20 papers · ranked by Valyu relevance
Katy Börner, Philip D. Blood, Jonathan C. Silverstein, Matthew Ruffalo + 16 more
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…
Yashvardhan Jain, Bhargav Desai, Danial Qaurooni, Antara Bhavsar + 7 more
Over the last five years, over 13,000 tissue datasets with 200+ million cells from 20 consortia have been spatially registered into the Human Reference Atlas (HRA) common coordinate framework (CCF). The shared 3D spatial and semantic reference system enables exploration of datasets in the context of all other data…
Katy Börner, Sarah A. Teichmann, Ellen M. Quardokus, James Gee + 32 more
This paper reviews efforts across 16 international consortia to construct human anatomical structures, cell types, and biomarkers (ASCT+B) tables and three-dimensional reference organs in support of a Human Reference Atlas. We detail the ontological descriptions and spatial three-dimensional anatomical representations…
Andreas Bueckle, Bruce W. Herr, Lu Chen, Daniel Bolin + 7 more
The human body contains ∼27–36 trillion cells of up to 10,000 cell types (CTs) within a volume of ∼62–120 liters (males) and 52–89 liters (females). The Human Reference Atlas (HRA) v2.3 provides a quantitative 3D framework of CTs across 73 reference organs and 1,283 3D anatomical structures (ASs). The HRA Cell Type…
Wieslaw L. Nowinski
Despite numerous efforts, a fairly complete (holistic) anatomical model of the whole, normal, adult human brain, which is required as the reference in brain studies and clinical applications, has not yet been constructed. Our ultimate objective is to build this kind of atlas from advanced in vivo imaging. This work…
Wieslaw L. Nowinski
Human brain atlas development is predominantly research-oriented and the use of atlases in clinical practice is limited. Here I introduce a new definition of a reference human brain atlas that serves education, research and clinical applications, and is extendable by its user. Subsequently, an architecture of a…
Heidi Kleven, Thomas H. Gillespie, Lyuba Zehl, Timo Dickscheid + 3 more
Brain atlases are important reference resources for accurate anatomical description of neuroscience data. Open access, three-dimensional atlases serve as spatial frameworks for integrating experimental data and defining regions-of-interest in analytic workflows. However, naming conventions, parcellation criteria, area…
Wieslaw L. Nowinski
Human brain atlases have been evolving tremendously, propelled recently by brain big projects, and driven by sophisticated imaging techniques, advanced brain mapping methods, vast data, analytical strategies, and powerful computing. We overview here this evolution in four categories: content, applications…
Heidi Kleven, Thomas H. Gillespie, Lyuba Zehl, Timo Dickscheid + 3 more
Brain atlases are important reference resources for accurate anatomical description of neuroscience data. Open access, three-dimensional atlases serve as spatial frameworks for integrating experimental data and defining regions-of-interest in analytic workflows. However, naming conventions, parcellation criteria, area…
Katy Börner, Ellen M. Quardokus, Bruce Herr, Leonard E. Cross + 13 more
'Elizabeth G. Record' 'Yingnan Ju' 'Andreas Bueckle' 'James P. Sluka' 'Jonathan C. Silverstein' 'Kristen Browne' 'Sanjay Jain' 'Clive Wasserfall' 'Marda Jorgensen' 'Jeffrey M. Spraggins' 'Nathan Heath Patterson' 'Mark A. Musen' 'Griffin M. Weber'] Katy Börner1 , Ellen M. Quardokus1 , Bruce W. Herr II1 , Leonard E.…
Sophie Starck, Vasiliki Sideri-Lampretsa, Jessica Johanna Maria Ritter, Veronika A. Zimmer + 3 more
'Jessica Johanna Maria Ritter' 'Veronika A. Zimmer' 'Rickmer Braren' 'Tamara T. Mueller' 'Daniel Rueckert'] Reliable reference data in medical imaging is largely unavailable. Developing tools that allow for the comparison of individual patient data to reference data has a high potential to enhance the sensitivity and…
Sara Ball, Terri L. Gilbert, Caroline C. Overly
This community page describes the database and associated Web application that comprise the Allen Human Brain Atlas, an open online resource that integrates genomic and anatomic human brain data.
Ho Hin Lee, Adam Saunders, Michael E. Kim, Samuel W. Remedios + 13 more
'Yucheng Tang' 'Qi Yang' 'Xin Yu' 'Shunxing Bao' 'Chloe Cho' 'Louise A. Mawn' 'Tonia S. Rex' 'Kevin L. Schey' 'Blake E. Dewey' 'Jeffrey M. Spraggins' 'Jerry L. Prince' 'Yuankai Huo' 'Bennett A. Landman'] **Ho Hin Lee, a,† Adam M. Saunders, b,†, Michael E. Kim, a Samuel W. Remedios, c Lucas W. Remedios,a Yucheng Tang, b…
Bryon Drown, Kevin Jooß, Rafael Melani, Cameron Lloyd-Jones + 2 more
A functional understanding of the human body requires structure-function studies of proteins at scale. The chemical structure of proteins is controlled at the transcriptional, translational, and post-translational levels, creating a variety of products with modulated functions within the cell. The term “proteoform”…
Halid Ziya Yerebakan, Kritika Iyer, Xueqi Guo, Yoshihisa Shinagawa + 1 more
'Gerardo Hermosillo Valadez'] We introduce a new type of foundational model for parsing human anatomy in medical images that works for different modalities. It supports supervised or unsupervised training and can perform matching, registration, classification, or segmentation with or without user interaction. We…
Ho Hin Lee, Yucheng Tang, Kaiwen Xu, Shunxing Bao + 7 more
'Raymond C. Harris' 'Mark P. de Caestecker' 'Mattias P. Heinrich\u202c' 'Jeffrey M. Spraggins' 'Yuankai Huo' 'Bennett A. Landman'] Abstract— The construction of three-dimensional multi-modal tissue maps provides an opportunity to spur interdisciplinary innovations across temporal and spatial scales through information…
Griffin M. Weber, Yingnan Ju, Katy Börner
Several ongoing international efforts are developing methods of localizing single cells within organs or mapping the entire human body at the single cell level, including the Chan Zuckerberg Initiative's Human Cell Atlas (HCA), and the Knut and Allice Wallenberg Foundation's Human Protein Atlas (HPA), and the National…
Authors not listed
One aim of the international Human Proteome Organization (HUPO) Human Proteome Project (HPP) is to obtain high-confidence translation evidence for every human protein-coding gene established in its target list of 19433 entries based on the protein-coding genes from Ensembl-GENCODE. However, 76 are annotated in…
Riley Hickman, Malcolm Sim, Sergio Pablo-García, Ivan Woolhouse + 6 more
Self-driving laboratories (SDLs) are next-generation research and development platforms for closed-loop, autonomous experimentation that combine ideas from artificial intelligence, robotics, and high-performance computing. A critical component of SDLs is the decision-making algorithm used to prioritize experiments to…
Authors not listed
The mechanisms underlying human odor recognition remain largely unclear, making it challenging to predict the scent of a novel molecule based solely on its molecular structure. Unlike taste, which is classified into a limited number of categories, odor perception is highly complex and lacks universally defined labels…