More is better: recent progress in multi-omics data integration methods
Multi-omics data integration is one of the major challenges in the era of precision medicine.
Considerable work has been done with the advent of high-throughput studies, which have …
Considerable work has been done with the advent of high-throughput studies, which have …
Community detection and stochastic block models: recent developments
E Abbe - Journal of Machine Learning Research, 2018 - jmlr.org
The stochastic block model (SBM) is a random graph model with planted clusters. It is widely
employed as a canonical model to study clustering and community detection, and provides …
employed as a canonical model to study clustering and community detection, and provides …
Pathway enrichment analysis and visualization of omics data using g: Profiler, GSEA, Cytoscape and EnrichmentMap
Pathway enrichment analysis helps researchers gain mechanistic insight into gene lists
generated from genome-scale (omics) experiments. This method identifies biological …
generated from genome-scale (omics) experiments. This method identifies biological …
Cytoscape StringApp: network analysis and visualization of proteomics data
Protein networks have become a popular tool for analyzing and visualizing the often long
lists of proteins or genes obtained from proteomics and other high-throughput technologies …
lists of proteins or genes obtained from proteomics and other high-throughput technologies …
UCSF ChimeraX: Meeting modern challenges in visualization and analysis
TD Goddard, CC Huang, EC Meng… - Protein …, 2018 - Wiley Online Library
UCSF ChimeraX is next‐generation software for the visualization and analysis of molecular
structures, density maps, 3D microscopy, and associated data. It addresses challenges in …
structures, density maps, 3D microscopy, and associated data. It addresses challenges in …
The whole-genome landscape of medulloblastoma subtypes
Current therapies for medulloblastoma, a highly malignant childhood brain tumour, impose
debilitating effects on the develo** child, and highlight the need for molecularly targeted …
debilitating effects on the develo** child, and highlight the need for molecularly targeted …
Single-cell analysis of two severe COVID-19 patients reveals a monocyte-associated and tocilizumab-responding cytokine storm
Several studies show that the immunosuppressive drugs targeting the interleukin-6 (IL-6)
receptor, including tocilizumab, ameliorate lethal inflammatory responses in COVID-19 …
receptor, including tocilizumab, ameliorate lethal inflammatory responses in COVID-19 …
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible
A system-wide understanding of cellular function requires knowledge of all functional
interactions between the expressed proteins. The STRING database aims to collect and …
interactions between the expressed proteins. The STRING database aims to collect and …
Lineage-specific genome architecture links enhancers and non-coding disease variants to target gene promoters
Long-range interactions between regulatory elements and gene promoters play key roles in
transcriptional regulation. The vast majority of interactions are uncharted, constituting a …
transcriptional regulation. The vast majority of interactions are uncharted, constituting a …
Coupled proliferation and apoptosis maintain the rapid turnover of microglia in the adult brain
Microglia play key roles in brain development, homeostasis, and function, and it is widely
assumed that the adult population is long lived and maintained by self-renewal. However …
assumed that the adult population is long lived and maintained by self-renewal. However …