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1. The International Virus Bioinformatics Meeting 2020.

Author

Hufsky, Franziska, Beerenwinkel, Niko, Meyer, Irmtraud M, Roux, Simon, Cook, Georgia May, Kinsella, Cormac M, Lamkiewicz, Kevin, Marquet, Mike, Nieuwenhuijse, David F, Olendraite, Ingrida, Paraskevopoulou, Sofia, Young, Francesca, Dijkman, Ronald, Ibrahim, Bashar, Kelly, Jenna, Le Mercier, Philippe, Marz, Manja, Ramette, Alban, and Thiel, Volker

Subjects
Humans, RNA Viruses, Computational Biology, Virology, Evolution, Molecular, Genome, Viral, Congresses as Topic, Metagenomics, COVID-19, genome evolution, identification, metagenomics, software, viral diversity, viral taxonomy, virology, virome, virus bioinformatics, Prevention, Infectious Diseases, 2.2 Factors relating to the physical environment, Infection, Microbiology
Abstract

The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.

Published
2020

3. The International Virus Bioinformatics Meeting 2023

Author

Hufsky, Franziska, primary, Abecasis, Ana B., additional, Babaian, Artem, additional, Beck, Sebastian, additional, Brierley, Liam, additional, Dellicour, Simon, additional, Eggeling, Christian, additional, Elena, Santiago F., additional, Gieraths, Udo, additional, Ha, Anh D., additional, Harvey, Will, additional, Jones, Terry C., additional, Lamkiewicz, Kevin, additional, Lovate, Gabriel L., additional, Lücking, Dominik, additional, Machyna, Martin, additional, Nishimura, Luca, additional, Nocke, Maximilian K., additional, Renard, Bernard Y., additional, Sakaguchi, Shoichi, additional, Sakellaridi, Lygeri, additional, Spangenberg, Jannes, additional, Tarradas-Alemany, Maria, additional, Triebel, Sandra, additional, Vakulenko, Yulia, additional, Wijesekara, Rajitha Yasas, additional, González-Candelas, Fernando, additional, Krautwurst, Sarah, additional, Pérez-Cataluña, Alba, additional, Randazzo, Walter, additional, Sánchez, Gloria, additional, and Marz, Manja, additional

Published
2023
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4. Women in the European Virus Bioinformatics Center

Author

Hufsky, Franziska, Abecasis, Ana, Agudelo-Romero, Patricia, Bletsa, Magda, Brown, Katherine, Claus, Claudia, Deinhardt-Emmer, Stefanie, Deng, Li, Friedel, Caroline C, Gismondi, María Inés, Kostaki, Evangelia Georgia, Kühnert, Denise, Kulkarni-Kale, Urmila, Metzner, Karin J, Meyer, Irmtraud M, Miozzi, Laura, Nishimura, Luca, Paraskevopoulou, Sofia, Pérez-Cataluña, Alba, Rahlff, Janina, Thomson, Emma, Tumescheit, Charlotte, van der Hoek, Lia, Van Espen, Lore, Vandamme, Anne-Mieke, Zaheri, Maryam, Zuckerman, Neta, Marz, Manja, Hufsky, Franziska [0000-0002-9489-3182], Abecasis, Ana [0000-0002-3903-5265], Agudelo-Romero, Patricia [0000-0002-3703-4111], Bletsa, Magda [0000-0003-3184-6618], Brown, Katherine [0000-0002-8400-6922], Claus, Claudia [0000-0003-4962-6568], Deinhardt-Emmer, Stefanie [0000-0003-4495-4052], Deng, Li [0000-0003-0225-0663], Friedel, Caroline C [0000-0003-3569-4877], Gismondi, María Inés [0000-0002-2566-1169], Kostaki, Evangelia Georgia [0000-0002-3346-0930], Kühnert, Denise [0000-0002-5657-018X], Kulkarni-Kale, Urmila [0000-0002-1168-2479], Metzner, Karin J [0000-0003-4862-1503], Meyer, Irmtraud M [0000-0002-4048-3479], Miozzi, Laura [0000-0003-0410-8230], Nishimura, Luca [0000-0003-2144-7867], Paraskevopoulou, Sofia [0000-0003-2608-2596], Pérez-Cataluña, Alba [0000-0002-4784-8346], Rahlff, Janina [0000-0002-2132-2709], Thomson, Emma [0000-0003-1482-0889], Tumescheit, Charlotte [0000-0002-7563-5575], van der Hoek, Lia [0000-0003-2803-642X], Van Espen, Lore [0000-0002-3870-4551], Vandamme, Anne-Mieke [0000-0002-6594-2766], Zaheri, Maryam [0000-0003-2777-835X], Zuckerman, Neta [0000-0001-6074-2100], Marz, Manja [0000-0003-4783-8823], Apollo - University of Cambridge Repository, Medical Microbiology and Infection Prevention, AII - Infectious diseases, University of Zurich, Hufsky, Franziska, and Marz, Manja

Subjects
10028 Institute of Medical Virology, virus evolution, virus discovery, Cancer Research, viral ecology, Virus Bioinformatics, Big Data, Networking, Virus Discovery, Virus Evolution, Viral Infection, Transcriptomics, Emerging Viruses, Epidemiology, Viral Ecology, networking, virus bioinformatics, Computational Biology, 610 Medicine & health, 2725 Infectious Diseases, Research Personnel, Europe, emerging viruses, transcriptomics, big data, Viruses, 2406 Virology, 570 Life sciences, biology, Humans, epidemiology, Female, viral infection
Abstract

Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics. ispartof: VIRUSES-BASEL vol:14 issue:7 ispartof: location:Switzerland status: published

Published
2022

5. The International Virus Bioinformatics Meeting 2023

Author

Hufsky, Franziska, Abecasis, Ana B., Babaian, Artem, Beck, Sebastian, Brierley, Liam, Dellicour, Simon, Eggeling, Christian, Elena, Santiago F., Gieraths, Udo, Ha, Anh D., Harvey, Will, Jones, Terry C., Lamkiewicz, Kevin, Lovate, Gabriel L., Lücking, Dominik, Machyna, Martin, Nishimura, Luca, Nocke, Maximilian K., Renard, Bernard Y., Sakaguchi, Shoichi, Sakellaridi, Lygeri, Spangenberg, Jannes, Tarradas-Alemany, Maria, Triebel, Sandra, Vakulenko, Yulia, Wijesekara, Rajitha Yasas, González-Candelas, Fernando, Krautwurst, Sarah, Pérez-Cataluña, Alba, Randazzo, Walter, Sánchez, Gloria, Marz, Manja, Hufsky, Franziska, Abecasis, Ana B., Babaian, Artem, Beck, Sebastian, Brierley, Liam, Dellicour, Simon, Eggeling, Christian, Elena, Santiago F., Gieraths, Udo, Ha, Anh D., Harvey, Will, Jones, Terry C., Lamkiewicz, Kevin, Lovate, Gabriel L., Lücking, Dominik, Machyna, Martin, Nishimura, Luca, Nocke, Maximilian K., Renard, Bernard Y., Sakaguchi, Shoichi, Sakellaridi, Lygeri, Spangenberg, Jannes, Tarradas-Alemany, Maria, Triebel, Sandra, Vakulenko, Yulia, Wijesekara, Rajitha Yasas, González-Candelas, Fernando, Krautwurst, Sarah, Pérez-Cataluña, Alba, Randazzo, Walter, Sánchez, Gloria, and Marz, Manja

Abstract

The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24–26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting.

Published
2023

6. The International Virus Bioinformatics Meeting 2023

Author

Federal Ministry of Health (Germany), European Commission, Fundação para a Ciência e a Tecnologia (Portugal), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), German Research Foundation, Federal Ministry of Education and Research (Germany), CSL Seqirus, Pandemic Institute, Tab Healthcare Research, National Science Foundation (US), Japan Society for the Promotion of Science, Russian Science Foundation, Hufsky, Franziska, Abecasis, Ana B., Babaian, Artem, Beck, Sebastian, Brierley, Liam, Dellicour, Simon, Eggeling, Christian, Elena, Santiago F., Gieraths, Udo, Ha, Anh D., Harvey, Will, Jones, Terry C., Lamkiewicz, Kevin, Lovate, Gabriel L., Lücking, Dominik, Machyna, Martin, Nishimura, Luca, Nocke, Maximilian K., Renard, Bernhard Y., Sakaguchi, Shoichi, Sakellaridi, Lygeri, Spangenberg, Jannes, Tarradas-Alemany, María, Triebel, Sandra, Vakulenko, Yulia, Wijesekara, Rajitha Yasas, González-Candelas, Fernando, Krautwurst, Sarah, Pérez-Cataluña, Alba, Randazzo, Walter, Sánchez Moragas, Gloria, Marz, Manja, Federal Ministry of Health (Germany), European Commission, Fundação para a Ciência e a Tecnologia (Portugal), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), German Research Foundation, Federal Ministry of Education and Research (Germany), CSL Seqirus, Pandemic Institute, Tab Healthcare Research, National Science Foundation (US), Japan Society for the Promotion of Science, Russian Science Foundation, Hufsky, Franziska, Abecasis, Ana B., Babaian, Artem, Beck, Sebastian, Brierley, Liam, Dellicour, Simon, Eggeling, Christian, Elena, Santiago F., Gieraths, Udo, Ha, Anh D., Harvey, Will, Jones, Terry C., Lamkiewicz, Kevin, Lovate, Gabriel L., Lücking, Dominik, Machyna, Martin, Nishimura, Luca, Nocke, Maximilian K., Renard, Bernhard Y., Sakaguchi, Shoichi, Sakellaridi, Lygeri, Spangenberg, Jannes, Tarradas-Alemany, María, Triebel, Sandra, Vakulenko, Yulia, Wijesekara, Rajitha Yasas, González-Candelas, Fernando, Krautwurst, Sarah, Pérez-Cataluña, Alba, Randazzo, Walter, Sánchez Moragas, Gloria, and Marz, Manja

Abstract

The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24–26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting.

Published
2023

7. NFDI4Microbiota - national research data infrastructure for microbiota research.

Author

Förstner, Konrad U., Becker, Anke, Blom, Jochen, Bork, Peer, Clavel, Thomas, Dieckmann, Marius, Goesmann, Alexander, Götz, Barbara, Gübitz, Thomas, Hufsky, Franziska, Jünemann, Sebastian, Körner, Marie-Louise, Marz, Manja, Da Rocha, Ulisses Nunes, Overmann, Jörg, Pühler, Alfred, Rebholz-Schuhmann, Dietrich, Sczyrba, Alexander, Stoye, Jens, and Vandendorpe, Justine

Subjects
MICROORGANISMS, ENVIRONMENTAL health, DRUG resistance in microorganisms, COVID-19 pandemic, WASTE management, INFRASTRUCTURE (Economics)
Abstract

Microbes - bacteria, archaea, unicellular eukaryotes, and viruses - play an important role in human and environmental health. Growing awareness of this fact has led to a huge increase in microbiological research and applications in a variety of fields. Driven by technological advances that allow high-throughput molecular characterization of microbial species and communities, microbiological research now offers unparalleled opportunities to address current and emerging needs. As well as helping to address global health threats such as antimicrobial resistance and viral pandemics, it also has a key role to play in areas such as agriculture, waste management, water treatment, ecosystems remediation, and the diagnosis, treatment and prevention of various diseases. Reflecting this broad potential, billions of euros have been invested in microbiota research programs worldwide. Though run independently, many of these projects are closely related. However, Germany currently has no infrastructure to connect such projects or even compare their results. Thus, the potential synergy of data and expertise is being squandered. The goal of the NFDI4Microbiota consortium is to serve and connect this broad and heterogeneous research community by elevating the availability and quality of research results through dedicated training, and by facilitating the generation, management, interpretation, sharing, and reuse of microbial data. In doing so, we will also foster interdisciplinary interactions between researchers. NFDI4Microbiota will achieve this by creating a German microbial research network through training and community-building activities, and by creating a cloud-based system that will make the storage, integration and analysis of microbial data, especially omics data, consistent, reproducible, and accessible across all areas of life sciences. In addition to increasing the quality of microbial research in Germany, our training program will support widespread and proper usage of these services. Through this dual emphasis on education and services, NFDI4Microbiota will ensure that microbial research in Germany is synergistic and efficient, and thus excellent. By creating a central resource for German microbial research, NDFDI4Microbiota will establish a connecting hub for all NFDI consortia that work with microbiological data, including GHGA, NFDI4Biodiversity, NFDI4Agri and several others. NFDI4Microbiota will provide nonmicrobial specialists from these consortia with direct and easy access to the necessary expertise and infrastructure in microbial research in order to facilitate their daily work and enhance their research. The links forged through NFDI4Microbiota will not only increase the synergy between NFDI consortia, but also elevate the overall quality and relevance of microbial research in Germany. [ABSTRACT FROM AUTHOR]

Published
2023
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8. 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

9. Women in the European Virus Bioinformatics Center

Author

Hufsky, Franziska; https://orcid.org/0000-0002-9489-3182, Abecasis, Ana; https://orcid.org/0000-0002-3903-5265, Agudelo-Romero, Patricia; https://orcid.org/0000-0002-3703-4111, Bletsa, Magda; https://orcid.org/0000-0003-3184-6618, Brown, Katherine; https://orcid.org/0000-0002-8400-6922, Claus, Claudia; https://orcid.org/0000-0003-4962-6568, Deinhardt-Emmer, Stefanie; https://orcid.org/0000-0003-4495-4052, Deng, Li; https://orcid.org/0000-0003-0225-0663, Friedel, Caroline C; https://orcid.org/0000-0003-3569-4877, Gismondi, María Inés; https://orcid.org/0000-0002-2566-1169, Kostaki, Evangelia Georgia; https://orcid.org/0000-0002-3346-0930, Kühnert, Denise; https://orcid.org/0000-0002-5657-018X, Kulkarni-Kale, Urmila; https://orcid.org/0000-0002-1168-2479, Metzner, Karin J; https://orcid.org/0000-0003-4862-1503, Meyer, Irmtraud M; https://orcid.org/0000-0002-4048-3479, Miozzi, Laura; https://orcid.org/0000-0003-0410-8230, Nishimura, Luca; https://orcid.org/0000-0003-2144-7867, Paraskevopoulou, Sofia; https://orcid.org/0000-0003-2608-2596, Pérez-Cataluña, Alba; https://orcid.org/0000-0002-4784-8346, Rahlff, Janina; https://orcid.org/0000-0002-2132-2709, Thomson, Emma; https://orcid.org/0000-0003-1482-0889, Tumescheit, Charlotte; https://orcid.org/0000-0002-7563-5575, van der Hoek, Lia; https://orcid.org/0000-0003-2803-642X, Van Espen, Lore; https://orcid.org/0000-0002-3870-4551, Vandamme, Anne-Mieke; https://orcid.org/0000-0002-6594-2766, Zaheri, Maryam; https://orcid.org/0000-0003-2777-835X, Zuckerman, Neta; https://orcid.org/0000-0001-6074-2100, Marz, Manja; https://orcid.org/0000-0003-4783-8823, Hufsky, Franziska; https://orcid.org/0000-0002-9489-3182, Abecasis, Ana; https://orcid.org/0000-0002-3903-5265, Agudelo-Romero, Patricia; https://orcid.org/0000-0002-3703-4111, Bletsa, Magda; https://orcid.org/0000-0003-3184-6618, Brown, Katherine; https://orcid.org/0000-0002-8400-6922, Claus, Claudia; https://orcid.org/0000-0003-4962-6568, Deinhardt-Emmer, Stefanie; https://orcid.org/0000-0003-4495-4052, Deng, Li; https://orcid.org/0000-0003-0225-0663, Friedel, Caroline C; https://orcid.org/0000-0003-3569-4877, Gismondi, María Inés; https://orcid.org/0000-0002-2566-1169, Kostaki, Evangelia Georgia; https://orcid.org/0000-0002-3346-0930, Kühnert, Denise; https://orcid.org/0000-0002-5657-018X, Kulkarni-Kale, Urmila; https://orcid.org/0000-0002-1168-2479, Metzner, Karin J; https://orcid.org/0000-0003-4862-1503, Meyer, Irmtraud M; https://orcid.org/0000-0002-4048-3479, Miozzi, Laura; https://orcid.org/0000-0003-0410-8230, Nishimura, Luca; https://orcid.org/0000-0003-2144-7867, Paraskevopoulou, Sofia; https://orcid.org/0000-0003-2608-2596, Pérez-Cataluña, Alba; https://orcid.org/0000-0002-4784-8346, Rahlff, Janina; https://orcid.org/0000-0002-2132-2709, Thomson, Emma; https://orcid.org/0000-0003-1482-0889, Tumescheit, Charlotte; https://orcid.org/0000-0002-7563-5575, van der Hoek, Lia; https://orcid.org/0000-0003-2803-642X, Van Espen, Lore; https://orcid.org/0000-0002-3870-4551, Vandamme, Anne-Mieke; https://orcid.org/0000-0002-6594-2766, Zaheri, Maryam; https://orcid.org/0000-0003-2777-835X, Zuckerman, Neta; https://orcid.org/0000-0001-6074-2100, and Marz, Manja; https://orcid.org/0000-0003-4783-8823

Abstract

Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.

Published
2022

11. 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
Full Text
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12. Women in the European Virus Bioinformatics Center

Author

Hufsky, Franziska, Abecasis, Ana, Agudelo-Romero, Patricia, Bletsa, Magda, Brown, Katherine, Claus, Claudia, Deinhardt-Emmer, Stefanie, Deng, Li, Friedel, Caroline C., Gismondi, María Inés, Kostaki, Evangelia Georgia, Kühnert, Denise, Kulkarni-Kale, Urmila, Metzner, Karin J., Meyer, Irmtraud M., Miozzi, Laura, Nishimura, Luca, Paraskevopoulou, Sofia, Pérez-Cataluña, Alba, Rahlff, Janina, Thomson, Emma, Tumescheit, Charlotte, van der Hoek, Lia, Van Espen, Lore, Vandamme, Anne-Mieke, Zaheri, Maryam, Zuckerman, Neta, and Marz, Manja

Subjects
Commentary, virus bioinformatics, big data, networking, virus discovery, virus evolution, viral infection, transcriptomics, emerging viruses, epidemiology, viral ecology, ddc
Published
2021

14. Computational strategies to combat COVID-19:useful tools to accelerate SARS-CoV-2 and coronavirus research

Author

Hufsky, Franziska, Lamkiewicz, Kevin, Almeida, Alexandre, Aouacheria, Abdel, Arighi, Cecilia, Bateman, Alex, Baumbach, Jan, Beerenwinkel, Niko, Brandt, Christian, Cacciabue, Marco, Chuguransky, Sara, Drechsel, Oliver, Finn, Robert D., Fritz, Adrian, Fuchs, Stephan, Hattab, Georges, Hauschild, Anne-Christin, Heider, Dominik, Hoffmann, Marie, Hölzer, Martin, Hoops, Stefan, Kaderali, Lars, Kalvari, Ioanna, von Kleist, Max, Kmiecinski, Renó, Kühnert, Denise, Lasso, Gorka, Libin, Pieter, List, Markus, Löchel, Hannah F., Martin, Maria J., Martin, Roman, Matschinske, Julian, McHardy, Alice C., Mendes, Pedro, Mistry, Jaina, Navratil, Vincent, Nawrocki, Eric P., O'Toole, Aíne Niamh, Ontiveros-Palacios, Nancy, Petrov, Anton I., Rangel-Pineros, Guillermo, Redaschi, Nicole, Reimering, Susanne, Reinert, Knut, Reyes, Alejandro, Richardson, Lorna, Robertson, David L., Sadegh, Sepideh, Singer, Joshua B., Theys, Kristof, Upton, Chris, Welzel, Marius, Williams, Lowri, Marz, Manja, Hufsky, Franziska, Lamkiewicz, Kevin, Almeida, Alexandre, Aouacheria, Abdel, Arighi, Cecilia, Bateman, Alex, Baumbach, Jan, Beerenwinkel, Niko, Brandt, Christian, Cacciabue, Marco, Chuguransky, Sara, Drechsel, Oliver, Finn, Robert D., Fritz, Adrian, Fuchs, Stephan, Hattab, Georges, Hauschild, Anne-Christin, Heider, Dominik, Hoffmann, Marie, Hölzer, Martin, Hoops, Stefan, Kaderali, Lars, Kalvari, Ioanna, von Kleist, Max, Kmiecinski, Renó, Kühnert, Denise, Lasso, Gorka, Libin, Pieter, List, Markus, Löchel, Hannah F., Martin, Maria J., Martin, Roman, Matschinske, Julian, McHardy, Alice C., Mendes, Pedro, Mistry, Jaina, Navratil, Vincent, Nawrocki, Eric P., O'Toole, Aíne Niamh, Ontiveros-Palacios, Nancy, Petrov, Anton I., Rangel-Pineros, Guillermo, Redaschi, Nicole, Reimering, Susanne, Reinert, Knut, Reyes, Alejandro, Richardson, Lorna, Robertson, David L., Sadegh, Sepideh, Singer, Joshua B., Theys, Kristof, Upton, Chris, Welzel, Marius, Williams, Lowri, and Marz, Manja

Abstract

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de

Published
2021

15. Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Author

Hufsky, Franziska, primary, Lamkiewicz, Kevin, additional, Almeida, Alexandre, additional, Aouacheria, Abdel, additional, Arighi, Cecilia, additional, Bateman, Alex, additional, Baumbach, Jan, additional, Beerenwinkel, Niko, additional, Brandt, Christian, additional, Cacciabue, Marco, additional, Chuguransky, Sara, additional, Drechsel, Oliver, additional, Finn, Robert D, additional, Fritz, Adrian, additional, Fuchs, Stephan, additional, Hattab, Georges, additional, Hauschild, Anne-Christin, additional, Heider, Dominik, additional, Hoffmann, Marie, additional, Hölzer, Martin, additional, Hoops, Stefan, additional, Kaderali, Lars, additional, Kalvari, Ioanna, additional, von Kleist, Max, additional, Kmiecinski, Renó, additional, Kühnert, Denise, additional, Lasso, Gorka, additional, Libin, Pieter, additional, List, Markus, additional, Löchel, Hannah F, additional, Martin, Maria J, additional, Martin, Roman, additional, Matschinske, Julian, additional, McHardy, Alice C, additional, Mendes, Pedro, additional, Mistry, Jaina, additional, Navratil, Vincent, additional, Nawrocki, Eric P, additional, O’Toole, Áine Niamh, additional, Ontiveros-Palacios, Nancy, additional, Petrov, Anton I, additional, Rangel-Pineros, Guillermo, additional, Redaschi, Nicole, additional, Reimering, Susanne, additional, Reinert, Knut, additional, Reyes, Alejandro, additional, Richardson, Lorna, additional, Robertson, David L, additional, Sadegh, Sepideh, additional, Singer, Joshua B, additional, Theys, Kristof, additional, Upton, Chris, additional, Welzel, Marius, additional, Williams, Lowri, additional, and Marz, Manja, additional

Published
2020
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17. The Third Annual Meeting of the European Virus Bioinformatics Center

Author

Sub Bioinformatics, Theoretical Biology and Bioinformatics, Hufsky, Franziska, Ibrahim, Bashar, Modha, Sejal, Clokie, Martha R J, Deinhardt-Emmer, Stefanie, Dutilh, Bas E, Lycett, Samantha, Simmonds, Peter, Thiel, Volker, Abroi, Aare, Adriaenssens, Evelien M, Escalera-Zamudio, Marina, Kelly, Jenna Nicole, Lamkiewicz, Kevin, Lu, Lu, Susat, Julian, Sicheritz, Thomas, Robertson, David L, Marz, Manja, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Hufsky, Franziska, Ibrahim, Bashar, Modha, Sejal, Clokie, Martha R J, Deinhardt-Emmer, Stefanie, Dutilh, Bas E, Lycett, Samantha, Simmonds, Peter, Thiel, Volker, Abroi, Aare, Adriaenssens, Evelien M, Escalera-Zamudio, Marina, Kelly, Jenna Nicole, Lamkiewicz, Kevin, Lu, Lu, Susat, Julian, Sicheritz, Thomas, Robertson, David L, and Marz, Manja

Published
2019

18. The Third Annual Meeting of the European Virus Bioinformatics Center

Author

Hufsky, Franziska, Ibrahim, Bashar, Modha, Sejal, Clokie, Martha R. J., Deinhardt-Emmer, Stefanie, Dutilh, Bas E., Lycett, Samantha, Simmonds, Peter, Thiel, Volker, Abroi, Aare, Adriaenssens, Evelien M., Escalera-Zamudio, Marina, Kelly, Jenna Nicole, Lamkiewicz, Kevin, Lu, Lu, Susat, Julian, Sicheritz, Thomas, Robertson, David L., Marz, Manja, Hufsky, Franziska, Ibrahim, Bashar, Modha, Sejal, Clokie, Martha R. J., Deinhardt-Emmer, Stefanie, Dutilh, Bas E., Lycett, Samantha, Simmonds, Peter, Thiel, Volker, Abroi, Aare, Adriaenssens, Evelien M., Escalera-Zamudio, Marina, Kelly, Jenna Nicole, Lamkiewicz, Kevin, Lu, Lu, Susat, Julian, Sicheritz, Thomas, Robertson, David L., and Marz, Manja

Published
2019

19. The Third Annual Meeting of the European Virus Bioinformatics Center

Author

Hufsky, Franziska, primary, Ibrahim, Bashar, additional, Modha, Sejal, additional, Clokie, Martha R. J., additional, Deinhardt-Emmer, Stefanie, additional, Dutilh, Bas E., additional, Lycett, Samantha, additional, Simmonds, Peter, additional, Thiel, Volker, additional, Abroi, Aare, additional, Adriaenssens, Evelien M., additional, Escalera-Zamudio, Marina, additional, Kelly, Jenna Nicole, additional, Lamkiewicz, Kevin, additional, Lu, Lu, additional, Susat, Julian, additional, Sicheritz, Thomas, additional, Robertson, David L., additional, and Marz, Manja, additional

Published
2019
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20. Swiftly Computing Center Strings

Author

Jahn Katharina, Kuchenbecker Léon, Hufsky Franziska, Stoye Jens, and Böcker Sebastian

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background The center string (or closest string) problem is a classic computer science problem with important applications in computational biology. Given k input strings and a distance threshold d, we search for a string within Hamming distance at most d to each input string. This problem is NP complete. Results In this paper, we focus on exact methods for the problem that are also swift in application. We first introduce data reduction techniques that allow us to infer that certain instances have no solution, or that a center string must satisfy certain conditions. We describe how to use this information to speed up two previously published search tree algorithms. Then, we describe a novel iterative search strategy that is effecient in practice, where some of our reduction techniques can also be applied. Finally, we present results of an evaluation study for two different data sets from a biological application. Conclusions We find that the running time for computing the optimal center string is dominated by the subroutine calls for d = dopt -1 and d = dopt. Our data reduction is very effective for both, either rejecting unsolvable instances or solving trivial positions. We find that this speeds up computations considerably.

Published
2011
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21. Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.

Author

Hufsky, Franziska, Lamkiewicz, Kevin, Almeida, Alexandre, Aouacheria, Abdel, Arighi, Cecilia, Bateman, Alex, Baumbach, Jan, Beerenwinkel, Niko, Brandt, Christian, Cacciabue, Marco, Chuguransky, Sara, Drechsel, Oliver, Finn, Robert D, Fritz, Adrian, Fuchs, Stephan, Hattab, Georges, Hauschild, Anne-Christin, Heider, Dominik, Hoffmann, Marie, and Hölzer, Martin

Subjects
*SARS-CoV-2, *COVID-19, *PANDEMICS, *COVID-19 pandemic, *COVID-19 treatment, *COMMUNICABLE diseases
Abstract

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact: evbc@unj-jena.de [ABSTRACT FROM AUTHOR]

Published
2021
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22. Virologists—Heroes need weapons

Author

Hufsky, Franziska, primary, Ibrahim, Bashar, additional, Beer, Martin, additional, Deng, Li, additional, Mercier, Philippe Le, additional, McMahon, Dino P., additional, Palmarini, Massimo, additional, Thiel, Volker, additional, and Marz, Manja, additional

Published
2018
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24. Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D

Author

Riege, Konstantin, primary, Hölzer, Martin, additional, Klassert, Tilman E., additional, Barth, Emanuel, additional, Bräuer, Julia, additional, Collatz, Maximilian, additional, Hufsky, Franziska, additional, Mostajo, Nelly, additional, Stock, Magdalena, additional, Vogel, Bertram, additional, Slevogt, Hortense, additional, and Marz, Manja, additional

Published
2017
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25. Correction: Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

Author

Hölzer, Martin, primary, Krähling, Verena, additional, Amman, Fabian, additional, Barth, Emanuel, additional, Bernhart, Stephan H., additional, Carmelo, Victor A. O., additional, Collatz, Maximilian, additional, Doose, Gero, additional, Eggenhofer, Florian, additional, Ewald, Jan, additional, Fallmann, Jörg, additional, Feldhahn, Lasse M., additional, Fricke, Markus, additional, Gebauer, Juliane, additional, Gruber, Andreas J., additional, Hufsky, Franziska, additional, Indrischek, Henrike, additional, Kanton, Sabina, additional, Linde, Jörg, additional, Mostajo, Nelly, additional, Ochsenreiter, Roman, additional, Riege, Konstantin, additional, Rivarola-Duarte, Lorena, additional, Sahyoun, Abdullah H., additional, Saunders, Sita J., additional, Seemann, Stefan E., additional, Tanzer, Andrea, additional, Vogel, Bertram, additional, Wehner, Stefanie, additional, Wolfinger, Michael T., additional, Backofen, Rolf, additional, Gorodkin, Jan, additional, Grosse, Ivo, additional, Hofacker, Ivo, additional, Hoffmann, Steve, additional, Kaleta, Christoph, additional, Stadler, Peter F., additional, Becker, Stephan, additional, and Marz, Manja, additional

Published
2017
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26. Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

Author

Hölzer, Martin, primary, Krähling, Verena, additional, Amman, Fabian, additional, Barth, Emanuel, additional, Bernhart, Stephan H., additional, Carmelo, Victor A. O., additional, Collatz, Maximilian, additional, Doose, Gero, additional, Eggenhofer, Florian, additional, Ewald, Jan, additional, Fallmann, Jörg, additional, Feldhahn, Lasse M., additional, Fricke, Markus, additional, Gebauer, Juliane, additional, Gruber, Andreas J., additional, Hufsky, Franziska, additional, Indrischek, Henrike, additional, Kanton, Sabina, additional, Linde, Jörg, additional, Mostajo, Nelly, additional, Ochsenreiter, Roman, additional, Riege, Konstantin, additional, Rivarola-Duarte, Lorena, additional, Sahyoun, Abdullah H., additional, Saunders, Sita J., additional, Seemann, Stefan E., additional, Tanzer, Andrea, additional, Vogel, Bertram, additional, Wehner, Stefanie, additional, Wolfinger, Michael T., additional, Backofen, Rolf, additional, Gorodkin, Jan, additional, Grosse, Ivo, additional, Hofacker, Ivo, additional, Hoffmann, Steve, additional, Kaleta, Christoph, additional, Stadler, Peter F., additional, Becker, Stephan, additional, and Marz, Manja, additional

Published
2016
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27. Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells:[Plus] Corrigendum

Author

Hölzer, Martin, Krähling, Verena, Amman, Fabian, Barth, Emanuel, Bernhart, Stephan H., Carmelo, Victor Adriano Okstoft, Collatz, Maximilian, Doose, Gero, Eggenhofer, Florian, Ewald, Jan, Fallmann, Jörg, Feldhahn, Lasse M., Fricke, Markus, Gebauer, Juliane, Gruber, Andreas J., Hufsky, Franziska, Indrischek, Henrike, Kanton, Sabina, Linde, Jörg, Mostajo, Nelly, Ochsenreiter, Roman, Riege, Konstantin, Rivarola-Duarte, Lorena, Sahyoun, Abdullah H., Saunders, Sita J., Seemann, Ernst Stefan, Tanzer, Andrea, Vogel, Bertram, Wehner, Stefanie, Wolfinger, Michael T., Backofen, Rolf, Gorodkin, Jan, Grosse, Ivo, Hofacker, Ivo, Hoffmann, Steve, Kaleta, Christoph, Stadler, Peter F., Becker, Stephan, Marz, Manja, Hölzer, Martin, Krähling, Verena, Amman, Fabian, Barth, Emanuel, Bernhart, Stephan H., Carmelo, Victor Adriano Okstoft, Collatz, Maximilian, Doose, Gero, Eggenhofer, Florian, Ewald, Jan, Fallmann, Jörg, Feldhahn, Lasse M., Fricke, Markus, Gebauer, Juliane, Gruber, Andreas J., Hufsky, Franziska, Indrischek, Henrike, Kanton, Sabina, Linde, Jörg, Mostajo, Nelly, Ochsenreiter, Roman, Riege, Konstantin, Rivarola-Duarte, Lorena, Sahyoun, Abdullah H., Saunders, Sita J., Seemann, Ernst Stefan, Tanzer, Andrea, Vogel, Bertram, Wehner, Stefanie, Wolfinger, Michael T., Backofen, Rolf, Gorodkin, Jan, Grosse, Ivo, Hofacker, Ivo, Hoffmann, Steve, Kaleta, Christoph, Stadler, Peter F., Becker, Stephan, and Marz, Manja

Abstract

The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the biology of this highly pathogenic virus to develop specific counter strategies. Two filoviruses, the Ebola and Marburg viruses, result in a severe and often fatal infection in humans. However, bats are natural hosts and survive filovirus infections without obvious symptoms. The molecular basis of this striking difference in the response to filovirus infections is not well understood. We report a systematic overview of differentially expressed genes, activity motifs and pathways in human and bat cells infected with the Ebola and Marburg viruses, and we demonstrate that the replication of filoviruses is more rapid in human cells than in bat cells. We also found that the most strongly regulated genes upon filovirus infection are chemokine ligands and transcription factors. We observed a strong induction of the JAK/STAT pathway, of several genes encoding inhibitors of MAP kinases (DUSP genes) and of PPP1R15A, which is involved in ER stress-induced cell death. We used comparative transcriptomics to provide a data resource that can be used to identify cellular responses that might allow bats to survive filovirus infections.

Published
2016

28. Finding characteristic substructures for metabolite classes

Author

Ludwig, Marcus, Hufsky, Franziska, Elshamy, Samy, and Böcker, Sebastian

Subjects
000 Computer science, knowledge, general works, Computer Science
Abstract

We introduce a method for finding a characteristic substructure for a set of molecular structures. Different from common approaches, such as computing the maximum common subgraph, the resulting substructure does not have to be contained in its exact form in all input molecules. Our approach is part of the identification pipeline for unknown metabolites using fragmentation trees. Searching databases using fragmentation tree alignment results in hit lists containing compounds with large structural similarity to the unknown metabolite. The characteristic substructure of the molecules in the hit list may be a key structural element of the unknown compound and might be used as starting point for structure elucidation. We evaluate our method on different data sets and find that it retrieves essential substructures if the input lists are not too heterogeneous. We apply our method to predict structural elements for five unknown samples from Icelandic poppy.

Published
2012

29. Comparing fragmentation trees from electron impact mass spectra with annotated fragmentation pathways

Author

Hufsky, Franziska and Böcker, Sebastian

Subjects
000 Computer science, knowledge, general works, Computer Science
Abstract

Electron impact ionization (EI) is the most common form of ionization for GC-MS analysis of small molecules. This ionization method results in a mass spectrum not necessarily containing the molecular ion peak. The fragmentation of small compounds during EI is well understood, but manual interpretation of mass spectra is tedious and time-consuming. Methods for automated analysis are highly sought, but currently limited to database searching and rule-based approaches. With the computation of hypothetical fragmentation trees from high mass GC-MS data the high-throughput interpretation of such spectra may become feasible. We compare these trees with annotated fragmentation pathways. We find that fragmentation trees explain the origin of the ions found in the mass spectra in accordance to the literature. No peak is annotated with an incorrect fragment formula and 78.7% of the fragmentation processes are correctly reconstructed.

Published
2012

30. OASIcs, Volume 26, GCB'12, Complete Volume

Author

B��cker, Sebastian, Hufsky, Franziska, Scheubert, Kerstin, Schleicher, Jana, and Schuster, Stefan

Subjects
Life and Medical Sciences, Data processing Computer science, ddc:004
Abstract

OASIcs, Volume 26, GCB'12, Complete Volume, OASIcs, Vol. 26, German Conference on Bioinformatics 2012, pages 0-0

Published
2012

32. OASIcs, Volume 26, GCB'12, Complete Volume

Author

Hufsky, Franziska, Scheubert, Kerstin, Schleicher, Jana, Schuster, Stefan, Hufsky, Franziska, Scheubert, Kerstin, Schleicher, Jana, and Schuster, Stefan

Abstract

OASIcs, Volume 26, GCB'12, Complete Volume

Published
2012
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34. Frontmatter, Table of Contents, Preface, Programm Committee, Supportes and Sponsors, Index of Authors

Author

Sebastian Böcker and Franziska Hufsky and Kerstin Scheubert and Jana Schleicher and Stefan Schuster, Böcker, Sebastian, Hufsky, Franziska, Scheubert, Kerstin, Schleicher, Jana, Schuster, Stefan, Sebastian Böcker and Franziska Hufsky and Kerstin Scheubert and Jana Schleicher and Stefan Schuster, Böcker, Sebastian, Hufsky, Franziska, Scheubert, Kerstin, Schleicher, Jana, and Schuster, Stefan

Abstract

Frontmatter, Table of Contents, Preface, Programm Committee, Supportes and Sponsors, Index of Authors

Published
2012
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35. Comparing Fragmentation Trees from Electron Impact Mass Spectra with Annotated Fragmentation Pathways

Author

Franziska Hufsky and Sebastian Böcker, Hufsky, Franziska, Böcker, Sebastian, Franziska Hufsky and Sebastian Böcker, Hufsky, Franziska, and Böcker, Sebastian

Abstract

Electron impact ionization (EI) is the most common form of ionization for GC-MS analysis of small molecules. This ionization method results in a mass spectrum not necessarily containing the molecular ion peak. The fragmentation of small compounds during EI is well understood, but manual interpretation of mass spectra is tedious and time-consuming. Methods for automated analysis are highly sought, but currently limited to database searching and rule-based approaches. With the computation of hypothetical fragmentation trees from high mass GC-MS data the high-throughput interpretation of such spectra may become feasible. We compare these trees with annotated fragmentation pathways. We find that fragmentation trees explain the origin of the ions found in the mass spectra in accordance to the literature. No peak is annotated with an incorrect fragment formula and 78.7% of the fragmentation processes are correctly reconstructed.

Published
2012
Full Text
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36. OASIcs, Volume 26, GCB'12, Complete Volume

Author

Sebastian Böcker and Franziska Hufsky and Kerstin Scheubert and Jana Schleicher and Stefan Schuster, Böcker, Sebastian, Hufsky, Franziska, Scheubert, Kerstin, Schleicher, Jana, Schuster, Stefan, Sebastian Böcker and Franziska Hufsky and Kerstin Scheubert and Jana Schleicher and Stefan Schuster, Böcker, Sebastian, Hufsky, Franziska, Scheubert, Kerstin, Schleicher, Jana, and Schuster, Stefan

Abstract

OASIcs, Volume 26, GCB'12, Complete Volume

Published
2012
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37. Finding Characteristic Substructures for Metabolite Classes

Author

Marcus Ludwig and Franziska Hufsky and Samy Elshamy and Sebastian Böcker, Ludwig, Marcus, Hufsky, Franziska, Elshamy, Samy, Böcker, Sebastian, Marcus Ludwig and Franziska Hufsky and Samy Elshamy and Sebastian Böcker, Ludwig, Marcus, Hufsky, Franziska, Elshamy, Samy, and Böcker, Sebastian

Abstract

We introduce a method for finding a characteristic substructure for a set of molecular structures. Different from common approaches, such as computing the maximum common subgraph, the resulting substructure does not have to be contained in its exact form in all input molecules. Our approach is part of the identification pipeline for unknown metabolites using fragmentation trees. Searching databases using fragmentation tree alignment results in hit lists containing compounds with large structural similarity to the unknown metabolite. The characteristic substructure of the molecules in the hit list may be a key structural element of the unknown compound and might be used as starting point for structure elucidation. We evaluate our method on different data sets and find that it retrieves essential substructures if the input lists are not too heterogeneous. We apply our method to predict structural elements for five unknown samples from Icelandic poppy.

Published
2012
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40. viromeBrowser: A Shiny App for Browsing Virome Sequencing Analysis Results.

Author

Nieuwenhuijse, David F., Oude Munnink, Bas B., Koopmans, Marion P. G., Marz, Manja, Ibrahim, Bashar, Hufsky, Franziska, Dijkman, Ronald, Ramette, Alban, and Kelly, Jenna

Subjects
SEQUENCE analysis, DATA science, METADATA, DATA analysis
Abstract

Experiments in which complex virome sequencing data is generated remain difficult to explore and unpack for scientists without a background in data science. The processing of raw sequencing data by high throughput sequencing workflows usually results in contigs in FASTA format coupled to an annotation file linking the contigs to a reference sequence or taxonomic identifier. The next step is to compare the virome of different samples based on the metadata of the experimental setup and extract sequences of interest that can be used in subsequent analyses. The viromeBrowser is an application written in the opensource R shiny framework that was developed in collaboration with end-users and is focused on three common data analysis steps. First, the application allows interactive filtering of annotations by default or custom quality thresholds. Next, multiple samples can be visualized to facilitate comparison of contig annotations based on sample specific metadata values. Last, the application makes it easy for users to extract sequences of interest in FASTA format. With the interactive features in the viromeBrowser we aim to enable scientists without a data science background to compare and extract annotation data and sequences from virome sequencing analysis results. [ABSTRACT FROM AUTHOR]

Published
2021
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41. Natural Selection Plays an Important Role in Shaping the Codon Usage of Structural Genes of the Viruses Belonging to the Coronaviridae Family.

Author

Nyayanit, Dimpal A., Yadav, Pragya D., Kharde, Rutuja, Cherian, Sarah, Marz, Manja, Ibrahim, Bashar, Hufsky, Franziska, Dijkman, Ronald, Ramette, Alban, and Kelly, Jenna

Subjects
NATURAL selection, CORONAVIRUSES, GENES, VIRUSES, GENE families
Abstract

Viruses belonging to the Coronaviridae family have a single-stranded positive-sense RNA with a poly-A tail. The genome has a length of ~29.9 kbps, which encodes for genes that are essential for cell survival and replication. Different evolutionary constraints constantly influence the codon usage bias (CUB) of different genes. A virus optimizes its codon usage to fit the host environment on which it savors. This study is a comprehensive analysis of the CUB for the different genes encoded by viruses of the Coronaviridae family. Different methods including relative synonymous codon usage (RSCU), an Effective number of codons (ENc), parity plot 2, and Neutrality plot, were adopted to analyze the factors responsible for the genetic evolution of the Coronaviridae family. Base composition and RSCU analyses demonstrated the presence of A-ended and U-ended codons being preferred in the 3rd codon position and are suggestive of mutational selection. The lesser ENc value for the spike 'S' gene suggests a higher bias in the codon usage of this gene compared to the other structural genes. Parity plot 2 and neutrality plot analyses demonstrate the role and the extent of mutational and natural selection towards the codon usage pattern. It was observed that the structural genes of the Coronaviridae family analyzed in this study were at the least under 84% influence of natural selection, implying a major role of natural selection in shaping the codon usage. [ABSTRACT FROM AUTHOR]

Published
2021
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42. Characterization of a Novel Mitovirus of the Sand Fly Lutzomyia longipalpis Using Genomic and Virus–Host Interaction Signatures.

Author

Fonseca, Paula, Ferreira, Flavia, da Silva, Felipe, Oliveira, Liliane Santana, Marques, João Trindade, Goes-Neto, Aristóteles, Aguiar, Eric, Gruber, Arthur, Marz, Manja, Ibrahim, habil. Bashar, Hufsky, Franziska, Dijkman, Ronald, Ramette, Alban, and Kelly, Jenna

Subjects
RNA replicase, SAND flies, LUTZOMYIA, BLOODSUCKING insects, GENETIC code, FUNGAL viruses, RNA polymerases
Abstract

Hematophagous insects act as the major reservoirs of infectious agents due to their intimate contact with a large variety of vertebrate hosts. Lutzomyia longipalpis is the main vector of Leishmania chagasi in the New World, but its role as a host of viruses is poorly understood. In this work, Lu. longipalpis RNA libraries were subjected to progressive assembly using viral profile HMMs as seeds. A sequence phylogenetically related to fungal viruses of the genus Mitovirus was identified and this novel virus was named Lul-MV-1. The 2697-base genome presents a single gene coding for an RNA-directed RNA polymerase with an organellar genetic code. To determine the possible host of Lul-MV-1, we analyzed the molecular characteristics of the viral genome. Dinucleotide composition and codon usage showed profiles similar to mitochondrial DNA of invertebrate hosts. Also, the virus-derived small RNA profile was consistent with the activation of the siRNA pathway, with size distribution and 5′ base enrichment analogous to those observed in viruses of sand flies, reinforcing Lu. longipalpis as a putative host. Finally, RT-PCR of different insect pools and sequences of public Lu. longipalpis RNA libraries confirmed the high prevalence of Lul-MV-1. This is the first report of a mitovirus infecting an insect host. [ABSTRACT FROM AUTHOR]

Published
2021
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43. Characterization and Diversity of 243 Complete Human Papillomavirus Genomes in Cervical Swabs Using Next Generation Sequencing.

Author

Latsuzbaia, Ardashel, Wienecke-Baldacchino, Anke, Tapp, Jessica, Arbyn, Marc, Karabegović, Irma, Chen, Zigui, Fischer, Marc, Mühlschlegel, Friedrich, Weyers, Steven, Pesch, Pascale, Mossong, Joël, Hufsky, Franziska, Ibrahim, Bashar, Marz, Manja, Dijkman, Ronald, Ramette, Alban, and Kelly, Jenna

Subjects
PAPILLOMAVIRUSES, GENOMES, GENOTYPES, HUMAN beings
Abstract

In recent years, next generation sequencing (NGS) technology has been widely used for the discovery of novel human papillomavirus (HPV) genotypes, variant characterization and genotyping. Here, we compared the analytical performance of NGS with a commercial PCR-based assay (Anyplex II HPV28) in cervical samples of 744 women. Overall, HPV positivity was 50.2% by the Anyplex and 45.5% by the NGS. With the NGS, we detected 25 genotypes covered by Anyplex and 41 additional genotypes. Agreement between the two methods for HPV positivity was 80.8% (kappa = 0.616) and 84.8% (kappa = 0.652) for 28 HPV genotypes and 14 high-risk genotypes, respectively. We recovered and characterized 243 complete HPV genomes from 153 samples spanning 40 different genotypes. According to phylogenetic analysis and pairwise distance, we identified novel lineages and sublineages of four high-risk and 16 low-risk genotypes. In total, 17 novel lineages and 14 novel sublineages were proposed, including novel lineages of HPV45, HPV52, HPV66 and a novel sublineage of HPV59. Our study provides important genomic insights on HPV types and lineages, where few complete genomes were publicly available. [ABSTRACT FROM AUTHOR]

Published
2020
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44. Advances in the Bioinformatics Knowledge of mRNA Polyadenylation in Baculovirus Genes.

Author

Peros, Iván Gabriel, Cerrudo, Carolina Susana, Pilloff, Marcela Gabriela, Belaich, Mariano Nicolás, Lozano, Mario Enrique, Ghiringhelli, Pablo Daniel, Marz, Manja, Ibrahim, Bashar, Hufsky, Franziska, Dijkman, Ronald, Ramette, Alban, and Kelly, Jenna

Subjects
BIOLOGICAL control of agricultural pests, INSECT viruses, MESSENGER RNA, GENES, GENE expression
Abstract

Baculoviruses are a group of insect viruses with large circular dsDNA genomes exploited in numerous biotechnological applications, such as the biological control of agricultural pests, the expression of recombinant proteins or the gene delivery of therapeutic sequences in mammals, among others. Their genomes encode between 80 and 200 proteins, of which 38 are shared by all reported species. Thanks to multi-omic studies, there is remarkable information about the baculoviral proteome and the temporality in the virus gene expression. This allows some functional elements of the genome to be very well described, such as promoters and open reading frames. However, less information is available about the transcription termination signals and, consequently, there are still imprecisions about what are the limits of the transcriptional units present in the baculovirus genomes and how is the processing of the 3′ end of viral mRNA. Regarding to this, in this review we provide an update about the characteristics of DNA signals involved in this process and we contribute to their correct prediction through an exhaustive analysis that involves bibliography information, data mining, RNA structure and a comprehensive study of the core gene 3′ ends from 180 baculovirus genomes. [ABSTRACT FROM AUTHOR]

Published
2020
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45. The International Virus Bioinformatics Meeting 2020

Author

Alban Ramette, Ronald Dijkman, Franziska Hufsky, Irmtraud M. Meyer, David F. Nieuwenhuijse, Georgia M. Cook, Manja Marz, Francesca Young, Mike Marquet, Philippe Le Mercier, Ingrida Olendraite, Kevin Lamkiewicz, Niko Beerenwinkel, Jenna N. Kelly, Cormac M. Kinsella, Simon Roux, Bashar Ibrahim, Sofia Paraskevopoulou, Volker Thiel, Virology, AII - Infectious diseases, Graduate School, Hufsky, Franziska [0000-0002-9489-3182], Roux, Simon [0000-0002-5831-5895], Lamkiewicz, Kevin [0000-0002-6375-6441], Nieuwenhuijse, David F [0000-0003-1310-5031], Young, Francesca [0000-0002-5236-1145], Dijkman, Ronald [0000-0003-0320-2743], Ibrahim, Bashar [0000-0001-7773-0122], Ramette, Alban [0000-0002-3437-4639], Thiel, Volker [0000-0002-5783-0887], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Viral metagenomics, Cancer Research, viral taxonomy, Coronavirus disease 2019 (COVID-19), Evolution, 030106 microbiology, lcsh:QR1-502, 610 Medicine & health, Genome, Viral, genome evolution, Bioinformatics, virology, virus bioinformatics, COVID-19, software, metagenomics, virome, viral diversity, identification, Microbiology, Virus, lcsh:Microbiology, Evolution, Molecular, 03 medical and health sciences, Pandemic, 2.2 Factors relating to the physical environment, Humans, RNA Viruses, Human virome, Viral, Aetiology, Virus classification, Genome, Notice, 630 Agriculture, Prevention, Molecular, Computational Biology, Conference Report, Congresses as Topic, Research findings, 030104 developmental biology, Infectious Diseases, 570 Life sciences, biology, Infection
Abstract

The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8–9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting., Viruses, 12 (12), ISSN:1999-4915

Published
2020

46. Women in the European Virus Bioinformatics Center.

Author

Hufsky F, Abecasis A, Agudelo-Romero P, Bletsa M, Brown K, Claus C, Deinhardt-Emmer S, Deng L, Friedel CC, Gismondi MI, Kostaki EG, Kühnert D, Kulkarni-Kale U, Metzner KJ, Meyer IM, Miozzi L, Nishimura L, Paraskevopoulou S, Pérez-Cataluña A, Rahlff J, Thomson E, Tumescheit C, van der Hoek L, Van Espen L, Vandamme AM, Zaheri M, Zuckerman N, and Marz M

Subjects
Europe, Female, Humans, Computational Biology, Research Personnel statistics & numerical data, Viruses genetics
Abstract

Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.

Published
2022
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47. Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.

Author

Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S, and Marz M

Published
2017
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