Jonathan Silverstein

Jan 10, 2025 | nature.com | Benjamin Stear |Jonathan Silverstein

AbstractThe Homo sapiens Chromosomal Location Ontology (HSCLO) is designed to facilitate the integration of human genomic features into biomedical knowledge graphs from releases GRCh37 and GRCh38 at multiple resolutions. HSCLO comprises two distinct versions, HSCLO37 and HSCLO38, each tailored to its respective human genome release.

Aug 14, 2024 | biorxiv.org | Katy Boerner |Philip Blood |Jonathan Silverstein |Matthew Ruffalo

AbstractThe Human BioMolecular Atlas Program (HuBMAP) aims to construct a reference 3D structural, cellular, and molecular atlas of the healthy adult human body. The HuBMAP Data Portal (https://portal.hubmapconsortium.org) serves experimental datasets and supports data processing, search, filtering, and visualization. The Human Reference Atlas (HRA) Portal (https://humanatlas.io) provides open access to atlas data, code, procedures, and instructional materials.

Jun 2, 2024 | nature.com | Vidyani Suryadevara |Adam D. Hudgins |Alberto Pappalardo |Alla Karpova |Amit K. Dey |Birgit Schilling | +23 more

AbstractOnce considered a tissue culture-specific phenomenon, cellular senescence has now been linked to various biological processes with both beneficial and detrimental roles in humans, rodents and other species. Much of our understanding of senescent cell biology still originates from tissue culture studies, where each cell in the culture is driven to an irreversible cell cycle arrest.

Apr 10, 2024 | nature.com | Tiffany J. Callahan |Sanya B. Taneja |Elena Casiraghi |Jonathan Silverstein |Charles Tapley Hoyt |Deepak R. Unni | +7 more

AbstractTranslational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled.

Apr 2, 2024 | biorxiv.org | Katy Boerner |Philip Blood |Jonathan Silverstein |Matthew Ruffalo

AbstractThe Human BioMolecular Atlas Program (HuBMAP) aims to construct a reference 3D structural, cellular, and molecular atlas of the healthy adult human body. The HuBMAP Data Portal (https://portal.hubmapconsortium.org) serves experimental datasets and supports data processing, search, filtering, and visualization. The Human Reference Atlas (HRA) Portal (https://humanatlas.io) provides open access to atlas data, code, procedures, and instructional materials.