Publications

Augmentation of wastewater-based epidemiology with machine learning to support global health surveillance
Wastewater-based epidemiology (WBE) has proven to be a valuable tool for monitoring the evolution and spread of global health threats, …
Eva Aßmann, Timo Greiner, Hugues Richard, Matthew Wade, Shelesh Agrawal, Fabian Amman, Sindy Böttcher, Susanne Lackner, Markus Landthaler, Serghei Mangul, Viorel Munteanu, Fotis Psomopoulos, Maureen Smith, Maria Trofimova, Alexander Ullrich, Max von Kleist, Emanuel Wyler, Martin Hölzer$, Christopher Irrgang$
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varVAMP: degenerate primer design for tiled full genome sequencing and qPCR
Time- and cost-saving surveillance of viral pathogens is achieved by tiled sequencing in which a viral genome is amplified in …
Jonas Fuchs, Johanna Kleine, Mathias Schemmerer, Julian Kreibich, Wolfgang Maier, Namuun Battur, Thomas Krannich, Somayyeh Sedaghatjoo, Lena Jaki, Anastasija Maks, Christina Boehm, Carina Wilhelm, Jessica Schulze, Christin Mache, Elischa Berger, Jessica Panajotov, Lisa Arnold, Björn Grüning, Markus Bauswein, Sindy Böttcher, Reimar Johne, Jürgen Wenzel, Martin Hölzer, Marcus Panning
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Decoding bacterial methylomes in four public health-relevant microbial species: nanopore sequencing enables reproducible analysis of DNA modifications
Investigating bacterial methylation profiles provides essential complementary information to the native DNA sequence, significantly …
Valentina Galeone, Johanna Dabernig-Heinz, Mara Lohde, Christian Brandt, Christian Kohler, Gabriel E. Wagner, Martin Hölzer
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SARS-CoV-2 evolution on a dynamic immune landscape
Since the onset of the pandemic, many SARS-CoV-2 variants have emerged, exhibiting substantial evolution in the virus’ spike protein, …
N. Alexia Raharinirina$, Nils Gubela$, Daniela Börnigen$, Maureen Rebecca Smith$, Djin-Ye Oh, Matthias Budt, Christin Mache, Claudia Schillings, Stephan Fuchs, Ralf Dürrwald, Thorsten Wolff, Martin Hölzer, Sofia Paraskevopoulou, Max von Kleist
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RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level
Microbial pangenome analysis identifies present or absent genes in prokaryotic genomes. However, current tools are limited when …
Kevin Lamkiewicz, Lisa-Marie Barf, Konrad Sachse, Martin Hölzer
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VIRify: an integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
The study of viral communities has revealed the enormous diversity and impact these biological entities have on various ecosystems. …
Guillermo Rangel-Pineros, Alexandre Almeida, Martin Beracochea, Ekaterina Sakharova, Manja Marz, Alejandro Reyes Muñoz, Martin Hölzer, Robert D Finn
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poreCov - an easy to use, fast, and robust workflow for SARS-CoV-2 genome reconstruction via nanopore sequencing
In response to the SARS-CoV-2 pandemic, a highly increased sequencing effort has been established worldwide to track and trace ongoing …
Christian Brandt, Sebastian Krautwurst, Riccardo Spott, Mara Lohde, Mateusz Jundzill, Mike Marquet, Martin Hölzer
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De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers
Background In recent years, massively parallel complementary DNA sequencing (RNA sequencing [RNA-Seq]) has emerged as a fast, …
Martin Hölzer, Manja Marz
Link Electronic Supplement Open Data