1. M. Hellmuth, D. Merkle, N. Nøjgaard
    Atom Tracking Using Cayley Graphs
    (submitted 2020)
  2. M. Lafond, M. Hellmuth
    Reconstruction of time-consistent species trees
    (submitted 2019)
  3. M. Hellmuth,  Carsten R. Seemann, P.F. Stadler
    Generalized Fitch Graphs III: Symmetrized Fitch maps and Sets of Symmetric Binary Relations that are explained by Unrooted Edge-labeled Trees
    (submitted 2020)
  4. Hierarchical Colorings of Cographs
    D.I. Valdivia, M. Geiß , M. Hellmuth, M. H.Rosales, P.F. Stadler
    (submitted 2019)
  5. C. Flamm, M. Hellmuth, D. Merkle, N. Nøjgaard, P.F. Stadler
    Generic Context-Aware Group Contributions
    (submitted 2019)

--------------PUBLISHED (PEER-REVIEWED)--------------
- - - - - - - - book-chapters and monographs:

  1. M. Hellmuth, N. Wieseke
    From Sequence Data incl. Orthologs, Paralogs, and Xenologs to Gene and Species Trees
    in Evolutionary Biology: Convergent Evolution, Evolution of Complex Traits, Concepts and Methods, Ed. Pierre Pontarotti, Springer, p. 373-392, ISBN 978-3-319-41323-5, 2016
    [publisher's page] [arXiv]
  2. Habilitation Thesis (2015)
    On the Decomposition and Reconstruction of Discrete Structures: Characterization, Approximation and Computation [Extended Abstract]
  3. PhD-Thesis (2010) "grade: summa cum laude"
    Local Prime Factor Decomposition of Approximate Strong Product Graphs [pdf]
  4. Diploma Thesis (2006)
    Konstruktion von Worten mit Matchingeigenschaften und Anwendung auf das RNA Design [pdf]

- - - - - - - - journals:

  1. P.F. Stadler, M. Geiss, D. Schaller, A. Lopez, M.G. Laffitte; D.I. Valdivia; M. Hellmuth; M. H. Rosales
    From Best Hits to Best Matches
    Algorithms for Molecular Biology, (to appear) 2020
  2. M. Hellmuth,  Carsten R. Seemann, P.F. Stadler
    Generalized Fitch Graphs II: Sets of Binary Relations that are explained by Edge-labeled Trees
    Discr. Appl. Math, DOI:10.1016/j.dam.2020.01.036, 2020
    [publisher's page][arXiv]
  3. A. Fritz, M. Hellmuth, P. F. Stadler , N. Wieseke
    Merging Modules is equivalent to Editing P4's
    Art Discrete Appl. Math. (to appear) 2020
  4. M. Geiß, M. Gonzalez Laffitte, A. Lopez  S anchez, D. Valdivia, M. H. Rosales, Marc Hellmuth, P.F. Stadler
    Best Match Graphs and Reconciliation of Gene Trees with SpeciesTrees
    J. Math. Biology, DOI:10.1007/s00285-020-01469-y, 2020
    [publisher's page][arXiv]
  5. M. Hellmuth,  M. Geiß, P.F. Stadler
    Complexity of Modification Problems for Reciprocal Best Match Graphs
    Theoretical Computer Science, 809, 384 - 393, 2020
    [publisher's page][preprint]
  6. M. Geiß, P.F. Stadler, M. Hellmuth
    Reciprocal Best Match Graphs
    J. Math. Biology, 80(3), 865-953, 2020
    [publisher's page][arXiv]
  7. M. Hellmuth
    Generalized Fitch Graphs: Edge-labeled Graphs that are explained by Edge-labeled Trees
    Discr. Appl. Math, 276, 1-11 2019
    [publisher's page][arXiv]
  8. M. Hellmuth, K.T. Huber, V. Moulton
    Reconciling Event-Labeled Gene Trees with MUL-trees and Species Networks
    J. Math. Biology, 79(5), 1885-1925, 2019
    [publisher's page][preprint]
  9. M. Hellmuth, C.R. Seemann
    Alternative Characterizations of Fitch's Xenology Relation
    J. Math. Biology, 79(3), 969–986, 2019
    [publisher's page][arXiv]
  10. M. Geiß, E. Chavez, M. Gonzalez, A. Lopez, D. Valdivia, M. H. Rosales, B.M.R. Stadler, Marc Hellmuth, P.F. Stadler
    Best Match Graphs
    J. Math. Biology, 78(7), 2015-2057, 2019
    [publisher's page][arXiv]
  11. M. Geiß, J. Anders, P. F. Stadler, N. Wieseke, M. Hellmuth
    Reconstructing Gene Trees From Fitch’s Xenology Relation
    J. Math. Biology,  77(5), 1459-1491, 2018
    [publisher's page][arXiv]
  12. T. Siems, M. Hellmuth, V. Liebscher
    Simultaneous Credible Regions for Multiple Changepoint Locations
    J. Comp. Graph. Statistics, 28(2), 290-298 2018
    [publisher's page][arXiv]
  13. M. Geiß, M Hellmuth, Y. Long, Peter F. Stadler
    A Short Note on Undirected Fitch Graphs
    Art Discrete Appl. Math., 1, 1, #P1.08, 2018
    [publisher's page][arXiv]
  14. M. Hellmuth, C.R. Seemann
    The Matroid Structure of Representative Triple Sets and Triple-Closure Computation
    Europ. J. of Combinatorics, 70, 384-407, 2018
    [publisher's page] [arXiv]
  15. N. Nøjgaard, M. Geiß, D. Merkle, P. F. Stadler, N. Wieske, M. Hellmuth
    Time-Consistent Reconciliation Maps and Forbidden Time Travel
    Algorithms for Molecular Biology, 13, 1, 2,  2018
    [publisher's page][biorXiv]
  16. M. Hellmuth, M. Hernandez-Rosales, Y. Long, Peter F. Stadler
    Inferring Phylogenetic Trees from the Knowledge of Rare Evolutionary Events
    J. Math. Biology, 76, 7, 1623-1653, 2018
    [publisher's page][arXiv]
  17. M. Hellmuth, N. Wieseke
    On Tree Representations of Relations and Graphs: Symbolic Ultrametrics and Cograph Edge Decompositions
    J. Combinatorial Optimization, 36, 2, 591–616, 2018
    [publisher's page] [arXiv]
  18. M. Hellmuth
    Biologically Feasible Gene Trees, Reconciliation Maps and Informative Triples
    Algorithms for Molecular Biology, 12, 1, 23, 2017
    [publisher's page][arXiv]
  19. R. Batra , N. Alcaraz , K. Gitzhofer , J. Pauling , H. Ditzel , M. Hellmuth , M. List, J. Baumbach
    On the performance of de novo pathway enrichment
    Nature Partner Journals Systems Biology and Applications, 3, 1, 6, 2017
    [publisher's page]
  20. M. Hellmuth, P.F. Stadler, N. Wieseke
    The Mathematics of Xenology: Di-cographs, Symbolic Ultrametrics, 2-structures and Tree-representable Systems of Binary Relations
    J. Math. Biology, 75, 1, 199-237, 2017
    [publisher's page][arXiv]
  21. R.H. Hammack, M. Hellmuth, L. Ostermeier, P.F. Stadler
    Associativity and non-associativity of some hypergraph products
    Mathematics in Computer Science, 10, 3, 403-408, 2016
    [publisher's page] [arXiv]
  22. M. Hellmuth, F. Lehner
    Fast Factorization of Cartesian products of (Directed) Hypergraphs
    Theor. Comp. Sci, 615, 1-11, 2016
    [publisher's page] [arXiv]
  23. S. Berkemer, R. Chaves, A. Fritz, M. Hellmuth, M. Hernandez-Rosales and P. F. Stadler
    Spiders can be recognized by counting their legs
    Mathematics in Computer Science, 9, 4, 437-441, 2015
    [publisher's page] [arXiv]
  24. M. Hellmuth, T. Marc, L. Ostermeier, P. F. Stadler
    The Relaxed Square Property
    Australasian Journal of Combinatorics, 62, 3, 240-270, 2015
    [publisher's page] [arXiv]
  25. M. Hellmuth, N. Wieseke, M. Lechner, H.-P. Lenhof, M. Middendorf, P. F. Stadler
    Phylogenomics with Paralogs
    Proceedings of the National Academy of Sciences (PNAS), 112, 7, 2058-2063, 2015
    [publisher's page] [ParaPhylo]
  26. M. Hellmuth, T. Marc
    On the Cartesian Skeleton and the Factorization of the Strong Product of Digraphs
    J. Theor. Comp. Sci, 565, 0, 16-29, 2015
    [publisher's page] [arXiv]
  27. M. Hellmuth, W. Imrich, T. Kupka
    Fast Recognition of Partial Star Products and Quasi Cartesian Products
    Ars Math. Contemporanea, 9, 2, 233-252, 2015
    [publisher's page] [arXiv]
  28. M. H.-Rosales, M. Hellmuth, N. Wieseke, P.F. Stadler,
    Simulation of gene family histories,
    BMC Bioinformatics, 15, Suppl 3, A8, 2014
    [publisher's page]
  29. M. Hellmuth, M. Noll, L. Ostermeier
    Strong Products of Hypergraphs: Unique Prime Factorization Theorems and Algorithms
    Discrete Applied Mathematics, 171, 60-71, 2014
    [publisher's page] [arXiv]
  30. M. Hellmuth, L. Ostermeier, P.F. Stadler
    Unique Square Property, Equitable Partitions, and Product-like Graphs,
    Discrete Mathematics, 320, 0, 92-103, 2014
    [publisher's page] [arXiv]
  31. M. Hellmuth, J. Leydold, P.F. Stadler,
    Convex Cycle Bases,
    Ars Math. Contemporanea, 7, 1, 123-140, 2014
    [publisher's page]
  32. M. Hellmuth, W. Imrich, T. Kupka
    Partial Star Products: A Local Covering Approach for the Recognition of Approximate Cartesian Product Graphs
    Mathematics in Computer Science, 7, 3, 255-273, 2013
    [publisher's page] [arXiv]
  33. M. Hellmuth
    On the Complexity of Recognizing S-composite and S-prime Graphs,
    Discrete Appl. Math., 161, 7-8, 1006-1013, 2013
    [publisher's page]  [arXiv]
  34. M. Hellmuth, M. H.-Rosales, K. T. Huber, V. Moulton, P.F. Stadler, N. Wieseke,
    Orthology Relations, Symbolic Ultrametrics, and Cographs,
    J. Math. Biol., 66, 1-2, 399-420, 2013
    [publisher's page] [preprint]
  35. M. H.-Rosales, M. Hellmuth, K. T. Huber, V. Moulton, N. Wieseke, P.F. Stadler,
    From Event-Labeled Gene Trees to Species Trees,
    BMC Bioinformatics, 13, Suppl 19, S6, 2012
    [publisher's page] [preprint]
  36. L. Gringmann, M. Hellmuth, P.F. Stadler,
    The Cartesian Product of Hypergraphs,
    Journal of Graph Theory, 70, 2, 180-196, 2012
    [publisher's page]
  37. M. Hellmuth, L. Ostermeier, P.F. Stadler,
    A Survey on Hypergraph Products,
    Mathematics in Computer Science, 6, 1, 1-32, 2012
    [publisher's page][arXiv - ERRATUM]
  38. M. Hellmuth, P.J. Ostermeier, P.F. Stadler,
    Minimum Cycle Bases of Lexicographic Products,
    Ars Math. Contemporanea, 5, 2, 223-234, 2012
    [publisher's page]
  39. M. Hellmuth, L. Gringmann, P.F. Stadler,
    Diagonalized Cartesian Products of S-prime graphs are S-prime,
    Discrete Mathematics, 312, 1, 74-80, 2012
    [publisher's page]
  40. M. Hellmuth
    A Local Prime Factor Decomposition Algorithm,
    Discrete Mathematics, 311, 12, 944-965, 2011
    [publisher's page][arXiv]
  41. C. Heine, S. Jaenicke, M. Hellmuth, P.F. Stadler, G. Scheuermann,
    Visualization of Graph Products,
    IEEE Transactions on Visualization and Computer Graphics, 16, 6, 1082 - 1089, 2010
    [publisher's page] [preprint]
  42. M. Hellmuth, D. Merkle, M. Middendorf,
    Extended Shapes for the Combinatorial Design of RNA Sequences,
    Int. J. of Computational Biology and Drug Design, 2, 4, 371 - 384, 2009
    [publisher's page]
  43. M. Hellmuth, W. Imrich, W. Kloeckl, P.F. Stadler,
    Local algorithms for the prime factorization of strong product graphs,
    Mathematics in Computer Science, 2009, 2, 4, 653-682, 2009
    [publisher's page][arXiv]
  44. P.J. Ostermeier, M. Hellmuth, K. Klemm, J. Leydold, P.F. Stadler,
    A Note on Quasi-Robust Cycle Bases,
    Ars Math. Contemporanea, 2, 2, 231-240, 2009
  45. T. Biyikoglu, M. Hellmuth, J. Leydold,
    Largest Eigenvalues of the Discrete p-Laplacian of Trees with Degree Sequences,
    Elec. J. Lin. Alg, 18, 202-210, 2009.
  46. M. Hellmuth, W. Imrich, W. Kloeckl, P.F. Stadler,
    Approximate graph products,
    Europ. J. of Combinatorics, 30, 5, Part Special Issue on Metric Graph Theory, 1119-1133, 2009.
    [publisher's page]


- - - - - - - - conference proceedings:

  1. A Graph-Based Tool to Embed the pi-Calculus into a Computational DPO Framework
    J.L. Andersen, M. Hellmuth, D. Merkle, N. Nøjgaard, M. Peressotti
    46th International Conference on Current Trends in Theory and Practice of Computer Science
    Doctoral Student Research Forum (SOFSEM), pp 121-132, 2020
    [publisher's page][arXiv]
  2. N. Nøjgaard, N. El-Mabrouk, D. Merkle, N. Wieske, M. Hellmuth
    Partial Homology Relations - Satisfiability in terms of Di-Cographs
    In Computing and Combinatorics: 24st International Conference (COCOON),
    Lecture Notes in Computer Science, vol 10976, Springer, pp. 403-415, 2018
    [publisher's page][arXiv]
  3. M. Hellmuth, A.S. Knudsen, M. Kotrbčík, D. Merkle and N. Nøjgaard
    Linear Time Canonicalization and Enumeration of Non-Isomorphic 1-Face Embeddings
    Proceedings of the 20th Workshop on Algorithm Engineering and Experiments (ALENEX), 154-168, 2018
    [publisher's page][preprint]
  4. N. Nøjgaard, M. Geiß, D. Merkle, P. F. Stadler, N. Wieske, M. Hellmuth
    Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps
    17th International Workshop on Algorithms in Bioinformatics (WABI 2017),
    Leibniz International Proceedings in Informatics (LIPIcs), 88, 17:1--17:12, 2017
    [publisher's page][arXiv]
  5. M. Hellmuth and N. Wieseke
    On Symbolic Ultrametrics, Cotree Representations, and Cograph Edge Decompositions and Partitions
    In Computing and Combinatorics: 21st International Conference (COCOON),
    Lecture Notes in Computer Science, vol 9198, Springer, pp. 609-623, 2015
    [publisher's page] [arXiv]
  6. T. Ingalls, G. Martius, M. Hellmuth, M. Marz, S.J. Prohaska,
    Converting DNA to Music: ComposAlign,
    German Conference on Bioinformatics 2009:Lecture Notes in Informatics, 93-103, 2009
    [publisher's page] [examples]
  7. M. Hellmuth, D. Merkle, M. Middendorf,
    On the Design of RNA Sequences for Realizing Extended Shapes,
    Bioinformatics, Systems Biology and Intelligent Computing, IJCBS '09, 167-173, 2009
    [publisher's page]

    BibFile of Publications