A parameter-adaptive dynamic programming approach for inferring cophylogenies. - Daniel Merkle; Martin Middendorf; Nicolas Wieseke (BMC Bioinform., 2010)

From event-labeled gene trees to species trees. - Maribel Hernandez-Rosales; Marc Hellmuth; Nicolas Wieseke; Katharina T. Huber; Vincent Moulton; Peter F. Stadler (BMC Bioinform., 2012)

On Weighting Schemes for Gene Order Analysis. - Matthias Bernt; Nicolas Wieseke; Martin Middendorf (GCB, 2013)

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

Unifying Parsimonious Tree Reconciliation. - Nicolas Wieseke; Matthias Bernt; Martin Middendorf (WABI, 2013)

Simulation of gene family histories. - Maribel Hernandez-Rosales; Nicolas Wieseke; Marc Hellmuth; Peter F. Stadler (BMC Bioinform., 2014)

On Symbolic Ultrametrics, Cotree Representations, and Cograph Edge Decompositions and Partitions. - Marc Hellmuth; Nicolas Wieseke (COCOON, 2015)

Techniques for the Cograph Editing Problem: Module Merge is equivalent to Editing P4s. - Marc Hellmuth; Adrian Fritz; Nicolas Wieseke; Peter F. Stadler (CoRR, 2015)

Cophylogenetic Reconciliation with ILP. - Nicolas Wieseke; Tom Hartmann; Matthias Bernt; Martin Middendorf (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies. - Henrike Indrischek; Nicolas Wieseke; Peter F. Stadler; Sonja J. Prohaska (Algorithms Mol. Biol., 2016)

The Mathematics of Xenology: Di-cographs, Symbolic Ultrametrics, 2-structures and Tree-representable Systems of Binary Relations. - Marc Hellmuth; Peter F. Stadler; Nicolas Wieseke (CoRR, 2016)

Construction of Gene and Species Trees from Sequence Data incl. Orthologs, Paralogs, and Xenologs. - Marc Hellmuth; Nicolas Wieseke (CoRR, 2016)

Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps. - Nikolai Nøjgaard; Manuela Geiß; Daniel Merkle; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (WABI, 2017)

Merging Modules is equivalent to Editing P4's. - Marc Hellmuth; Adrian Fritz; Nicolas Wieseke; Peter F. Stadler (CoRR, 2017)

Partial Orthology, Paralogy and Xenology Relations - Satisfiability in terms of Di-Cographs. - Nikolai Nøjgaard; Nadia El-Mabrouk; Daniel Merkle; Nicolas Wieseke; Marc Hellmuth (CoRR, 2017)

Reconstructing Gene Trees From Fitch's Xenology Relation. - Manuela Geiß; John Anders; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (CoRR, 2017)

Phylogenomics with Paralogs. - Marc Hellmuth; Nicolas Wieseke; Marcus Lechner; Hans-Peter Lenhof; Martin Middendorf; Peter F. Stadler (CoRR, 2017)

From Homologous Genes to Phylogenetic Species Trees: On Tree Representations of Binary Relations - Nicolas Wieseke (2017)

Partial Homology Relations - Satisfiability in Terms of Di-Cographs. - Nikolai Nøjgaard; Nadia El-Mabrouk; Daniel Merkle; Nicolas Wieseke; Marc Hellmuth (COCOON, 2018)

Time-consistent reconciliation maps and forbidden time travel. - Nikolai Nøjgaard; Manuela Geiß; Daniel Merkle; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (Algorithms Mol. Biol., 2018)

On tree representations of relations and graphs: symbolic ultrametrics and cograph edge decompositions. - Marc Hellmuth; Nicolas Wieseke (J. Comb. Optim., 2018)

Genome Rearrangement with ILP. - Tom Hartmann; Nicolas Wieseke; Roded Sharan; Martin Middendorf; Matthias Bernt (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Cograph editing: Merging modules is equivalent to editing P_4s. - Adrian Fritz; Marc Hellmuth; Peter F. Stadler; Nicolas Wieseke (Art Discret. Appl. Math., 2020)

Indirect Identification of Horizontal Gene Transfer. - David Schaller 001; Manuel Lafond; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (CoRR, 2020)

Complete edge-colored permutation graphs. - Tom Hartmann; Max Bannach; Martin Middendorf; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (Adv. Appl. Math., 2022)

Relative timing information and orthology in evolutionary scenarios. - David Schaller 001; Tom Hartmann; Manuel Lafond; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (Algorithms Mol. Biol., 2023)

Orthology and Near-Cographs in the Context of Phylogenetic Networks. - Anna Lindeberg; Guillaume E. Scholz; Nicolas Wieseke; Marc Hellmuth (CoRR, 2025)