Publications

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

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; & Niko Beerenwinkel, Timothy R. Julian

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

In: Nat Microbiol, 2022.

Abstract | Links | BibTeX | Tags:

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

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