Roser Vento‐Tormo

Multi-scale modeling of human tissues from spatial transcriptomics with TERRA

TERRA is a foundation model for spatial transcriptomics that predicts tissue behavior under perturbation and identifies multi-scale biological insights across tissues.

Full-thickness spatial transcriptomics of the human uterus reveals basalis niche architecture and regeneration gradients during menstrual breakdown

This study uses spatial transcriptomics to map gene expression gradients in the human endometrium, revealing coordinated regeneration and niche architecture during menstrual breakdown.

T cell receptor-ligand affinity quantitatively tunes transcriptome remodelling in vivo, inversely regulating cell division and interferon response

This study shows that TCR-ligand affinity quantitatively modulates transcriptome remodelling in vivo, affecting cell division and interferon response.

An integrated multimodal pan-organ atlas of the female reproductive system across the lifespan contextualises gynaecological pathologies

This paper creates an integrated multimodal atlas of the female reproductive system across the lifespan, identifying cell types and linking them to gynaecological pathologies.

Human 3D epithelioids enable continuous long-term clonal evolution studies across multiple epithelial tissues

This study develops human epithelioids as a 3D culture system that maintains architecture, heterogeneity, and clonal evolution over time, enabling long-term studies of tissue dynamics and therapeutic responses.

Spatial atlas of the ovary identifies molecular events in primordial follicle activation in humans

This study creates a comprehensive spatial atlas of the human ovarian cortex, revealing molecular mechanisms of primordial follicle activation and follicle niche organization.

A transient epithelial plasticity state defines the developmental window for uterine gland specification

The paper identifies a transient epithelial plasticity state that regulates uterine gland specification through ESR1, retinoic acid signaling, and FOXA2.

An integrated single cell and spatial omics atlas of human prenatal development

Human Developmental Cell Atlas integrates ~4.6 million cells/nuclei from 4-22 post-conception weeks into 454 refined cell types and maps 114 spatial niches across 6PCW whole-embryo sections.

Self-supervised learning for a gene program-centric view of cell states

Tripso, a self-supervised transformer model, identifies gene program-specific embeddings and discovers novel gene programs, revealing biological insights in hematopoietic development and disease.

Decoding human B cell ontogeny in prenatal and adult bone marrow and in vitro models via single-cell multiomics

This study creates a single-cell multiomics atlas of B cell development in prenatal and adult bone marrow and in vitro models, identifying novel cell subsets and molecular signatures.

A blastocyst-derived in vitro model of the human chorion

This paper develops an in vitro model of the human chorion using blastocysts to generate trophoblast organoids and extraembryonic mesoderm cells, enabling study of placental development and pathophysiology.

Atlas-scale metabolic activities inferred from single-cell and spatial transcriptomics

The paper introduces scCellFie, a framework to infer metabolic activities from single-cell and spatial transcriptomics data, revealing organ-specific metabolic programs and disease-associated alterations.

inVAE: Conditionally invariant representation learning for generating multivariate single-cell reference maps

inVAE improves cell state identification by disentangling biological and technical variation in single-cell data, outperforming existing methods across multiple human tissues.

Spatiotemporal map of the developing human reproductive tract at single-cell resolution

This study creates a single-cell spatial atlas of the developing human reproductive tract, identifying genes and mechanisms involved in sexual dimorphism and organ development.

An integrated single-cell reference atlas of the human endometrium

The paper constructs a high-resolution single-cell reference atlas of the human endometrium, identifying cell types, states, and signaling networks, and links them to endometriosis.

A developmental cell atlas of the human thyroid gland

This study creates a developmental cell atlas of the human thyroid gland using single-cell sequencing, revealing cell type heterogeneity and its implications in thyroid disorders and cancer.

Early infection response of the first trimester human placenta at single-cell scale

This study uses single-cell transcriptomics to map the early placental response to three pathogens in first-trimester human placenta, identifying coordinated inflammatory responses and pathogen-specific effects.

Successful placentation in human pregnancy is regulated by reciprocal interactions between maternal uterine NK cells and fetal placental trophoblast

The paper identifies a uNK-derived cytokine signal that promotes trophoblast differentiation and influences placental function and pregnancy outcomes.

A human prenatal skin cell atlas reveals immune cell regulation of skin morphogenesis

This study creates a prenatal human skin cell atlas, revealing immune cells' role in skin development and showing their impact on vascular and hair follicle formation.

Epigenetic and transcriptomic reprogramming in monocytes of severe COVID-19 patients reflects alterations in myeloid differentiation and the influence of inflammatory cytokines

The paper examines DNA methylation and transcriptomic changes in monocytes from severe COVID-19 patients, identifying epigenetic and transcriptional reprogramming linked to myeloid differentiation and inflammatory cytokines.

X-inactivation states of single cell transcriptomes reveal cellular phylogenies in human females

The paper introduces a method to determine X-inactivation states in single-cell transcriptomes and uses it to infer cellular phylogenies in human females.

Spatially resolved single-cell multiomics map of human trophoblast differentiation in early pregnancy

This study creates a spatially resolved single-cell multiomics atlas of human trophoblast differentiation in early pregnancy, revealing key regulatory programs and cell-cell communication events involved in EVT invasion and arterial transformation.

Multi-organ functions of yolk sac during human early development

The paper maps the multi-organ functions of the human yolk sac during early development, revealing its roles in hematopoiesis, nutrition, and oxygen regulation.

Robust temporal map of human in vitro myelopoiesis using single-cell genomics

The paper generates a molecular map of human in vitro myelopoiesis from iPSC to macrophages, revealing conserved regulatory networks and new myeloid progenitors.

Cell2location maps fine-grained cell types in spatial transcriptomics

cell2location uses a Bayesian model to integrate single-cell and spatial transcriptomics, mapping cell types in situ across mouse brain regions and human lymph node immune compartments.

Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

This study maps the temporal and spatial dynamics of the human endometrium using single-cell and spatial reference maps, identifying key signaling pathways regulating cell fate in vivo and in vitro.

SpatialDE2: Fast and localized variance component analysis of spatial transcriptomics

SpatialDE2 unifies tissue zone mapping and spatially variable gene detection for spatial transcriptomics within a fast Bayesian framework that directly models Poisson count noise.

Somatic mutations reveal widespread mosaicism and mutagenesis in human placentas

This study uses whole genome sequencing of placental biopsies to show that human placentas exhibit clonal expansions, copy number changes, and developmental bottlenecks similar to childhood cancer.

CellPhoneDB v2.0: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes

CellPhoneDB infers cell-cell communication by analyzing the combined expression of multi-subunit ligand-receptor complexes across cell types.

Decoding the development of the blood and immune systems during human fetal liver haematopoiesis

The paper uses single-cell transcriptomics to map hematopoiesis in human fetal liver, identifying cell differentiation trajectories and shifts in hematopoietic composition during development.