A5090269921- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Cell Image Analysis Techniques
- Mitochondrial Function and Pathology
- Nitric Oxide and Endothelin Effects
- Genomics and Phylogenetic Studies
- Single-cell and spatial transcriptomics
- Epigenetics and DNA Methylation
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- Anesthesia and Neurotoxicity Research
- Genetics, Aging, and Longevity in Model Organisms
- Neurogenesis and neuroplasticity mechanisms
- Mesenchymal stem cell research
- Renin-Angiotensin System Studies
- Memory and Neural Mechanisms
- Electron Spin Resonance Studies
- Machine Learning in Bioinformatics
- ATP Synthase and ATPases Research
- Radiation Dose and Imaging
- Neural dynamics and brain function
- Anatomy and Medical Technology
- Gastrointestinal Bleeding Diagnosis and Treatment
- Psychological and Temporal Perspectives Research
University of Szeged
2022-2024
Age UK
2019-2024
Wellcome/MRC Cambridge Stem Cell Institute
2019
European Bioinformatics Institute
2012-2018
Wellcome Trust
2012-2018
CHI Health Creighton University Medical Center - Bergan Mercy
2010-2017
Zero to Three
2014
Center for Systems Biology
2014
Digital Proteomics (United States)
2014
Rutgers, The State University of New Jersey
2013
The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data, and one founding members global ProteomeXchange (PX) consortium. In this manuscript, we summarize developments in PRIDE resources related tools since previous update manuscript was published Nucleic Acids Research 2016. last 3 years, public sharing through (as part PX) has definitely become norm field. parallel, re-use increased...
The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories mass spectrometry (MS)-based proteomics data. Since beginning 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) new archival system, replacing original database. Here we summarize developments in resources and related tools since previous update manuscript Database Issue 2013. constitutes a complete redevelopment PRIDE, comprising storage backend, submission system web interface, among other...
The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of most prominent data repositories mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in PRIDE and related tools. First, provide up-to-date statistics content, splitting figures by groups organisms species, including peptide protein identifications, post-translational modifications. We then describe tools that are part submission...
The ProteomeXchange (PX) Consortium of proteomics resources (http://www.proteomexchange.org) was formally started in 2011 to standardize data submission and dissemination mass spectrometry worldwide. We give an overview the current consortium activities describe advances past few years. Augmenting PX founding members (PRIDE PeptideAtlas, including PASSEL resource), two new have joined consortium: MassIVE jPOST. ProteomeCentral remains as common access portal, providing ability search for...
The most prominent feature of the Basal Forebrain (BF) is collection large cortically projecting neurons (basal nucleus Meynert) that serve as primary source cholinergic input to entire cortical mantle. Despite its broad involvement in activation, attention, and memory, functional details BF are not well understood due anatomical complexity region. This study tested hypothesis basalocortical connections reflect connectivity patterns. Distinct retrograde tracers were deposited into various...
The original PRIDE Inspector tool was developed as an open source standalone to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before submission or already publicly available in Proteomics Identifications (PRIDE) database. initial implementation focused on visualizing by supporting XML format a direct access private (password protected) public experiments PRIDE.The ProteomeXchange (PX) Consortium has been set up better integration existing...
The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to database. However, after much user feedback, it was noted that had some limitations and could not handle several requirements were now becoming commonplace. This prompted us design implement a whole new suite tools would build on successes allow users generate submission-ready, well-annotated XML files. 2 allows convert search result files into (the format needed for...
The ProteomeXchange (PX) consortium has been established to standardize and facilitate submission dissemination of MS-based proteomics data in the public domain. In consortium, PRIDE database at European Bioinformatics Institute, acts as initial point MS/MS sets. this manuscript, we explain step by process sets PX via PRIDE. We describe detail two available workflows: 'complete' 'partial' submissions, together with tools streamline process. Throughout will use one example set containing...
For shotgun mass spectrometry based proteomics the most computationally expensive step is in matching spectra against an increasingly large database of sequences and their post-translational modifications with known masses. Each spectrometer can generate data at astonishingly high rate, scope what searched for continually increasing. Therefore solutions improving our ability to perform these searches are needed. We present a sequence search engine that specifically designed run efficiently...
The PRoteomics IDEntifications (PRIDE) database is a large public proteomics data repository, containing over 270 million mass spectra (by November 2011). PRIDE an archival database, providing the supporting specific scientific publications in computationally accessible manner. While faces rapid increases deposition size as well number of depositions, major challenge to ensure high quality depositions context highly diverse work flows and representations. Here, we describe curation pipeline...
We measured the contribution of mitochondrial nitric oxide synthase (mtNOS) and respiratory chain enzymes to reactive nitrogen species (RNS) production. Diaminofluorescein (DAF) was applied for assessment RNS production in isolated mouse brain, heart liver mitochondria also a cultured neuroblastoma cell line by confocal microscopy flow cytometry. Mitochondria produced RNS, which inhibited catalysts peroxynitrite decomposition but not (NO) inhibitors. Disrupting organelles or withdrawing...
The PRIDE database, developed and maintained at the European Bioinformatics Institute (EBI), is one of most prominent data repositories dedicated to high throughput MS-based proteomics data. Peptidome, by National Center for Biotechnology Information (NCBI) as a sibling resource PRIDE, was discontinued due funding constraints in April 2011. A joint effort between two teams started soon after Peptidome closure ensure that were not "lost" wider community exporting it PRIDE. As result, low...
Abstract Biological age is typically estimated using biomarkers whose states have been observed to correlate with chronological age. A persistent limitation of such aging clocks that it difficult establish how the biomarker are related mechanisms aging. Somatic mutations could potentially form basis for a more fundamental clock since both markers and drivers natural timescale. Cell lineage trees inferred from these reflect somatic evolutionary process, thus, has conjectured, status body....