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  • ELIXIR GR
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Carlos Pérez Cantalapiedra; Ana Hernández-Plaza; Ivica Letunic; Peer Bork; +1 Authors

    Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows for: 1) de novo gene prediction from raw contigs, 2) built-in pairwise orthology prediction, 3) fast protein domain discovery, and 4) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de. This research was supported by the National Programme for Fostering Excellence in Scientific and Technical Research (Grant No. PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE, to J.H.C.) and the Severo Ochoa Centres of Excellence Programme (Grant No. SEV-2016-0672 (2017–2021) to C.P.C.) from the State Research Agency (AEI) of Spain, as well as a Research Technical Support Staff Aid (PTA2019-017593-I/AEI/10.13039/501100011033 to A.H.P.); European Research Council grant MicroBioS (ERC-2014-AdG)—GA669830 (to P.B.). Cloud computing is supported by BMBF (de.NBI network #031A537B). Centro de Biotecnología y Genómica de Plantas (CBGP) Peer reviewed 5 Pág.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    Molecular Biology and Evolution
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Molecular Biology and Evolution
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Jose Ramon Macias; Rubén J. Sánchez-García; Pablo Conesa; Erney Ramírez-Aportela; +8 Authors

    The web platform 3DBionotes-WS integrates multiple Web Services and an interactive Web Viewer to provide a unified environment in which biological annotations can be analyzed in their structural context. Since the COVID-19 outbreak, new structural data from many viral proteins have been provided at a very fast pace. This effort includes many cryogenic Electron Microscopy (cryo-EM) studies, together with more traditional ones (X-rays, NMR), using several modeling approaches and complemented with structural predictions. At the same time, a plethora of new genomics and interactomics information (including fragment screening and structure-based virtual screening efforts) have been made available from different servers. In this context we have developed 3DBionotes-COVID-19 as an answer to: (1) The need to explore multi-omics data in a unified context with a special focus on structural information and (2) the drive to incorporate quality measurements, especially in the form of advanced validation metrics for cryogenic Electron Microscopy. We acknowledge financial support from: CSIC (PIE/COVID-19 number 202020E079), the Comunidad de Madrid through grant CAM (S2017/BMD-3817), the Spanish Ministry of Science and Innovation through projects (SEV 2017-0712, FPU-2015/264, PID2019-104757RB-I00 / AEI / 10.13039/501100011033), the Instituto de Salud Carlos III: PT17/0009/0010 (ISCIII-SGEFI / ERDF-) and the European Union and Horizon 2020 through grant: CORBEL (INFRADEV-01-2014- 1, Proposal 654248) and EOSC Life (INFRAEOSC-04-2018, Proposal: 824087). This work was supported by Instruct-ULTRA (Grant 731005), an EU H2020 project to further develop the services of Instruct-ERIC. Contributions from the Coronavirus Structural Task Force were supported by the German Federal Ministry of Education and Research [grant no. 05K19WWA] and Deutsche Forschungsgemeinschaft [project TH2135/2-1]. The authors acknowledge the support and the use of resources of Instruct, a Landmark ESFRI project. https://3dbionotes.cnb.csic.es/ws/covid19 Peer reviewed

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    Bioinformatics
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Acta Crystallographica Section A Foundations and Advances
    Article . 2021 . Peer-reviewed
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      Bioinformatics
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Acta Crystallographica Section A Foundations and Advances
      Article . 2021 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Gerard Minuesa; Cristina Alsina; Juan Antonio Garcia-Martin; Juan Carlos Oliveros; +1 Authors

    Novel tools for in silico design of RNA constructs such as riboregulators are required in order to reduce time and cost to production for the development of diagnostic and therapeutic advances. Here, we present MoiRNAiFold, a versatile and user-friendly tool for de novo synthetic RNA design. MoiRNAiFold is based on Constraint Programming and it includes novel variable types, heuristics and restart strategies for Large Neighborhood Search. Moreover, this software can handle dozens of design constraints and quality measures and improves features for RNA regulation control of gene expression, such as Translation Efficiency calculation. We demonstrate that MoiRNAiFold outperforms any previous software in benchmarking structural RNA puzzles from EteRNA. Importantly, with regard to biologically relevant RNA designs, we focus on RNA riboregulators, demonstrating that the designed RNA sequences are functional both in vitro and in vivo. Overall, we have generated a powerful tool for de novo complex RNA design that we make freely available as a web server (https://moiraibiodesign.com/design/ Gerard Minuesa leading to these results has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie SklodowskaCurie grant agreement No 712949 (TECNIOspring PLUS) and from the Agency for Business and Competitiveness (ACCIO) of the Government of Catalonia. Fund- ´ ing for open access charge: European Union’s Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie grant agreement No 712949 (TECNIOspring PLUS) and from the Agency for Business and Competitiveness (ACCIO) of the Government of Catalonia. © The Author(s) 2021.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Nucleic Acids Resear...arrow_drop_down
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    Nucleic Acids Research
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    Nucleic Acids Research
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    Nucleic Acids Research
    Article . 2021 . Peer-reviewed
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Nucleic Acids Resear...arrow_drop_down
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      Nucleic Acids Research
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      Nucleic Acids Research
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      Nucleic Acids Research
      Article . 2021 . Peer-reviewed
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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    Authors: Martín Garrido-Rodríguez; Daniel Lopez-Lopez; Francisco M. Ortuño; Maria Peña-Chilet; +3 Authors

    [Author summary] Currently, RNA massive sequencing RNA-seq is the most extensively used technique for gene expression profiling in a single assay. The output of RNA-seq experiments contains millions of sequences, generated from cDNA libraries produced by the retro-transcription of RNA samples, that need to be processed by computational methods to be transformed into meaningful biological information. Thus, a number of bioinformatic workflows and pipelines have been proposed to produce different types of gene expression measurements, including in some cases, functional annotations to facilitate biological interpretation. While most pipelines focus exclusively on transcriptional data, the ultimate activity of the resulting gene product also depends critically on its integrity. Although traditional hybridization-based transcriptomics methodologies (microarrays) miss this information, RNA-seq data also contains information on variants present in the transcripts that can affect the function of the gene product, which is systematically ignored by current RNA-seq pipelines. MIGNON is the first workflow able to perform an integrative analysis of transcriptomic and genomic data in the proper functional context, provided by a mechanistic model of signaling pathway activity, making thus the most of the information contained in RNA-Seq data. MIGNON is easy to use and to deploy and may become a valuable asset in fields such as personalized medicine. [Abstract] MIGNON is a workflow for the analysis of RNA-Seq experiments, which not only efficiently manages the estimation of gene expression levels from raw sequencing reads, but also calls genomic variants present in the transcripts analyzed. Moreover, this is the first workflow that provides a framework for the integration of transcriptomic and genomic data based on a mechanistic model of signaling pathway activities that allows a detailed biological interpretation of the results, including a comprehensive functional profiling of cell activity. MIGNON covers the whole process, from reads to signaling circuit activity estimations, using state-of-the-art tools, it is easy to use and it is deployable in different computational environments, allowing an optimized use of the resources available. JD has received these grants: SAF2017-88908-R from the Ministerio de Economía y Competitividad and PT17/0009/0006 from the Instituto de Salud Carlos III, as well as an FP7 People Marie-Curie Actions 813533 and and Horizon 2020 Framework Programme 676559. This is a PLOS Computational Biology Software paper. Peer reviewed

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    PLoS Computational Biology
    Article . 2021 . Peer-reviewed
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      PLoS Computational Biology
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    Authors: Segura, J.; Sánchez-García, Rubén; Sorzano, Carlos Óscar S.; Carazo, José M.;

    MOTIVATION: Many diseases are associated to single nucleotide polymorphisms that affect critical regions of proteins as binding sites or post translational modifications. Therefore, analysing genomic variants with structural and molecular biology data is a powerful framework in order to elucidate the potential causes of such diseases. RESULTS: A new version of our web framework 3DBIONOTES is presented. This version offers new tools to analyse and visualize protein annotations and genomic variants, including a contingency analysis of variants and amino acid features by means of a Fisher exact test, the integration of a gene annotation viewer to highlight protein features on gene sequences and a protein-protein interaction viewer to display protein annotations at network level. AVAILABILITY AND IMPLEMENTATION: The web server is available at https://3dbionotes.cnb.csic.es. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: Spanish National Institute for Bioinformatics (INB ELIXIR-ES) and Biocomputing Unit, National Centre of Biotechnology (CSIC)/Instruct Image Processing Centre, C/ Darwin nº 3, Campus of Cantoblanco, 28049 Madrid, Spain. This work was supported by Ministerio de Economía, Industria y Competitividad, Gobierno de España [grant No. BIO2016-76400-R(AEI/FEDER, UE)]; Comunidad de Madrid [grant No. S2017/BMD-3817]; Instituto de Salud Carlos III [grant No. PT13/0001/0009; INB Grant PT17/0009/0010 -ISCIII-SGEFI/ERDF]; Horizon 2020 [grant No. Elixir – EXCELERATEINFRADEV-3-2015, Proposal 676559] and iNEXT [INFRAIA-1-2014-2015,Proposal 653706].

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    Authors: José M. Juanes; Asunción Gallego; Joaquín Tárraga; Felipe J. Chaves; +4 Authors

    [Background] The possibility of integrating viral vectors to become a persistent part of the host genome makes them a crucial element of clinical gene therapy. However, viral integration has associated risks, such as the unintentional activation of oncogenes that can result in cancer. Therefore, the analysis of integration sites of retroviral vectors is a crucial step in developing safer vectors for therapeutic use. This work is supported by grants BIO2014–57291-R from the Spanish Ministry of Economy and Competitiveness (MINECO), and Plataforma de Recursos Biomoleculares y Bioinformáticos PT13/0001/0007 from the ISCIII, both co-funded with European Regional Development Funds (ERDF); H2020-INFRADEV-1-2015-1 ELIXIR-EXCELERATE (ref. 676,559). [Conclusions] Because it uses novel mapping algorithms VISMapper is remarkably faster than previous available programs. It also provides a useful graphical interface to analyze the integration sites found in the genomic context. [Results] Here we present VISMapper, a vector integration site analysis web server, to analyze next-generation sequencing data for retroviral vector integration sites. VISMapper can be found at: http://vismapper.babelomics.org . Peer reviewed

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    Authors: Tabas-Madrid, D; Segura, J; Sanchez-Garcia, R; Cuenca-Alba, J; +2 Authors

    With the advent of high throughput techniques like Next Generation Sequencing, the amount of biological information for genes and proteins is growing faster than ever. Structural information is also rapidly growing, especially in the cryo Electron Microscopy area. However, in many cases, the proteomic and genomic data are spread in multiple databases and with no simple connection to structural information. In this work we present a new web platform that integrates EMDB/PDB structures and UniProt sequences with different sources of protein annotations. The application provides an interactive interface linking sequence and structure, including EM maps, presenting the different sources of information at sequence and structural level. The web application is available at http://3dbionotes.cnb.csic.es. Peer Reviewed

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Carlos Pérez Cantalapiedra; Ana Hernández-Plaza; Ivica Letunic; Peer Bork; +1 Authors

    Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows for: 1) de novo gene prediction from raw contigs, 2) built-in pairwise orthology prediction, 3) fast protein domain discovery, and 4) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de. This research was supported by the National Programme for Fostering Excellence in Scientific and Technical Research (Grant No. PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE, to J.H.C.) and the Severo Ochoa Centres of Excellence Programme (Grant No. SEV-2016-0672 (2017–2021) to C.P.C.) from the State Research Agency (AEI) of Spain, as well as a Research Technical Support Staff Aid (PTA2019-017593-I/AEI/10.13039/501100011033 to A.H.P.); European Research Council grant MicroBioS (ERC-2014-AdG)—GA669830 (to P.B.). Cloud computing is supported by BMBF (de.NBI network #031A537B). Centro de Biotecnología y Genómica de Plantas (CBGP) Peer reviewed 5 Pág.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    Molecular Biology and Evolution
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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      Molecular Biology and Evolution
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Jose Ramon Macias; Rubén J. Sánchez-García; Pablo Conesa; Erney Ramírez-Aportela; +8 Authors

    The web platform 3DBionotes-WS integrates multiple Web Services and an interactive Web Viewer to provide a unified environment in which biological annotations can be analyzed in their structural context. Since the COVID-19 outbreak, new structural data from many viral proteins have been provided at a very fast pace. This effort includes many cryogenic Electron Microscopy (cryo-EM) studies, together with more traditional ones (X-rays, NMR), using several modeling approaches and complemented with structural predictions. At the same time, a plethora of new genomics and interactomics information (including fragment screening and structure-based virtual screening efforts) have been made available from different servers. In this context we have developed 3DBionotes-COVID-19 as an answer to: (1) The need to explore multi-omics data in a unified context with a special focus on structural information and (2) the drive to incorporate quality measurements, especially in the form of advanced validation metrics for cryogenic Electron Microscopy. We acknowledge financial support from: CSIC (PIE/COVID-19 number 202020E079), the Comunidad de Madrid through grant CAM (S2017/BMD-3817), the Spanish Ministry of Science and Innovation through projects (SEV 2017-0712, FPU-2015/264, PID2019-104757RB-I00 / AEI / 10.13039/501100011033), the Instituto de Salud Carlos III: PT17/0009/0010 (ISCIII-SGEFI / ERDF-) and the European Union and Horizon 2020 through grant: CORBEL (INFRADEV-01-2014- 1, Proposal 654248) and EOSC Life (INFRAEOSC-04-2018, Proposal: 824087). This work was supported by Instruct-ULTRA (Grant 731005), an EU H2020 project to further develop the services of Instruct-ERIC. Contributions from the Coronavirus Structural Task Force were supported by the German Federal Ministry of Education and Research [grant no. 05K19WWA] and Deutsche Forschungsgemeinschaft [project TH2135/2-1]. The authors acknowledge the support and the use of resources of Instruct, a Landmark ESFRI project. https://3dbionotes.cnb.csic.es/ws/covid19 Peer reviewed

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    Bioinformatics
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Acta Crystallographica Section A Foundations and Advances
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Acta Crystallographica Section A Foundations and Advances
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Gerard Minuesa; Cristina Alsina; Juan Antonio Garcia-Martin; Juan Carlos Oliveros; +1 Authors

    Novel tools for in silico design of RNA constructs such as riboregulators are required in order to reduce time and cost to production for the development of diagnostic and therapeutic advances. Here, we present MoiRNAiFold, a versatile and user-friendly tool for de novo synthetic RNA design. MoiRNAiFold is based on Constraint Programming and it includes novel variable types, heuristics and restart strategies for Large Neighborhood Search. Moreover, this software can handle dozens of design constraints and quality measures and improves features for RNA regulation control of gene expression, such as Translation Efficiency calculation. We demonstrate that MoiRNAiFold outperforms any previous software in benchmarking structural RNA puzzles from EteRNA. Importantly, with regard to biologically relevant RNA designs, we focus on RNA riboregulators, demonstrating that the designed RNA sequences are functional both in vitro and in vivo. Overall, we have generated a powerful tool for de novo complex RNA design that we make freely available as a web server (https://moiraibiodesign.com/design/ Gerard Minuesa leading to these results has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie SklodowskaCurie grant agreement No 712949 (TECNIOspring PLUS) and from the Agency for Business and Competitiveness (ACCIO) of the Government of Catalonia. Fund- ´ ing for open access charge: European Union’s Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie grant agreement No 712949 (TECNIOspring PLUS) and from the Agency for Business and Competitiveness (ACCIO) of the Government of Catalonia. © The Author(s) 2021.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Nucleic Acids Resear...arrow_drop_down
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    Nucleic Acids Research
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    Nucleic Acids Research
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      Nucleic Acids Research
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    Authors: Martín Garrido-Rodríguez; Daniel Lopez-Lopez; Francisco M. Ortuño; Maria Peña-Chilet; +3 Authors

    [Author summary] Currently, RNA massive sequencing RNA-seq is the most extensively used technique for gene expression profiling in a single assay. The output of RNA-seq experiments contains millions of sequences, generated from cDNA libraries produced by the retro-transcription of RNA samples, that need to be processed by computational methods to be transformed into meaningful biological information. Thus, a number of bioinformatic workflows and pipelines have been proposed to produce different types of gene expression measurements, including in some cases, functional annotations to facilitate biological interpretation. While most pipelines focus exclusively on transcriptional data, the ultimate activity of the resulting gene product also depends critically on its integrity. Although traditional hybridization-based transcriptomics methodologies (microarrays) miss this information, RNA-seq data also contains information on variants present in the transcripts that can affect the function of the gene product, which is systematically ignored by current RNA-seq pipelines. MIGNON is the first workflow able to perform an integrative analysis of transcriptomic and genomic data in the proper functional context, provided by a mechanistic model of signaling pathway activity, making thus the most of the information contained in RNA-Seq data. MIGNON is easy to use and to deploy and may become a valuable asset in fields such as personalized medicine. [Abstract] MIGNON is a workflow for the analysis of RNA-Seq experiments, which not only efficiently manages the estimation of gene expression levels from raw sequencing reads, but also calls genomic variants present in the transcripts analyzed. Moreover, this is the first workflow that provides a framework for the integration of transcriptomic and genomic data based on a mechanistic model of signaling pathway activities that allows a detailed biological interpretation of the results, including a comprehensive functional profiling of cell activity. MIGNON covers the whole process, from reads to signaling circuit activity estimations, using state-of-the-art tools, it is easy to use and it is deployable in different computational environments, allowing an optimized use of the resources available. JD has received these grants: SAF2017-88908-R from the Ministerio de Economía y Competitividad and PT17/0009/0006 from the Instituto de Salud Carlos III, as well as an FP7 People Marie-Curie Actions 813533 and and Horizon 2020 Framework Programme 676559. This is a PLOS Computational Biology Software paper. Peer reviewed

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    PLoS Computational Biology
    Article . 2021 . Peer-reviewed
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      PLoS Computational Biology
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    Authors: Segura, J.; Sánchez-García, Rubén; Sorzano, Carlos Óscar S.; Carazo, José M.;

    MOTIVATION: Many diseases are associated to single nucleotide polymorphisms that affect critical regions of proteins as binding sites or post translational modifications. Therefore, analysing genomic variants with structural and molecular biology data is a powerful framework in order to elucidate the potential causes of such diseases. RESULTS: A new version of our web framework 3DBIONOTES is presented. This version offers new tools to analyse and visualize protein annotations and genomic variants, including a contingency analysis of variants and amino acid features by means of a Fisher exact test, the integration of a gene annotation viewer to highlight protein features on gene sequences and a protein-protein interaction viewer to display protein annotations at network level. AVAILABILITY AND IMPLEMENTATION: The web server is available at https://3dbionotes.cnb.csic.es. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: Spanish National Institute for Bioinformatics (INB ELIXIR-ES) and Biocomputing Unit, National Centre of Biotechnology (CSIC)/Instruct Image Processing Centre, C/ Darwin nº 3, Campus of Cantoblanco, 28049 Madrid, Spain. This work was supported by Ministerio de Economía, Industria y Competitividad, Gobierno de España [grant No. BIO2016-76400-R(AEI/FEDER, UE)]; Comunidad de Madrid [grant No. S2017/BMD-3817]; Instituto de Salud Carlos III [grant No. PT13/0001/0009; INB Grant PT17/0009/0010 -ISCIII-SGEFI/ERDF]; Horizon 2020 [grant No. Elixir – EXCELERATEINFRADEV-3-2015, Proposal 676559] and iNEXT [INFRAIA-1-2014-2015,Proposal 653706].

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    Authors: José M. Juanes; Asunción Gallego; Joaquín Tárraga; Felipe J. Chaves; +4 Authors

    [Background] The possibility of integrating viral vectors to become a persistent part of the host genome makes them a crucial element of clinical gene therapy. However, viral integration has associated risks, such as the unintentional activation of oncogenes that can result in cancer. Therefore, the analysis of integration sites of retroviral vectors is a crucial step in developing safer vectors for therapeutic use. This work is supported by grants BIO2014–57291-R from the Spanish Ministry of Economy and Competitiveness (MINECO), and Plataforma de Recursos Biomoleculares y Bioinformáticos PT13/0001/0007 from the ISCIII, both co-funded with European Regional Development Funds (ERDF); H2020-INFRADEV-1-2015-1 ELIXIR-EXCELERATE (ref. 676,559). [Conclusions] Because it uses novel mapping algorithms VISMapper is remarkably faster than previous available programs. It also provides a useful graphical interface to analyze the integration sites found in the genomic context. [Results] Here we present VISMapper, a vector integration site analysis web server, to analyze next-generation sequencing data for retroviral vector integration sites. VISMapper can be found at: http://vismapper.babelomics.org . Peer reviewed

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    BMC Bioinformatics
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    Authors: Tabas-Madrid, D; Segura, J; Sanchez-Garcia, R; Cuenca-Alba, J; +2 Authors

    With the advent of high throughput techniques like Next Generation Sequencing, the amount of biological information for genes and proteins is growing faster than ever. Structural information is also rapidly growing, especially in the cryo Electron Microscopy area. However, in many cases, the proteomic and genomic data are spread in multiple databases and with no simple connection to structural information. In this work we present a new web platform that integrates EMDB/PDB structures and UniProt sequences with different sources of protein annotations. The application provides an interactive interface linking sequence and structure, including EM maps, presenting the different sources of information at sequence and structural level. The web application is available at http://3dbionotes.cnb.csic.es. Peer Reviewed

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