Cool Papers

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 Yimin Zheng · 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! import optimuskg nodes, edges = optimuskg.load_graph(lcc=True)

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: Model weights:

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. 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 - 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 Yimin Zheng · Nature Medicine

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:

A 3D morphogenetic blueprint for metastatic outgrowth in breast cancer

2026-04-27 · shared by Yimin Zheng · 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 Yimin Zheng · 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.

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 "NetWAS trains a support vector machine classifier using nominally significant (P < 0.01) genes as …

annbatch unlocks terabyte-scale training of biological data in anndata

2026-04-13 · shared by Ernesto Abila · arXiv

PRET is a few-shot system for pan-cancer recognition without example training

2026-04-10 · shared by Yimin Zheng · 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. Lisa

Generative machine learning unlocks the first proteome-wide image of human cells

2026-04-07 · shared by Andre Rendeiro · bioRxiv

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: see a full discussion on adopting these technologies for biological imaging here:

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

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

latest from the Mahmood lab

Reimagining systematic anatomy: The conclusion of the quartet

2026-03-27 · shared by Andre Rendeiro · Clinical Anatomy

Reimagining systematic anatomy: The conclusion of the quartet - Neumann - 2022 - Clinical Anatomy - Wiley Online Library

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

Hidden immune memory niches in inflammatory skin diseases

2026-03-27 · shared by Ernesto Abila · bioRxiv

Another interesting Skin paper, in which they profile 113 Xenium skin sections together with histology images for healthy, atopic dermatitis and psoriasis - likely relevant for @Lisa Kleissl

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.

Thymic health consequences in adults

2026-03-23 · shared by Lisa Kleissl · Nature

"We developed a d eep 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 ( = 25,031) and the Fr…

Whole-organ and whole-body 3D atlases enable cellome-wide profiling

2026-03-23 · shared by Yimin Zheng · 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).

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

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."

Toward Computationally Complete Spatial Omics

2026-03-11 · shared by Andre Rendeiro · bioRxiv

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

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.

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

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 the imbalance in age in the GTEx dataset.

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

Circulating Cell Type Senescence Signatures Reveal High-Resolution Health Status and 2 Trajectories in Human Longitudinal Studies

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

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:

Unifying the genetic landscape of common and rare diseases via latent neighborhoods

2026-02-04 · shared by Andre Rendeiro · bioRxiv

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

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. Probably relevant for everybody, but especially for the slide hub project and @Ariadna Villanueva M…

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:

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

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

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 Yimin Zheng · Nature Reviews Molecular Cell Biology

High-parameter spatial multi-omics through histology-anchored integration

2026-01-08 · shared by Andre Rendeiro · Nature Methods