Publications

2024

Rozwalak, Piotr; Barylski, Jakub; Wijesekara, Yasas; Dutilh, Bas E.; Zielezinski, Andrzej

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

In: Nat Commun, vol. 15, iss. 1, pp. 495, 2024.

Abstract | Links | BibTeX | Tags: Project 12, WP 1.1 Virus identification

2023

Lezcano, Oscar M.; Fuhrmann, Lara; Ramakrishnan, Gayatri; Beerenwinkel, Niko; Huynen, Martijn A.; van Rij, Ronald P.

Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster. Journal Article

In: Virus Evol, vol. 9, iss. 2, pp. vead074, 2023.

Abstract | Links | BibTeX | Tags: Project 03, Project 09, WP 1.3 Virus-host interactions

Luo, Shiqi; Ru, Jinlong; Mirzaei, Mohammadali Khan; Xue, Jinling; Peng, Xue; Ralser, Anna; Hadi, Joshua Lemuel; Mejías-Luque, Raquel; Gerhard, Markus; Deng, Li

Helicobacter pylori infection alters gut virome by expanding temperate phages linked to increased risk of colorectal cancer Journal Article

In: Gut, pp. gutjnl-2023-330362, 2023.

Abstract | Links | BibTeX | Tags: Project 05, WP 1.2 Host prediction

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 Lencioni; 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, Yasas; González-Candelas, Fernando; Krautwurst, Sarah; Pérez-Cataluña, Alba; Randazzo, Walter; Sánchez, Gloria; Marz, Manja

The International Virus Bioinformatics Meeting 2023. Journal Article

In: Viruses, vol. 15, iss. 10, pp. 2031, 2023.

Abstract | Links | BibTeX | Tags: Project 01, Project 06, WP 1.3 Virus-host interactions, WP 1.4 Virus regulation

Luo, Shiqi; Ru, Jinlong; Mirzaei, Mohammadali Khan; Xue, Jinling; Peng, Xue; Ralser, Anna; Luque, Raquel Mejías; Gerhard, Markus; Deng, Li

Gut virome profiling identifies an association between temperate phages and colorectal cancer promoted by Helicobacter pylori infection Journal Article

In: Gut Microbes, vol. 15, iss. 2, pp. 2257291, 2023.

Abstract | Links | BibTeX | Tags: Project 05, WP 1.1 Virus identification, WP 1.2 Host prediction

Adriaenssens, Evelien M.; Roux, Simon; Brister, J. Rodney; Karsch-Mizrachi, Ilene; Kuhn, Jens H.; Varsani, Arvind; Yigang, Tong; Reyes, Alejandro; Lood, Cédric; Lefkowitz, Elliot J.; Sullivan, Matthew B.; Edwards, Robert A.; Simmonds, Peter; Rubino, Luisa; Sabanadzovic, Sead; Krupovic, Mart; Dutilh, Bas E.

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

In: Nature Biotechnology, vol. 41, pp. 898–902, 2023.

Abstract | Links | BibTeX | Tags:

Rummel, Teresa; Sakellaridi, Lygeri; Erhard, Florian

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

In: Nat Commun, vol. 14, iss. 1, pp. 3559, 2023.

Abstract | Links | BibTeX | Tags: Project 06, WP 1.3 Virus-host interactions

Jakob, Celia; Lovate, Gabriel Lencioni; Desirò, Daniel; Gießler, Lara; Smyth, Redmond P.; Marquet, Roland; Lamkiewicz, Kevin; Marz, Manja; Schwemmle, Martin; Bolte, Hardin

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

In: Nucleic Acids Research, vol. 51, iss. 12, pp. 6479-6494, 2023.

Abstract | Links | BibTeX | Tags: Project 01, WP 1.4 Virus regulation

Siddell, Stuart G.; Smith, Donald B.; Adriaenssens, Evelien; Alfenas-Zerbini, Poliane; Dutilh, Bas E.; Garcia, Maria Laura; Junglen, Sandra; Krupovic, Mart; Kuhn, Jens H.; Lambert, Amy J.; Lefkowitz, Elliot J.; Łobocka, Małgorzata; Mushegian, Arcady R.; Oksanen, Hanna M.; Robertson, David L.; Rubino, Luisa; Sabanadzovic, Sead; Simmonds, Peter; Suzuki, Nobuhiro; Doorslaer, Koenraad Van; Vandamme, Anne-Mieke; Varsani, Arvind; Zerbini, F. Murilo

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

In: Journal of General Virology, vol. 104, iss. 5, 2023.

Links | BibTeX | Tags:

Wu, Ling-Yi; Pappas, Nikolaos; Wijesekara, Yasas; Piedade, Gonçalo J.; Brussaard, Corina P. D.; Dutilh, Bas E.

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

In: bioRxiv, 2023.

Abstract | Links | BibTeX | Tags: Project 12, Project 13, WP 1.1 Virus identification, WP 1.2 Host prediction

Roux, Simon; Camargo, Antonio Pedro; Coutinho, Felipe H.; Dabdoub, Shareef M.; Dutilh, Bas E.; Nayfach, Stephen; Tritt, Andrew

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

In: PLOS Biology, 2023.

Abstract | Links | BibTeX | Tags:

Liu, Dan; Young, Francesca; Robertson, David L.; Yuan, Ke

Prediction of virus-host association using protein language models and multiple instance learning Journal Article

In: bioRxiv, 2023.

Abstract | Links | BibTeX | Tags: Project 10, WP 1.2 Host prediction, WP 1.3 Virus-host interactions

Ru, Jinlong; Mirzaei, Mohammadali Khan; Xue, Jinling; Peng, Xue; Deng, Li

ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis Journal Article

In: Gut Microbes, vol. 15, iss. 1, pp. 2192522, 2023.

Abstract | Links | BibTeX | Tags: Project 05, WP 1.1 Virus identification, WP 1.2 Host prediction

Graf, Christiana; Fuhrmann, Lara; Lutz, Thomas; Stephan, Christoph; Knecht, Gaby; Gute, Peter; Bickel, Markus; Peiffer, Kai-Henrik; Finkelmeier, Fabian; Dultz, Georg; Mondorf, Antonia; Wetzstein, Nils; Filmann, Natalie; Herrmann, Eva; Zeuzem, Stefan; Beerenwinkel, Niko; Dietz, Julia; Sarrazin, Christoph

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

In: JHEP Rep, vol. 5, iss. 7, pp. 100701, 2023.

Abstract | Links | BibTeX | Tags: Project 03, WP 1.3 Virus-host interactions

Oliveira, Liliane S.; Reyes, Alejandro; Dutilh, Bas E.; Gruber, Arthur

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

In: Viruses, vol. 15, iss. 2, pp. 519, 2023.

Links | BibTeX | Tags:

Turner, Dann; Shkoporov, Andrey N.; Lood, Cédric; Millard, Andrew D.; Dutilh, Bas E.; Alfenas-Zerbini, Poliane; van Zyl, Leonardo J.; Aziz, Ramy K.; Oksanen, Hanna M.; Poranen, Minna M.; Kropinski, Andrew M.; Barylski, Jakub; Brister, J Rodney; Chanisvili, Nina; Edwards, Rob A.; Enault, François; Gillis, Annika; Knezevic, Petar; Krupovic, Mart; Kurtböke, Ipek; Kushkina, Alla; Lavigne, Rob; Lehman, Susan; Lobocka, Malgorzata; Moraru, Cristina; Switt, Andrea Moreno; Morozova, Vera; Nakavuma, Jesca; Muñoz, Alejandro Reyes; Rūmnieks, Jānis; Sarkar, BL; Sullivan, Matthew B.; Uchiyama, Jumpei; Wittmann, Johannes; Yigang, Tong; Adriaenssens, Evelien M.

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

In: Virology Division News, vol. 168, pp. 74, 2023.

Abstract | Links | BibTeX | Tags:

2022

Rummel, Teresa; Sakellaridi, Lygeri; Erhard, Florian

grandR: a comprehensive package for nucleotide conversion sequencing data analysis Journal Article

In: bioRxiv, 2022.

Abstract | Links | BibTeX | Tags: Project 06, WP 1.3 Virus-host interactions

Besson, Benoit; Lezcano, Oscar M.; Overheul, Gijs J; Janssen, Kirsten; Spruijt, Cornelia G.; Vermeulen, Michiel; Qu, Jieqiong; van Rij, Ronald P.

Arbovirus-vector protein interactomics identifies Loquacious as a co-factor for dengue virus replication in Aedes mosquitoes Journal Article

In: PLoS Pathogens, vol. 18, iss. 9, pp. e1010329, 2022.

Abstract | Links | BibTeX | Tags: Project 09, WP 1.3 Virus-host interactions

Jakob, Celia; Paul-Stansilaus, Rithu; Schwemmle, Martin; Marquet, Roland; Bolte, Hardin

The influenza A virus genome packaging network - complex, flexible and yet unsolved Journal Article

In: Nucleic Acids Res., 2022.

Abstract | Links | BibTeX | Tags: Project 02, WP 1.4 Virus regulation

Peng, Xue; Ru, Jinlong; Mirzaei, Mohammadali Khan; Deng, Li

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

In: bioRxiv, 2022.

Abstract | Links | BibTeX | Tags: Project 05, WP 1.2 Host prediction

Jahn, Katharina; Dreifuss, David; Topolsky, Ivan; Kull, Anina; Ganesanandamoorthy, Pravin; Fernandez-Cassi, Xavier; Bänziger, Carola; Devaux, Alexander J.; Stachler, Elyse; Caduff, Lea; Cariti, Federica; Corzón, Alex Tuñas; Fuhrmann, Lara; Chen, Chaoran; Jablonski, Kim Philipp; Nadeau, Sarah; Feldkamp, Mirjam; Beisel, Christian; Aquino, Catharine; Stadler, Tanja; Ort, Christoph; Kohn, Tamar; Julian, Timothy R.; Beerenwinkel, Niko

Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC Journal Article

In: Nat Microbiol, 2022.

Abstract | Links | BibTeX | Tags: Project 03, WP 1.3 Virus-host interactions

McCallin, Shawna; Menzi, Carmen; Lassen, Swenja; Daraspe, Jean; Oechslin, Frank; Moreillon, Philippe

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

In: Antimicrob Agents Chemother, 2022.

Abstract | Links | BibTeX | Tags: Project 07, WP 1.5 Virus products

2021

Chen, Chaoran; Nadeau, Sarah Ann; Topolsky, Ivan; Manceau, Marc; Huisman, Jana S.; Jablonski, Kim Philipp; Fuhrmann, Lara; Dreifuss, David; Jahn, Katharina; Beckmann, Christiane; Redondo, Maurice; Noppen, Christoph; Risch, Lorenz; Risch, Martin; Wohlwend, Nadia; Kas, Sinem; Bodmer, Thomas; Roloff, Tim; Stange, Madlen; Egli, Adrian; Eckerle, Isabella; Kaiser, Laurent; Denes, Rebecca; Feldkamp, Mirjam; Nissen, Ina; Santacroce, Natascha; Burcklen, Elodie; Aquino, Catharine; de Gouvea, Andreia Cabral; Moccia, Maria Domenica; Grüter, Simon; Sykes, Timothy; Opitz, Lennart; White, Griffin; Neff, Laura; Popovic, Doris; Patrignani, Andrea; Tracy, Jay; Schlapbach, Ralph; Dermitzakis, Emmanouil T; Harshman, Keith; Xenarios, Ioannis; Pegeot, Henri; Cerutti, Lorenzo; Penet, Deborah; Blin, Anthony; Elies, Melyssa; Althaus, Christian L.; Beisel, Christian; Beerenwinkel, Niko; Ackermann, Martin; Stadler, Tanja

Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland Journal Article

In: Epidemics, vol. 37, pp. 100480, 2021.

Abstract | Links | BibTeX | Tags: Project 03, WP 1.3 Virus-host interactions

Fuhrmann, Lara; Jablonski, Kim Philipp; Beerenwinkel, Niko

Quantitative measures of within-host viral genetic diversity Journal Article

In: Curr Opin Virol, vol. 49, pp. 157-163, 2021.

Abstract | Links | BibTeX | Tags: Project 03, WP 1.3 Virus-host interactions

Goettsch, Winfried; Beerenwinkel, Niko; Deng, Li; Dölken, Lars; Dutilh, Bas E.; Erhard, Florian; Kaderali, Lars; von Kleist, Max; Marquet, Roland; Matthijnssens, Jelle; McCallin, Shawna; McMahon, Dino; Rattei, Thomas; van Rij, Ronald P.; Robertson, David L.; Schwemmle, Martin; Stern-Ginossar, Noam; Marz, Manja

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

In: Viruses, vol. 13, no. 5, pp. 766, 2021.

Abstract | Links | BibTeX | Tags: Project 01, Project 02, Project 03, Project 04, Project 05, Project 06, Project 07, Project 08, Project 09, Project 10, Project 11, Project 12, Project 13, Project 14, Project 15, WP 1.1 Virus identification, WP 1.2 Host prediction, WP 1.3 Virus-host interactions, WP 1.4 Virus regulation, WP 1.5 Virus products, WP 2.1 Microevolution: Virus quasispecies, WP 2.2 Macroevolution: Natural selection of viruses