A5036680074- Advanced Electron Microscopy Techniques and Applications
- Electron and X-Ray Spectroscopy Techniques
- Metabolomics and Mass Spectrometry Studies
- Enzyme Structure and Function
- Machine Learning in Materials Science
- Advanced X-ray Imaging Techniques
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Advanced Proteomics Techniques and Applications
- Advanced Fluorescence Microscopy Techniques
- Force Microscopy Techniques and Applications
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- COVID-19 diagnosis using AI
- Lipid Membrane Structure and Behavior
- Integrated Circuits and Semiconductor Failure Analysis
- Image Processing Techniques and Applications
- Microbial Metabolic Engineering and Bioproduction
- Scientific Computing and Data Management
- SARS-CoV-2 and COVID-19 Research
- Distributed and Parallel Computing Systems
- Computational Physics and Python Applications
- Microstructure and mechanical properties
- Marine Bivalve and Aquaculture Studies
Centro Nacional de Biotecnología
2016-2024
Universidad Autónoma de Madrid
2016-2022
Biocom
2018-2021
Consejo Superior de Investigaciones Científicas
2021
European Bioinformatics Institute
2012-2017
Wellcome Trust
2012-2017
University of Cambridge
2013
Instituto Volcanológico de Canarias
2001
Instituto Español de Oceanografía
2001
MetaboLights (http://www.ebi.ac.uk/metabolights) is the first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained by one of major providers in molecular biology. Metabolomic profiling an important tool research into biological functioning systemic perturbations caused diseases, diet environment. The effectiveness such methods depends on availability public open across a broad range conditions. repository, powered...
Abstract MetaboLights is the first general purpose, open‐access database repository for cross‐platform and cross‐species metabolomics research at European Bioinformatics Institute (EMBL‐EBI). Based upon open‐source ISA framework, provides Metabolomics Standard Initiative (MSI) compliant metadata raw experimental data associated with experiments. Users can upload their study datasets into Repository. These studies are then automatically assigned a stable unique identifier (e.g., MTBLS1) that...
Metabolomics has become a crucial phenotyping technique in range of research fields including medicine, the life sciences, biotechnology and environmental sciences. This necessitates transfer experimental information between groups, as well potentially to publishers funders. After initial efforts metabolomics standards initiative, minimum reporting were proposed which included concepts for databases. Built by community, infrastructure are still needed allow storage, exchange, comparison...
Recent technological advances and computational developments have allowed the reconstruction of Cryo-Electron Microscopy (cryo-EM) maps at near-atomic resolution. On a typical workflow once cryo-EM map has been calculated, sharpening process is usually performed to enhance visualization, step that proven very important in key task structural modeling. However, approaches, general, neglects local quality map, which clearly suboptimal.Here, new method for density proposed. The algorithm, named...
Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination analysis. This is based on a rich ecosystem of resources around world, which has been build during past ten years, including but not limited to such as MassBank Japan Human Metabolome Database Canada. Now, European Bioinformatics Institute launched MetaboLights, database experiments associated metadata (http://www.ebi.ac.uk/metabolights). It first comprehensive,...
In this article, a method is presented to estimate new local quality measure for 3D cryoEM maps that adopts the form of 'local resolution' type information. The algorithm (
Image processing in cryogenic electron tomography (cryoET) is currently at a similar state as Single Particle Analysis (SPA) microscopy (cryoEM) was few years ago. Its data workflows are far from being well defined and the user experience still not smooth. Moreover, file formats of different software packages their associated metadata standardized, mainly since developed by groups, focusing on steps pipeline. The Scipion framework, originally for SPA (de la Rosa-Trevín et al., 2016), has...
Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of SARS-CoV-2 spike in prefusion state have been analysed. These studies revealed concerted motions involving receptor-binding domain (RBD), N-terminal domain, subdomains 1 2 around previously characterized 1-RBD-up state, which modeled as elastic deformations. It is shown that this data set there are not well defined, stable conformations, but...
Abstract In recent years, advances in cryoEM have dramatically increased the resolution of reconstructions and, with it, number solved atomic models. It is widely accepted that quality maps varies locally; therefore, evaluation maps-derived structural models must be done locally as well. this article, a method for local analysis map-to-model fit presented. The algorithm uses comparison two maps. first FSC (Fourier shell correlation) between full map and model, while second calculated half...
Cryo-electron microscopy (cryoEM) has become a well established technique to elucidate the 3D structures of biological macromolecules. Projection images from thousands macromolecules that are assumed be structurally identical combined into single map representing Coulomb potential macromolecule under study. This article discusses possible caveats along image-processing path and how avoid them obtain reliable structure. Some these problems very known in community. These may referred as...
MetaboLights is the first general-purpose open-access curated repository for metabolomic studies, their raw experimental data and associated metadata, maintained by one of major providers in molecular biology. Increases number depositions, samples per study file size submitted to present a challenge objective ensuring high-quality standardized context diverse workflows representations. Here, we describe curation pipeline, its challenges practical application quality control complex...
The presence of preferred orientations in single particle analysis (SPA) by cryo-Electron Microscopy (cryoEM) is currently one the hurdles preventing many structural analyses from yielding high-resolution structures. Although existence mostly related to grid preparation, this technical note, we show that some image processing algorithms used for angular assignment and three-dimensional (3D) reconstruction are more robust than others these detrimental conditions. We exemplify argument with...
Three dimensional electron microscopy is becoming a very data-intensive field in which vast amounts of experimental images are acquired at high speed. To manage such large-scale projects, we had previously developed modular workflow system called Scipion (de la Rosa-Trevín et al., 2016). We present here major extension that allows processing EM while the data being acquired. This approach helps to detect problems early stages, saves computing time and provides users with detailed evaluation...
Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and tomography, designed managed by the Biocomputing Unit Spanish National Center Biotechnology, although with contributions many other developers over world. During its 25 years existence, underwent changes updates. While there were publications related to new functionality added Xmipp, no single publication on as a since 2013. In this article, we give overview...
Advances in cryo-electron microscopy (cryo-EM) have made it possible to obtain structures of large biological macromolecules at near-atomic resolution. This "resolution revolution" has encouraged the use and development modeling tools able produce high-quality atomic models from cryo-EM density maps. Unfortunately, many practical problems appear when combining different packages same processing workflow, which make difficult these by non-experts and, therefore, reduce their utility. We...
Abstract Image-processing pipelines require the design of complex workflows combining many different steps that bring raw acquired data to a final result with biological meaning. In image-processing domain cryo-electron microscopy single-particle analysis (cryo-EM SPA), hundreds must be performed obtain three-dimensional structure macromolecule by integrating spread over thousands micrographs containing millions copies allegedly same macromolecule. The execution such complicated demands...
Abstract Macromolecular structural determination by Electron Microscopy under cryogenic conditions is revolutionizing the field of biology, interesting a large community potential users. Still, path from raw images to density maps complex, and sophisticated image processing suites are required in this process, often demanding installation understanding different software packages. Here, we present Scipion Web Tools, web‐based set tools/workflows derived framework, specially tailored...
Understanding how structure and function meet to drive biological processes is progressively shifting the cryoEM field towards a more advanced analysis of macromolecular flexibility. Thanks techniques such as single-particle electron tomography, it possible image macromolecule in different states, information that can subsequently be extracted through image-processing methods build richer approximation conformational landscape. However, interoperability all these algorithms remains...
Electron microscopy of macromolecular structures is an approach that in increasing demand the field structural biology. The automation image acquisition has greatly increased potential throughput electron microscopy. Here, focus on possibilities Scipion to implement flexible and robust image-processing workflows allow electron-microscope operator user monitor quality acquisition, assessing very simple measures or obtaining a first estimate initial volume, data resolution heterogeneity,...
Abstract With the help of novel processing workflows and algorithms, we have obtained a better understanding flexibility conformational dynamics SARS-CoV-2 spike in prefusion state. We re-analyzed previous cryo-EM data combining 3D clustering approaches with ways to explore continuous space based on Principal Component Analysis. These advanced analyses revealed concerted motion involving receptor-binding domain (RBD), N-terminal (NTD), subdomain 1 2 (SD1 & SD2) around previously...