Orchestrating single-cell analysis with Bioconductor

RA Amezquita, ATL Lun, E Becht, VJ Carey… - Nature …, 2020 - nature.com
Recent technological advancements have enabled the profiling of a large number of
genome-wide features in individual cells. However, single-cell data present unique …

Discovery and validation of biomarkers to aid the development of safe and effective pain therapeutics: challenges and opportunities

KD Davis, N Aghaeepour, AH Ahn, MS Angst… - Nature Reviews …, 2020 - nature.com
Pain medication plays an important role in the treatment of acute and chronic pain
conditions, but some drugs, opioids in particular, have been overprescribed or prescribed …

Guidelines for the use of flow cytometry and cell sorting in immunological studies

A Cossarizza, HD Chang, A Radbruch… - European journal of …, 2019 - Wiley Online Library
These guidelines are a consensus work of a considerable number of members of the
immunology and flow cytometry community. They provide the theory and key practical …

Guidelines for the use of flow cytometry and cell sorting in immunological studies*

A Cossarizza, HD Chang, A Radbruch… - European journal of …, 2017 - Wiley Online Library
From a technical point of view a flow cytometer is a light detection device capable of
detecting photons of different wavelengths over a high dynamic range. In order to achieve a …

Mass cytometry: single cells, many features

MH Spitzer, GP Nolan - Cell, 2016 - cell.com
Technology development in biological research often aims to either increase the number of
cellular features that can be surveyed simultaneously or enhance the resolution at which …

[HTML][HTML] A systematic performance evaluation of clustering methods for single-cell RNA-seq data

A Duò, MD Robinson, C Soneson - F1000Research, 2018 - ncbi.nlm.nih.gov
Subpopulation identification, usually via some form of unsupervised clustering, is a
fundamental step in the analysis of many single-cell RNA-seq data sets. This has motivated …

An immune clock of human pregnancy

N Aghaeepour, EA Ganio, D Mcilwain, AS Tsai… - Science …, 2017 - science.org
The maintenance of pregnancy relies on finely tuned immune adaptations. We demonstrate
that these adaptations are precisely timed, reflecting an immune clock of pregnancy in …

FlowSOM: Using self‐organizing maps for visualization and interpretation of cytometry data

S Van Gassen, B Callebaut, MJ Van Helden… - Cytometry Part …, 2015 - Wiley Online Library
The number of markers measured in both flow and mass cytometry keeps increasing
steadily. Although this provides a wealth of information, it becomes infeasible to analyze …

[HTML][HTML] CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets

M Nowicka, C Krieg, HL Crowell, LM Weber… - …, 2017 - ncbi.nlm.nih.gov
High-dimensional mass and flow cytometry (HDCyto) experiments have become a method
of choice for high-throughput interrogation and characterization of cell populations. Here, we …

Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis

JH Levine, EF Simonds, SC Bendall, KL Davis… - Cell, 2015 - cell.com
Acute myeloid leukemia (AML) manifests as phenotypically and functionally diverse cells,
often within the same patient. Intratumor phenotypic and functional heterogeneity have been …