de

Dr. Malte Petersen

Bioinformatics Research Scientist

I design and implement workflows to efficiently analyse large-scale genomic and transcriptomic datasets; I also support research projects with statistical modelling and data visualisation.

I am the main contact person for requests from the life sciences.

Fields of expertise

I can support you in the following topics:

  • Usage of HPC clusters and batch systems/schedulers such as SLURM on Bonna
  • Writing workflows that scale to hundreds or thousands of samples
  • Identifying and resolving performance bottlenecks in your pipeline
  • Genome analysis:
    • Assembly (short read/long read/hybrid)
    • Annotation (protein-coding genes, non-coding regions, repeats)
    • Variant calling (structural/single nucleotide)
    • Comparative genomics
  • Transcriptome analysis:
    • Assembly
    • Annotation
    • Differential gene expression
  • Single-cell RNA-seq:
    • Mapping and read counting
    • Denoising and dimensionality reduction
    • Plotting (t-SNE/UMAP)
  • Phylogenetics:
    • Workstreams towards large phylogenies, also from whole genomes
    • Orthology prediction
    • Bayesian/Maximum Likelihood phylogeny inference
    • Comparative phylogenetic methods

Curriculum vitae

2022 -- dato HPC/A Lab, Digital Science Center, University of Bonn

2019 -- 2022 Max Planck Institute of Immunobiology and Epigenetics, Freiburg

2018 -- 2019 Senckenberg Biodiversity and Climate Research Centre, Frankfurt

2018 PhD (Dr. rer. nat.), Zoological Research Museum A. Koenig, Bonn

2013 Diploma (Dipl. Biol.), Zoological Research Museum A. Koenig, Bonn

Publications

Excerpt. Full publication list on Orcid .

Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae

Malte Petersen, Sven Winter, Raphael Coimbra, Menno J. de Jong, Vladimir V. Kapitonov, Maria A. Nilsson

Mobile DNA (2021). DOI: 10.1186/s13100-021-00254-y

The immunogenetics of sexual parasitism

Jeremy B. Swann, Stephen J. Holland, Malte Petersen, Theodore W. Pietsch, Thomas Boehm

Science (2020). DOI: 10.1126/science.aaz9445

Improving the Chromosome-Level Genome Assembly of the Siamese Fighting Fish (Betta splendens) in a University Master's Course

Stefan Prost, Malte Petersen, Martin Grethlein, Sarah Joy Hahn, Nina Kuschik-Maczollek, Martyna E.  Olesiuk, Jan-Olaf Reschke, Tamara E.  Schmey, Caroline Zimmer, Deepak K Gupta, Tilman Schell, Raphael Coimbra, Jordi De Raad, Fritjof Lammers, Sven Winter, Axel Janke

G3 Genes|Genomes|Genetics (2020). DOI: 10.1534/g3.120.401205

Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects

Malte Petersen, David Armisén, Richard A. Gibbs, Lars Hering, Abderrahman Khila, Georg Mayer, Stephen Richards, Oliver Niehuis, Bernhard Misof

BMC Ecology and Evolution (2019). DOI: 10.1186/s12862-021-01778-w

Re-assessing the diversity of negative strand RNA viruses in insects

Simon Käfer, Sofia Paraskevopoulou, Florian Zirkel, Nicolas Wieseke, Alexander Donath, Malte Petersen, Terry C. Jones, Shanlin Liu, Xin Zhou, Martin Middendorf, Sandra Junglen, Bernhard Misof, Christian Drosten  

PLOS Pathogens (2019). DOI: 10.1371/journal.ppat.1008224

Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes

Malte Petersen, Karen Meusemann, Alexander Donath, Daniel Dowling, Shanlin Liu, Ralph S. Peters, Lars Podsiadlowski, Alexandros Vasilikopoulos, Xin Zhou, Bernhard Misof, Oliver Niehuis

BMC Bioinformatics (2017). DOI: 10.1186/s12859-017-1529-8

Phylogenomics resolves the timing and pattern of insect evolution

Bernhard Misof*, Shanlin Liu*, Karen Meusemann*, Ralph S. Peters*, Alexander Donath*, Christoph Mayer*, Paul B. Frandsen*, Jessica Ware*, Tomáš Flouri*, Rolf G. Beutel*, Oliver Niehuis*, Malte Petersen*, Fernando Izquierdo-Carrasco*, Torsten Wappler*, Jes Rust*, et al.

*: major contributors

Science (2014). DOI: 10.1126/science.1257570