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
Dr. Malte Petersen
3.036
Friedrich-Hirzebruch-Allee 8
53115 Bonn
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
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