Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023 - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

Organoids

Z Zhao, X Chen, AM Dowbaj, A Sljukic… - Nature Reviews …, 2022 - nature.com
Organoids are simple tissue-engineered cell-based in vitro models that recapitulate many
aspects of the complex structure and function of the corresponding in vivo tissue. They can …

[HTML][HTML] TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines

D Ershov, MS Phan, JW Pylvänäinen, SU Rigaud… - Nature …, 2022 - nature.com
TrackMate is an automated tracking software used to analyze bioimages and is distributed
as a Fiji plugin. Here, we introduce a new version of TrackMate. TrackMate 7 is built to …

[HTML][HTML] Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

WL Hwang, KA Jagadeesh, JA Guo, HI Hoffman… - Nature …, 2022 - nature.com
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory
cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet …

[HTML][HTML] High-content CRISPR screening

C Bock, P Datlinger, F Chardon, MA Coelho… - Nature Reviews …, 2022 - nature.com
CRISPR screens are a powerful source of biological discovery, enabling the unbiased
interrogation of gene function in a wide range of applications and species. In pooled …

[HTML][HTML] Identification of essential sites of lipid peroxidation in ferroptosis

AN von Krusenstiern, RN Robson, N Qian… - Nature chemical …, 2023 - nature.com
Ferroptosis, an iron-dependent form of cell death driven by lipid peroxidation, provides a
potential treatment avenue for drug-resistant cancers and may play a role in the pathology of …

Spatial profiling technologies illuminate the tumor microenvironment

O Elhanani, R Ben-Uri, L Keren - Cancer cell, 2023 - cell.com
The tumor microenvironment (TME) is composed of many different cellular and acellular
components that together drive tumor growth, invasion, metastasis, and response to …

CellProfiler 4: improvements in speed, utility and usability

DR Stirling, MJ Swain-Bowden, AM Lucas… - BMC …, 2021 - Springer
Background Imaging data contains a substantial amount of information which can be difficult
to evaluate by eye. With the expansion of high throughput microscopy methodologies …

[HTML][HTML] Spatial components of molecular tissue biology

G Palla, DS Fischer, A Regev, FJ Theis - Nature Biotechnology, 2022 - nature.com
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly
evolving, making it possible to comprehensively characterize cells and tissues in health and …

Cancer-associated fibroblast classification in single-cell and spatial proteomics data

L Cords, S Tietscher, T Anzeneder… - Nature …, 2023 - nature.com
Cancer-associated fibroblasts (CAFs) are a diverse cell population within the tumour
microenvironment, where they have critical effects on tumour evolution and patient …