BMC Bioinformatics, 2023 Background Quantifying cell-type abundance in bulk tissue RNA-sequencing enables researchers to better understand complex systems. Newer deconvolution methodologies, such as MuSiC, use cell-type signatures derived from single-cell RNA-sequencing (scRNA ...
Nicholas K. O’Neill +7 more
doaj +1 more source
Reconstruction of Cell-type-Specific Interactomes at Single-Cell Resolution [PDF]
Cell Systems, 2019 The human interactome is instrumental in the systems-level study of the cell and the contextualization of disease-associated gene perturbations. However, reference organismal interactomes do not capture the cell-type-specific context in which proteins and modules preferentially act. Here, we introduce SCINET, a computational framework that reconstructs
Mohammadi, Shahin +2 more
openaire +3 more sources
A single–cell type transcriptomics map of human tissues [PDF]
Science Advances, 2021 Single-cell RNA analysis has been integrated with spatial protein profiling to create a single–cell type map of human tissues.
Max Karlsson +24 more
openaire +7 more sources
Defining cell types and states with single-cell genomics [PDF]
Genome Research, 2015 A revolution in cellular measurement technology is under way: For the first time, we have the ability to monitor global gene regulation in thousands of individual cells in a single experiment. Such experiments will allow us to discover new cell types and states and trace their developmental origins.
openaire +2 more sources
Lineage dynamics of murine pancreatic development at single-cell resolution. [PDF]
, 2018 Organogenesis requires the complex interactions of multiple cell lineages that coordinate their expansion, differentiation, and maturation over time.
Byrnes, Lauren E +8 more
core +2 more sources
Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data [PDF]
, 2013 Genome-wide association studies (GWASs) identify single nucleotide polymorphisms (SNPs) that are enriched in individuals suffering from a given disease. Most disease-associated SNPs fall into non-coding regions, so that it is not straightforward to infer
A Milosavljevic +57 more
core +3 more sources
scPred: Cell type prediction at single-cell resolution [PDF]
, 2018 AbstractSingle-cell RNA sequencing has enabled the characterization of highly specific cell types in many human tissues, as well as both primary and stem cell-derived cell lines. An important facet of these studies is the ability to identify the transcriptional signatures that define a cell type or state.
Alquicira-Hernández, José +4 more
openaire +1 more source
MARS: discovering novel cell types across heterogeneous single-cell experiments [PDF]
Nature Methods, 2020 Although tremendous effort has been put into cell-type annotation, identification of previously uncharacterized cell types in heterogeneous single-cell RNA-seq data remains a challenge. Here we present MARS, a meta-learning approach for identifying and annotating known as well as new cell types.
Maria Brbić +6 more
openaire +2 more sources
Single-Cell Transcriptomes Reveal a Complex Cellular Landscape in the Middle Ear and Differential Capacities for Acute Response to Infection. [PDF]
, 2020 Single-cell transcriptomics was used to profile cells of the normal murine middle ear. Clustering analysis of 6770 transcriptomes identified 17 cell clusters corresponding to distinct cell types: five epithelial, three stromal, three lymphocyte, two ...
Draf, Clara +6 more
core
Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity. [PDF]
, 2018 Here we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing (Pi-ATAC) that combines single-cell chromatin and proteomic profiling. In conjunction with DNA transposition, the levels of multiple cell surface or intracellular
Chang, Howard Y +8 more
core +2 more sources