U7 snRNAs: A Computational Survey. - Manja Marz; Axel Mosig; Bärbel M. R. Stadler; Peter F. Stadler (Genom. Proteom. Bioinform., 2007)

Converting DNA to Music: ComposAlign. - Todd Ingalls; Georg Martius; Manja Marz; Sonja J. Proshaka; Marc Hellmuth (GCB, 2009)

Temperature-Dependent Structural Variability of RNAs: spliced Leader RNAs and their Evolutionary History. - Manja Marz; Nathalie Vanzo; Peter F. Stadler (J. Bioinform. Comput. Biol., 2010)

RNA-RNA interaction prediction based on multiple sequence alignments. - Andrew X. Li; Manja Marz; Jing Qin 006; Christian M. Reidys (Bioinform., 2011)

Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis. - Marcus Lechner; Sven Findeiß; Lydia Steiner; Manja Marz; Peter F. Stadler; Sonja J. Prohaska (BMC Bioinform., 2011)

POMAGO: Multiple Genome-Wide Alignment Tool for Bacteria. - Nicolas Wieseke; Marcus Lechner; Marcus Ludwig; Manja Marz (ISBRA, 2013)

Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures. - Rolf Backofen; Markus Fricke; Manja Marz; Jing Qin 006; Peter F. Stadler (WABI, 2013)

The correlation of genome size and DNA methylation rate in metazoans. - Marcus Lechner; Manja Marz; Christian Ihling; Andrea Sinz; Peter F. Stadler; Veiko Krauss (Theory Biosci., 2013)

Explorative Analysis of Heterogeneous, Unstructured, and Uncertain Data - A Computer Science Perspective on Biodiversity Research. - Clemens Beckstein; Sebastian Böcker; Martin Bogdan; Helge Bruelheide; H. Martin Bücker; Joachim Denzler; Peter Dittrich; Ivo Grosse; Alexander Hinneburg; Birgitta König-Ries; Felicitas Löffler; Manja Marz; et al. (DATA, 2014)

Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures. - Jing Qin 006; Markus Fricke; Manja Marz; Peter F. Stadler; Rolf Backofen (Algorithms Mol. Biol., 2014)

Challenges in RNA virus bioinformatics. - Manja Marz; Niko Beerenwinkel; Christian Drosten; Markus Fricke; Dmitrij Frishman; Ivo L. Hofacker; Dieter Hoffmann; Martin Middendorf; Thomas Rattei; Peter F. Stadler; Armin Töpfer (Bioinform., 2014)

Prediction of conserved long-range RNA-RNA interactions in full viral genomes. - Markus Fricke; Manja Marz (Bioinform., 2016)

Global importance of RNA secondary structures in protein-coding sequences. - Markus Fricke; Ruman Gerst; Bashar Ibrahim; Michael Niepmann; Manja Marz (Bioinform., 2019)

Tissue-specific Gene Expression Changes Are Associated with Aging in Mice. - Akash Srivastava; Emanuel Barth; Maria A. Ermolaeva; Madlen Guenther; Christiane Frahm; Manja Marz; Otto W. Witte (Genom. Proteom. Bioinform., 2020)

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. - Franziska Hufsky; Kevin Lamkiewicz; Alexandre Almeida; Abdel Aouacheria; Cecilia N. Arighi; Alex Bateman; Jan Baumbach; Niko Beerenwinkel; Christian Brandt; Marco Cacciabue; Sara Chuguransky; Oliver Drechsel; et al. (Briefings Bioinform., 2021)

EpiDope: a deep neural network for linear B-cell epitope prediction. - Maximilian Collatz; Florian Mock; Emanuel Barth; Martin Hölzer; Konrad Sachse; Manja Marz (Bioinform., 2021)

PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection. - Martin Hölzer; Manja Marz (Bioinform., 2021)

VIDHOP, viral host prediction with deep learning. - Florian Mock; Adrian Viehweger; Emanuel Barth; Manja Marz (Bioinform., 2021)

Rfam 14: expanded coverage of metagenomic, viral and microRNA families. - Ioanna Kalvari; Eric P. Nawrocki; Nancy Ontiveros-Palacios; Joanna Argasinska; Kevin Lamkiewicz; Manja Marz; Sam Griffiths-Jones; Claire Toffano-Nioche; Daniel Gautheret; Zasha Weinberg; Elena Rivas; Sean R. Eddy; et al. (Nucleic Acids Res., 2021)

VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models. - Guillermo Rangel-Pineros; Alexandre Almeida; Martin Beracochea; Ekaterina A. Sakharova; Manja Marz; Alejandro Reyes; Martin Hölzer; Robert D. Finn (PLoS Comput. Biol., 2023)

Go Game Capture and Reconstruction of Missing Moves Using Deep Learning Techniques. - Roman Gerloff; Manja Marz; Florian Wahl (CoG, 2025)