Joachim Fritscher

Postgraduate Student

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Microbial Genomes, Strains and Evolution

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I am a bioinformatician in the Hildebrand Group based at the Quadram Institute, with a strong interest in metagenomics, k-mer and alignment based analysis of metagenomes, C++ tool development all aimed towards improving metagenomic analysis and pushing the taxonomic resolution beyond species/subspecies level.

I have both a bachelor’s and master’s degree in bioinformatics from the University of Tuebingen. After I focused on immunomics in my bachelors, I developed an interest for metagenomics during my masters. As a result, my masters thesis is about k-mer based taxonomic profiling using protein reference. In order to follow this passion for metagenomics, I joined Falk Hildebrand’s group as a PhD student.

In my PhD I focus on k-mer and alignment-based methods for taxonomic and strain-level profiling as well as investigating methods to improve the taxonomic resolution. To achieve this, I use C++ for high performance tool development, data structures such as specialised hash maps for efficient data storage as well as Python and R for scripting and statistical analysis, respectively.

 


Key Publications

Özkurt, E., Fritscher, J., Soranzo, N. et al. LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis. Microbiome 10, 176 (2022). https://doi.org/10.1186/s40168-022-01365-1

 

Netherway T, Bengtsson J, Buegger F, Fritscher J, Oja J, Pritsch K, Hildebrand F, Krab EJ, Bahram . (2024)

Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe.

Nature communications


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Sidorczuk K, Burdukiewicz M, Cerk K, Fritscher J, Kingsley RA, Schierack P, Hildebrand F, Kolenda . (2024)

adhesiomeR: a tool for Escherichia coli adhesin classification and analysis

BMC Genomics


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Diaz M, Aird H, Le Viet T, Gutierrez AV, Larke-Mejia N, Omelchenko O, Moragues-Solanas L, Fritscher J, Som N, McLauchlin J, Hildebrand F, Jørgensen F, Gilmour M. (2024)

Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonization of Listeria monocytogenes

Food Microbiology


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Frioux C, Ansorge R, Özkurt E, Ghassemi Nedjad, Fritscher J, Quince C, Waszak SM, Hildebrand . (2023)

Enterosignatures define common bacterial guilds in the human gut microbiome.

Cell host & microbe


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Ozkurt E, Fritscher J, Soranzo N, Ng D, Davey R, Bahram M, Hildebrand . (2022)

LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Microbiome


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