Transfer learning enables predictions in network biology
Mapping gene networks requires large amounts of transcriptomic data to learn the
connections between genes, which impedes discoveries in settings with limited data …
connections between genes, which impedes discoveries in settings with limited data …
[HTML][HTML] Interpretation of T cell states from single-cell transcriptomics data using reference atlases
Single-cell RNA sequencing (scRNA-seq) has revealed an unprecedented degree of
immune cell diversity. However, consistent definition of cell subtypes and cell states across …
immune cell diversity. However, consistent definition of cell subtypes and cell states across …
[HTML][HTML] Integrated analysis of single-cell and bulk RNA sequencing data reveals a pan-cancer stemness signature predicting immunotherapy response
Background Although immune checkpoint inhibitor (ICI) is regarded as a breakthrough in
cancer therapy, only a limited fraction of patients benefit from it. Cancer stemness can be the …
cancer therapy, only a limited fraction of patients benefit from it. Cancer stemness can be the …
[HTML][HTML] A single-cell atlas of glioblastoma evolution under therapy reveals cell-intrinsic and cell-extrinsic therapeutic targets
Recent longitudinal studies of glioblastoma (GBM) have demonstrated a lack of apparent
selection pressure for specific DNA mutations in recurrent disease. Single-cell lineage …
selection pressure for specific DNA mutations in recurrent disease. Single-cell lineage …
[HTML][HTML] ATRX regulates glial identity and the tumor microenvironment in IDH-mutant glioma
Background Recent single-cell transcriptomic studies report that IDH-mutant gliomas share
a common hierarchy of cellular phenotypes, independent of genetic subtype. However, the …
a common hierarchy of cellular phenotypes, independent of genetic subtype. However, the …
[HTML][HTML] Lymph node and tumor-associated PD-L1+ macrophages antagonize dendritic cell vaccines by suppressing CD8+ T cells
Current immunotherapies provide limited benefits against T cell-depleted tumors, calling for
therapeutic innovation. Using multi-omics integration of cancer patient data, we predict a …
therapeutic innovation. Using multi-omics integration of cancer patient data, we predict a …
[HTML][HTML] The evolution of alternative splicing in glioblastoma under therapy
Background Alternative splicing is a rich source of tumor-specific neoantigen targets for
immunotherapy. This holds promise for glioblastomas (GBMs), the most common primary …
immunotherapy. This holds promise for glioblastomas (GBMs), the most common primary …
Learning deep features and topological structure of cells for clustering of scRNA-sequencing data
H Wang, X Ma - Briefings in Bioinformatics, 2022 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) measures gene transcriptome at the cell level,
paving the way for the identification of cell subpopulations. Although deep learning has …
paving the way for the identification of cell subpopulations. Although deep learning has …
[HTML][HTML] TIGIT and PD-1 immune checkpoint pathways are associated with patient outcome and anti-tumor immunity in glioblastoma
I Raphael, R Kumar, LH McCarl, K Shoger… - Frontiers in …, 2021 - frontiersin.org
Glioblastoma (GBM) remains an aggressive brain tumor with a high rate of mortality. Immune
checkpoint (IC) molecules are expressed on tumor infiltrating lymphocytes (TILs) and …
checkpoint (IC) molecules are expressed on tumor infiltrating lymphocytes (TILs) and …
CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data
Motivation Effective identification of cell types is of critical importance in single-cell RNA-
sequencing (scRNA-seq) data analysis. To date, many supervised machine learning-based …
sequencing (scRNA-seq) data analysis. To date, many supervised machine learning-based …