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Applications of single-cell RNA sequencing in drug discovery and development
B Van de Sande, JS Lee, E Mutasa-Gottgens… - Nature Reviews Drug …, 2023 - nature.com
Single-cell technologies, particularly single-cell RNA sequencing (scRNA-seq) methods,
together with associated computational tools and the growing availability of public data …
together with associated computational tools and the growing availability of public data …
Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers
The rapid growth of high-throughput technologies has transformed biomedical research.
With the increasing amount and complexity of data, scalability and reproducibility have …
With the increasing amount and complexity of data, scalability and reproducibility have …
Pangenome graph construction from genome alignments with Minigraph-Cactus
Pangenome references address biases of reference genomes by storing a representative
set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles …
set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles …
[HTML][HTML] Expanding PROTACtable genome universe of E3 ligases
Proteolysis-targeting chimera (PROTAC) and other targeted protein degradation (TPD)
molecules that induce degradation by the ubiquitin-proteasome system (UPS) offer new …
molecules that induce degradation by the ubiquitin-proteasome system (UPS) offer new …
[HTML][HTML] Conserved pan-cancer microenvironment subtypes predict response to immunotherapy
The clinical use of molecular targeted therapy is rapidly evolving but has primarily focused
on genomic alterations. Transcriptomic analysis offers an opportunity to dissect the …
on genomic alterations. Transcriptomic analysis offers an opportunity to dissect the …
Sustainable data analysis with Snakemake
Data analysis often entails a multitude of heterogeneous steps, from the application of
various command line tools to the usage of scripting languages like R or Python for the …
various command line tools to the usage of scripting languages like R or Python for the …
[HTML][HTML] A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells
Tumor-infiltrating myeloid cells (TIMs) are key regulators in tumor progression, but the
similarity and distinction of their fundamental properties across different tumors remain …
similarity and distinction of their fundamental properties across different tumors remain …
[HTML][HTML] CDKN2A deletion remodels lipid metabolism to prime glioblastoma for ferroptosis
Malignant tumors exhibit heterogeneous metabolic reprogramming, hindering the
identification of translatable vulnerabilities for metabolism-targeted therapy. How molecular …
identification of translatable vulnerabilities for metabolism-targeted therapy. How molecular …
Visualizing and interpreting cancer genomics data via the Xena platform
MJ Goldman, B Craft, M Hastie, K Repečka… - Nature …, 2020 - nature.com
To the Editor—There is a great need for easy-to-use cancer genomics visualization tools for
both large public data resources such as TCGA (The Cancer Genome Atlas) 1 and the GDC …
both large public data resources such as TCGA (The Cancer Genome Atlas) 1 and the GDC …
Interrogation of the microenvironmental landscape in brain tumors reveals disease-specific alterations of immune cells
Brain malignancies encompass a range of primary and metastatic cancers, including low-
grade and high-grade gliomas and brain metastases (BrMs) originating from diverse …
grade and high-grade gliomas and brain metastases (BrMs) originating from diverse …