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2. Neighbourhood watch: genomic epidemiology of SARS-CoV-2 variants circulating in a German federal state, Mecklenburg-Western Pomerania, in 2020–2022

Author

Kohler, Christian, primary, King, Jacqueline, additional, Stacker, Lina, additional, Goller, Katja V., additional, Moritz, Juliane, additional, Pohlmann, Anne, additional, Nath, Neetika, additional, Tzvetkova, Ana, additional, Rieck, Maximilian, additional, Paraskevopoulou, Sofia, additional, Beslic, Denis, additional, Hölzer, Martin, additional, Fuchs, Stephan, additional, Ziemann, Janine, additional, Kaderali, Lars, additional, Beer, Martin, additional, Hübner, Nils-Olaf, additional, and Becker, Karsten, additional

Published
2023
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5. The International Virus Bioinformatics Meeting 2022

Author

Consejo Superior de Investigaciones Científicas (España), Ministerio de Ciencia, Innovación y Universidades (España), Instituto de Salud Carlos III, European Commission, Fundación Ramón Areces, Banco Santander, European Centre for Disease Prevention and Control, Research Foundation - Flanders, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, National Science Foundation (US), Gordon and Betty Moore Foundation, European Research Council, Wellcome Trust, National Institutes of Health (US), Japan Society for the Promotion of Science, German Research Foundation, Hufsky, Franziska, Beslic, Denis, Boeckaerts, Dimitri, Duchene, Sebastian, González-Tortuero, Enrique, Gruber, Andreas J., Guo, Jiarong, Jansen, Daan, Juma, John, Kongkitimanon, Kunaphas, Luque, Antoni, Ritsch, Muriel, Lencioni Lovate, Gabriel, Nishimura, Luca, Pas, Célia, Domingo, Esteban, Hodcroft, Emma, Lemey, Philippe, Sullivan, Matthew B., Weber, Friedemann, González-Candelas, Fernando, Krautwurst, Sarah, Pérez-Cataluña, Alba, Randazzo, Walter, Sánchez, Gloria, Marz, Manja, Consejo Superior de Investigaciones Científicas (España), Ministerio de Ciencia, Innovación y Universidades (España), Instituto de Salud Carlos III, European Commission, Fundación Ramón Areces, Banco Santander, European Centre for Disease Prevention and Control, Research Foundation - Flanders, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, National Science Foundation (US), Gordon and Betty Moore Foundation, European Research Council, Wellcome Trust, National Institutes of Health (US), Japan Society for the Promotion of Science, German Research Foundation, Hufsky, Franziska, Beslic, Denis, Boeckaerts, Dimitri, Duchene, Sebastian, González-Tortuero, Enrique, Gruber, Andreas J., Guo, Jiarong, Jansen, Daan, Juma, John, Kongkitimanon, Kunaphas, Luque, Antoni, Ritsch, Muriel, Lencioni Lovate, Gabriel, Nishimura, Luca, Pas, Célia, Domingo, Esteban, Hodcroft, Emma, Lemey, Philippe, Sullivan, Matthew B., Weber, Friedemann, González-Candelas, Fernando, Krautwurst, Sarah, Pérez-Cataluña, Alba, Randazzo, Walter, Sánchez, Gloria, and Marz, Manja

Abstract

The International Virus Bioinformatics Meeting 2022 took place online, on 23-25 March 2022, and has attracted about 380 participants from all over the world. The goal of the meeting was to provide a meaningful and interactive scientific environment to promote discussion and collaboration and to inspire and suggest new research directions and questions. The participants created a highly interactive scientific environment even without physical face-to-face interactions. This meeting is a focal point to gain an insight into the state-of-the-art of the virus bioinformatics research landscape and to interact with researchers in the forefront as well as aspiring young scientists. The meeting featured eight invited and 18 contributed talks in eight sessions on three days, as well as 52 posters, which were presented during three virtual poster sessions. The main topics were: SARS-CoV-2, viral emergence and surveillance, virus-host interactions, viral sequence analysis, virus identification and annotation, phages, and viral diversity. This report summarizes the main research findings and highlights presented at the meeting.

Published
2022

6. The International Virus Bioinformatics Meeting 2022

Author

Hufsky, Franziska, primary, Beslic, Denis, additional, Boeckaerts, Dimitri, additional, Duchene, Sebastian, additional, González-Tortuero, Enrique, additional, Gruber, Andreas J., additional, Guo, Jiarong, additional, Jansen, Daan, additional, Juma, John, additional, Kongkitimanon, Kunaphas, additional, Luque, Antoni, additional, Ritsch, Muriel, additional, Lencioni Lovate, Gabriel, additional, Nishimura, Luca, additional, Pas, Célia, additional, Domingo, Esteban, additional, Hodcroft, Emma, additional, Lemey, Philippe, additional, Sullivan, Matthew B., additional, Weber, Friedemann, additional, González-Candelas, Fernando, additional, Krautwurst, Sarah, additional, Pérez-Cataluña, Alba, additional, Randazzo, Walter, additional, Sánchez, Gloria, additional, and Marz, Manja, additional

Published
2022
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7. MALDI-TOF-MS-Based Identification of Monoclonal Murine Anti-SARS-CoV-2 Antibodies within One Hour

Author

Tscheuschner, Georg, primary, Kaiser, Melanie N., additional, Lisec, Jan, additional, Beslic, Denis, additional, Muth, Thilo, additional, Krüger, Maren, additional, Mages, Hans Werner, additional, Dorner, Brigitte G., additional, Knospe, Julia, additional, Schenk, Jörg A., additional, Sellrie, Frank, additional, and Weller, Michael G., additional

Published
2022
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8. Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly.

Author

Beslic, Denis, Tscheuschner, Georg, Renard, Bernhard Y, Weller, Michael G, and Muth, Thilo

Subjects
*PEPTIDES, *AMINO acid sequence, *MONOCLONAL antibodies, *PROTEOMICS, *MASS spectrometry
Abstract

Monoclonal antibodies are biotechnologically produced proteins with various applications in research, therapeutics and diagnostics. Their ability to recognize and bind to specific molecule structures makes them essential research tools and therapeutic agents. Sequence information of antibodies is helpful for understanding antibody–antigen interactions and ensuring their affinity and specificity. De novo protein sequencing based on mass spectrometry is a valuable method to obtain the amino acid sequence of peptides and proteins without a priori knowledge. In this study, we evaluated six recently developed de novo peptide sequencing algorithms (Novor, pNovo 3, DeepNovo, SMSNet, PointNovo and Casanovo), which were not specifically designed for antibody data. We validated their ability to identify and assemble antibody sequences on three multi-enzymatic data sets. The deep learning-based tools Casanovo and PointNovo showed an increased peptide recall across different enzymes and data sets compared with spectrum-graph-based approaches. We evaluated different error types of de novo peptide sequencing tools and their performance for different numbers of missing cleavage sites, noisy spectra and peptides of various lengths. We achieved a sequence coverage of 97.69–99.53% on the light chains of three different antibody data sets using the de Bruijn assembler ALPS and the predictions from Casanovo. However, low sequence coverage and accuracy on the heavy chains demonstrate that complete de novo protein sequencing remains a challenging issue in proteomics that requires improved de novo error correction, alternative digestion strategies and hybrid approaches such as homology search to achieve high accuracy on long protein sequences. [ABSTRACT FROM AUTHOR]

Published
2023
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