Digital histopathology by infrared spectroscopic imaging

R Bhargava - Annual Review of Analytical Chemistry, 2023 - annualreviews.org
Infrared (IR) spectroscopic imaging records spatially resolved molecular vibrational spectra,
enabling a comprehensive measurement of the chemical makeup and heterogeneity of …

Single-cell genomics meets human genetics

ASE Cuomo, A Nathan, S Raychaudhuri… - Nature Reviews …, 2023 - nature.com
Single-cell genomic technologies are revealing the cellular composition, identities and
states in tissues at unprecedented resolution. They have now scaled to the point that it is …

[HTML][HTML] Dissecting the treatment-naive ecosystem of human melanoma brain metastasis

J Biermann, JC Melms, AD Amin, Y Wang, LA Caprio… - Cell, 2022 - cell.com
Melanoma brain metastasis (MBM) frequently occurs in patients with advanced melanoma;
yet, our understanding of the underlying salient biology is rudimentary. Here, we performed …

Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response

S Liu, JB Iorgulescu, S Li, M Borji, IA Barrera-Lopez… - Immunity, 2022 - cell.com
T cells mediate antigen-specific immune responses to disease through the specificity and
diversity of their clonotypic T cell receptors (TCRs). Determining the spatial distributions of T …

SCS: cell segmentation for high-resolution spatial transcriptomics

H Chen, D Li, Z Bar-Joseph - Nature methods, 2023 - nature.com
Spatial transcriptomics promises to greatly improve our understanding of tissue organization
and cell–cell interactions. While most current platforms for spatial transcriptomics only offer …

Benchmarking spatial clustering methods with spatially resolved transcriptomics data

Z Yuan, F Zhao, S Lin, Y Zhao, J Yao, Y Cui… - Nature …, 2024 - nature.com
Spatial clustering, which shares an analogy with single-cell clustering, has expanded the
scope of tissue physiology studies from cell-centroid to structure-centroid with spatially …

Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope

X Wan, J Xiao, SST Tam, M Cai, R Sugimura… - Nature …, 2023 - nature.com
The rapid emergence of spatial transcriptomics (ST) technologies is revolutionizing our
understanding of tissue spatial architecture and biology. Although current ST methods …

Integrating spatial transcriptomics data across different conditions, technologies and developmental stages

X Zhou, K Dong, S Zhang - Nature Computational Science, 2023 - nature.com
With the rapid generation of spatial transcriptomics (ST) data, integrative analysis of multiple
ST datasets from different conditions, technologies and developmental stages is becoming …

Streamlining spatial omics data analysis with Pysodb

S Lin, F Zhao, Z Wu, J Yao, Y Zhao, Z Yuan - Nature Protocols, 2024 - nature.com
Advances in spatial omics technologies have improved the understanding of cellular
organization in tissues, leading to the generation of complex and heterogeneous data and …

STAMarker: determining spatial domain-specific variable genes with saliency maps in deep learning

C Zhang, K Dong, K Aihara, L Chen… - Nucleic Acids …, 2023 - academic.oup.com
Spatial transcriptomics characterizes gene expression profiles while retaining the
information of the spatial context, providing an unprecedented opportunity to understand …