Understanding (harmful) virus-host interactions by linking virology and bioinformatics

Deliverables

Providing webpage, Twitter and YouTube about VIROINF

Providing webpage Twitter and YouTube about VIROINF

Publications

VILOCA: Sequencing quality-aware haplotype reconstruction and mutation calling for short- and long-read data

Author(s): Lara Fuhrmann, Benjamin Langer, Ivan Topolsky, Niko Beerenwinkel
Published in: bioRxiv, 2024, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.06.06.597712

High Resolution Kinetic Characterization and Dynamic Mathematical Modeling of the RIG-I Signaling Pathway and the Antiviral Responses

Author(s): Sandy S. Burkart, Darius Schweinoch, Jamie Frankish, Carola Sparn, Sandra Wüst, Christian Urban, Antonio Piras, Andreas Pichlmair, Joschka Willemsen, Lars Kaderali, Marco Binder
Published in: bioRxiv, 2024, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.08.05.502818

The International Virus Bioinformatics Meeting 2022

Author(s): Franziska Hufsky; Denis Beslic; Dimitri Boeckaerts; Sebastian Duchene; Enrique González-Tortuero; Andreas J. Gruber; Jiarong Guo; Daan Jansen; John Juma; Kunaphas Kongkitimanon; Antoni Luque; Muriel Ritsch; Gabriel Lencioni Lovate; Luca Nishimura; Célia Pas; Esteban Domingo; Emma Hodcroft; Philippe Lemey; Matthew B. Sullivan; Friedemann Weber; Fernando González-Candelas; Sarah Krautwurst; Alba
Published in: Viruses, Issue 19994915, 2022, Page(s) 973, ISSN 1999-4915
Publisher: MDPI
DOI: 10.3390/v14050973

Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing

Author(s): Wiep van der Toorn, Patrick Bohn, Wang Liu-Wei, Marco Olguin-Nava, Redmond P Smyth, Max von Kleist
Published in: bioRxiv, 2024, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.07.22.604276

Prediction of virus-host associations using protein language models and multiple instance learning

Author(s): Dan Liu, Francesca Young, David L Robertson, Ke Yuan
Published in: bioRxiv, 2023, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.04.07.536023

Metagenomic analyses of single phages and phage cocktails show instances of contamination with temperate phages and bacterial DNA

Author(s): Xue Peng, Sophie Elizabeth Smith, Wanqi Huang, Jinlong Ru, Mohammadali Khan Mirzaei, Li Deng
Published in: bioRxiv, 2024, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.09.12.612727

Screening great ape museum specimens for DNA viruses

Author(s): Michelle Hämmerle, Meriam Guellil, Olivia Cheronet, Susanna Sawyer, Irune Ruiz-Gartzia, Esther Lizano, Aigerim Rymbekova, Pere Gelabert, Paolo Bernardi, Sojung Han, Lovro Trgovec-Greif, Thomas Rattei, Verena J. Schuenemann, Tomas Marques-Bonet, Katerina Guschanski, Sebastien Calvignac-Spencer, Ron Pinhasi, Martin Kuhlwilm
Published in: bioRxiv, 2024, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.04.25.591107

HCMV exploits STING signaling and counteracts IFN and ISG induction to facilitate dendritic cell infection

Author(s): Bibiana Costa, Jennifer Becker, Tobias Krammer, Felix Mulenge, Verónica Durán, Andreas Pavlou, Xiaojing Chu, Yang Li, Luka Cicin-Sain, Britta Eiz-Vesper, Lars Dolken, Antoine-Emmanuel Saliba, Florian Erhard, Ulrich Kalinke
Published in: Research Square, 2024, ISSN 2693-5015
Publisher: Research Square Platform LLC
DOI: 10.21203/rs.3.rs-953016/v1

Replidec - Use naive Bayes classifier to identify virus lifecycle from metagenomics data

Author(s): Xue Peng, Jinlong Ru, Mohammadali Khan Mirzaei, Li Deng
Published in: bioRxiv, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.07.18.500415

FrameRate: learning the coding potential of unassembled metagenomic reads

Author(s): Wang Liu-Wei, Wayne Aubrey, Amanda Clare, Robert Hoehndorf, Christopher J. Creevey, Nicholas J. Dimonaco
Published in: bioRxiv, 2023, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.09.16.508314

Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences

Author(s): Yasas Wijesekara, Ling-Yi Wu, Rick Beeloo, Piotr Rozwalak, Ernestina Hauptfeld, Swapnil P. Doijad, Bas E. Dutilh, Lars Kaderali
Published in: bioRxiv, 2024, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.09.24.612722

ITN—VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics

Author(s): Winfried Goettsch; Niko Beerenwinkel; Li Deng; Lars Dölken; Bas E. Dutilh; Florian Erhard; Lars Kaderali; Max von Kleist; Roland Marquet; Jelle Matthijnssens; Shawna McCallin; Dino McMahon; Thomas Rattei; Ronald P. Van Rij; David L. Robertson; Martin Schwemmle; Noam Stern-Ginossar; Manja Marz
Published in: Viruses, Issue 13(5), 2021, Page(s) 766, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.17169/refubium-30621

Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)

Author(s): Stuart G. Siddell, Donald B. Smith, Evelien Adriaenssens, Poliane Alfenas-Zerbini, Bas E. Dutilh, Maria Laura Garcia, Sandra Junglen, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Elliot J. Lefkowitz, Małgorzata Łobocka, Arcady R. Mushegian, Hanna M. Oksanen, David L. Robertson, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Nobuhiro Suzuki, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind V
Published in: Journal of General Virology, Issue 104, 2023, ISSN 0022-1317
Publisher: Society for General Microbiology
DOI: 10.1099/jgv.0.001840

Antibiotic Exposure Leads to Reduced Phage Susceptibility in Vancomycin Intermediate Staphylococcus aureus (VISA)

Author(s): Shawna McCallin; Carmen Menzi; Swenja Lassen; Jean Daraspe; Frank Oechslin; Philippe Moreillon
Published in: Antimicrobial Agents and Chemotherapy, Issue Ahead of Print, 2022, ISSN 0066-4804
Publisher: American Society for Microbiology
DOI: 10.1128/aac.02247-21

Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage

Author(s): Patrick A. de Jonge, Bert-Jan H. van den Born, Aeilko H. Zwinderman, Max Nieuwdorp, Bas E. Dutilh, Hilde Herrema
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-50777-0

Human cytomegalovirus exploits STING signaling and counteracts IFN/ISG induction to facilitate infection of dendritic cells

Author(s): Bibiana Costa, Jennifer Becker, Tobias Krammer, Felix Mulenge, Verónica Durán, Andreas Pavlou, Olivia Luise Gern, Xiaojing Chu, Yang Li, Luka Čičin-Šain, Britta Eiz-Vesper, Martin Messerle, Lars Dölken, Antoine-Emmanuel Saliba, Florian Erhard, Ulrich Kalinke
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-45614-3

Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author(s): Dann Turner, Andrey N. Shkoporov, Cédric Lood, Andrew D. Millard, Bas E. Dutilh, Poliane Alfenas-Zerbini, Leonardo J. van Zyl, Ramy K. Aziz, Hanna M. Oksanen, Minna M. Poranen, Andrew M. Kropinski, Jakub Barylski, J Rodney Brister, Nina Chanisvili, Rob A. Edwards, François Enault, Annika Gillis, Petar Knezevic, Mart Krupovic, Ipek Kurtböke, Alla Kushkina, Rob Lavigne, Susan Lehman, Malgorzata L
Published in: Archives of Virology, Issue 168, 2023, ISSN 0304-8608
Publisher: Springer Verlag
DOI: 10.1007/s00705-022-05694-2

Rational Design of Profile HMMs for Sensitive and Specific Sequence Detection with Case Studies Applied to Viruses, Bacteriophages, and Casposons

Author(s): Liliane S. Oliveira, Alejandro Reyes, Bas E. Dutilh, Arthur Gruber
Published in: Viruses, Issue 15, 2023, Page(s) 519, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v15020519

Known and novel viruses in Belgian honey bees: yearly differences, spatial clustering, and associations with overwintering loss

Author(s): Ward Deboutte, Lina De Smet, Marleen Brunain, Nikolas Basler, Riet De Rycke, Lena Smets, Dirk C. de Graaf, Jelle Matthijnssens
Published in: Microbiology Spectrum, Issue 12, 2024, ISSN 2165-0497
Publisher: ASM Press
DOI: 10.1128/spectrum.03581-23

Quantitative measures of within-host viral genetic diversity

Author(s): Lara Fuhrmann, Kim Philipp Jablonski, Niko Beerenwinkel
Published in: Current Opinion in Virology, Issue 49, 2022, Page(s) 157-163, ISSN 1879-6257
Publisher: Elsevier BV
DOI: 10.1016/j.coviro.2021.06.002

Expanding epidemic of recently acquired HCV in HIV-coinfected patients over a period of 10 years

Author(s): Christiana Graf, Lara Fuhrmann, Thomas Lutz, Christoph Stephan, Gaby Knecht, Peter Gute, Markus Bickel, Kai-Henrik Peiffer, Fabian Finkelmeier, Georg Dultz, Antonia Mondorf, Nils Wetzstein, Natalie Filmann, Eva Herrmann, Stefan Zeuzem, Niko Beerenwinkel, Julia Dietz, Christoph Sarrazin
Published in: JHEP Reports, Issue 5, 2023, Page(s) 100701, ISSN 2589-5559
Publisher: Elsevier B.V.
DOI: 10.1016/j.jhepr.2023.100701

Comprehensive Survey of Conserved RNA Secondary Structures in Full-Genome Alignment of Hepatitis C Virus

Author(s): Sandra Triebel, Kevin Lamkiewicz, Nancy Ontiveros, Blake Sweeney, Peter F. Stadler, Anton I. Petrov, Michael Niepmann, Manja Marz
Published in: Scientific Reports, Issue 14, 2023, Page(s) 15145, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1101/2023.11.15.567179

Sequential disruption of SPLASH-identified vRNA–vRNA interactions challenges their role in influenza A virus genome packaging

Author(s): Celia Jakob, Gabriel L. Lovate, Daniel Desir, Lara Gießler, Redmond P. Smyth, Roland Marquet, Kevin Lamkiewicz, Manja Marz, Martin Schwemmle, and Hardin Bolte
Published in: Nucleic Acids Research, Issue 51 (12), 2023, Page(s) 6479–6494, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad442

Navigating the Landscape: A Comprehensive Review of Current Virus Databases

Author(s): Muriel Ritsch, Noriko A. Cassman, Shahram Saghaei, Manja Marz
Published in: Viruses, Issue 15, 2023, Page(s) 1834, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v15091834

Benchmarking Bioinformatic Virus Identification Tools Using Real-World Metagenomic Data across Biomes

Author(s): Ling-Yi Wu, Nikolaos Pappas, Yasas Wijesekara, Gonçalo J. Piedade, Corina P.D. Brussaard, Bas E. Dutilh
Published in: Genome Biology, Issue 25, 2023, Page(s) 97, ISSN 1474-760X
Publisher: BioMed Central Ltd
DOI: 10.1101/2023.04.26.538077

Endogenous Bornavirus-like Elements in Bats: Evolutionary Insights from the Conserved Riboviral L-Gene in Microbats and Its Antisense Transcription in Myotis daubentonii

Author(s): Muriel Ritsch, Tom Eulenfeld, Kevin Lamkiewicz, Andreas Schoen, Friedemann Weber, Martin Hölzer, Manja Marz
Published in: Viruses, Issue 16, 2024, Page(s) 1210, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v16081210

V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation

Author(s): Lara Fuhrmann, Kim Philipp Jablonski, Ivan Topolsky, Aashil A Batavia, Nico Borgsmüller, Pelin Icer Baykal, Matteo Carrara, Chaoran Chen, Arthur Dondi, Monica Dragan, David Dreifuss, Anika John, Benjamin Langer, Michal Okoniewski, Louis du Plessis, Uwe Schmitt, Franziska Singer, Tanja Stadler, Niko Beerenwinkel
Published in: GigaScience, Issue 13, 2024, ISSN 2047-217X
Publisher: Oxford University Press
DOI: 10.1093/gigascience/giae065

iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria

Author(s): Simon Roux, Antonio Pedro Camargo, Felipe H. Coutinho, Shareef M. Dabdoub, Bas E. Dutilh, Stephen Nayfach, Andrew Tritt
Published in: PLOS Biology, Issue 21, 2023, Page(s) e3002083, ISSN 1544-9173
Publisher: Public Library of Science
DOI: 10.1371/journal.pbio.3002083

grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis

Author(s): Teresa Rummel, Lygeri Sakellaridi, Florian Erhard
Published in: Nature Communications, Issue 14, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-39163-4

VOGDB—Database of Virus Orthologous Groups

Author(s): Lovro Trgovec-Greif, Hans-Jörg Hellinger, Jean Mainguy, Alexander Pfundner, Dmitrij Frishman, Michael Kiening, Nicole Suzanne Webster, Patrick William Laffy, Michael Feichtinger, Thomas Rattei
Published in: Viruses, Issue 16, 2024, Page(s) 1191, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v16081191

Parallel evolution and enhanced virulence upon <i>in vivo</i> passage of an RNA virus in <i>Drosophila melanogaster</i>

Author(s): Oscar M Lezcano, Lara Fuhrmann, Gayatri Ramakrishnan, Niko Beerenwinkel, Martijn A Huynen, Ronald P van Rij
Published in: Virus Evolution, Issue 9, 2023, ISSN 2057-1577
Publisher: Oxford Academic Press
DOI: 10.1093/ve/vead074

Sequencing accuracy and systematic errors of nanopore direct RNA sequencing

Author(s): Wang Liu-Wei, Wiep van der Toorn, Patrick Bohn, Martin Hölzer, Redmond P. Smyth, Max von Kleist
Published in: BMC Genomics, Issue 25, 2024, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-024-10440-w

The influenza A virus genome packaging network — complex, flexible and yet unsolved.

Author(s): Celia Jakob; Rithu Paul-Stansilaus,; Martin Schwemmle; Roland Marquet; Hardin Bolte.
Published in: Nucleic Acids Research, Issue 03051048, 2022, Page(s) 9023-9038, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac688

Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces

Author(s): Piotr Rozwalak, Jakub Barylski, Yasas Wijesekara, Bas E. Dutilh, Andrzej Zielezinski
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-44370-0

The International Virus Bioinformatics Meeting 2023

Author(s): Franziska Hufsky, Ana B. Abecasis, Artem Babaian, Sebastian Beck, Liam Brierley, Simon Dellicour, Christian Eggeling, Santiago F. Elena, Udo Gieraths, Anh D. Ha, Will Harvey, Terry C. Jones, Kevin Lamkiewicz, Gabriel L. Lovate, Dominik Lücking, Martin Machyna, Luca Nishimura, Maximilian K. Nocke, Bernard Y. Renard, Shoichi Sakaguchi, Lygeri Sakellaridi, Jannes Spangenberg, Maria Tarradas-Alemany,
Published in: Viruses, Issue 15, 2023, Page(s) 2031, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v15102031

Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape

Author(s): Gonçalo J. Piedade, Max E. Schön, Cédric Lood, Mikhail V. Fofanov, Ella M. Wesdorp, Tristan E. G. Biggs, Lingyi Wu, Henk Bolhuis, Matthias G. Fischer, Natalya Yutin, Bas E. Dutilh, Corina P. D. Brussaard
Published in: Nature Communications, Issue 15, 2024, Page(s) 9192, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-53317-y

How might bacteriophages shape biological invasions?

Author(s): Jannick Van Cauwenberghe, Ellen L. Simms
Published in: mBio, Issue 14, 2024, ISSN 2150-7511
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.01886-23

Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification

Author(s): Evelien M. Adriaenssens, Simon Roux, J. Rodney Brister, Ilene Karsch-Mizrachi, Jens H. Kuhn, Arvind Varsani, Tong Yigang, Alejandro Reyes, Cédric Lood, Elliot J. Lefkowitz, Matthew B. Sullivan, Robert A. Edwards, Peter Simmonds, Luisa Rubino, Sead Sabanadzovic, Mart Krupovic, Bas E. Dutilh
Published in: Nature Biotechnology, Issue 41, 2023, Page(s) 898-902, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-023-01844-2

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