Graph representation learning in biomedicine and healthcare
Networks—or graphs—are universal descriptors of systems of interacting elements. In
biomedicine and healthcare, they can represent, for example, molecular interactions …
biomedicine and healthcare, they can represent, for example, molecular interactions …
Single-cell analyses of aging, inflammation and senescence
Single-cell gene expression (transcriptomics) data are becoming robust and abundant, and
are increasingly used to track organisms along their life-course. This allows investigation …
are increasingly used to track organisms along their life-course. This allows investigation …
SIGNOR 3.0, the SIGnaling network open resource 3.0: 2022 update
P Lo Surdo, M Iannuccelli, S Contino… - Nucleic acids …, 2023 - academic.oup.com
Abstract The SIGnaling Network Open Resource (SIGNOR 3.0, https://signor. uniroma2. it) is
a public repository that captures causal information and represents it according to an 'activity …
a public repository that captures causal information and represents it according to an 'activity …
A computational tool (H-MAGMA) for improved prediction of brain-disorder risk genes by incorporating brain chromatin interaction profiles
NYA Sey, B Hu, W Mah, H Fauni, JC McAfee… - Nature …, 2020 - nature.com
Most risk variants for brain disorders identified by genome-wide association studies reside in
the noncoding genome, which makes deciphering biological mechanisms difficult. A …
the noncoding genome, which makes deciphering biological mechanisms difficult. A …
Metabolic network analysis reveals altered bile acid synthesis and metabolism in Alzheimer's disease
Increasing evidence suggests Alzheimer's disease (AD) pathophysiology is influenced by
primary and secondary bile acids, the end product of cholesterol metabolism. We analyze …
primary and secondary bile acids, the end product of cholesterol metabolism. We analyze …
Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application
Alzheimer's disease (AD) is the most common form of dementia, characterized by
progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic …
progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic …
Single-cell network biology for resolving cellular heterogeneity in human diseases
Understanding cellular heterogeneity is the holy grail of biology and medicine. Cells
harboring identical genomes show a wide variety of behaviors in multicellular organisms …
harboring identical genomes show a wide variety of behaviors in multicellular organisms …
Single-cell transcriptomic analyses define distinct peripheral B cell subsets and discrete development pathways
Separation of B cells into different subsets has been useful to understand their different
functions in various immune scenarios. In some instances, the subsets defined by …
functions in various immune scenarios. In some instances, the subsets defined by …
Machine intelligence in single-cell data analysis: advances and new challenges
The rapid development of single-cell technologies allows for dissecting cellular
heterogeneity at different omics layers with an unprecedented resolution. In-dep analysis of …
heterogeneity at different omics layers with an unprecedented resolution. In-dep analysis of …
Mapping the multiscale structure of biological systems
LV Schaffer, T Ideker - Cell systems, 2021 - cell.com
Biological systems are by nature multiscale, consisting of subsystems that factor into
progressively smaller units in a deeply hierarchical structure. At any level of the hierarchy …
progressively smaller units in a deeply hierarchical structure. At any level of the hierarchy …