The Human Biomolecular Atlas Program (HuBMAP) is a program funded by the US National Institutes of Health to characterize the human body at single cell resolution, integrated to other efforts such as the Human Cell Atlas. [1] Among the products of the program is the Azimuth reference datasets for single-cell RNA seq data [2] [3] and the ASCT+B Reporter, a visualization tool for anatomical structures, cell types and biomarkers. [4] [5]
Millitomes are used to create uniformly sized tissue blocks that match the shape and size of organs from HuBMAP's 3D Reference Object Library. [6]
The HuBMAP received 27 million US dollars of funding from the NIH in 2020 and about 28.5 million in 2021. [7]
The National Institutes of Health, commonly referred to as NIH, is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late 1880s and is now part of the United States Department of Health and Human Services. Many NIH facilities are located in Bethesda, Maryland, and other nearby suburbs of the Washington metropolitan area, with other primary facilities in the Research Triangle Park in North Carolina and smaller satellite facilities located around the United States. The NIH conducts its own scientific research through the NIH Intramural Research Program (IRP) and provides major biomedical research funding to non-NIH research facilities through its Extramural Research Program.
An integral, or intrinsic, membrane protein (IMP) is a type of membrane protein that is permanently attached to the biological membrane. All transmembrane proteins can be classified as IMPs, but not all IMPs are transmembrane proteins. IMPs comprise a significant fraction of the proteins encoded in an organism's genome. Proteins that cross the membrane are surrounded by annular lipids, which are defined as lipids that are in direct contact with a membrane protein. Such proteins can only be separated from the membranes by using detergents, nonpolar solvents, or sometimes denaturing agents.
An epigenome consists of a record of the chemical changes to the DNA and histone proteins of an organism; these changes can be passed down to an organism's offspring via transgenerational stranded epigenetic inheritance. Changes to the epigenome can result in changes to the structure of chromatin and changes to the function of the genome.
EcoHealth Alliance is a US-based non-governmental organization with a stated mission of protecting people, animals, and the environment from emerging infectious diseases. The nonprofit focuses on research aimed at preventing pandemics and promoting conservation in hotspot regions worldwide.
Brain mapping is a set of neuroscience techniques predicated on the mapping of (biological) quantities or properties onto spatial representations of the brain resulting in maps.
Single-stranded DNA-binding protein 2 is a protein that in humans is encoded by the SSBP2 gene.
The Human Microbiome Project (HMP) was a United States National Institutes of Health (NIH) research initiative to improve understanding of the microbiota involved in human health and disease. Launched in 2007, the first phase (HMP1) focused on identifying and characterizing human microbiota. The second phase, known as the Integrative Human Microbiome Project (iHMP) launched in 2014 with the aim of generating resources to characterize the microbiome and elucidating the roles of microbes in health and disease states. The program received $170 million in funding by the NIH Common Fund from 2007 to 2016.
Nader Pourmand is a Professor of Biomolecular Engineering leading the Biosensors and Bioelectrical Technology Group at the Baskin School of Engineering at the University of California Santa Cruz, Baskin School of Engineering.
Mark Atkinson is an American medical researcher best known for his contributions to research seeking to predict, prevent, and cure type 1 diabetes. He is the author of over 600 publications and is one of the world's most cited diabetes researchers.
Aviv Regev is a computational biologist and systems biologist and Executive Vice President and Head of Genentech Research and Early Development in Genentech/Roche. She is a core member at the Broad Institute of MIT and Harvard and professor at the Department of Biology of the Massachusetts Institute of Technology. Regev is a pioneer of single cell genomics and of computational and systems biology of gene regulatory circuits. She founded and leads the Human Cell Atlas project, together with Sarah Teichmann.
Extracellular RNA (exRNA) describes RNA species present outside of the cells in which they were transcribed. Carried within extracellular vesicles, lipoproteins, and protein complexes, exRNAs are protected from ubiquitous RNA-degrading enzymes. exRNAs may be found in the environment or, in multicellular organisms, within the tissues or biological fluids such as venous blood, saliva, breast milk, urine, semen, menstrual blood, and vaginal fluid. Although their biological function is not fully understood, exRNAs have been proposed to play a role in a variety of biological processes including syntrophy, intercellular communication, and cell regulation. The United States National Institutes of Health (NIH) published in 2012 a set of Requests for Applications (RFAs) for investigating extracellular RNA biology. Funded by the NIH Common Fund, the resulting program was collectively known as the Extracellular RNA Communication Consortium (ERCC). The ERCC was renewed for a second phase in 2019.
Dana Pe'er, Chair and Professor in Computational and Systems Biology Program at Sloan Kettering Institute is a researcher in computational systems biology. A Howard Hughes Medical Institute (HHMI) Investigator since 2021, she was previously a professor at Columbia Department of Biological Sciences. Pe'er's research focuses on understanding the organization, function and evolution of molecular networks, particularly how genetic variations alter the regulatory network and how these genetic variations can cause cancer.
Multiomics, multi-omics, integrative omics, "panomics" or "pan-omics" is a biological analysis approach in which the data sets are multiple "omes", such as the genome, proteome, transcriptome, epigenome, metabolome, and microbiome ; in other words, the use of multiple omics technologies to study life in a concerted way. By combining these "omes", scientists can analyze complex biological big data to find novel associations between biological entities, pinpoint relevant biomarkers and build elaborate markers of disease and physiology. In doing so, multiomics integrates diverse omics data to find a coherently matching geno-pheno-envirotype relationship or association. The OmicTools service lists more than 99 softwares related to multiomic data analysis, as well as more than 99 databases on the topic.
The Ray and Stephanie Lane Computational Biology Department (CBD) is a one of the seven departments within the School of Computer Science at Carnegie Mellon University in Pittsburgh, Pennsylvania, United States. Now situated in the Gates-Hillman Center, CBD was established in 2007 as the Lane Center for Computational Biology by founding department head Robert F. Murphy. The establishment was supported by funding from Raymond J. Lane and Stephanie Lane, CBD officially became a department within the School of Computer Science in 2009. In November 2023, Carnegie Mellon named the department as the Ray and Stephanie Lane Computational Biology Department, in recognition of the Lanes' significant investment in computational biology at CMU.
James M. Anderson is an American Professor of Medicine and Cell Biology and is a Chief of Section of Digestive Diseases at the Yale School of Medicine. Anderson is also a director of the Division of Program Coordination, Planning, and Strategic Initiatives at the National Institutes of Health.
Jin Zhang is a Chinese-American biochemist. She is a professor of pharmacology, chemistry and biochemistry, and biomedical engineering at the University of California, San Diego.
The Human Cell Atlas is a project to describe all cell types in the human body. The initiative was announced by a consortium after its inaugural meeting in London in October 2016, which established the first phase of the project. Aviv Regev and Sarah Teichmann defined the goals of the project at that meeting, which was convened by the Broad Institute, the Wellcome Trust Sanger Institute and Wellcome Trust. Regev and Teichmann lead the project.
Sandro Santagata is an associate professor at Harvard Medical School and a physician-scientist at Brigham and Women’s Hospital where he practices neuropathology. His research focuses on precision medicine in cancer biology.
A millitome is a device designed to hold a freshly procured organ and facilitate cutting it into many small tissue blocks for usage in single-cell analysis. A millitome has discrete, equally placed cutting grooves in both the x and y directions to guide a carbon steel cutting knife to produce uniformly sized slices or cubes of tissue material. Millitome design and usage was developed by the HIVE MC-IU Team, Indiana University and members of the Cyberinfrastructure for Network Science Center (CNS) for the Human Reference Atlas project, which is part of the U.S. National Institutes of Health Common Fund’s Human Biomolecular Atlas Program (HuBMAP).