Computational approaches and challenges in spatial transcriptomics
The development of spatial transcriptomics (ST) technologies has transformed genetic
research from a single-cell data level to a two-dimensional spatial coordinate system and …
research from a single-cell data level to a two-dimensional spatial coordinate system and …
Subcellular proteomics
The eukaryotic cell is compartmentalized into subcellular niches, including membrane-
bound and membrane-less organelles. Proteins localize to these niches to fulfil their …
bound and membrane-less organelles. Proteins localize to these niches to fulfil their …
[HTML][HTML] QuPath: Open source software for digital pathology image analysis
P Bankhead, MB Loughrey, JA Fernández… - Scientific reports, 2017 - nature.com
QuPath is new bioimage analysis software designed to meet the growing need for a user-
friendly, extensible, open-source solution for digital pathology and whole slide image …
friendly, extensible, open-source solution for digital pathology and whole slide image …
Shared and distinct transcriptomic cell types across neocortical areas
The neocortex contains a multitude of cell types that are segregated into layers and
functionally distinct areas. To investigate the diversity of cell types across the mouse …
functionally distinct areas. To investigate the diversity of cell types across the mouse …
High-definition spatial transcriptomics for in situ tissue profiling
Spatial and molecular characteristics determine tissue function, yet high-resolution methods
to capture both concurrently are lacking. Here, we developed high-definition spatial …
to capture both concurrently are lacking. Here, we developed high-definition spatial …
NIH Image to ImageJ: 25 years of image analysis
CA Schneider, WS Rasband, KW Eliceiri - Nature methods, 2012 - nature.com
For the past 25 years NIH Image and ImageJ software have been pioneers as open tools for
the analysis of scientific images. We discuss the origins, challenges and solutions of these …
the analysis of scientific images. We discuss the origins, challenges and solutions of these …
Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy
Intratumoral immune cells are crucial for tumor control and antitumor responses during
immunotherapy. Immune cell trafficking into tumors is mediated by binding of specific …
immunotherapy. Immune cell trafficking into tumors is mediated by binding of specific …
CellProfiler: image analysis software for identifying and quantifying cell phenotypes
Biologists can now prepare and image thousands of samples per day using automation,
enabling chemical screens and functional genomics (for example, using RNA interference) …
enabling chemical screens and functional genomics (for example, using RNA interference) …
SARS-CoV2-mediated suppression of NRF2-signaling reveals potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate
D Olagnier, E Farahani, J Thyrsted… - Nature …, 2020 - nature.com
Antiviral strategies to inhibit Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-
CoV2) and the pathogenic consequences of COVID-19 are urgently required. Here, we …
CoV2) and the pathogenic consequences of COVID-19 are urgently required. Here, we …
Single-nucleus and single-cell transcriptomes compared in matched cortical cell types
Transcriptomic profiling of complex tissues by single-nucleus RNA-sequencing (snRNA-seq)
affords some advantages over single-cell RNA-sequencing (scRNA-seq). snRNA-seq …
affords some advantages over single-cell RNA-sequencing (scRNA-seq). snRNA-seq …