Publications

Submitted

  1. Complexity of Modification Problems for Best Match Graphs
    D. Schaller, P.F. Stadler, M. Hellmuth
    (submitted 2020)
    [arXiv]
  2. Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs
    D. Schaller, M. Geiß, P.F. Stadler, M. Hellmuth
    (submitted 2020)
    [arXiv]
  3. Complete Edge-Colored Permutation Graphs
    T. Hartmann, M. Bannach, M. Middendorf, P.F. Stadler, N. Wieseke, M. Hellmuth
    (submitted 2020)
    [arXiv]
  4. Hierarchical and Modularly-Minimal Vertex Colorings
    D.I. Valdivia, M. Geiß, M. H.Rosales, P.F. Stadler, M. Hellmuth
    (submitted 2020)
    [arXiv]
  5. 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)
    [arXiv]

Published (peer-reviewed)

    MONOGRAPHS / BOOK CHAPTERS
  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]

  5. JOURNALS
  6. M. Lafond, M. Hellmuth
    Reconstruction of time-consistent species trees
    Algorithms for Molecular Biology, DOI: 10.1186/s13015-020-00175-0 (in press), 2020
    [arXiv]
  7. C. Flamm, M. Hellmuth, D. Merkle, N. Nøjgaard, P.F. Stadler
    Generic Context-Aware Group Contributions
    IEEE/ACM Trans Comput Biol Bioinform, DOI:10.1109/TCBB.2020.2998948, 2020
    [publisher's page]
  8. P.F. Stadler, M. Geiß, D. Schaller, A. Lopez, M.G. Laffitte, D.I. Valdivia, M. Hellmuth, M. H.Rosales
    From pairs of most similar sequences to phylogenetic best matches
    Algorithms for Molecular Biology, 15, 5, 1-20, 2020
    [publisher's page][arXiv]
  9. 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, 283, 495-511, 2020
    [publisher's page][arXiv]
  10. A. Fritz, M. Hellmuth, P.F. Stadler, N. Wieseke
    Cograph Editing: Merging Modules is equivalent to Editing P4's
    Art Discrete Appl. Math., 3, #P2.01, 2020
    [publisher's page][arXiv]
  11. 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, 80, 1459-1495, 2020
    [publisher's page][arXiv]
  12. 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]
  13. M. Geiß, P.F. Stadler, M. Hellmuth
    Reciprocal Best Match Graphs
    J. Math. Biology, 80(3), 865-953, 2020
    [publisher's page][arXiv]
  14. 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]
  15. 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]
  16. M. Hellmuth, C.R. Seemann
    Alternative Characterizations of Fitch's Xenology Relation
    J. Math. Biology, 79(3), 969-986, 2019
    [publisher's page][arXiv]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. M. Hellmuth
    Biologically Feasible Gene Trees, Reconciliation Maps and Informative Triples
    Algorithms for Molecular Biology, 12, 1, 23, 2017
    [publisher's page][arXiv]
  26. 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]
  27. 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]
  28. 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]
  29. M. Hellmuth, F. Lehner
    Fast Factorization of Cartesian products of (Directed) Hypergraphs
    Theor. Comp. Sci, 615, 1-11, 2016
    [publisher's page] [arXiv]
  30. 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]
  31. 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]
  32. 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]
  33. 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]
  34. 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]
  35. 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]
  36. 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]
  37. 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]
  38. M. Hellmuth, J. Leydold, P.F. Stadler,
    Convex Cycle Bases,
    Ars Math. Contemporanea, 7, 1, 123-140, 2014
    [publisher's page]
  39. 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]
  40. 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]
  41. 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]
  42. 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]
  43. L. Gringmann, M. Hellmuth, P.F. Stadler,
    The Cartesian Product of Hypergraphs,
    Journal of Graph Theory, 70, 2, 180-196, 2012
    [publisher's page]
  44. 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]
  45. 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]
  46. 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]
  47. M. Hellmuth
    A Local Prime Factor Decomposition Algorithm,
    Discrete Mathematics, 311, 12, 944-965, 2011
    [publisher's page][arXiv]
  48. 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]
  49. 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]
  50. 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]
  51. 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
    [pdf]
  52. 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.
    [pdf]
  53. 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]

  54. CONFERENCE PROCEEDINGS
  55. M. Hellmuth, D. Merkle, N. Nøjgaard
    Atom Tracking Using Cayley Graphs
    16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020)
    (to appear), 2020
    [preprint]
  56. J.L. Andersen, M. Hellmuth, D. Merkle, N. Nøjgaard, M. Peressotti
    A Graph-Based Tool to Embed the pi-Calculus into a Computational DPO Framework
    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]
  57. 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]
  58. M. Hellmuth, A.S. Knudsen, M. Kotrbcik, 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]
  59. 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]
  60. 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]
  61. 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]
  62. 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]