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

On the Design of RNA Sequences for Realizing Extended Shapes. - Marc Hellmuth; Daniel Merkle; Martin Middendorf (IJCBS, 2009)

A note on quasi-robust cycle bases. - Philipp-Jens Ostermeier; Marc Hellmuth; Josef Leydold; Konstantin Klemm; Peter F. Stadler (Ars Math. Contemp., 2009)

Approximate graph products. - Marc Hellmuth; Wilfried Imrich; Werner Klöckl; Peter F. Stadler (Eur. J. Comb., 2009)

Extended shapes for the combinatorial design of RNA sequences. - Marc Hellmuth; Daniel Merkle; Martin Middendorf (Int. J. Comput. Biol. Drug Des., 2009)

Local Algorithms for the Prime Factorization of Strong Product Graphs. - Marc Hellmuth; Wilfried Imrich; Werner Klöckl; Peter F. Stadler (Math. Comput. Sci., 2009)

Visualization of Graph Products. - Stefan Jänicke; Christian Heine 002; Marc Hellmuth; Peter F. Stadler; Gerik Scheuermann (IEEE Trans. Vis. Comput. Graph., 2010)

Local Prime Factor Decomposition of Approximate Strong Product Graphs: Local Prime Factor Decompositionof Approximate Strong Product Graphs - Marc Hellmuth (2010)

A local prime factor decomposition algorithm. - Marc Hellmuth (Discret. Math., 2011)

Minimum cycle bases of lexicographic products. - Marc Hellmuth; Philipp-Jens Ostermeier; Peter F. Stadler (Ars Math. Contemp., 2012)

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)

Diagonalized Cartesian products of s-prime graphs are s-prime. - Marc Hellmuth; Lydia Ostermeier; Peter F. Stadler (Discret. Math., 2012)

The Cartesian product of hypergraphs. - Lydia Ostermeier; Marc Hellmuth; Peter F. Stadler (J. Graph Theory, 2012)

A Survey on Hypergraph Products. - Marc Hellmuth; Lydia Ostermeier; Peter F. Stadler (Math. Comput. Sci., 2012)

Square Property, Equitable Partitions, and Product-like Graphs - Marc Hellmuth; Lydia Ostermeier; Peter F. Stadler (CoRR, 2013)

On the complexity of recognizing S-composite and S-prime graphs. - Marc Hellmuth (Discret. Appl. Math., 2013)

Partial Star Products: A Local Covering Approach for the Recognition of Approximate Cartesian Product Graphs. - Marc Hellmuth; Wilfried Imrich; Tomas Kupka (Math. Comput. Sci., 2013)

Convex cycle bases. - Marc Hellmuth; Josef Leydold; Peter F. Stadler (Ars Math. Contemp., 2014)

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

Strong products of hypergraphs: Unique prime factorization theorems and algorithms. - Marc Hellmuth; Manuel Noll; Lydia Ostermeier (Discret. Appl. Math., 2014)

Unique square property, equitable partitions, and product-like graphs. - Marc Hellmuth; Lydia Ostermeier; Peter F. Stadler (Discret. Math., 2014)

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

The relaxed square property. - Marc Hellmuth; Tilen Marc; Lydia Ostermeier; Peter F. Stadler (Australas. J Comb., 2015)

Fast recognition of partial star products and quasi cartesian products. - Marc Hellmuth; Wilfried Imrich; Tomas Kupka (Ars Math. Contemp., 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)

Fast Factorization of Cartesian products of Hypergraphs. - Marc Hellmuth; Florian Lehner (CoRR, 2015)

Spiders can be Recognized by Counting Their Legs. - Sarah Berkemer; Ricardo Régis Cavalcante Chaves; Adrian Fritz; Marc Hellmuth; Maribel Hernandez-Rosales; Peter F. Stadler (Math. Comput. Sci., 2015)

On the Cartesian skeleton and the factorization of the strong product of digraphs. - Marc Hellmuth; Tilen Marc (Theor. Comput. Sci., 2015)

Inference of Phylogenetic Trees from the Knowledge of Rare Evolutionary Events. - Marc Hellmuth; Maribel Hernandez-Rosales; Yangjing Long; Peter F. Stadler (CoRR, 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)

Associativity and Non-Associativity of Some Hypergraph Products. - Richard H. Hammack; Marc Hellmuth; Lydia Ostermeier; Peter F. Stadler (Math. Comput. Sci., 2016)

Fast factorization of Cartesian products of (directed) hypergraphs. - Marc Hellmuth; Florian Lehner (Theor. Comput. Sci., 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)

Biologically feasible gene trees, reconciliation maps and informative triples. - Marc Hellmuth (Algorithms Mol. Biol., 2017)

From event-labeled gene trees with horizontal gene transfer to species trees. - Marc Hellmuth (CoRR, 2017)

A Local Prime Factor Decomposition Algorithm for Strong Product Graphs. - Marc Hellmuth (CoRR, 2017)

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

A Survey on Hypergraph Products (Erratum). - Marc Hellmuth; Lydia Ostermeier; 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)

Linear Time Canonicalization and Enumeration of Non-Isomorphic 1-Face Embeddings. - Marc Hellmuth; Anders S. Knudsen; Michal Kotrbcík; Daniel Merkle; Nikolai Nøjgaard (ALENEX, 2018)

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

A short note on undirected Fitch graphs. - Marc Hellmuth; Yangjing Long; Manuela Geiß; Peter F. Stadler (Art Discret. Appl. Math., 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)

The matroid structure of representative triple sets and triple-closure computation. - Carsten R. Seemann; Marc Hellmuth (Eur. J. Comb., 2018)

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

Best Match Graphs and Reconciliation of Gene Trees with Species Trees. - Manuela Geiß; Marcos González; Alitzel López Sánchez; Dulce I. Valdivia; Marc Hellmuth; Maribel Hernández-Rosales; Peter F. Stadler (CoRR, 2019)

Hierarchical Colorings of Cographs. - Dulce I. Valdivia; Manuela Geiß; Marc Hellmuth; Maribel Hernández-Rosales; Peter F. Stadler (CoRR, 2019)

Generalized Fitch Relations II: Sets of Binary Relations that are explained by Edge-labeled Trees. - Marc Hellmuth; Carsten R. Seemann; Peter F. Stadler (CoRR, 2019)

Generalized Fitch graphs: Edge-labeled graphs that are explained by edge-labeled trees. - Marc Hellmuth (Discret. Appl. Math., 2019)

Atom Tracking Using Cayley Graphs. - Marc Hellmuth; Daniel Merkle; Nikolai Nøjgaard (ISBRA, 2020)

A Graph-Based Tool to Embed the π-Calculus into a Computational DPO Framework. - Jakob Lykke Andersen; Marc Hellmuth; Daniel Merkle; Nikolai Nøjgaard; Marco Peressotti (SOFSEM (Doctoral Student Research Forum), 2020)

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

Reconstruction of time-consistent species trees. - Manuel Lafond; Marc Hellmuth (Algorithms Mol. Biol., 2020)

From pairs of most similar sequences to phylogenetic best matches. - Peter F. Stadler; Manuela Geiß; David Schaller 001; Alitzel López Sánchez; Marcos E. González Laffitte; Dulce I. Valdivia; Marc Hellmuth; Maribel Hernandez-Rosales (Algorithms Mol. Biol., 2020)

Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs. - David Schaller 001; Manuela Geiß; Peter F. Stadler; Marc Hellmuth (CoRR, 2020)

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

Generalized Fitch graphs II: Sets of binary relations that are explained by edge-labeled trees. - Marc Hellmuth; Carsten R. Seemann; Peter F. Stadler (Discret. Appl. Math., 2020)

Complexity of modification problems for reciprocal best match graphs. - Marc Hellmuth; Manuela Geiß; Peter F. Stadler (Theor. Comput. Sci., 2020)

Combining Orthology and Xenology Data in a Common Phylogenetic Tree. - Marc Hellmuth; Mira Michel; Nikolai N. Nøjgaard; David Schaller 001; Peter F. Stadler (BSB, 2021)

Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable Best Match Graphs. - David Schaller 001; Manuela Geiß; Marc Hellmuth; Peter F. Stadler (Algorithms, 2021)

Heuristic algorithms for best match graph editing. - David Schaller 001; Manuela Geiß; Marc Hellmuth; Peter F. Stadler (Algorithms Mol. Biol., 2021)

A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set. - David Schaller 001; Marc Hellmuth; Peter F. Stadler (Algorithms Mol. Biol., 2021)

Compatibility of Partitions, Hierarchies, and Split Systems. - Marc Hellmuth; David Schaller 001; Peter F. Stadler (CoRR, 2021)

A Linear-Time Algorithm for the Common Refinement of Rooted Phylogenetic Trees on a Common Leaf Set. - David Schaller 001; Marc Hellmuth; Peter F. Stadler (CoRR, 2021)

Construction of k-matchings and k-regular subgraphs in graph products. - Anna Lindeberg; Marc Hellmuth (CoRR, 2021)

Orientation of Fitch Graphs and Detection of Horizontal Gene Transfer in Gene Trees. - David Schaller 001; Marc Hellmuth; Peter F. Stadler (CoRR, 2021)

Pseudo-Cographs, Polar-Cats and Level-1 Network Explainable Graphs. - Marc Hellmuth; Guillaume E. Scholz (CoRR, 2021)

Generalized Fitch Graphs III: Symmetrized Fitch maps and Sets of Symmetric Binary Relations that are explained by Unrooted Edge-labeled Trees. - Marc Hellmuth; Carsten R. Seemann; Peter F. Stadler (Discret. Math. Theor. Comput. Sci., 2021)

Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry. - Nikolai Nøjgaard; Walter Fontana; Marc Hellmuth; Daniel Merkle (J. Comput. Biol., 2021)

Least resolved trees for two-colored best match graphs. - David Schaller 001; Manuela Geiß; Marc Hellmuth; Peter F. Stadler (J. Graph Algorithms Appl., 2021)

Complexity of modification problems for best match graphs. - David Schaller 001; Peter F. Stadler; Marc Hellmuth (Theor. Comput. Sci., 2021)

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

From modular decomposition trees to rooted median graphs. - Carmen Bruckmann; Peter F. Stadler; Marc Hellmuth (Discret. Appl. Math., 2022)

From modular decomposition trees to level-1 networks: Pseudo-cographs, polar-cats and prime polar-cats. - Marc Hellmuth; Guillaume E. Scholz (Discret. Appl. Math., 2022)

Compatibility of partitions with trees, hierarchies, and split systems. - Marc Hellmuth; David Schaller 001; Peter F. Stadler (Discret. Appl. Math., 2022)

Generic Context-Aware Group Contributions. - Christoph Flamm; Marc Hellmuth; Daniel Merkle; Nikolai Nøjgaard; Peter F. Stadler (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Construction of k-matchings in graph products. - Anna Lindeberg; Marc Hellmuth (Art Discret. Appl. Math., 2022)

Hierarchical and modularly-minimal vertex colorings. - Dulce I. Valdivia; Maribel Hernández-Rosales; Manuela Geiß; Peter F. Stadler; Marc Hellmuth (Art Discret. Appl. Math., 2022)

Linear Time Algorithms for NP-Hard Problems Restricted to GaTEx Graphs. - Marc Hellmuth; Guillaume E. Scholz (COCOON (1), 2023)

Fitch Graph Completion. - Marc Hellmuth; Peter F. Stadler; Sandhya Thekkumpadan Puthiyaveedu (COCOON (2), 2023)

The Theory of Gene Family Histories. - Marc Hellmuth; Peter F. Stadler (CoRR, 2023)

Best Match Graphs With Binary Trees. - David Schaller 001; Manuela Geiß; Marc Hellmuth; Peter F. Stadler (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Quasi-best match graphs. - Annachiara Korchmaros; David Schaller 001; Marc Hellmuth; Peter F. Stadler (Discret. Appl. Math., 2023)

Planar median graphs and cubesquare-graphs. - Carsten R. Seemann; Vincent Moulton; Peter F. Stadler; Marc Hellmuth (Discret. Appl. Math., 2023)

Injective Split Systems. - Marc Hellmuth; Katharina T. Huber; Vincent Moulton; Guillaume E. Scholz; Peter F. Stadler (Graphs Comb., 2023)

Orientation of Fitch Graphs and Reconciliation-Free Inference of Horizontal Gene Transfer in Gene Trees. - David Schaller 001; Marc Hellmuth; Peter F. Stadler (SIAM J. Discret. Math., 2023)

Clustering systems of phylogenetic networks. - Marc Hellmuth; David Schaller 001; Peter F. Stadler (Theory Biosci., 2023)

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)

Unique Least Common Ancestors and Clusters in Directed Acyclic Graphs. - Ameera Vaheeda Shanavas; Manoj Changat; Marc Hellmuth; Peter F. Stadler (CALDAM, 2024)

REvolutionH-tl: Reconstruction of Evolutionary Histories tool. - José Antonio Ramírez-Rafael; Annachiara Korchmaros; Katia Aviña-Padilla; Alitzel López Sánchez; Andrea Arlette España-Tinajero; Marc Hellmuth; Peter F. Stadler; Maribel Hernández-Rosales (RECOMB-CG, 2024)

Network Representation and Modular Decomposition of Combinatorial Structures: A Galled-Tree Perspective. - Anna Lindeberg; Guillaume E. Scholz; Marc Hellmuth (CoRR, 2024)

Nesting of Touching Polygons. - Carsten R. Seemann; Peter F. Stadler; Marc Hellmuth (CoRR, 2024)

Simplifying and Characterizing DAGs and Phylogenetic Networks via Least Common Ancestor Constraints. - Anna Lindeberg; Marc Hellmuth (CoRR, 2024)

Characterizing and Transforming DAGs within the I-LCA Framework. - Marc Hellmuth; Anna Lindeberg (CoRR, 2024)

The weighted total cophenetic index: A novel balance index for phylogenetic networks. - Linda Knüver; Mareike Fischer 001; Marc Hellmuth; Kristina Wicke (Discret. Appl. Math., 2024)

Resolving prime modules: The structure of pseudo-cographs and galled-tree explainable graphs. - Marc Hellmuth; Guillaume E. Scholz (Discret. Appl. Math., 2024)

On a generalization of median graphs: k-median graphs. - Marc Hellmuth; Sandhya Thekkumpadan Puthiyaveedu (Ars Math. Contemp., 2025)

The complement of the Djoković-Winkler relation. - Marc Hellmuth; Bruno J. Schmidt; Guillaume E. Scholz; Sandhya Thekkumpadan Puthiyaveedu (Discret. Math., 2025)

Solving NP-hard problems on GaTEx graphs: Linear-time algorithms for perfect orderings, cliques, colorings, and independent sets. - Marc Hellmuth; Guillaume E. Scholz (Theor. Comput. Sci., 2025)

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

On Finding All Connected Maximum-Sized Common Subgraphs in Multiple Labeled Graphs. - Johannes B. S. Petersen; Akbar Davoodi; Thomas Gärtner 001; Marc Hellmuth; Daniel Merkle (CoRR, 2025)