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Neuroinformatics is the field that combines informatics and neuroscience. Neuroinformatics is related with neuroscience data and information processing by artificial neural networks. There are three main directions where neuroinformatics has to be applied:
Citation impact is a measure of how many times an academic journal article or book or author is cited by other articles, books or authors. Citation counts are interpreted as measures of the impact or influence of academic work and have given rise to the field of bibliometrics or scientometrics, specializing in the study of patterns of academic impact through citation analysis. The journal impact factor, the two-year average ratio of citations to articles published, is a measure of the importance of journals. It is used by academic institutions in decisions about academic tenure, promotion and hiring, and hence also used by authors in deciding which journal to publish in. Citation-like measures are also used in other fields that do ranking, such as Google's PageRank algorithm, software metrics, college and university rankings, and business performance indicators.
In immunology, an immunological synapse is the interface between an antigen-presenting cell or target cell and a lymphocyte such as a T/B cell or Natural Killer cell. The interface was originally named after the neuronal synapse, with which it shares the main structural pattern. An immunological synapse consists of molecules involved in T cell activation, which compose typical patterns—activation clusters. Immunological synapses are the subject of much ongoing research.
Mark Bender Gerstein is an American scientist working in bioinformatics and Data Science. As of 2009, he is co-director of the Yale Computational Biology and Bioinformatics program.
The Cancer Genome Atlas (TCGA) is a project to catalogue the genetic mutations responsible for cancer using genome sequencing and bioinformatics. The overarching goal was to apply high-throughput genome analysis techniques to improve the ability to diagnose, treat, and prevent cancer through a better understanding of the genetic basis of the disease.
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system.
A connectome is a comprehensive map of neural connections in the brain, and may be thought of as its "wiring diagram". An organism's nervous system is made up of neurons which communicate through synapses. A connectome is constructed by tracing the neuron in a nervous system and mapping where neurons are connected through synapses.
28S ribosomal RNA is the structural ribosomal RNA (rRNA) for the large subunit (LSU) of eukaryotic cytoplasmic ribosomes, and thus one of the basic components of all eukaryotic cells. It has a size of 25S in plants and 28S in mammals, hence the alias of 25S–28S rRNA.
Tobias Bonhoeffer is a German-American neurobiologist. He is director of the department Synapses – Circuits – Plasticity and current managing director at the Max Planck Institute for Biological Intelligence, in foundation ). His father, the neurobiologist Friedrich Bonhoeffer, was director at the Max Planck Institute for Developmental Biology in Tübingen.
Foldit is an online puzzle video game about protein folding. It is part of an experimental research project developed by the University of Washington, Center for Game Science, in collaboration with the UW Department of Biochemistry. The objective of Foldit is to fold the structures of selected proteins as perfectly as possible, using tools provided in the game. The highest scoring solutions are analyzed by researchers, who determine whether or not there is a native structural configuration that can be applied to relevant proteins in the real world. Scientists can then use these solutions to target and eradicate diseases and create biological innovations. A 2010 paper in the science journal Nature credited Foldit's 57,000 players with providing useful results that matched or outperformed algorithmically computed solutions.
Connectomics is the production and study of connectomes: comprehensive maps of connections within an organism's nervous system. More generally, it can be thought of as the study of neuronal wiring diagrams with a focus on how structural connectivity, individual synapses, cellular morphology, and cellular ultrastructure contribute to the make up of a network. The nervous system is a network made of billions of connections and these connections are responsible for our thoughts, emotions, actions, memories, function and dysfunction. Therefore, the study of connectomics aims to advance our understanding of mental health and cognition by understanding how cells in the nervous system are connected and communicate. Because these structures are extremely complex, methods within this field use a high-throughput application of functional and structural neural imaging, most commonly magnetic resonance imaging (MRI), electron microscopy, and histological techniques in order to increase the speed, efficiency, and resolution of these nervous system maps. To date, tens of large scale datasets have been collected spanning the nervous system including the various areas of cortex, cerebellum, the retina, the peripheral nervous system and neuromuscular junctions.
Alice Yen-Ping Ting is Taiwanese-born American chemist. She is a professor of Genetics, of Biology, and by courtesy, of Chemistry at Stanford University. She is also a Chan Zuckerberg Biohub investigator.
The ribbon synapse is a type of neuronal synapse characterized by the presence of an electron-dense structure, the synaptic ribbon, that holds vesicles close to the active zone. It is characterized by a tight vesicle-calcium channel coupling that promotes rapid neurotransmitter release and sustained signal transmission. Ribbon synapses undergo a cycle of exocytosis and endocytosis in response to graded changes of membrane potential. It has been proposed that most ribbon synapses undergo a special type of exocytosis based on coordinated multivesicular release. This interpretation has recently been questioned at the inner hair cell ribbon synapse, where it has been instead proposed that exocytosis is described by uniquantal release shaped by a flickering vesicle fusion pore.
The PhenX Toolkit is a web-based catalog of high-priority measures related to complex diseases, phenotypic traits and environmental exposures. These measures were selected by working groups of experts using a consensus process. Use of PhenX measures facilitates combining data from a variety of studies, and makes it easy for investigators to expand a study design beyond the primary research focus. The Toolkit is funded by the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) with co-funding by the Office of Behavioral and Social Sciences Research (OBSSR) and the National Institute on Drug Abuse (NIDA). Supplemental funding is provided by the National Heart, Lung, and Blood Institute (NHLBI) and the National Institute on Minority Health and Health Disparities (NIMHD). The PhenX Toolkit is available to the scientific community at no cost.
Sage Bionetworks is a nonprofit organization in Seattle that promotes open science and patient engagement in the research process. It is led by Lara Mangravite. It was co-founded by Stephen Friend and Eric Schadt.
The replication crisis is an ongoing methodological crisis in which the results of many scientific studies are difficult or impossible to reproduce. Because the reproducibility of empirical results is an essential part of the scientific method, such failures undermine the credibility of theories building on them and potentially call into question substantial parts of scientific knowledge.
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.
SciCrunch is a collaboratively edited knowledge base about scientific resources. It is a community portal for researchers and a content management system for data and databases. It is intended to provide a common source of data to the research community and the data about Research Resource Identifiers (RRIDs), which can be used in scientific publications. After starting as a pilot of two journals in 2014, by 2022 over 1,000 journals have been using them and over half a million RRIDs have been quoted in the scientific literature. In some respect, it is for science and scholarly publishing, similar to what Wikidata is for Wikimedia Foundation projects. Hosted by the University of California, San Diego, SciCrunch was also designed to help communities of researchers create their own portals to provide access to resources, databases and tools of relevance to their research areas
Robin Angus Silver is Professor of Neuroscience and a Wellcome Trust Principal Research Fellow at University College London. His laboratory studies neurotransmission and artificial neural networks by combining in vitro and in vivo experimental approaches with quantitative analysis and computational models developed in silico.
References
- ↑ Eduati, Federica; Mangravite, Lara M; Saez-Rodriguez, Julio (August 10, 2015). "Prediction of human population responses to toxic compounds by a collaborative competition". Nature Biotechnology . 33 (9): 933–940. doi:10.1038/nbt.3299. PMC 4568441 . PMID 26258538.
- ↑ Bot, Brian M.; Suver, Christine; Neto, Elias Chaibub; Kellen, Michael; Klein, Arno; Bare, Christopher; Doerr, Megan; Pratap, Abhishek; Wilbanks, John; Dorsey, E. Ray; Friend, Stephen H. (2016-03-03). "The mPower study, Parkinson disease mobile data collected using ResearchKit". Scientific Data. 3 (1): 160011. Bibcode:2016NatSD...360011B. doi: 10.1038/sdata.2016.11 . ISSN 2052-4463. PMC 4776701 . PMID 26938265.
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