Best practices for single-cell analysis across modalities
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …
[HTML][HTML] Automated methods for cell type annotation on scRNA-seq data
G Pasquini, JER Arias, P Schäfer… - Computational and …, 2021 - Elsevier
The advent of single-cell sequencing started a new era of transcriptomic and genomic
research, advancing our knowledge of the cellular heterogeneity and dynamics. Cell type …
research, advancing our knowledge of the cellular heterogeneity and dynamics. Cell type …
Dictionary learning for integrative, multimodal and scalable single-cell analysis
Mapping single-cell sequencing profiles to comprehensive reference datasets provides a
powerful alternative to unsupervised analysis. However, most reference datasets are …
powerful alternative to unsupervised analysis. However, most reference datasets are …
Multi-omics single-cell data integration and regulatory inference with graph-linked embedding
ZJ Cao, G Gao - Nature Biotechnology, 2022 - nature.com
Despite the emergence of experimental methods for simultaneous measurement of multiple
omics modalities in single cells, most single-cell datasets include only one modality. A major …
omics modalities in single cells, most single-cell datasets include only one modality. A major …
The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans
The Tabula Sapiens Consortium*, RC Jones… - Science, 2022 - science.org
Molecular characterization of cell types using single-cell transcriptome sequencing is
revolutionizing cell biology and enabling new insights into the physiology of human organs …
revolutionizing cell biology and enabling new insights into the physiology of human organs …
A cellular hierarchy framework for understanding heterogeneity and predicting drug response in acute myeloid leukemia
The treatment landscape of acute myeloid leukemia (AML) is evolving, with promising
therapies entering clinical translation, yet patient responses remain heterogeneous, and …
therapies entering clinical translation, yet patient responses remain heterogeneous, and …
Mapping single-cell data to reference atlases by transfer learning
Large single-cell atlases are now routinely generated to serve as references for analysis of
smaller-scale studies. Yet learning from reference data is complicated by batch effects …
smaller-scale studies. Yet learning from reference data is complicated by batch effects …
[HTML][HTML] Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution
Tumor evolution is driven by the progressive acquisition of genetic and epigenetic
alterations that enable uncontrolled growth and expansion to neighboring and distal tissues …
alterations that enable uncontrolled growth and expansion to neighboring and distal tissues …
High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer
Non-small cell lung cancer (NSCLC) is characterized by molecular heterogeneity with
diverse immune cell infiltration patterns, which has been linked to therapy sensitivity and …
diverse immune cell infiltration patterns, which has been linked to therapy sensitivity and …
[HTML][HTML] A Python library for probabilistic analysis of single-cell omics data
To the Editor—Methods for analyzing single-cell data 1, 2, 3, 4 perform a core set of
computational tasks. These tasks include dimensionality reduction, cell clustering, cell-state …
computational tasks. These tasks include dimensionality reduction, cell clustering, cell-state …