Publications

This list is also available on Google Scholar and under ORCID.

Submitted journal publications & preprints

poreCov – an easy to use, fast, and robust workflow for SARS-CoV-2 genome reconstruction via nanopore sequencing.
Christian Brandt, Sebastian Krautwurst, Riccardo Spott, Mara Lohde, Mateusz Jundzill, Mike Marquet, Martin Hölzer
bioRxiv (2021), supplement

Chromosome-level genome assembly and transcriptome-based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14.
Giselle De La Caridad Martin Hernandez, Bettina Müller, Mikolaj Chmielarz, Christian Brandt, Martin Hölzer, Adrian Viehweger, Volkmar Passoth
bioRxiv (2021)

CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance.
Alice Wittig, Fabio Miranda, Ming Tang, Martin Hölzer, Bernhard Renard, Stephan Fuchs
bioRxiv (2021), supplement

Molecular epidemiology of SARS-CoV-2 – a regional to global perspective.
Christian Brandt, Riccardo Spott, Martin Hölzer, Denise Kühnert, Stephan Fuchs, Mara Lohde, Mike Marquet, Adrian Viehweger, Dagmar Rimek, Matthias Pletz
medRxiv (2021)

DarkQ: Continuous genomic monitoring using message queues.
Adrian Viehweger, Christian Brandt, Martin Hölzer
bioRxiv (2020), supplement

What the Phage: A scalable workflow for the identification and analysis of phage sequences.
Maik Marquet, Martin Hölzer, Mathias W Pletz, Adrian Viehweger, Oliwia Makarewicz, Ralf Ehricht, Christian Brandt
bioRxiv (2020), supplement

Addressing dereplication crisis: Taxonomy-free reduction of massive genome collections using embeddings of protein content.
Adrian Viehweger, Martin Hölzer, Christian Brandt
bioRxiv (2019), supplement

PCAGO: An interactive tool to analyze RNA-Seq data with principal component analysis.
Ruman Gerst, Martin Hölzer
bioRxiv (2018)

Peer reviewed

Transcriptomics

RUNX3 transcript variants have dichotomous roles in ovarian carcinoma and influence platin sensitivity and angiogenesis
Karolin Heinze, Martin Hölzer, M Ungelenk, M Gerth, J Thomale, R Heller, CR Morden, KJ McManus, A Mosig, Matthias Dürst, Ingo B Runnebaum, Norman Häfner
MDPI Cancers (2021)

A decade of de novo transcriptome assembly: Are we there yet?
Martin Hölzer
Molecular Ecology Resources (2020)

De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers.
Martin Hölzer, Manja Marz
GigaScience (2019), supplement

Virus- and interferon alpha-induced transcriptomes of cells from the microbat Myotis daubentonii.
Martin Hölzer, Andreas Schoen, Julia Wulle, Marcel A Müller, Christian Drosten, Manja Marz, Friedemann Weber
iScience (2019), supplement

Cohesin-mediated NF-κB signaling limits hematopoietic stem cell self-renewal in aging and inflammation.
Zhiyang Chen, Elias Moris Amro, Friedrich Becker, Martin Hölzer, Seyed Mohammad Mahdi Rasa, Sospeter Ngoci Njeru, Bing Han, Simone Di Sanzo, Yulin Chen, Duozhuang Tang, Si Tao, Ronny Haenold et al.
Journal of Experimental Medicine (2018)

Massive effect on lncRNAs in human monocytes during fungal and bacterial infections and in response to vitamins A and D.
Konstantin Riege, Martin Hölzer, Tilman E Klassert, Emanuel Barth, Julia Bräuer, Maximilian Collatz, Franziska Hufsky, Nelly Mostajo, Magdalena Stock, Bertram Vogel, Hortense Slevogt, Manja Marz.
Scientific Reports (2017), supplement

Differential Effects of Vitamins A and D on the Transcriptional Landscape of Human Monocytes during Infection.
Tilman E Klassert, Julia Bräuer, Martin Hölzer, Magdalena Stock, Konstantin Riege, Cristina Zubiría-Barrera, Mario M Müller, Silke Rummler, Christine Skerka, Manja Marz, Hortense Slevogt
Scientific Reports (2017), supplement

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.
Martin Hölzer, Verena Krähling, Fabian Amman, Emanuel Barth, Stephan H Bernhart, Victor A O Carmelo, Maximilian Collatz, Gero Doose, Florian Eggenhofer, Jan Ewald, Jörg Fallmann, Lasse M Feldhahn et al.
Scientific Reports (2016), supplement

Genomics & metagenomics

Evidence for the existence of a new genus Chlamydiifrater gen. nov. inside the family Chlamydiaceae with two new species isolated from flamingo (Phoenicopterus roseus): Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov.
F Vorimore, M Hölzer, EM Liebler-Tenorio, LM Barf, S Delannoy, M Vittecoq, R Wedlarski, A L{'e}cu, S Scharf, Y Blanchard, P Fach, RC Hsia et al.
Systematic and Applied Microbiology (2021), supplement

Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome-assembled genomes from a complex aquifer system.
Will A Overholt, Martin Hölzer, Patricia Geesink, Celia Diezel, Manja Marz, Kirsten Küsel
Environmental Microbiology (2020), supplement

Comparative genome analysis of 33 Chlamydia strains reveals characteristic features of Chlamydia psittaci and closely related species.
Martin Hölzer, Lisa Barf, Kevin Lamkiewicz, Fabien Vorimore, Marie Lataretu, Alison Favaroni, Christiane Schnee, Karine Laroucau, Manja Marz, Konrad Sachse
MDPI Pathogens (2020), supplement

Chlamydia buteonis, a new Chlamydia species isolated from a red-shouldered hawk.
K Laroucau, F Vorimore, R Aaziz, L Solmonson, RC Hsia, PM Bavoil, P Fach, Martin Hölzer, A Wuenschmann, K Sachse
Systematic and Applied Microbiology (2019)

Analysis of molecular mechanism of progression of non-muscle-invasive bladder cancer (NMIBC) by genome-wide exome and UTR mutation analysis.
Daniel Steinbach, Martin Hölzer, Manja Marz, Mieczyslaw Gajda, Friedrich-Carl von Rundstedt, Marc-Oliver Grimm
European Urology Supplements (2018)

Complete genome sequence of JII-1961, a bovine Mycobacterium avium subsp. paratuberculosis field isolate from Germany.
Petra Möbius, Gabriele Nordsiek, Martin Hölzer, Michael Jarek, Manja Marz, Heike Köhler
Genome Announcements (2017)

Whole-Genome Sequence of Chlamydia gallinacea Type Strain 08-1274/3.
Martin Hölzer, Karine Laroucau, Heather Huot Creasy, Sandra Ott, Fabien Vorimore, Patrik M Bavoil, Manja Marz, Konrad Sachse
Genome Announcements (2016)

Comprehensive insights in the Mycobacterium avium subsp. paratuberculosis genome using new WGS data of sheep strain JIII-386 from Germany.
Petra Möbius, Martin Hölzer, Marius Felder, Gabriele Nordsiek, Marco Groth, Heike Köhler, Kathrin Reichwald, Matthias Platzer, Manja Marz
Genome Biology and Evolution (2015), supplement

Viruses

SARS-CoV-2-Varianten: Evolution im Zeitraffer
Djin-Ye Oh, Stefan Kröger, Marianne Wedde, Felix Hartkopf, Matthias Budt, Janna Seifried, Aleksandar Radonic, Essia Belarbi, Martin Hölzer, Sindy Böttcher, Grit Schubert, Sandra Kaiser et al.
Dtsch Arztebl International (2021)

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.
F. Hufsky, K. Lamkiewicz, A. Almeida, A. Aouacheria, C. Arighi, A. Bateman, J. Baumbach, N. Beerenwinkel, C. Brandt, M. Cacciabue, S. Chuguransky, O. Drechsel et al.
Briefings in Bioinformatics (2020), supplement

Structure and hierarchy of influenza virus models revealed by reaction network analysis.
Stephan Peter, Martin Hölzer, Kevin Lamkiewicz, Pietro Speroni di Fenizio, Hassan Al Hwaeer, Manja Marz, Stefan Schuster, Peter Dittrich, Bashar Ibrahim
Viruses (2019)

Evaluation of sequencing library preparation protocols for viral metagenomic analysis from pristine aquifer groundwaters.
René Kallies, Martin Hölzer, Rodolfo Brizola Toscan, Ulisses Nunes da Rocha, John Anders, Manja Marz, Antonis Chatzinotas
Viruses (2019)

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis.
Adrian Viehweger, Sebastian Krautwurst, Kevin Lamkiewicz, Ramakanth Madhugiri, John Ziebuhr, Martin Hölzer, Manja Marz
Genome Research (2019), supplement

Evolution and antiviral specificity of interferon-induced Mx proteins of bats against Ebola-, Influenza-, and other RNA viruses.
Jonas Fuchs, Martin Hölzer, Mirjam Schilling, Corinna Patzina, Andreas Schoen, Thomas Hoenen, Gert Zimmer, Manja Marz, Friedemann Weber, Marcel A Müller, Georg Kochs
Journal of Virology (2017), supplement

Bioinformatic tools & workflows

Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis (MUFFIN).
Renaud Van Damme, Martin Hölzer, Adrian Viehweger, Müller Bettina, Erik Bongcam-Rudloff, Christian Brandt
Plos Comp Biol (2021), supplement

PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection.
Martin Hölzer, Manja Marz
OUP Bioinformatics (2020), supplement

EpiDope: A Deep neural network for linear B-cell epitope prediction.
Maximilian Collatz, Forian Mock, Martin Hölzer, Emmanuel Barth, Konrad Sachse, Manja Marz
OUP Bioinformatics (2020), supplement

RNAflow: An effective and simple RNA-Seq differential gene expression pipeline using Nextflow.
Marie Lataretu, Martin Hölzer
MDPI Genes (2020), supplement

SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structured RNAs.
Daniel Desirò, Martin Hölzer, Bashar Ibrahim, Manja Marz
Virus Research (2018)

Other

SLC35F2, a Transporter Sporadically Mutated in the Untranslated Region, Promotes Growth, Migration, and Invasion of Bladder Cancer Cells.
Roland Kotolloshi, Martin Hölzer, Mieczyslaw Gajda, Marc-Oliver Grimm, Daniel Steinbach
MDPI Cells (2021)

A marine Chlamydomonas sp. emerging as an algal model.
David C Flores, Markus Fricke, Valentin Wesp, Daniel Desirò, Anja Kniewasser, Martin Hölzer, Manja Marz, Maria Mittag
Journal of Phycology (2020)

A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
Nelly F Mostajo, Marie Lataretu, Sebastian Krautwurst, Florian Mock, Daniel Desirò, Kevin Lamkiewicz, Maximilian Collatz, Andreas Schoen, Friedemann Weber, Manja Marz, Martin Hölzer
NAR Genomics and Bioinformatics (2019), supplement

Evaluation of associations between genotypes of Mycobacterium avium subsp. paratuberculosis and presence of intestinal lesions characteristic of paratuberculosis.
Petra Möbius, Elisabeth Liebler-Tenorio, Martin Hölzer, Heike Köhler
Veterinary Microbiology (2017)

Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes.
Abdullah H Sahyoun, Martin Hölzer, Frank Jühling, Christian Höner Zu Siederdissen, Marwa Al-Arab, Kifah Tout, Manja Marz, Martin Middendorf, Peter F. Stadler, Matthias Bernt
Nucleic Acids Res. (2015)

Book chapter

Virus Bioinformatics
Nikolaos Pappas, Simon Roux, Martin Hölzer, Kevin Lamkiewicz, Florian Mock, Manja Marz, Bas E Dutilh
Reference Module in Life Sciences (2020)

Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral”
Martin Hölzer, Manja Marz
Advances in Virus Research (2017)

Publications with acknowledgement

The Definition of Open Reading Frame Revisited.
Patricia Sieber, Matthias Platzer, Stefan Schuster
Trends in Genetics (2018)

A host subtraction database for virus discovery in human cell line sequencing data.
Jason R Miller, Kari A Dilley, Derek M Harkins, Timothy B Stockwell, Reed S Shabman, Granger G Sutton
F1000Research (2018)

Comparative study on alternative splicing in human fungal pathogens suggests its involvement during host invasion.
Patricia Sieber, Kerstin Voigt, Philipp Kämmer, Sascha Brunke, Stefan Schuster, Jörg Linde
Frontiers in microbiology (2018)