2023
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
@article{nokey,
title = {The International Virus Bioinformatics Meeting 2023.},
author = {Franziska Hufsky and Ana B. Abecasis and Artem Babaian and Sebastian Beck and Liam Brierley and Simon Dellicour and Christian Eggeling and Santiago F. Elena and Udo Gieraths and Anh D. Ha and Will Harvey and Terry C. Jones and Kevin Lamkiewicz and Gabriel Lencioni Lovate and Dominik Lücking and Martin Machyna and Luca Nishimura and Maximilian K. Nocke and Bernard Y. Renard and Shoichi Sakaguchi and Lygeri Sakellaridi and Jannes Spangenberg and Maria Tarradas-Alemany and Sandra Triebel and Yulia Vakulenko and Yasas Wijesekara and Fernando González-Candelas and Sarah Krautwurst and Alba Pérez-Cataluña and Walter Randazzo and Gloria Sánchez and Manja Marz },
doi = {10.3390/v15102031},
year = {2023},
date = {2023-09-30},
urldate = {2023-09-30},
journal = {Viruses},
volume = {15},
issue = {10},
pages = {2031},
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.},
keywords = {Project 01, Project 06, WP 1.3 Virus-host interactions, WP 1.4 Virus regulation},
pubstate = {published},
tppubtype = {article}
}
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.
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
@article{nokey,
title = {grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis},
author = {Teresa Rummel and Lygeri Sakellaridi and Florian Erhard
},
doi = {10.1038/s41467-023-39163-4},
year = {2023},
date = {2023-06-15},
journal = {Nat Commun},
volume = {14},
issue = {1},
pages = {3559},
abstract = {Metabolic labeling of RNA is a powerful technique for studying the temporal dynamics of gene expression. Nucleotide conversion approaches greatly facilitate the generation of data but introduce challenges for their analysis. Here we present grandR, a comprehensive package for quality control, differential gene expression analysis, kinetic modeling, and visualization of such data. We compare several existing methods for inference of RNA synthesis rates and half-lives using progressive labeling time courses. We demonstrate the need for recalibration of effective labeling times and introduce a Bayesian approach to study the temporal dynamics of RNA using snapshot experiments.},
keywords = {Project 06, WP 1.3 Virus-host interactions},
pubstate = {published},
tppubtype = {article}
}
Metabolic labeling of RNA is a powerful technique for studying the temporal dynamics of gene expression. Nucleotide conversion approaches greatly facilitate the generation of data but introduce challenges for their analysis. Here we present grandR, a comprehensive package for quality control, differential gene expression analysis, kinetic modeling, and visualization of such data. We compare several existing methods for inference of RNA synthesis rates and half-lives using progressive labeling time courses. We demonstrate the need for recalibration of effective labeling times and introduce a Bayesian approach to study the temporal dynamics of RNA using snapshot experiments.
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
@article{Rummel2022,
title = {grandR: a comprehensive package for nucleotide conversion sequencing data analysis},
author = {Teresa Rummel and Lygeri Sakellaridi and Florian Erhard },
doi = {10.1101/2022.09.12.507665},
year = {2022},
date = {2022-09-15},
urldate = {2022-09-15},
journal = {bioRxiv},
abstract = {Metabolic labeling of RNA is a powerful technique for studying the temporal dynamics of gene expression. Nucleotide conversion approaches greatly facilitate the generation of data but introduce challenges for their analysis. We here present grandR, a comprehensive package for quality control, differential gene expression analysis, kinetic modeling, and visualization of such data. We compare several existing methods for inference of RNA synthesis rates and half-lives using progressive labeling time courses. We demonstrate the need for recalibration of effective labeling times and introduce a Bayesian approach to study the temporal dynamics of RNA using snapshot experiments.},
keywords = {Project 06, WP 1.3 Virus-host interactions},
pubstate = {published},
tppubtype = {article}
}
Metabolic labeling of RNA is a powerful technique for studying the temporal dynamics of gene expression. Nucleotide conversion approaches greatly facilitate the generation of data but introduce challenges for their analysis. We here present grandR, a comprehensive package for quality control, differential gene expression analysis, kinetic modeling, and visualization of such data. We compare several existing methods for inference of RNA synthesis rates and half-lives using progressive labeling time courses. We demonstrate the need for recalibration of effective labeling times and introduce a Bayesian approach to study the temporal dynamics of RNA using snapshot experiments.
2021
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
@article{nokey,
title = {ITN -- VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics},
author = {Winfried Goettsch and Niko Beerenwinkel and Li Deng and Lars Dölken and Bas E. Dutilh and Florian Erhard and Lars Kaderali and Max von Kleist and Roland Marquet and Jelle Matthijnssens and Shawna McCallin and Dino McMahon and Thomas Rattei and Ronald P. {van Rij} and David L. Robertson and Martin Schwemmle and Noam Stern-Ginossar and Manja Marz},
doi = {10.3390/v13050766},
year = {2021},
date = {2021-04-27},
urldate = {2021-04-27},
journal = {Viruses},
volume = {13},
number = {5},
pages = {766},
abstract = {Many recent studies highlight the fundamental importance of viruses. Besides their important role as human and animal pathogens, their beneficial, commensal or harmful functions are poorly understood. By developing and applying tailored bioinformatical tools in important virological models, the Marie Skłodowska-Curie Initiative International Training Network VIROINF will provide a better understanding of viruses and the interaction with their hosts. This will open the door to validate methods of improving viral growth, morphogenesis and development, as well as to control strategies against unwanted microorganisms. The key feature of VIROINF is its interdisciplinary nature, which brings together virologists and bioinformaticians to achieve common goals.},
keywords = {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},
pubstate = {published},
tppubtype = {article}
}
Many recent studies highlight the fundamental importance of viruses. Besides their important role as human and animal pathogens, their beneficial, commensal or harmful functions are poorly understood. By developing and applying tailored bioinformatical tools in important virological models, the Marie Skłodowska-Curie Initiative International Training Network VIROINF will provide a better understanding of viruses and the interaction with their hosts. This will open the door to validate methods of improving viral growth, morphogenesis and development, as well as to control strategies against unwanted microorganisms. The key feature of VIROINF is its interdisciplinary nature, which brings together virologists and bioinformaticians to achieve common goals.