Deep learning in cancer diagnosis, prognosis and treatment selection

KA Tran, O Kondrashova, A Bradley, ED Williams… - Genome Medicine, 2021 - Springer
Deep learning is a subdiscipline of artificial intelligence that uses a machine learning
technique called artificial neural networks to extract patterns and make predictions from …

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

SK Longo, MG Guo, AL Ji, PA Khavari - Nature Reviews Genetics, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but
does not capture their spatial distribution nor reveal local networks of intercellular …

Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH

R Fang, C Xia, JL Close, M Zhang, J He, Z Huang… - Science, 2022 - science.org
The human cerebral cortex has tremendous cellular diversity. How different cell types are
organized in the human cortex and how cellular organization varies across species remain …

Applications of multi‐omics analysis in human diseases

C Chen, J Wang, D Pan, X Wang, Y Xu, J Yan… - MedComm, 2023 - Wiley Online Library
Multi‐omics usually refers to the crossover application of multiple high‐throughput screening
technologies represented by genomics, transcriptomics, single‐cell transcriptomics …

The spatial landscape of progression and immunoediting in primary melanoma at single-cell resolution

AJ Nirmal, Z Maliga, T Vallius, B Quattrochi, AA Chen… - Cancer Discovery, 2022 - AACR
Cutaneous melanoma is a highly immunogenic malignancy that is surgically curable at early
stages but life-threatening when metastatic. Here we integrate high-plex imaging, 3D high …

Undisclosed, unmet and neglected challenges in multi-omics studies

S Tarazona, A Arzalluz-Luque, A Conesa - Nature Computational …, 2021 - nature.com
Multi-omics approaches have become a reality in both large genomics projects and small
laboratories. However, the multi-omics research community still faces a number of issues …

Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities

BF Miller, D Bambah-Mukku, C Dulac… - Genome …, 2021 - genome.cshlp.org
Recent technological advances have enabled spatially resolved measurements of
expression profiles for hundreds to thousands of genes in fixed tissues at single-cell …

scDFC: a deep fusion clustering method for single-cell RNA-seq data

D Hu, K Liang, S Zhou, W Tu, M Liu… - Briefings in …, 2023 - academic.oup.com
Clustering methods have been widely used in single-cell RNA-seq data for investigating
tumor heterogeneity. Since traditional clustering methods fail to capture the high-dimension …

[HTML][HTML] Unravelling glioblastoma heterogeneity by means of single-cell RNA sequencing

AH Martínez, R Madurga, N García-Romero… - Cancer letters, 2022 - Elsevier
Glioblastoma (GBM) is the most invasive and deadliest brain cancer in adults. Its inherent
heterogeneity has been designated as the main cause of treatment failure. Thus, a deeper …

Domain generalization enables general cancer cell annotation in single-cell and spatial transcriptomics

Z Zhong, J Hou, Z Yao, L Dong, F Liu, J Yue… - Nature …, 2024 - nature.com
Single-cell and spatial transcriptome sequencing, two recently optimized transcriptome
sequencing methods, are increasingly used to study cancer and related diseases. Cell …