Publications
--------------SUBMITTED--------------
- M. Hellmuth, D. Merkle, N. Nøjgaard
Atom Tracking Using Cayley Graphs
(submitted 2020)
- M. Lafond, M. Hellmuth
Reconstruction of time-consistent species trees
(submitted 2019)
[arXiv]
- 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]
- Hierarchical Colorings of Cographs
D.I. Valdivia, M. Geiß , M. Hellmuth, M. H.Rosales, P.F. Stadler
(submitted 2019)
[arXiv]
- 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:
- 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]
- Habilitation Thesis (2015)
On the Decomposition and Reconstruction of Discrete Structures: Characterization, Approximation and Computation [Extended Abstract]
- PhD-Thesis (2010) "grade: summa cum laude"
Local Prime Factor Decomposition of Approximate Strong Product Graphs [pdf]
- Diploma Thesis (2006)
Konstruktion von Worten mit Matchingeigenschaften und Anwendung auf das RNA Design [pdf]
- - - - - - - - journals:
- 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
[arXiv]
- 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]
- A. Fritz, M. Hellmuth, P. F. Stadler , N. Wieseke
Merging Modules is equivalent to Editing P4's
Art Discrete Appl. Math. (to appear) 2020
[arXiv]
- 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]
- 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]
- M. Geiß, P.F. Stadler, M. Hellmuth
Reciprocal Best Match Graphs
J. Math. Biology, 80(3), 865-953, 2020
[publisher's page][arXiv]
- 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]
- 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]
- M. Hellmuth, C.R. Seemann
Alternative Characterizations of Fitch's Xenology Relation
J. Math. Biology, 79(3), 969–986, 2019
[publisher's page][arXiv]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- M. Hellmuth
Biologically Feasible Gene Trees, Reconciliation Maps and Informative Triples
Algorithms for Molecular Biology, 12, 1, 23, 2017
[publisher's page][arXiv]
- 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]
- 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]
- 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]
- M. Hellmuth, F. Lehner
Fast Factorization of Cartesian products of (Directed) Hypergraphs
Theor. Comp. Sci, 615, 1-11, 2016
[publisher's page] [arXiv]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- M. Hellmuth, J. Leydold, P.F. Stadler,
Convex Cycle Bases,
Ars Math. Contemporanea, 7, 1, 123-140, 2014
[publisher's page]
- 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]
- 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]
- 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]
- 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]
- L. Gringmann, M. Hellmuth, P.F. Stadler,
The Cartesian Product of Hypergraphs,
Journal of Graph Theory, 70, 2, 180-196, 2012
[publisher's page]
- 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]
- 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]
- 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]
- M. Hellmuth
A Local Prime Factor Decomposition Algorithm,
Discrete Mathematics, 311, 12, 944-965, 2011
[publisher's page][arXiv]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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:
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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