Graph representation learning in biomedicine and healthcare

MM Li, K Huang, M Zitnik - Nature Biomedical Engineering, 2022 - nature.com
Networks—or graphs—are universal descriptors of systems of interacting elements. In
biomedicine and healthcare, they can represent, for example, molecular interactions …

RNA-binding proteins in human genetic disease

F Gebauer, T Schwarzl, J Valcárcel… - Nature Reviews …, 2021 - nature.com
RNA-binding proteins (RBPs) are critical effectors of gene expression, and as such their
malfunction underlies the origin of many diseases. RBPs can recognize hundreds of …

HMDB 5.0: the human metabolome database for 2022

DS Wishart, AC Guo, E Oler, F Wang… - Nucleic acids …, 2022 - academic.oup.com
Abstract The Human Metabolome Database or HMDB (https://hmdb. ca) has been providing
comprehensive reference information about human metabolites and their associated …

OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity

D Kuznetsov, F Tegenfeldt, M Manni… - Nucleic Acids …, 2023 - academic.oup.com
OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling of
eukaryotes, prokaryotes, and viruses. Genomics continues to accelerate our exploration of …

Highly accurate protein structure prediction for the human proteome

K Tunyasuvunakool, J Adler, Z Wu, T Green, M Zielinski… - Nature, 2021 - nature.com
Protein structures can provide invaluable information, both for reasoning about biological
processes and for enabling interventions such as structure-based drug development or …

[PDF][PDF] clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng… - The innovation, 2021 - cell.com
Functional enrichment analysis is pivotal for interpreting high-throughput omics data in life
science. It is crucial for this type of tool to use the latest annotation databases for as many …

Acute inflammatory response via neutrophil activation protects against the development of chronic pain

M Parisien, LV Lima, C Dagostino… - Science translational …, 2022 - science.org
The transition from acute to chronic pain is critically important but not well understood. Here,
we investigated the pathophysiological mechanisms underlying the transition from acute to …

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

B Amos, C Aurrecoechea, M Barba… - Nucleic Acids …, 2022 - academic.oup.com
Abstract The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB,
https://veupathdb. org) represents the 2019 merger of VectorBase with the EuPathDB …

Single-cell dissection of the human brain vasculature

FJ Garcia, N Sun, H Lee, B Godlewski, H Mathys… - Nature, 2022 - nature.com
Despite the importance of the cerebrovasculature in maintaining normal brain physiology
and in understanding neurodegeneration and drug delivery to the central nervous system …

Gene set knowledge discovery with Enrichr

Z Xie, A Bailey, MV Kuleshov, DJB Clarke… - Current …, 2021 - Wiley Online Library
Profiling samples from patients, tissues, and cells with genomics, transcriptomics,
epigenomics, proteomics, and metabolomics ultimately produces lists of genes and proteins …