Map** cellular interactions from spatially resolved transcriptomics data

J Zhu, Y Wang, WY Chang, A Malewska, F Napolitano… - Nature …, 2024 - nature.com
Cell–cell communication (CCC) is essential to how life forms and functions. However,
accurate, high-throughput map** of how expression of all genes in one cell affects …

A bird's eye view of fibroblast heterogeneity: a pan‐disease, pan‐cancer perspective

RN Pradhan, AT Krishnamurty, AL Fletcher… - Immunological …, 2021 - Wiley Online Library
Fibroblasts, custodians of tissue architecture and function, are no longer considered a
monolithic entity across tissues and disease indications. Recent advances in single‐cell …

Sprod for de-noising spatially resolved transcriptomics data based on position and image information

Y Wang, B Song, S Wang, M Chen, Y **e, G **ao… - Nature …, 2022 - nature.com
Spatially resolved transcriptomics (SRT) provide gene expression close to, or even superior
to, single-cell resolution while retaining the physical locations of sequencing and often also …

Comparative analysis of dimension reduction methods for cytometry by time-of-flight data

K Wang, Y Yang, F Wu, B Song, X Wang… - Nature …, 2023 - nature.com
While experimental and informatic techniques around single cell sequencing (scRNA-seq)
are advanced, research around mass cytometry (CyTOF) data analysis has severely lagged …

CanCellVar: a database for single-cell variants map in human cancer

C Yang, Y Liu, C Lv, M Xu, K Xu, J Shi, T Tan… - The American Journal of …, 2024 - cell.com
Numerous variants, including both single-nucleotide variants (SNVs) in DNA and A> G RNA
edits in mRNA as essential drivers of cellular proliferation and tumorigenesis, are commonly …

[HTML][HTML] Immunotherapy of cancer in single-cell RNA sequencing era: A precision medicine perspective

N Erfanian, A Derakhshani, S Nasseri… - Biomedicine & …, 2022 - Elsevier
Immunotherapy has revolutionized cancer treatment and brought new aspects into tumor
immunology. Effective immunotherapy will require using the suitable target antigens …

SpotGF: Denoising spatially resolved transcriptomics data using an optimal transport-based gene filtering algorithm

L Du, J Kang, Y Hou, HX Sun, B Zhang - Cell Systems, 2024 - cell.com
Spatially resolved transcriptomics (SRT) combines gene expression profiles with the
physical locations of cells in their native states but suffers from unpredictable spatial noise …

Benchmarking bulk and single-cell variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries

M Wiens, H Farahani, RW Scott, TM Underhill… - Genome …, 2024 - genome.cshlp.org
Single-cell sequencing methodologies such as scRNA-seq and scATAC-seq have become
widespread and effective tools to interrogate tissue composition. Increasingly, variant callers …

Netie: inferring the evolution of neoantigen–T cell interactions in tumors

T Lu, S Park, Y Han, Y Wang, SM Hubert, PA Futreal… - Nature …, 2022 - nature.com
Neoantigens are the key targets of antitumor immune responses from cytotoxic T cells and
play a critical role in affecting tumor progressions and immunotherapy treatment responses …

A novel graph-based k-partitioning approach improves the detection of gene-gene correlations by single-cell RNA sequencing

H Xu, Y Hu, X Zhang, BE Aouizerat, C Yan, K Xu - BMC genomics, 2022 - Springer
Background Gene expression is regulated by transcription factors, cofactors, and epigenetic
mechanisms. Coexpressed genes indicate similar functional categories and gene networks …