[HTML][HTML] Spatial components of molecular tissue biology

G Palla, DS Fischer, A Regev, FJ Theis - Nature Biotechnology, 2022 - nature.com
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly
evolving, making it possible to comprehensively characterize cells and tissues in health and …

Spatial omics technologies at multimodal and single cell/subcellular level

J Park, J Kim, T Lewy, CM Rice, O Elemento… - Genome Biology, 2022 - Springer
Spatial omics technologies enable a deeper understanding of cellular organizations and
interactions within a tissue of interest. These assays can identify specific compartments or …

Multi-omics single-cell data integration and regulatory inference with graph-linked embedding

ZJ Cao, G Gao - Nature Biotechnology, 2022 - nature.com
Despite the emergence of experimental methods for simultaneous measurement of multiple
omics modalities in single cells, most single-cell datasets include only one modality. A major …

[HTML][HTML] Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain

SE Marsh, AJ Walker, T Kamath, L Dissing-Olesen… - Nature …, 2022 - nature.com
A key aspect of nearly all single-cell sequencing experiments is dissociation of intact tissues
into single-cell suspensions. While many protocols have been optimized for optimal cell …

Computational approaches and challenges in spatial transcriptomics

S Fang, B Chen, Y Zhang, H Sun, L Liu… - Genomics …, 2023 - academic.oup.com
The development of spatial transcriptomics (ST) technologies has transformed genetic
research from a single-cell data level to a two-dimensional spatial coordinate system and …

Single-cell multiomics

E Flynn, A Almonte-Loya… - Annual review of …, 2023 - annualreviews.org
Single-cell RNA sequencing methods have led to improved understanding of the
heterogeneity and transcriptomic states present in complex biological systems. Recently, the …

Modal-nexus auto-encoder for multi-modality cellular data integration and imputation

Z Tang, G Chen, S Chen, J Yao, L You… - Nature …, 2024 - nature.com
Heterogeneous feature spaces and technical noise hinder the cellular data integration and
imputation. The high cost of obtaining matched data across modalities further restricts …

Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics

AA Almet, YC Tsai, M Watanabe, Q Nie - Nature Methods, 2024 - nature.com
From single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST), one can
extract high-dimensional gene expression patterns that can be described by intercellular …

Cross-linked unified embedding for cross-modality representation learning

X Tu, ZJ Cao, S Mostafavi… - Advances in Neural …, 2022 - proceedings.neurips.cc
Multi-modal learning is essential for understanding information in the real world. Jointly
learning from multi-modal data enables global integration of both shared and modality …

Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution

LM Murrow, RJ Weber, JA Caruso, CS McGinnis… - Cell systems, 2022 - cell.com
The rise and fall of estrogen and progesterone across menstrual cycles and during
pregnancy regulates breast development and modifies cancer risk. How these hormones …