The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

The tumor microenvironment (TME) is composed of many different cellular and acellular
components that together drive tumor growth, invasion, metastasis, and response to …

Single-cell technologies have transformed our understanding of human tissues. Yet, studies
typically capture only a limited number of donors and disagree on cell type definitions …

Large pretrained models have become foundation models leading to breakthroughs in
natural language processing and related fields. Develo** foundation models for …

Map** single-cell sequencing profiles to comprehensive reference datasets provides a
powerful alternative to unsupervised analysis. However, most reference datasets are …

Hundreds of millions of single cells have been analyzed using high-throughput
transcriptomic methods. The cumulative knowledge within these datasets provides an …

Abstract The Human BioMolecular Atlas Program (HuBMAP) aims to create a multi-scale
spatial atlas of the healthy human body at single-cell resolution by applying advanced …

Understanding kidney disease relies on defining the complexity of cell types and states, their
associated molecular profiles and interactions within tissue neighbourhoods. Here we …

A principal challenge in the analysis of tissue imaging data is cell segmentation—the task of
identifying the precise boundary of every cell in an image. To address this problem we …

Single-molecule spatial transcriptomics protocols based on in situ sequencing or
multiplexed RNA fluorescent hybridization can reveal detailed tissue organization. However …