Gene regulatory network inference in the era of single-cell multi-omics
P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
Spatial profiling technologies illuminate the tumor microenvironment
O Elhanani, R Ben-Uri, L Keren - Cancer cell, 2023 - cell.com
The tumor microenvironment (TME) is composed of many different cellular and acellular
components that together drive tumor growth, invasion, metastasis, and response to …
components that together drive tumor growth, invasion, metastasis, and response to …
[HTML][HTML] An integrated cell atlas of the lung in health and disease
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 …
typically capture only a limited number of donors and disagree on cell type definitions …
[HTML][HTML] Dictionary learning for integrative, multimodal and scalable single-cell analysis
Mapping single-cell sequencing profiles to comprehensive reference datasets provides a
powerful alternative to unsupervised analysis. However, most reference datasets are …
powerful alternative to unsupervised analysis. However, most reference datasets are …
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning
NF Greenwald, G Miller, E Moen, A Kong, A Kagel… - Nature …, 2022 - nature.com
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 …
identifying the precise boundary of every cell in an image. To address this problem we …
[HTML][HTML] An atlas of healthy and injured cell states and niches in the human kidney
Understanding kidney disease relies on defining the complexity of cell types and states, their
associated molecular profiles and interactions within tissue neighbourhoods. Here we …
associated molecular profiles and interactions within tissue neighbourhoods. Here we …
[HTML][HTML] Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography
Imaging intact human organs from the organ to the cellular scale in three dimensions is a
goal of biomedical imaging. To meet this challenge, we developed hierarchical phase …
goal of biomedical imaging. To meet this challenge, we developed hierarchical phase …
The human proteoform project: defining the human proteome
Proteins are the primary effectors of function in biology, and thus, complete knowledge of
their structure and properties is fundamental to deciphering function in basic and …
their structure and properties is fundamental to deciphering function in basic and …
Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)
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 …
spatial atlas of the healthy human body at single-cell resolution by applying advanced …
Cell segmentation in imaging-based spatial transcriptomics
Single-molecule spatial transcriptomics protocols based on in situ sequencing or
multiplexed RNA fluorescent hybridization can reveal detailed tissue organization. However …
multiplexed RNA fluorescent hybridization can reveal detailed tissue organization. However …