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 …

Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers

L Wratten, A Wilm, J Göke - Nature methods, 2021 - nature.com
The rapid growth of high-throughput technologies has transformed biomedical research.
With the increasing amount and complexity of data, scalability and reproducibility have …

Pangenome graph construction from genome alignments with Minigraph-Cactus

G Hickey, J Monlong, J Ebler, AM Novak… - Nature …, 2024 - nature.com
Pangenome references address biases of reference genomes by storing a representative
set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles …

[HTML][HTML] Expanding PROTACtable genome universe of E3 ligases

Y Liu, J Yang, T Wang, M Luo, Y Chen, C Chen… - Nature …, 2023 - nature.com
Proteolysis-targeting chimera (PROTAC) and other targeted protein degradation (TPD)
molecules that induce degradation by the ubiquitin-proteasome system (UPS) offer new …

[HTML][HTML] Conserved pan-cancer microenvironment subtypes predict response to immunotherapy

A Bagaev, N Kotlov, K Nomie, V Svekolkin, A Gafurov… - Cancer cell, 2021 - cell.com
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 …

Sustainable data analysis with Snakemake

F Mölder, KP Jablonski, B Letcher, MB Hall… - …, 2021 - pmc.ncbi.nlm.nih.gov
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 …

[HTML][HTML] A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells

S Cheng, Z Li, R Gao, B **ng, Y Gao, Y Yang, S Qin… - Cell, 2021 - cell.com
Tumor-infiltrating myeloid cells (TIMs) are key regulators in tumor progression, but the
similarity and distinction of their fundamental properties across different tumors remain …

[HTML][HTML] CDKN2A deletion remodels lipid metabolism to prime glioblastoma for ferroptosis

JK Minami, D Morrow, NA Bayley, EG Fernandez… - Cancer cell, 2023 - cell.com
Malignant tumors exhibit heterogeneous metabolic reprogramming, hindering the
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 …

Interrogation of the microenvironmental landscape in brain tumors reveals disease-specific alterations of immune cells

F Klemm, RR Maas, RL Bowman, M Kornete, K Soukup… - Cell, 2020 - cell.com
Brain malignancies encompass a range of primary and metastatic cancers, including low-
grade and high-grade gliomas and brain metastases (BrMs) originating from diverse …