Articles by Jonathan Silverstein
HuBMAP Data Portal: a resource for multimodal spatial and single-cell data of healthy human tissues
Abstract The NIH Human BioMolecular Atlas Program (HuBMAP) Data Portal (https://portal.hubmapconsortium.org/) serves as a comprehensive repository for multimodal, multi-scale spatial and single-cell data from healthy human tissues. As of August 2026, the portal hosts 9,316 public datasets from 26 data types spanning 29 organ classes across 501 donors. Portal infrastructure and user interfaces support data search and discovery, visualization, and analysis directly in web browsers.
Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage - Nature Methods
Abstract The Human BioMolecular Atlas Program (HuBMAP) aims to construct a 3D Human Reference Atlas (HRA) of the healthy adult body. Experts from 20+ consortia collaborate to develop a Common Coordinate Framework (CCF), knowledge graphs and tools that describe the multiscale structure of the human body (from organs and tissues down to cells, genes and biomarkers) and to use the HRA to characterize changes that occur with aging, disease and other perturbations.
Homo Sapiens Chromosomal Location Ontology: A Framework for Genomic Data in Biomedical Knowledge Graphs - Scientific Data
Abstract The 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.
Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage
Abstract The 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.
SenNet recommendations for detecting senescent cells in different tissues - Nature Reviews Molecular Cell Biology
|
Abstract Once 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.
By Vidyani Suryadevara, Adam D. Hudgins, Alberto Pappalardo, Alla Karpova, Amit K. Dey, Birgit Schilling, Cristina Aguayo-Mazzucato, Darren Baker, Diana Jurk, Elizabeth Schmidt, George A. Kuchel, Jonathan Silverstein, Kanako Iwasaki, Karina O Barbosa, Madison L. Doolittle, Marissa J. Schafer, Ming Xu, Mozhgan Boroumand, Paul Robson, Peter Adams, Ramalakshmi Ramasamy, Rong Fan, Ruth R. Montgomery, Sundeep Khosla, Yizhe Song, Helene Martini, Marcos G. Teneche, Periklis Vasilikos, Rolando Perez-Lorenzo
|
Nature
Verified
An open source knowledge graph ecosystem for the life sciences - Scientific Data
Abstract Translational 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.
Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage
Abstract The 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.
Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging - Nature Methods
|
Abstract Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Advances in the field now allow high-parameter data collection (>60 targets); however, considerable expertise and capital are needed to construct the antibody panels employed by these methods.
By Ellen Quardokus, Diane Saunders, Elizabeth Zephyrine McDonough, John Hickey Verified, Christopher Werlein, Hua Tian, Josh Croteau, Anne E. Wiblin, Jeremy Fisher, Jonathan Silverstein, Jeffrey M. Spraggins, Gloria Pryhuber, Simon Melov, Danny Jonigk, Ioannis S. Vlachos, Werner Müller, Nils Gehlenborg, Brent R. Stockwell, Emma Lundberg, Michael Snyder, Ronald N Germain, Neil L. Kelleher, Katy Börner
|
Nature
Verified
Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis - Nature Cancer
|
Abstract The AURORA US Metastasis Project was established with the goal to identify molecular features associated with metastasis. We assayed 55 females with metastatic breast cancer (51 primary cancers and 102 metastases) by RNA sequencing, tumor/germline DNA exome and low-pass whole-genome sequencing and global DNA methylation microarrays. Expression subtype changes were observed in ~30% of samples and were coincident with DNA clonality shifts, especially involving HER2.
By Gregory Wheeler, Ana C. Garrido-Castro, Brooke M. Felsheim, Markia Smith, Paula Ericsson, Chad J. Creighton, Jay Bowen, Joel Parker, Carey Anders, Mothaffar F. Rimawi, Rita Nanda, Jonathan Silverstein, Alexander J. Ropelewski, Minetta C. Liu, W. Fraser Symmans, Lisa Carey, Adrian Lee, Justin M. Balko, Katherine A. Hoadley, Peter W. Laird, Elaine R. Mardis
|
Nature
Verified
Tissue registration and exploration user interfaces in support of a human reference atlas - Communications Biology
The RUI and EUI were released in May 2021 with continuous updates following. Since then, they have been adopted by six consortia contributing data toward the HRA. Both user interfaces are available as web components, which have been successfully integrated in the HuBMAP portal and rebranded for the GTEx33 and SenNet portals34,35. The CCF-HRA’s three ontologies have been fully implemented for 25 organs.
Xtant Medical Holdings, Inc. Changes to Beneficial Ownership: Orbimed ROF II LLC (Director, 10%+) (Form4) (0001790300-19-000006)
SEC Form 4 FORM 4 UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934 or Section 30(h) of the Investment Company Act of 1940 OMB APPROVAL OMB Number: 3235-0287 Estimated average burden hours per response: 0.5 Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b). 1.
Gain recognition agreements: US corporation’s transfer of a foreign corporation followed by the foreign corporation’s disposition of its assets
By Emily Arjani Barnhart, CPA, and Jonathan Silverstein, J.D., Washington, D.C. Editor: Christine M. Turgeon, CPA U.S. corporations regularly transfer property to subsidiaries in transactions that qualify for tax-deferred treatment for U.S. federal income tax purposes (see, e.g., Secs. 351 and 354).
Heschel Heat Girls Hockey Repeat as MYHSAL Champions
You are here: Home Sports Teaneck Doghouse Sportstar of the Week: Shoshana Lofstock By Jonathan Silverstein | June 06, 2019 The Heschel Heat team. The seniors on the team. Prev 1 of 2 Next On Wednesday night May 29, the MYHSAL girls varsity hockey championship was played out in Ma’ayanot girls high school gym between the 2018 defending champion Heschel Heat and the up and coming Ramaz Rams, who were making their first appearance in the championship game.
Review: They Meet Again in ‘Later Life.’ Will Fireworks Follow?
His version of the character is upright, forthright and transparent almost to the point of invisibility. Similarly, the revival in which he appears, directed by Jonathan Silverstein, is most notable for its lucidity. It’s a gentle production that lets Gurney speak for himself, without flashy interpretive obstructions. While this approach may not make for thrilling theater, it does allow you to see Gurney plain.
Review: In ‘Lonely Planet,’ Mismatched Friends and an Unnamed Plague
But Mr. Dietz has something besides humor in mind (even if there is plenty of it) and that something — the weight of grief, the paralyzing fear of illness — emerges over the course of the show, like a photograph coming into focus in a dark room. The first sign of unsettlement is when Carl starts bringing mismatched chairs to Jody’s shop, where the play takes place, claiming his own apartment is too small. As the chairs progressively take over the space, we learn that Jody has stopped going home.
We need to approach rare diseases with a hive mind to find a cure
After my diagnosis, my professional life suddenly took a very personal turn. I went public with my story in Forbes on April 27, and was quickly inundated by emails and calls from all over the globe. I realized my unique position to make a real impact on Parkinson's disease. I can raise awareness and the funds necessary to accelerate research into therapies that provide not only incremental improvement in the symptoms, but hopefully, a cure.
Review: In ‘When It’s You,’ Isolation Has Consequences
Ginnifer hasn’t had many boyfriends, and frankly the last one was a creep. But the first? A boy named Jason Hanley back in high school? For two decades, she’s remembered him fondly. When her mom died a few years ago, he came to the funeral and brought a Key lime pie. So it is with more than the usual kind of horror that she reacts to a mass shooting in their city. She learns the news on Facebook, when scores of old classmates direct-message her, thinking she’ll have some insight.
How Activision Is Keeping "Call Of Duty" Cutting Edge 13 Years And $15 Billion Later
The near-deafening pulse of electronic base from the Prodigy’s "The Day Is My Enemy" echoed through the massive arena, muffling the screams and cheers of the hundreds amassed for the event. Two massive screens lit up the crowd, displaying images of sci-fi soldiers on alien worlds battling in fierce combat at breakneck speeds.
Show More
loading
Actions
Is this you?
As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work.Get in touch with Jonathan
Contact Jonathan, search articles and posts on X, monitor coverage, and track replies from one place.
Learn more about Muck Rack