Outreach

@misc{nokey,

title = {The honey bee gut microbiome – a diversity profile of different gut parts and seasons across eight European countries},

author = {Nikolas Basler and Dirk C. de Graaf and Lina De Smet and Jelle Matthijnssens},

year  = {2022},

date = {2022-09-20},

urldate = {2022-09-20},

abstract = {As a highly productive pollinator of flowering plants, the honey bee (Apis mellifera) plays an important role in ecology and agriculture. However, managed honey bee colonies are suffering from a number of stressors, including pathogens, parasites, and the use of pesticides. Studying and improving the health of honey bees is therefore of great ecologic and economic interest. Previous studies have shown that the honey bee gut houses a stable bacterial microbiome of only approximately eight core species. On the other hand, recent studies described a higher diversity in bacteria on the sub-species level as well as in bacteriophages (or phages, i.e. viruses that infect bacteria). Additionally, it has been shown that the gut microbiome affects the bees’ development, immune signalling and behaviour. 

This project is part of the EU-funded Innovative Training Network VIROINF (grant agreement No 955974) which revolves around virus-host interactions and aims to facilitate the connections between the fields of virology and bioinformatics. Honey bees from eight different European countries (Belgium, France, Germany, Netherlands, Portugal, Romania, Switzerland and United Kingdom) were collected during spring, summer and autumn 2020 as part of the EU-funded B-GOOD project (grant agreement No 817622). From each sample, midguts, ileums and rectums of 10 individual bees have been pooled and processed to generate Illumina libraries for shotgun sequencing. From the resulting data, the diversity of the microbiome was assessed based on species-level abundances as well as shared fractions of single-nucleotide variations (SNVs) in orthologous core genes within species. Preliminary analysis of the core species abundance profiles suggests that the rectum contains the entire bacterial community, of which ileum and midgut contain nested subsets. Unlike species abundances, SNV profiles within some core species appear to separate by geographic origin. 

These findings will also inform future experiments to gain more insight into the complex interactions between the honey bee, its gut bacteria and their viruses. We thereby aim to contribute to a better understanding of honey bee health and disease.},

howpublished = {Oral presentation at 9th European Congress of Apidology (EurBee9)},

note = {Best Oral Presentation},

keywords = {Project 11, WP 1.1 Virus identification},

pubstate = {published},

tppubtype = {presentation}

}

@misc{Liu-Wei2022,

title = {Systematic benchmarking and error evaluation of basecallers for Nanopore Direct RNA-seq},

author = {Wang Liu-Wei and Patrick Bohn and Wiep van der Toorn and Redmond P. Smyth and Max von Kleist},

year  = {2022},

date = {2022-09-20},

urldate = {2022-09-20},

howpublished = {Poster at 21st European Conference on Computational Biology 2022},

keywords = {Project 08, WP 2.1 Microevolution: Virus quasispecies},

pubstate = {published},

tppubtype = {presentation}

}

@misc{Liu-Wei2022b,

title = {FrameRate: predicting coding frames direct from unassembled DNA reads},

author = {Wang Liu-Wei and Robert Hoehndorf and Wayne Aubrey and Christopher Creevey and Amanda Clare and Nicholas Dimonaco},

year  = {2022},

date = {2022-09-19},

urldate = {2022-09-19},

howpublished = {Poster at 21st European Conference on Computational Biology 2022},

keywords = {Project 08, WP 2.1 Microevolution: Virus quasispecies},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {Experimental evolution of Deformed Wing Virus in developing honeybees (\textit{Apis mellifera})},

author = {Harshit Kumar Prajapati

},

year  = {2022},

date = {2022-09-07},

howpublished = {Poster at Ecological immunology workshop 2022: Resistance, tolerance & symbionts},

keywords = {Project 04, WP 2.2 Macroevolution: Natural selection of viruses},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {Computational prediction of virus-host interactions by pre-trained transformer and Multiple Instance Learning},

author = {Dan Liu},

url = {https://cbc.dcs.gla.ac.uk/},

year  = {2022},

date = {2022-09-01},

urldate = {2022-09-01},

abstract = {Viruses exist in the environment extensively and live in different hosts including plants, animals, eukaryotes, and bacteria and generate offspring depending on the replication mechanisms of the hosts. Detecting virus-host interactions is essential for us to understand interaction mechanisms between virus and host and explore clues regarding diseases caused by viruses. The virus mimics the host's patterns for escaping the immune response, so viral contain predictive signals for host prediction. Here, we proposed a computational strategy to predict hosts for viruses, which extracted representative vectors of viral protein sequences through a pre-trained transformer language model and then passed protein features to attention-based Multiple instance learning for host prediction and obtaining each weighted protein for viruses. Protein weight is helpful for understanding essential proteins contributing to virus-host interactions, and it is explainable for prediction signals of host prediction at the species level. Our results demonstrated that transformer embedding is potential for virus-host interaction prediction and is able to explain essential virus proteins leading to host infection.

},

howpublished = {Oral presentation at Computational Biology Conference 2022, Glasgow, UK},

keywords = {Project 10, WP 1.2 Host prediction},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {Replidec - Use naive bayes classifier to identify virus lifecycle from metagenomics data},

author = {Xue Peng},

year  = {2022},

date = {2022-08-01},

howpublished = {Poster at VIRO retreat 2022, Munich, Germany},

keywords = {Project 05, WP 1.2 Host prediction},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {Antibiotic Exposure Leads to Reduced Phage Susceptibility in Vancomycin Intermediate Staphylococcus aureus (VISA)},

author = {Swenja Lassen},

year  = {2022},

date = {2022-07-19},

howpublished = {Poster at Viruses of Microbes (VoM) meeting 2022},

keywords = {Project 07, WP 1.5 Virus products},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {The database of Virus Orthologous Groups and its application in phage cocktail genomics},

author = {Lovro Trgovec-Greif

},

year  = {2022},

date = {2022-07-18},

howpublished = {Poster at Viruses of Microbes (VoM) meeting 2022},

keywords = {Project 14, WP 1.5 Virus products},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {Inferring expression trajectories from metabolically labeled cells},

author = {Lygeri Sakellaridi},

year  = {2022},

date = {2022-06-22},

howpublished = {Poster at International symposium on immune control and its evasion by CMV and other DNA viruses (Deep-DV) 2022},

keywords = {Project 06, WP 1.3 Virus-host interactions},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {Using high-throughput analysis to understand RNA-RNA interactions of Influenza},

author = {Gabriel Lencioni Lovate},

url = {https://www.infectognostics.de/termine/rnaswarm},

year  = {2022},

date = {2022-04-29},

urldate = {2022-04-29},

abstract = {As a segmented RNA virus, Influenza is a frequently changing its genome. Each year, this leads to pandemic strains and continuous efforts to adapt  vaccines to newly emerging antigens of Influenza. To improve the understanding of this antigenic diversity, researchers from the European Virus Bioinformatics Center (EVBC) are analysing the specific RNA-RNA interactions that play an essential role in the packaging and the corresponding selective reassortment of Influenza (A) genomes.



In this lecture, EVBC scientist Gabriel Lencioni Lovate will present "RNAswarm", a new software pipeline that is expanding the scope of high-throughput analyses of RNA-RNA interactions. In particular, RNAswarm allows for statistically comparing the frequency of RNA interactions among different strains or experimental settings. Thus, RNAswarm offers virologists an automated and consistent method for prioritising and comparing the RNA-RNA interactions, a time-consuming job prone to individual biases when performed manually.},

howpublished = {Talk at DiagnosTech Lecture},

keywords = {Project 01, WP 1.4 Virus regulation},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {Identification of RNA-RNA interactions that drive genetic reassortment between human H1N1 and H3N2 viruses},

author = {Rithu Paul-Stansilaus},

year  = {2022},

date = {2022-04-13},

howpublished = {Oral presentation at 3rd ResaFlu meeting 2022},

keywords = {Project 02, WP 1.4 Virus regulation},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {Identification of RNA-RNA interactions that drive genetic reassortment between human H1N1 and H3N2 viruses},

author = {Rithu Paul-Stansilaus},

year  = {2022},

date = {2022-04-11},

howpublished = {Poster at XXIVemes Journées Francophones de Virologie 2022},

keywords = {Project 02, WP 1.4 Virus regulation},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {RNAswarm: A pipeline for differential RNA-RNA Interaction probing},

author = {Gabriel Lencioni Lovate},

year  = {2022},

date = {2022-03-30},

urldate = {2022-03-30},

howpublished = {Oral poster at 31st Annual Meeting of the Society for Virology 2022, Munich, Germany},

keywords = {Project 01, WP 1.4 Virus regulation},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {Read error correction for heterogeneous NGS samples using Dirichlet mixture models},

author = {Lara Fuhrmann },

url = {https://bsse.ethz.ch/cbg/cbg-news/ascona-2022.html},

year  = {2022},

date = {2022-03-27},

howpublished = {Poster at Asonca 2022 - Biological systems: from first principles to data-​driven modelling and back },

keywords = {Project 03, WP 2.1 Microevolution: Virus quasispecies},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {Reproducible RNA-RNA interaction probing for RNA proximity ligation data with RNAswarm},

author = {Gabriel Lencioni Lovate},

url = {https://evbc.uni-jena.de/events/vibiom2022/},

year  = {2022},

date = {2022-03-24},

howpublished = {Poster at International Virus Bioinformatics Meeting 2022},

note = {Best Poster Award},

keywords = {Project 01, WP 1.4 Virus regulation},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {Error correction and local haplotype reconstruction for NGS data},

author = {Lara Fuhrmann},

url = {https://evbc.uni-jena.de/events/vibiom2022/},

year  = {2022},

date = {2022-03-24},

urldate = {2022-03-24},

howpublished = {Poster at International Virus Bioinformatics Meeting 2022},

keywords = {Project 03, WP 2.1 Microevolution: Virus quasispecies},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {GRAND-R: Leveraging the power of RNA metabolic labeling to record transcriptional activity in single cells},

author = {Lygeri Sakellaridi},

url = {https://evbc.uni-jena.de/events/vibiom2022/},

year  = {2022},

date = {2022-03-24},

howpublished = {Poster at International Virus Bioinformatics Meeting 2022},

keywords = {Project 06, WP 1.3 Virus-host interactions},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {Inferring expression trajectories from metabolically labeled cells},

author = {Lygeri Sakellaridi



},

year  = {2021},

date = {2021-10-07},

urldate = {2022-10-05},

howpublished = {Poster at EUREKA Symposium 2021},

keywords = {Project 06, WP 1.3 Virus-host interactions},

pubstate = {published},

tppubtype = {presentation}

}

@misc{nokey,

title = {VOGDB - Virus Orthologous Groups database},

author = {Lovro Trgovec-Greif},

url = {https://applbio.biologie.uni-frankfurt.de/conferences/qfo6-5/QfO6-5_Program.pdf},

year  = {2021},

date = {2021-08-02},

howpublished = {Oral presentation at Quest for Orthologs 2021},

keywords = {Project 14, WP 1.5 Virus products},

pubstate = {published},

tppubtype = {presentation}

}