Artificial intelligence in cancer immunotherapy: applications in neoantigen recognition, antibody design and immunotherapy response prediction

T Li, Y Li, X Zhu, Y He, Y Wu, T Ying, Z Xie - Seminars in Cancer Biology, 2023 - Elsevier
Cancer immunotherapy is a method of controlling and eliminating tumors by reactivating the
body's cancer-immunity cycle and restoring its antitumor immune response. The increased …

Spatial transcriptomics in breast cancer: providing insight into tumor heterogeneity and promoting individualized therapy

J An, Y Lu, Y Chen, Y Chen, Z Zhou, J Chen… - Frontiers in …, 2024 - frontiersin.org
A comprehensive understanding of tumor heterogeneity, tumor microenvironment and the
mechanisms of drug resistance is fundamental to advancing breast cancer research. While …

EnDecon: cell type deconvolution of spatially resolved transcriptomics data via ensemble learning

JJ Tu, HS Li, H Yan, XF Zhang - Bioinformatics, 2023 - academic.oup.com
Motivation Spatially resolved gene expression profiles are the key to exploring the cell type
spatial distributions and understanding the architecture of tissues. Many spatially resolved …

Cell composition inference and identification of layer-specific spatial transcriptional profiles with POLARIS

J Chen, T Luo, M Jiang, J Liu, GP Gupta, Y Li - Science Advances, 2023 - science.org
Spatial transcriptomics (ST) technology, providing spatially resolved transcriptional profiles,
facilitates advanced understanding of key biological processes related to health and …

Cellular neighborhood analysis in spatial omics reveals new tissue domains and cell subtypes

MJ Ruitenberg, QH Nguyen - Nature Genetics, 2024 - nature.com
Spatial omics enables the molecular profiling of cells with the tissue context preserved. A
new analytic approach shows how cellular neighborhood analysis and feature …

A framework for comparison and assessment of synthetic RNA-seq data

F Shakola, D Palejev, I Ivanov - Genes, 2022 - mdpi.com
The ever-growing number of methods for the generation of synthetic bulk and single cell
RNA-seq data have multiple and diverse applications. They are often aimed at …

[HTML][HTML] A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity

AG Patel, O Ashenberg, NB Collins, Å Segerstolpe… - bioRxiv, 2024 - ncbi.nlm.nih.gov
Neuroblastoma is a pediatric cancer arising from the developing sympathoadrenal lineage
with complex inter-and intra-tumoral heterogeneity. To chart this complexity, we generated a …

A Review of the Application of Spatial Transcriptomics in Neuroscience

L Zhang, Z Xiong, M Xiao - Interdisciplinary Sciences: Computational Life …, 2024 - Springer
Since spatial transcriptomics can locate and distinguish the gene expression of functional
genes in special regions and tissue, it is important for us to investigate the brain …

Cross-expression analysis reveals patterns of coordinated gene expression in spatial transcriptomics

A Sarwar, M Rue, L French, H Cross, X Chen, J Gillis - bioRxiv, 2024 - pmc.ncbi.nlm.nih.gov
Spatial transcriptomics promises to transform our understanding of tissue biology by
molecularly profiling individual cells in situ. A fundamental question they allow us to ask is …

CellPie: a fast spatial transcriptomics topic discovery method via joint factorization of gene expression and imaging data

S Georgaka, WG Morgans, Q Zhao… - bioRxiv, 2023 - biorxiv.org
Motivation Spatially resolved transcriptomics has enabled the study of expression of genes
within tissues while retaining their spatial identity. The lack of single-cell resolution for most …