List of Past Projects

    Prediction of antibiotic susceptibility profiles from whole-genome sequencing

    In order to limit the spread of pathogenic drug-resistant bacteria and to maintain treatment options the analysis of clinical samples and their AMR profiles are essential. Particularly, in low-resource settings a timely analysis of AMR profiles is often impaired due to lengthy culturing procedures for antibiotic susceptibility testing or lack of laboratory capacity. Because of the relatively low costs, the possibility for real-time data analyses, and portability, the Oxford Nanopore Technologies MinION sequencing platform — especially in light of an upcoming less error-prone technology for the platform — appears to be well suited for pathogen genomic analyses. We developed the pipeline CholerAegon for the in silico prediction of AMR profiles of Vibrio cholerae genomes assembled from long and/or short sequencing reads. We aim to adapt our pipeline to other pathogenic microorganisms.

    People involved: Sebastian Krautwurst

    Collaborations: Kathrin Schuldt, Valeria Fuesslin

    Related publications:

    Fuesslin, Valeria; Krautwurst, Sebastian; Srivastava, Akash; Winter, Doris; Liedigk, Britta; Thye, Thorsten; Herrera-León, Silvia; Wohl, Shirlee; May, Jürgen; Fobil, Julius N.; Eibach, Daniel; Marz, Manja; Schuldt, Kathrin

    Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon Journal Article

    In: Front Microbiol, vol. 13, pp. 909692, 2022.

    Abstract | Links | BibTeX

    Workflow development for HTS data

    High-throughput sequencing (HTS) of DNA and RNA has become a standard procedure in molecular biology. Widely used methods include next-generation sequencing (NGS) of short reads, offered primarily by Illumina, and third-generation sequencing (TGS) of long reads e.g. using Nanopore ONT. With decreasing costs, technological improvements, and wider use, there are more and more HTS datasets. The amount and size of the data can make the analysis difficult. We are developing reproducible, scalable, and portable workflows for processing and analyzing HTS data by deploying workflow management frameworks such as Nextflow. The goal is to provide easy-to-use workflows with state-of-the-art tools for different HTS types and applications.

    People involved: Marie Lataretu, Sebastian Krautwurst, Martin Hölzer

    Related publications:

    Lataretu, Marie; Hölzer, Martin

    RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow Journal Article

    In: Genes, vol. 11, no. 12, pp. 1487, 2020.

    Abstract | Links | BibTeX

    Molecular serology for rapid determination of vaccination titers

    The Permanent Vaccination Commission (STIKO) annually publishes a list of recommended vaccinations. A high vaccination rate in a population is the best requirement to prevent the spread of vaccine-preventable diseases. However, the present system is being challenged by massive migration of people from crisis areas. Therefore, we want to develop a novel diagnostic tool to determine, in a single test run, the antibody status against all vaccinations recommended by the STIKO. For this purpose, new bioinformatic tools for in silico identification of diagnostically relevant epitopes will be developed. This will render the diagnosis faster, less expensive and less time consuming and, at the same time, considerably more informative.

    People involved: Konrad Sachse, Maximilian Collatz

    Grants: Zwanzig20 – InfectControl 2020: Molekulare Serologie zur schnellen Bestimmung der Impftiter gegen impf-präventable Infektionskrankheiten (STIKO-Liste) bei Migranten und anderen Patientengruppen; Subproject: STIKO-Serologie

    Related publications:

    Collatz, Maximilian; Mock, Florian; Barth, Emanuel; Hölzer, Martin; Sachse, Konrad; Marz, Manja

    EpiDope: A Deep Neural Network for linear B-cell epitope prediction Journal Article

    In: Bioinformatics, vol. 37, no. 4, pp. 448–455, 2020.

    Abstract | Links | BibTeX

    Towards solving the puzzle of aging

    Aging is still an enigma, which has challenged scientists and philosophers for centuries. For example, individuals within one species or population show a divers range of life spans (most humans die around 80 years of age, whereas some reach the age of 100 or even more). Which genes are responsible for this variance in lifespan and how exactly is aging caused? We try to help answer these questions by the means of transcriptomic data analysis, including the identification of genes and biological processes that are differentially regulated through time, in different species and tissues.

    People involved: Emanuel BarthAkash Srivastava

    Collaborations: Alessandro Cellerino, Otto Witte

    Grants: RegenerAging — Analyzing the regulation of aging

    Related publications:

    Barth, Emanuel; Srivastava, Akash; Wengerodt, Diane; Stojiljkovic, Milan; Axer, Hubertus; Witte, Otto W; Kretz, Alexandra; Marz, Manja

    Age-dependent expression changes of circadian system-related genes reveal a potentially conserved link to aging Journal Article

    In: Aging, vol. 13, no. 24, pp. 25694-25716, 2021.

    Abstract | Links | BibTeX

    Srivastava, Akash; Barth, Emanuel; Ermolaeva, Maria A.; Guenther, Madlen; Frahm, Christiane; Marz, Manja; Witte, Otto W.

    Tissue-specific Gene Expression Changes Are Associated with Aging in Mice Journal Article

    In: Genomics Proteomics Bioinformatics, vol. 18, no. 4, pp. 430–442, 2020.

    Abstract | Links | BibTeX

    Srivastava, Akash

    Whole-transcriptome changes in gene expression in multiple tissues across various organisms during aging PhD Thesis


    Links | BibTeX

    Barth, Emanuel; Srivastava, Akash; Stojiljkovic, Milan; Frahm, Christiane; Axer, Hubertus; Witte, Otto W; Marz, Manja

    Conserved aging-related signatures of senescence and inflammation in different tissues and species. Journal Article

    In: Aging, vol. 11, no. 19, pp. 8556—8572, 2019.

    Abstract | Links | BibTeX

    Finding mitogenomes in fungi using short-read NGS data

    Mitochondria are essential energy producing cell organelles in eukaryotes. Their genomes are common objects for phylogenetic studies. For fungi, mitochondria play also a key role for pathogenicity and drug resistance. The structure and evolution of the mitogenomes differs between plants, animals and fungi, whereby fungal mitogenomes have been less studied than in plants or animals. The loss of tRNAs and ribosomal proteins has been reported in fungal mitogenome, as well as recombination and variable gene distribution. Hence de novo tools for reconstructing the mitogenome in silico should work with as few information from related species as possible. We will develop a pipeline to find and annotate mitogenomes of fungal short-read NGS data automatically.

    People involved: Marie Lataretu

    Collaborations: Matthias Bernt

    Multiplex-sequencing for different kingdoms 

    The concept of the German Centre for Integrative Biodiversity Research (iDiv) encompasses the detection of biodiversity, understanding its emergence, exploring its consequences for ecosystem functions and services, and developing strategies to safeguard biodiversity under global change.
    To record biological diversity is fundamental but faces many challenges. To analyse genomes and transcriptomes from all organisms e.g. in soil or gut of insects, we usually use different (wet-lab) extraction protocols for bacteria, fungi and viruses. Sometimes also a common host needs to be sequenced. Instead of sequencing about 10 times the same sample from different extraction protocols to obtain the complete biodiversity, we aim to develop a method to multiplex organisms from different kingdoms into one sequencing approach.

    People involved: Franziska Hufsky

    Grants: DFG iDiv: All-in-one Multiplex-Sequencing