vascular and nervous system development
2026-04-15 · shared by Ernesto Abila · bioRxiv
A new paper from the Wirtz lab where they developed a computational pipeline for whole-organism 3D imaging (z stacked H&E) to reconstruct the complete vascular and nervous systems of rhesus macaque, mouse, and turtle embryos. Data is apparently available upon request.
Perturbational phenotyping of human blood cells reveals genetically determined latent traits associated with subsets of common diseases
2026-04-15 · shared by Andre Rendeiro · Nature Genetics
not directly relevant, but just sharing this super impressive work using flow cytometry without any staining on perturbed PBMCs of 2600 donors
Understanding multicellular function and disease with human tissue-specific networks
2026-04-14 · shared by Andre Rendeiro · Nature Genetics
an older method which was added to HumanBase which has something that could be of interest to us, in particular Tamas and Ariadna: NetWAS - Network-wide Association Study — HumanBase 1.0 documentation https://humanbase.readthedocs.io/en/latest/netwas.html "NetWAS trains a support vector machine clas…
annbatch unlocks terabyte-scale training of biological data in anndata
2026-04-13 · shared by Ernesto Abila · arXiv
A new toolbox for model training that provides AnnData native mini batching with a Rust-based I/O.
PRET is a few-shot system for pan-cancer recognition without example training
2026-04-10 · shared by YZheng · Nature Cancer
A way to build clinical AI without training.
scAgeClock: a single-cell transcriptome-based human aging clock model using gated multi-head attention neural networks
2026-04-08 · shared by Lisa Kleissl · npj Aging
Not really a paper rather a publicly available model for network-based single-cell aging clock model. Maybe interesting for someone.
Generative machine learning unlocks the first proteome-wide image of human cells
2026-04-07 · shared by Andre Rendeiro · bioRxiv
Odon: An ultra-fast viewer for spatial proteomics
2026-04-03 · shared by Andre Rendeiro · bioRxiv
https://github.com/alexcoulton/odon https://alexcoulton.github.io/odon/ https://www.linkedin.com/posts/alexander-coulton_spatial-proteomics-has-a-data-problem-around-share-7445410643526045696-rsS6
rewrites.bio - A manifesto for bioinformatics
2026-04-03 · shared by Andre Rendeiro
https://www.linkedin.com/posts/introducing-rustqc-60x-faster-rna-seq-quality-ugcPost-7445494545481437186-affE
Scaling and quantization of large-scale foundation model enables resource-efficient predictions in network biology
2026-04-03 · shared by Andre Rendeiro · Nature Computational Science
maybe you'll find this paper interesting
tracel-ai/burn: a next generation tensor library and Deep Learning Framework
2026-04-02 · shared by Andre Rendeiro
the next big thing on model training and inference? for those interested in rust, there's also a nice image algorithm library: https://github.com/imgal-sc/imgal/ see a full discussion on adopting these technologies for biological imaging here: https://forum.image.sc/t/pytorch-vs-burn-rust/119776
p16High-expressing immune cells control disease tolerance as a defense and health span-extending strategy
2026-04-02 · shared by Lisa Kleissl · Immunity
MIPHEI-ViT: Multiplex Immunofluorescence Prediction from H&E Images using ViT Foundation Models
2026-04-01 · shared by Andre Rendeiro · arXiv
a multiplex imaging prediction model from Sanofi
Functional hierarchy of the human neocortex across the lifespan
2026-04-01 · shared by Andre Rendeiro · Nature
relevant for the VITA dataset
CytoSyn: a Foundation Diffusion Model for Histopathology -- Tech Report
2026-04-01 · shared by Andre Rendeiro · arXiv
the write-up of Owkin's generative model
MOOZY: A Patient-First Foundation Model for Computational Pathology
2026-04-01 · shared by Andre Rendeiro · arXiv
https://atlasanalyticslab.github.io/MOOZY/ https://github.com/AtlasAnalyticsLab/MOOZY
Toward Computationally Complete Spatial Omics
2026-03-29 · shared by Ernesto Abila · bioRxiv
A new framework to integrate histology, epigenome, transcriptome, proteome, and metabolome into a unified representation.
Mixture of Mini Experts: Overcoming the Linear Layer Bottleneck in Multiple Instance Learning
2026-03-27 · shared by Andre Rendeiro · OpenReview
latest from the Mahmood lab
Reimagining systematic anatomy: The conclusion of the quartet
2026-03-27 · shared by Andre Rendeiro · Clinical Anatomy
a nice theory article on systematic anatomy which we should cite and learn from (i.e. a less cell-centric view of anatomy) Gist: - before: - proposed:
Single-cell atlas of human lung aging identifies cell type dyssynchrony and increased transcriptional entropy
2026-03-27 · shared by Andre Rendeiro · Nature Communications
potentially useful dataset to validate insights from lung tissue aging
Single-cell spatial transcriptomic analysis of human skin anatomy
2026-03-26 · shared by Ernesto Abila · Nature Genetics
Potentially a nice dataset, where they also study tissue units/ neighborhoods in the skin in healthy, pathology, but also age. They find e.g., a stromal unit decreasing with age and an immune-poor perivascular niche increasing with age. They also use GTEx bulk RNA-seq, but so far not the images. MER…
Adapting a Pre-trained Single-Cell Foundation Model to Spatial Gene Expression Generation from Histology Images
2026-03-26 · shared by Clemens Kohl · arXiv
Interesting method that allows for retrofitting of foundation models to another modality.
Genetic architectures of brain-related traits are shaped by strong selective constraints
2026-03-25 · shared by Andre Rendeiro · bioRxiv
Reprogramming of stroma-derived chemokine networks drives the loss of tissue organization in nodal B cell lymphoma
2026-03-25 · shared by Andre Rendeiro · Nature Cancer
sounds interesting
Trajectory-based differential expression analysis for single-cell sequencing data
2026-03-23 · shared by Andre Rendeiro · Nature Communications
an interesting paper which I think you'll find relevant
Thymic health consequences in adults
2026-03-23 · shared by Lisa Kleissl · Nature
"We developed a deep learning framework to quantify thymic health from routine radiographic images and evaluated its association with longevity and risk of major age-associated diseases in two large prospective cohorts of asymptomatic adults: the National Lung Screening Trial (n = 25,031) and the Fr…
Whole-organ and whole-body 3D atlases enable cellome-wide profiling
2026-03-23 · shared by YZheng · Cell
HistoAtlas: A Pan-Cancer Morphology Atlas Linking Histomics to Molecular Programs and Clinical Outcomes
2026-03-18 · shared by Ernesto Abila · arXiv
A solo paper by one of the software developers of HistoPlus (Pierre, who we also met with for HistoPlus).
Fractal: Towards FAIR bioimage analysis at scale with OME-Zarr-native workflows
2026-03-16 · shared by Andre Rendeiro · bioRxiv
HistoGWAS: An AI Framework for Automated and Interpretable Genetic Analysis of Tissue Phenotypes
2026-03-16 · shared by Andre Rendeiro · bioRxiv
Intestinal interoceptive dysfunction drives age-associated cognitive decline
2026-03-12 · shared by Andre Rendeiro · Nature
particularly relevant in the context of the CeMM 'flagship' project - let's have a look so we are familiar with the scientific language, methods, ideas
The DNA virome varies with human genes and environments
2026-03-12 · shared by Andre Rendeiro · bioRxiv
super cool work - had a similar idea for GTEx and then trying to anatomically localize the impact of viral infection/load in the body
Ageing promotes metastasis via activation of the integrated stress response
2026-03-12 · shared by Andre Rendeiro · Nature
Simultaneous spatial transcriptomics and morphology profiling as tools to explore how microglia change with age
2026-03-11 · shared by Lisa Kleissl · Nature Aging
imAgeScore, a Cell Painting-Based Predictor of Cellular Age for High-throughput Drug Screening Applications
2026-03-11 · shared by Ernesto Abila · bioRxiv
Scoring of primary human dermal fibroblasts with Cell Painting. "imAgeScore correlates with chronological and DNA methylation-based age estimates and captures coordinated morphological changes across nuclear and cytoplasmic compartments."
RNA-seq analysis in seconds using GPUs
2026-03-11 · shared by Andre Rendeiro · bioRxiv
a bit of a curiosity/niche but pretty interesting to see how people are GPU-accelerating very standard areas of biology which are no longer a bottleneck for routine tasks but can then enable very large scale analysis
Estropausal gut microbiota transplant improves measures of ovarian function in adult mice
2026-03-11 · shared by Andre Rendeiro · Nature Aging
interesting study with lots of valuable resources for ovarian aging and histology - particularly relevant to Parijat
TransBrain: a computational framework for translating brain-wide phenotypes between humans and mice
2026-03-11 · shared by Andre Rendeiro · Nature Methods
sounds cool and probably a lot to learn here
Ten mouse organs proteome and metabolome atlas from adult to aging
2026-03-09 · shared by Andre Rendeiro · Genome Medicine
if we ever want a dataset of mouse proteomics during aging
MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy
2026-03-05 · shared by Andre Rendeiro · arXiv
model for microscopy data where some ideas may be useful to us
Tissue-specific impacts of aging and genetics on gene expression patterns in humans
2026-03-04 · shared by Andre Rendeiro · Nature Communications
I believe I had already shared this one, but just in case
Confounding factors and biases abound when predicting molecular biomarkers from histological images
2026-03-04 · shared by Andre Rendeiro · Nature Biomedical Engineering
Foundation model for cancer imaging biomarkers
2026-03-04 · shared by Andre Rendeiro · Nature Machine Intelligence
good to keep an eye on the radiology side of things
GrapHist: Graph Self-Supervised Learning for Histopathology
2026-03-04 · shared by Andre Rendeiro · arXiv
cool work on graph-based learning - we could try it out already in basically every project in which we learn slide labels; especially relevant for Shrestha, Simon
3D-Guided Scalable Flow Matching for Generating Volumetric Tissue Spatial Transcriptomics from Serial Histology
2026-02-27 · shared by Ernesto Abila · arXiv
Revisiting the blueprint for an interpretable virtual cell
2026-02-27 · shared by Andre Rendeiro · Nature Reviews Genetics
important historical insights, and a provoking thought we should all be having
Cellular Aging Signatures in the Plasma Proteome 2 Record Human Health and Disease
2026-02-25 · shared by Ernesto Abila · bioRxiv
New paper from the Wyss-Coray lab.
Combining xenium in situ spatial transcriptomics and imaging mass cytometry on a single tissue section
2026-02-23 · shared by Andre Rendeiro · bioRxiv
Towards Spatial Transcriptomics-driven Pathology Foundation Models
2026-02-23 · shared by Andre Rendeiro · arXiv
latest from Mahmood lab - would be good to run inference for a small set of GTEx slides and benchmark how aggregation recovers the bulk RNA-seq profiles
Deep Label Distribution Learning for Leveraging Image Ambiguity
2026-02-17 · shared by SSrivastava
"https://www.semanticscholar.org/paper/Deep-Label-Distribution-Learning-With-Label-Gao-Xing/02567fd428a675ca91a0c6786f47f3e35881bcbd" Converts the hard labels into a distribution and then calculates loss between prediction probability and ground truth probabilities, maybe we can use this to solve th…
immgenT: A Comprehensive Reference of Convergent T-cell States in the Mouse
2026-02-11 · shared by Andre Rendeiro · bioRxiv
seems like a good reference for all sorts of T cell states which includes lymph nodes also in some cancer models. There are also some other companion papers
Circulating Cell Type Senescence Signatures Reveal High-Resolution Health Status and 2 Trajectories in Human Longitudinal Studies
2026-02-10 · shared by Ernesto Abila · medRxiv
A lightweight, ultrafast and general embedding framework for large-scale spatial omics data
2026-02-09 · shared by Andre Rendeiro · bioRxiv
very impressive work, we should study it (method and paper); maybe particularly relevant for Simon regarding previous foundation model ideas
Trans-eQTLs reveal the architecture of human gene regulatory networks
2026-02-09 · shared by Andre Rendeiro · medRxiv
the latest in QTL land
AtlasPatch: An Efficient and Scalable Tool for Whole Slide Image Preprocessing in Computational Pathology
2026-02-05 · shared by Ernesto Abila · arXiv
maybe another Grandqc competitor. They also have or plan a patch writing database functionality: https://github.com/AtlasAnalyticsLab/AtlasPatch
Unifying the genetic landscape of common and rare diseases via latent neighborhoods
2026-02-04 · shared by Andre Rendeiro · bioRxiv
Revealing the genetic architectures underlying organ-specific aging based on proteomic data
2026-02-04 · shared by Andre Rendeiro · Nature Communications
not sure I sent this one around - look at the bell curve in figure 1... that's what I'm thinking
HistoSweep enables cellular-resolution tissue quality control for gigapixel images in digital pathology and spatial omics
2026-02-04 · shared by Andre Rendeiro · bioRxiv
looks like there is a competitor to GrandQC
PaperBanana: Automating Academic Illustration for AI Scientists
2026-02-04 · shared by Ernesto Abila · arXiv
https://dwzhu-pku.github.io/PaperBanana/
A cross-population compendium of gene–environment interactions
2026-02-04 · shared by Andre Rendeiro · Nature
Aging reshapes the adaptive immune system from healer to saboteur
2026-02-03 · shared by Andre Rendeiro · Nature Aging
https://www-nature-com.ez.srv.meduniwien.ac.at/articles/s43587-025-00906-1
Skin health and biological aging
2026-02-03 · shared by Andre Rendeiro · Nature Aging
https://www-nature-com.ez.srv.meduniwien.ac.at/articles/s43587-025-00901-6
An atlas of human histological diversity
2026-02-03 · shared by Ernesto Abila · bioRxiv
A new very relevant study on the GTEx dataset, associating "morphemes" (histology signatures) with the patho-clinical and multi-omics data, to reveal influences of age, sex, genetics, and pathologies. Furthermore, they provide a web Version of the atlas (https://histologyatlas.ulb.be/), where among …
Heritability of intrinsic human life span is about 50% when confounding factors are addressed
2026-01-29 · shared by Andre Rendeiro · Science
commentary also here: https://www.science.org/doi/10.1126/science.aee3844
Targeting modulated vascular smooth muscle cells in atherosclerosis via FAP-directed immunotherapy
2026-01-29 · shared by Andre Rendeiro · Science
VISTA-PATH: An interactive foundation model for pathology image segmentation and quantitative analysis in computational pathology
2026-01-27 · shared by Samir Moustafa · arXiv
interactive pathology segmentation foundation model combining vision, language, and expert prompts, strong gains on complex tissue segmentation and useful for clinically grounded benchmarks
STPath: a generative foundation model for integrating spatial transcriptomics and whole-slide images
2026-01-22 · shared by Andre Rendeiro · npj Digital Medicine
another ST-generating models from H&E; would be good to add to LazySlide
CELLama: Foundation Model for Single Cell and Spatial Transcriptomics by Cell Embedding Leveraging Language Model Abilities
2026-01-22 · shared by Andre Rendeiro · Advanced Science
interesting model combining ST and language; would be good to add to LazySlide
A Foundational Generative Model for Cross-platform Unified Enhancement of Spatial Transcriptomics
2026-01-22 · shared by Andre Rendeiro · bioRxiv
a model for ST prediction from histology; potentially useful paper to understand how to benchmark/validate these types of models; when available would be good to include in LazySlide
A multimodal sleep foundation model for disease prediction
2026-01-21 · shared by Andre Rendeiro · Nature Medicine
A foundation model for continuous glucose monitoring data
2026-01-21 · shared by Andre Rendeiro · Nature
Automated Detection of Portal Fields and Central Veins in Whole-Slide Images of Liver Tissue
2026-01-16 · shared by Andre Rendeiro · Cell Press
maybe a dataset to benchmark on, but also a paper with a template for some downstream tasks we could also adopt (e.g. slide-level classification)
AI-enabled virtual spatial proteomics from histopathology for interpretable biomarker discovery in lung cancer
2026-01-16 · shared by Ernesto Abila · Nature Medicine
HEDeST: An Integrative Approach to Enhance Spatial Transcriptomic Deconvolution with Histology
2026-01-12 · shared by Andre Rendeiro · bioRxiv
Combining Graph Neural Network and Mamba to Capture Local and Global Tissue Spatial Relationships in Whole Slide Images
2026-01-09 · shared by SSrivastava · arXiv
This paper uses Mamba a specific type of state space model (SSM) (these are proposed to be faster and efficient alternative for the attention mechanism). SSM combines the fast nature of RNNs during inference along with the complexity of transformers during training.
Advancing single-cell omics and cell-based therapeutics with quantum computing
2026-01-09 · shared by YZheng · Nature Reviews Molecular Cell Biology
High-parameter spatial multi-omics through histology-anchored integration
2026-01-08 · shared by Andre Rendeiro · Nature Methods