Deciphering cell–cell interactions and communication from gene expression

E Armingol, A Officer, O Harismendy… - Nature Reviews …, 2021 - nature.com
Cell–cell interactions orchestrate organismal development, homeostasis and single-cell
functions. When cells do not properly interact or improperly decode molecular messages …

Artificial intelligence in cancer research and precision medicine

B Bhinder, C Gilvary, NS Madhukar, O Elemento - Cancer discovery, 2021 - AACR
Artificial intelligence (AI) is rapidly reshaping cancer research and personalized clinical
care. Availability of high-dimensionality datasets coupled with advances in high …

Key parameters of tumor epitope immunogenicity revealed through a consortium approach improve neoantigen prediction

DK Wells, MM van Buuren, KK Dang… - Cell, 2020 - cell.com
Many approaches to identify therapeutically relevant neoantigens couple tumor sequencing
with bioinformatic algorithms and inferred rules of tumor epitope immunogenicity. However …

Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics

AS Nam, R Chaligne, DA Landau - Nature Reviews Genetics, 2021 - nature.com
Cancer represents an evolutionary process through which growing malignant populations
genetically diversify, leading to tumour progression, relapse and resistance to therapy. In …

The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma

CB Steen, BA Luca, MS Esfahani, A Azizi, BJ Sworder… - Cancer cell, 2021 - cell.com
Biological heterogeneity in diffuse large B cell lymphoma (DLBCL) is partly driven by cell-of-
origin subtypes and associated genomic lesions, but also by diverse cell types and cell …

[HTML][HTML] Tumor heterogeneity reshapes the tumor microenvironment to influence drug resistance

A Zhang, K Miao, H Sun, CX Deng - International journal of …, 2022 - ncbi.nlm.nih.gov
Tumor heterogeneity is one of the hallmarks of cancer and a challenge in the field of
oncology. Tumor heterogeneity is the main cause of drug resistance, leading to therapeutic …

FunRich enables enrichment analysis of OMICs datasets

P Fonseka, M Pathan, SV Chitti, T Kang… - Journal of molecular …, 2021 - Elsevier
High‐throughput methods to profile the genome, transcriptome, proteome and metabolome
of various systems has become a routine in multiple research laboratories around the world …

Recent developments in application of single-cell RNA sequencing in the tumour immune microenvironment and cancer therapy

PH Li, XY Kong, YZ He, Y Liu, X Peng, ZH Li… - Military Medical …, 2022 - Springer
The advent of single-cell RNA sequencing (scRNA-seq) has provided insight into the tumour
immune microenvironment (TIME). This review focuses on the application of scRNA-seq in …

[HTML][HTML] Tumor-infiltrating dendritic cell states are conserved across solid human cancers

GM Gerhard, R Bill, M Messemaker, AM Klein… - Journal of Experimental …, 2021 - rupress.org
Dendritic cells (DCs) contribute a small fraction of the tumor microenvironment but are
emerging as an essential antitumor component based on their ability to foster T cell …

Neoantigens: promising targets for cancer therapy

N Xie, G Shen, W Gao, Z Huang, C Huang… - Signal transduction and …, 2023 - nature.com
Recent advances in neoantigen research have accelerated the development and regulatory
approval of tumor immunotherapies, including cancer vaccines, adoptive cell therapy and …