Tools of the Trade

In this Tools of the Trade article, Zuzana Tatarova describes the development of MIMA, an integrated analytical platform providing the quantitative information on tumour microenvironment drug responses required for effective treatment design.

In this Tools of the Trade article, Daniel Kirschenbaum describes the development of Zman-seq and its utility for capturing dynamic changes in cellular state within single-cell RNA sequencing data.

In this Tools of the Trade article, Kaile Wang describes the development and use of Arc-well, a high-throughput single-cell DNA sequencing method tailored to analyse archival formalin-fixed paraffin-embedded (FFPE) materials.

In this Tools of the Trade, Juliann Shih describes the development of BISCUT, which detects genomic loci that are subject to fitness advantages or disadvantages by interrogating the length distributions of partial somatic copy-number alterations to enable the discovery of new drivers of aneuploidy in cancer.

In this Tools of the Trade article, Vakul Mohanty describes the development and use of METAFlux, a computational framework that infers metabolic flux from bulk and single-cell RNA-sequencing data.

In this Tools of the Trade article, Xiwen Tang describes the development of in vivo reporters detecting mutant p53 at the protein level, which enables the visualization of precancerous cells during cancer initiation.

In this Tools of the Trade article, Hongcheng Mai describes the development of wildDISCO, an approach for whole-body immunolabelling, optical clearing and imaging in mice.

In this Tool of the Trade article, Nicolas Mathey-Andrews describes the generation and use of a prime editor mouse that enables in vivo modelling of the multitude of cancer alleles found in human tumours.

In this Tools of the Trade article, Dezhong Ji describes the development and use of a chimeric antigenic peptide influenza virus (CAP-Flu) system as a cancer vaccine strategy to promote tumour-infiltrating T cell activation in lung metastasis.

In this Tools of the Trade article, Chiara Cattaneo describes the development of HANSolo, a high-throughput genetic platform for the personalized identification of CD4⁺ and CD8⁺ T cell-recognized (neo)antigens, that can be used to generate patient-specific TCR gene therapies or cancer vaccines.

In this Tools of the Trade article, Emmanuel Olivier describes an approach to reprogramming AML cancer cells into induced pluripotent stem cells, which provide faithful genetic models of the most common genetic subgroups of AML.

In this Tools of the Trade article, Yuan Ma describes the development and use of ARPLA, a spatial imaging tool that can be used to visualize glycoRNAs in single cells, including cancer cells in situ.

In this Tools of the Trade article, Ciaran Seath describes the development and use of a proximity labelling method to study how cancer driving mutations and small molecule ligands remodel the chromatin microenvironment.

In this Tools of the Trade article, Isabel Esain-Garcia describes the development and use of a 6-letter whole-genome sequencing technology, which enables the simultaneous acquisition of genetic and epigenetic information from human genomic and cell-free DNA, which has implications for improving our biological understanding of cancer as well as cancer diagnosis and early intervention.

In this Tool of the Trade article, Eva Freckmann describes the development of Traject3d, a workflow that enables the detection of heterogeneous phenotypes in 3D culture by analysing label-free multi-day time-lapse imaging.

In this Tools of the Trade article, Zhenqin Wu describes the development and use of SPACE-GM, a graph deep learning tool that enables the detection of spatial cellular structures predictive of outcomes of patients with cancer.

In this Tool of the Trade article, Tatiana Flisikowska describes the development and use of humanized minipigs that allow the preclinical safety testing of human therapeutic antibodies.

In this Tool of the Trade article, Mateusz Legut describes the development and use of OverCITE-seq, a new single-cell multiomics approach enabling the high-throughput quantification of the transcriptome and surface antigens in cells expressing a library of open reading frames.

In this Tools of the Trade article, Alexandros P. Drainas describes the development and use of EpicMIBI, a multiplexed imaging technology that enables the study of spatial clonality in cancer.

In this article, Efrat Shema describes EPINUC, a liquid biopsy method based on epigenetic profiling of nucleosomes from cell-free DNA in the plasma. EPINUC, combined with protein biomarker measurements, enables the accurate differentiation of samples from healthy volunteers and patients.