Cool Papers — Rendeiro Lab

The molecular asynchrony of single cells

Lisa Kleissl — Mon, 15 Jun 2026 10:13:16 +0200

[bioRxiv]

General-purpose large language models outperform specialized clinical AI tools on medical benchmarks

arendeiro — Mon, 15 Jun 2026 08:50:39 +0200

[Nature Medicine] General-purpose large language models outperform specialized clinical AI tools on medical benchmarks

Back to basics: Observed statistics are sufficient to predict drug responses

arendeiro — Mon, 15 Jun 2026 08:03:10 +0200

[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:

Spatial biomarker discovery via interpretable semantic learning in histopathology

Ernesto Abila — Fri, 12 Jun 2026 14:56:00 +0200

[Cancer Cell]

Plasma signals of lung tumor promotion for molecular cancer prevention

arendeiro — Tue, 09 Jun 2026 20:08:16 +0200

[Cell] they identified a 14-protein plasma signature predicting lung cancer more than 5 years before diagnosis!

DaX: Learning General Pathology Representations Across Scales

Ernesto Abila — Mon, 08 Jun 2026 10:10:32 +0200

[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

Andre Rendeiro — Fri, 05 Jun 2026 12:33:16 +0200

[bioRxiv]

The Human Pleiotropic Map of GWAS Associations and Therapeutic Implications

Ariadna Villanueva Marijuan — Wed, 03 Jun 2026 13:11:11 +0200

[bioRxiv] genome-wide target prioritization

Cracks in the Foundation: How Data-Hungry and Sensitive to Domain Shift are Vision Foundation Models for Computational Pathology?

Andre Rendeiro — Tue, 02 Jun 2026 17:50:04 +0200

[medRxiv]

Thousandfold Expansion Microscopy

Ernesto Abila — Tue, 02 Jun 2026 13:27:38 +0200

[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

Andre Rendeiro — Tue, 02 Jun 2026 07:01:30 +0200

[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

Andre Rendeiro — Tue, 02 Jun 2026 06:57:41 +0200

[Proceedings of the National Academy of Sciences]

Cophenetic Spatial Topology Embedding reveals multiscale tissue architecture in spatial omics

Andre Rendeiro — Mon, 01 Jun 2026 08:00:00 +0200

[bioRxiv]

Pan-cancer spatial atlas of tertiary lymphoid structures

Andre Rendeiro — Fri, 29 May 2026 09:37:27 +0200

[Science]

MORPHE: Bridging Image Generation and Spatial Omics for Tissue Synthesis

Andre Rendeiro — Thu, 28 May 2026 18:40:44 +0200

[bioRxiv]

Universal transcriptomic hallmarks of mammalian ageing and mortality

Ernesto Abila — Thu, 28 May 2026 10:43:04 +0200

[Nature]

Spatiotemporal transcriptome atlas of human embryos after gastrulation

Yimin Zheng — Thu, 28 May 2026 10:42:24 +0200

[Nature] Typically BGI work

TopoSlide: Topologically-Informed Histopathology Whole Slide Image Representation Learning

Ernesto Abila — Wed, 27 May 2026 11:03:23 +0200

[CVF Open Access] Might be useful for Simon & Shrestha

A Spatial Proteomic Atlas of Tertiary Lymphoid Structures in Non-Small Cell Lung Cancer Identifies a Novel Predictive Class of Lymphoid Aggregates

Andre Rendeiro — Tue, 26 May 2026 09:00:00 +0200

[bioRxiv]

A deep-learning framework reveals whole-body perturbations at cell level

Ernesto Abila — Wed, 20 May 2026 22:30:00 +0200

[Nature]

Systematic common and rare variant association testing in 392,030 whole genomes in All of Us

Andre Rendeiro — Tue, 19 May 2026 12:13:30 +0200

[medRxiv] potentially useful to cross-check on age/age-gap variants

Multiplexed magnetic resonance imaging

Andre Rendeiro — Tue, 19 May 2026 12:12:09 +0200

[Nature] the latest in cutting-edge MRI

Differential Analysis of Gene Spatial Organisation with Minkowski Functionals and Tensors

Andre Rendeiro — Tue, 19 May 2026 12:11:03 +0200

[bioRxiv] please have a close look

Integrated multi-omics identifies distinct macrophage alterations during progression of metabolic dysfunction-associated steatohepatitis

Andre Rendeiro — Tue, 19 May 2026 12:10:36 +0200

[Nature Genetics] seems like a cool and potentially useful dataset

A Perturb-seq screen guided by species divergence uncovers pathways for collateral artery formation

Andre Rendeiro — Tue, 19 May 2026 12:09:54 +0200

[bioRxiv] seems like a super cool approach, would love to hear your thoughts

Sleep chart of biological ageing clocks in middle and late life

Andre Rendeiro — Tue, 19 May 2026 12:08:27 +0200

[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

Andre Rendeiro — Tue, 19 May 2026 12:06:35 +0200

[Nature Computational Science] one more for the collection

Plasma proteomic signature of frailty in 50,506 adults - ScienceDirect

Andre Rendeiro — Mon, 18 May 2026 09:45:04 +0200

[Cell Press] Plasma proteomic signature of frailty in 50,506 adults

Hidden immune memory niches in inflammatory skin diseases

Lisa Kleissl — Wed, 13 May 2026 16:22:09 +0200

[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

Lisa Kleissl — Wed, 13 May 2026 15:39:00 +0200

[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

Ernesto Abila — Wed, 13 May 2026 12:27:43 +0200

[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

Ernesto Abila — Wed, 13 May 2026 12:09:07 +0200

[medRxiv]

IBDome: An integrated molecular, histopathological, and clinical atlas of inflammatory bowel diseases

Andre Rendeiro — Mon, 11 May 2026 08:00:00 +0200

[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

Yimin Zheng — Fri, 08 May 2026 14:49:21 +0200

[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

Andre Rendeiro — Wed, 06 May 2026 08:55:32 +0200

[arXiv] finally an easy way to load the Zitnik lab Knowledge-graph! import optimuskg nodes, edges = optimuskg.load_graph(lcc=True)

Pleiotropy and disease interactors: the dual nature of genes linking ageing and ageing-related diseases

Andre Rendeiro — Wed, 06 May 2026 08:38:57 +0200

[Biogerontology] probably worth a look e.g.

Linking spatial biology and clinical histology via Haiku

Ernesto Abila — Tue, 05 May 2026 09:51:30 +0200

[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

Andre Rendeiro — Mon, 04 May 2026 13:59:28 +0200

[bioRxiv] spatial gene expression prediction from H&E via flow matching. Code available now: Weights not available yet. Full TCGA dataset with inference will be available.

AI framework for multidisease detection via retinal imaging

Andre Rendeiro — Mon, 04 May 2026 09:37:05 +0200

[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

Andre Rendeiro — Thu, 30 Apr 2026 14:51:53 +0200

[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

Yimin Zheng — Thu, 30 Apr 2026 06:59:52 +0200

[Nature Medicine]

Discovery of candidate therapeutic targets with Geneformer

Andre Rendeiro — Tue, 28 Apr 2026 15:37:30 +0200

[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

Ernesto Abila — Tue, 28 Apr 2026 10:57:18 +0200

[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

Yimin Zheng — Mon, 27 Apr 2026 09:49:15 +0200

[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

Andre Rendeiro — Fri, 24 Apr 2026 11:22:24 +0200

[Nature]

Weighted Genetic Risk Scores and Prediction of Weight Gain in Solid Organ Transplant Populations

Ariadna Villanueva Marijuan — Wed, 22 Apr 2026 11:30:07 +0200

[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 group#3) from candidate genes. Briefly, genotypes from each SNP were coded as 0, 1 or 2 according to the number of BMI risk alleles and each polymorphism was then weighted by its �-coefficient (allele eff

A spatial atlas of the healthy human liver from live donors

Andre Rendeiro — Fri, 17 Apr 2026 17:35:25 +0200

[Nature]

95% of Experimental Life-Science Papers in Three Months of Nature Used Hypothesis Testing Without Justifying Sample Sizes

Andre Rendeiro — Fri, 17 Apr 2026 16:42:59 +0200

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

Yimin Zheng — Thu, 16 Apr 2026 11:04:00 +0200

[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

Ernesto Abila — Wed, 15 Apr 2026 19:05:18 +0200

[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

Andre Rendeiro — Wed, 15 Apr 2026 11:18:00 +0200

[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

Andre Rendeiro — Tue, 14 Apr 2026 08:30:36 +0200

[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 positive examples and 10,000 randomly selected non-significant (P ≥ 0.01) genes as negatives. The classifier is constructed using a tissue network relevant to a disease (e.g. kidney for hypertension),

annbatch unlocks terabyte-scale training of biological data in anndata

Ernesto Abila — Mon, 13 Apr 2026 19:28:31 +0200

[arXiv]

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

Yimin Zheng — Fri, 10 Apr 2026 13:04:14 +0200

[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

Lisa Kleissl — Wed, 08 Apr 2026 09:58:32 +0200

[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

Andre Rendeiro — Tue, 07 Apr 2026 08:00:00 +0200

[bioRxiv]

Scaling and quantization of large-scale foundation model enables resource-efficient predictions in network biology

Andre Rendeiro — Fri, 03 Apr 2026 08:00:00 +0200

[Nature Computational Science] maybe you'll find this paper interesting

Odon: An ultra-fast viewer for spatial proteomics

Andre Rendeiro — Fri, 03 Apr 2026 08:00:00 +0200

[bioRxiv]

rewrites.bio - A manifesto for bioinformatics

Andre Rendeiro — Fri, 03 Apr 2026 08:00:00 +0200

tracel-ai/burn: a next generation tensor library and Deep Learning Framework

Andre Rendeiro — Thu, 02 Apr 2026 09:57:37 +0200

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

Lisa Kleissl — Thu, 02 Apr 2026 09:37:27 +0200

[Immunity]

MIPHEI-ViT: Multiplex Immunofluorescence Prediction from H&E Images using ViT Foundation Models

Andre Rendeiro — Wed, 01 Apr 2026 16:41:56 +0200

[arXiv] a multiplex imaging prediction model from Sanofi

Functional hierarchy of the human neocortex across the lifespan

Andre Rendeiro — Wed, 01 Apr 2026 16:40:29 +0200

[Nature] relevant for the VITA dataset

CytoSyn: a Foundation Diffusion Model for Histopathology -- Tech Report

Andre Rendeiro — Wed, 01 Apr 2026 16:39:23 +0200

[arXiv] the write-up of Owkin's generative model

MOOZY: A Patient-First Foundation Model for Computational Pathology

Andre Rendeiro — Wed, 01 Apr 2026 16:37:50 +0200

Toward Computationally Complete Spatial Omics

Ernesto Abila — Sun, 29 Mar 2026 13:38:31 +0200

[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

Andre Rendeiro — Fri, 27 Mar 2026 18:40:39 +0100

latest from the Mahmood lab

Reimagining systematic anatomy: The conclusion of the quartet

Andre Rendeiro — Fri, 27 Mar 2026 16:37:56 +0100

[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

Andre Rendeiro — Fri, 27 Mar 2026 13:47:48 +0100

[Nature Communications] potentially useful dataset to validate insights from lung tissue aging

Single-cell spatial transcriptomic analysis of human skin anatomy

Ernesto Abila — Thu, 26 Mar 2026 16:29:59 +0100

[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. MERFISH and histology image data is available at:

Adapting a Pre-trained Single-Cell Foundation Model to Spatial Gene Expression Generation from Histology Images

Clemens Kohl — Thu, 26 Mar 2026 12:55:54 +0100

[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

Andre Rendeiro — Wed, 25 Mar 2026 18:20:56 +0100

[bioRxiv]

Reprogramming of stroma-derived chemokine networks drives the loss of tissue organization in nodal B cell lymphoma

Andre Rendeiro — Wed, 25 Mar 2026 17:17:06 +0100

[Nature Cancer]

Trajectory-based differential expression analysis for single-cell sequencing data

Andre Rendeiro — Mon, 23 Mar 2026 13:43:22 +0100

[Nature Communications] an interesting paper which I think you'll find relevant

Thymic health consequences in adults

Lisa Kleissl — Mon, 23 Mar 2026 10:19:34 +0100

[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 Framingham Heart Study (

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

Yimin Zheng — Mon, 23 Mar 2026 08:01:53 +0100

[Cell]

HistoAtlas: A Pan-Cancer Morphology Atlas Linking Histomics to Molecular Programs and Clinical Outcomes

Ernesto Abila — Wed, 18 Mar 2026 08:55:39 +0100

[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

Andre Rendeiro — Mon, 16 Mar 2026 15:27:43 +0100

[bioRxiv]

HistoGWAS: An AI Framework for Automated and Interpretable Genetic Analysis of Tissue Phenotypes

Andre Rendeiro — Mon, 16 Mar 2026 08:00:00 +0100

[bioRxiv]

Intestinal interoceptive dysfunction drives age-associated cognitive decline

Andre Rendeiro — Thu, 12 Mar 2026 08:48:11 +0100

[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

Andre Rendeiro — Thu, 12 Mar 2026 08:46:42 +0100

[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

Andre Rendeiro — Thu, 12 Mar 2026 08:45:05 +0100

[Nature]

Simultaneous spatial transcriptomics and morphology profiling as tools to explore how microglia change with age

Lisa Kleissl — Wed, 11 Mar 2026 11:12:29 +0100

[Nature Aging]

imAgeScore, a Cell Painting-Based Predictor of Cellular Age for High-throughput Drug Screening Applications

Ernesto Abila — Wed, 11 Mar 2026 09:36:55 +0100

[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

Andre Rendeiro — Wed, 11 Mar 2026 09:03:27 +0100

[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

Andre Rendeiro — Wed, 11 Mar 2026 09:01:32 +0100

[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

Andre Rendeiro — Wed, 11 Mar 2026 08:58:36 +0100

[Nature Methods] sounds cool and probably a lot to learn here

Ten mouse organs proteome and metabolome atlas from adult to aging

Andre Rendeiro — Mon, 09 Mar 2026 08:00:00 +0100

[Genome Medicine] if we ever want a dataset of mouse proteomics during aging

MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy

Andre Rendeiro — Thu, 05 Mar 2026 10:48:08 +0100

[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

Andre Rendeiro — Wed, 04 Mar 2026 18:11:21 +0100

[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

Andre Rendeiro — Wed, 04 Mar 2026 08:00:00 +0100

[Nature Biomedical Engineering]

Foundation model for cancer imaging biomarkers

Andre Rendeiro — Wed, 04 Mar 2026 08:00:00 +0100

[Nature Machine Intelligence] good to keep an eye on the radiology side of things

GrapHist: Graph Self-Supervised Learning for Histopathology

Andre Rendeiro — Wed, 04 Mar 2026 08:00:00 +0100

[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

Ernesto Abila — Fri, 27 Feb 2026 18:00:02 +0100

[arXiv]

Revisiting the blueprint for an interpretable virtual cell

Andre Rendeiro — Fri, 27 Feb 2026 07:08:04 +0100

[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

Ernesto Abila — Wed, 25 Feb 2026 15:56:48 +0100

[bioRxiv] New paper from the Wyss-Coray lab.

Combining xenium in situ spatial transcriptomics and imaging mass cytometry on a single tissue section

Andre Rendeiro — Mon, 23 Feb 2026 12:51:21 +0100

[bioRxiv]

Towards Spatial Transcriptomics-driven Pathology Foundation Models

Andre Rendeiro — Mon, 23 Feb 2026 12:26:47 +0100

[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

SSrivastava — Tue, 17 Feb 2026 17:12:16 +0100

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.

immgenT: A Comprehensive Reference of Convergent T-cell States in the Mouse

Andre Rendeiro — Wed, 11 Feb 2026 12:37:53 +0100

[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