Publikationen

• Articles in journals and refereed conference proceedings
• Articles in a book
• Editorial Work
• Preprints
• PhD-Thesis
• Other publications

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Editorial Work

• Matthias Müller-Hannemann and Federico Perea (eds.)
  21st Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2021), Open Access Series in Informatics (OASIcs), Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, vol. 96, 2021.
• M. Müller-Hannemann and S. Schirra (eds.)
  Algorithm Engineering - Bridging the Gap between Algorithm Theory and Practice
  LNCS 5971, Springer, 2010.
• R. K. Ahuja, R. Jacob and M. M.-H. (guest eds.)
  Focused Issue on Rail Transportation, Transportation Science, volume 42, number 4, pp. 405 - 507, 2008.
• R. Jacob and M. M.-H. (eds.)
  ATMOS 2006 - 6th Workshop on Algorithmic Methods and Models for Optimization of Railways
  Dagstuhl Seminar Proceedings 06002, ISSN 1862-4405
  Preface and abstract collection
• A. Eriksson, K. Marti, M. M.-H., B.H.V. Topping, and C.A. Mota- Soares (eds.)
  Engineering Computational Technology, special issue of Advances in Engineering Software, volume 38, issues 11-12, pp. 723-896, 2007.

Articles in journals and refereed conference proceedings

• Frederik L. Jatzkowski, Antonia Schmidt, Robert Mank, Steffen Schüler, and Matthias Müller-Hannemann
  Barcode Selection and Layout Optimization in Spatial Transcriptomics. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 17:1-17:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024) https://doi.org/10.4230/LIPIcs.SEA.2024.17
• Julian Patzner, Ralf Rückert, Matthias Müller-Hannemann
  Passenger-Aware Real-Time Planning of Short Turns to Reduce Delays in Public Transport, 22nd Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2022), Open Access Series in Informatics (OASIcs), Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, vol. 106, pp. 13:1-13:18, DOI: 10.4230/OASIcs.ATMOS.2022.13
• Matthias Müller-Hannemann, Ralf Rückert, Alexander Schiewe and Anita Schöbel
  Estimating the robustness of public transport schedules using machine learning, Transportation Research Part C 137 (2022) 103566
• Matthias Müller-Hannemann, Ralf Rückert, Alexander Schiewe and Anita Schöbel
  Towards improved robustness of public transport by a machine-learned oracle, 21st Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2021), Open Access Series in Informatics (OASIcs), Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, vol. 96, pp. 3:1-3:20, DOI: 10.4230/OASIcs.ATMOS.2021.3.
• Jördis-Ann Schüler, Steffen Rechner, and Matthias Müller-Hannemann
  MET: a Java package for fast molecule equivalence testing.
  J Cheminform 12, 73 (2020). https://doi.org/10.1186/s13321-020-00480-1
• Matthias Müller-Hannemann, Ralf Rückert, and Sebastian S. Schmidt
  Vehicle Capacity-Aware Rerouting of Passengers in Delay Management.
  In Proceedings of 19th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2019), OpenAccess Series in Informatics (OASIcs), Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, vol. 75, pages 7:1-7:14 (2019). DOI: 10.4230/OASIcs.ATMOS.2019.7
• Markus Friedrich, Matthias Müller-Hannemann, Ralf Rückert, Alexander Schiewe, and Anita Schöbel
  Robustness as a Third Dimension for Evaluating Public Transport Plans
  18th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2018), OpenAccess Series in Informatics (OASIcs), Schloss Dagstuhl-- Leibniz-Zentrum fuer Informatik, 2018, volume 65, article 4, 1-17.
• Jördis-Ann Schüler, Steffen Neumann, Matthias Müller-Hannemann, and Wolfgang Brandt
  ChemFrag: Chemically meaningful annotation of fragment ion mass spectra
  Journal of Mass Spectrometry, 53 (11), 1104-1115, 2018, doi: 10.1002/jms.4278
• Steffen Rechner, Linda Strowick, and M. M.-H.
  Uniform sampling of bipartite graphs with degrees in prescribed intervals
  Journal of Complex Networks, published online on Dec. 22, 2017, cnx059.
• Markus Friedrich, Matthias Müller-Hannemann, Ralf Rückert, Alexander Schiewe, and Anita Schöbel
  Robustness Tests for Public Transport Planning
  17th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2017), OpenAccess Series in Informatics (OASIcs), vol. 59, 16 pages, Schloss Dagstuhl-- Leibniz-Zentrum fuer Informatik
• Matthias Müller-Hannemann and Ralf Rückert
  Dynamic Event-Activity Networks in Public Transportation - Timetable Information and Delay Management
  Datenbank Spektrum. doi:10.1007/s13222-017-0252-y
• Ivo Hedtke, Ioana Lemnian, Ivo Große and Matthias Müller- Hannemann
  Optimal Block-Based Trimming for Next Generation Sequencing
  IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 15, issue 2 (2018)
• Marius Erbert, Steffen Rechner, and Matthias Müller- Hannemann
  Gerbil: A fast and memory-efficient k-mer counter with GPU-support
  Algorithms for Molecular Biology (2017) 12:9, open access
• Hannah Bast, Daniel Delling, Andrew Goldberg, Matthias Müller- Hannemann, Thomas Pajor, Peter Sanders, Dorothea Wagner and Renato Werneck
  Route Planning in Transportation Networks,
  in Algorithm Engineering: Selected Results and Surveys, Volume 9220 of the series Lecture Notes in Computer Science, pages 19-80, Springer, 2016
  See also arXiv version.
• Martin Lemnian, M. M.-H. and Ralf Rückert
  Sensitivity analysis and coupled decisions in passenger flow-based train dispatching
  16th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2016), OpenAccess Series in Informatics (OASIcs), vol. 54, 15 pages, Schloss Dagstuhl-- Leibniz-Zentrum fuer Informatik
• Marius Erbert, Steffen Rechner, and M. M.- H.
  G erbil: A fast and memory-efficient k-mer counter with GPU- support
  M. Frith and C.N.S. Pedersen (Eds.): WABI 2016, LNBI 9838, pp. 150– 161, Springer. DOI: 10.1007/978-3-319-43681-4 12
• Ralf Rückert, Martin Lemnian, Steffen Rechner, Christoph Blendinger, and Matthias Müller-Hannemann
  PANDA: a software tool for improved train dispatching with focus on passenger flows,
  Public Transport, Springer (open access), 2016. A preliminary version appeared in Proceedings of CASPT 2015, Rotterdam.
• Martin Lemnian, Ralf Rückert, Steffen Rechner, Christoph Blendinger, and M. M.-H.
  Timing of Train Disposition: Towards Early Passenger Rerouting in Case of Delays,
  in Proceedings of ATMOS 2014, Wroclaw, Poland, September 11, 2014,pages 122-137.
• Clemens Beckstein, Sebastian Böcker, Martin Bogdan, Helge Bruelheide, H. Martin Bücker, Joachim Denzler, Peter Dittrich, Ivo Grosse, Alexander Hinneburg, Birgitta König-Ries, Felicitas Löffler, Manja Marz, M. M.-H., Marten Winter, and Wolf Zimmermann.
  Explorative analysis of heterogeneous, unstructured, and uncertain data: A computer science perspective on biodiversity research.
  In Proceedings of the 3rd International Conference on Data Management Technologies and Applications, DATA 2014, Vienna, Austria, August 29--31, 2014, pages 251-257.
• Sarah Hart, Ivo Hedtke, M. M.-H., and Sandeep Murthy,
  A Fast Search Algorithm for (m, m, m) Triple Product Property Triples and an Application for 5 × 5 Matrix Multiplication,
  Groups - Complexity - Cryptology, ISSN 1867-1144, Volume 7 Issue 1 (2015), Pages 31-46, De Gruyter
• Ivo Hedtke, Ioana Lemnian, M. M.-H. and Ivo Grosse
  On Optimal Read Trimming in Next Generation Sequencing and its Complexity, Proceedings of AlCoB 2014, LNBI 8542, pp. 83-94, Springer, 2014.
• Marc Goerigk, Sascha Heße, M. M.-H., Marie Schmidt, and Anita Schöbel
  Recoverable Robust Timetable Information, Proceedings of ATMOS 2013. OpenAccess Series in Informatics (OASIcs), vol. 33, pp. 1-14, Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik.
• Marc Goerigk, Martin Knoth, M. M.-H., Marie Schmidt, and Anita Schöbel
  The price of strict and light robustness in timetable information, Transportation Science, Vol. 48, No. 2, May 2014, pp. 225–242.
• Moritz Emanuel Beber, Christoph Fretter, Shubham Jain, Nikolaus Sonnenschein, M. M.-H., and Marc-Thorsten Hütt
  Artefacts in statistical analyses of network motifs: general framework and application to metabolic networks, J. R. Soc. Interface vol. 9, nr. 77, 3426-3435, doi:10.1098/rsif.2012.0490, 2012
• Annabell Berger and M. M.-H.
  How to Attack the NP-complete Dag Realization Problem in Practice,
  Proceedings of SEA 2012, LNCS 7276, pages 51-62, Springer, 2012
• Christoph Fretter, M. M.-H., and Marc-Thorsten Hütt
  Subgraph fluctuations in random graphs,
  Physical Review E 85, 056119, 2012
• Steffen Schiele, Markus Möller, Holger Blaar, Detlev Thürkow, and M. M.-H.
  Parallelization strategies to deal with non-localities in the calculation of regional land-surface parameters,
  Computers and Geosciences, vol. 44, pages 1-9, 2012
• Steffen Schiele, Holger Blaar, Detlev Thürkow, Markus Möller and M. M.-H.
  Parallelization Strategies to Speed-Up Computations for Terrain Analysis on Multi-Core Processors,
  Mühl, G., Herkersdorf, A. (Eds.) ARCS 2012 Workshops, Lecture Notes in Informatics (Vol. 200), pages 457-468, 2012.
• Siamak Tazari and M. M.-H.
  Dealing with large hidden constants: engineering a planar Steiner tree PTAS
  Journal of Experimental Algorithmics (JEA), volume 16, article 3.6, 2011
• Annabell Berger, Christian Blaar, Andreas Gebhardt, Matthias Müller-Hannemann and Mathias Schnee
  Passe nger Flow-Oriented Train Disposition, Proceedings of ESA 2011, Saarbrücken, LNCS 6942, pp. 227-238, Springer, Heidelberg. Full version: Technical Report 2011/2, Institut für Informatik, MLU Halle-Wittenberg
• A. Berger, A. Gebhardt, M. Müller-Hannemann and M. Ostrowski
  Stochastic Delay Prediction in Large Train Networks,
  ATMOS 2011, OpenAccess Series in Informatics (OASIcs), vol. 20, pp. 100-111, Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik,
• M. Goerigk, M. Knoth, M. Müller-Hannemann, A. Schöbel and M. Schmidt
  The Price of Robustness in Timetable Information,
  ATMOS 2011, OpenAccess Series in Informatics (OASIcs), vol. 20, pp. 76-87, Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik,
• A. Berger and M. Müller-Hannemann
  Dag Realizations of Directed Degree Sequences
  Proceedings of FCT 2011, Oslo, Norway, LNCS 6914, pp. 264-275, Springer, Heidelberg. Full version: Technical Report 2011/5, Institut für Informatik, MLU Halle-Wittenberg
• L. Krumov, C. Fretter, M. M.-H., K. Weihe, and M.-T. Hütt
  Motifs in co-authorship networks and their relation to the impact of scientific publications
  European Physical Journal B, volume 84, no.4, pp. 535-540 (2011)
• A. Berger, M. M.-H., S. Rechner, and A. Zock
  Efficient Computation of Time-Dependent Centralities in Air Transportation Networks
  Proceedings of WALCOM 2011, LNCS 6552, pp. 77-88, Springer, 2011.
• C. Fretter, L. Krumov, K.Weihe, M. M.-H., and M.-T. Hütt
  Phase synchronization in railway timetables
  Eur. Phys. J. B 77, 281–289 (2010).
• A. Berger and M. M.-H.
  Uniform Sampling of Undirected and Directed Graphs with a Fixed Degree Sequence
  extended abstract in Proceedings of WG 2010, LNCS 6410, pp. 220-231, Springer, 2010.
• A. Berger, M. Grimmer, and M. M.-H.
  Fully dynamic speed-up techniques for multi-criteria shortest paths searches in time-dependent networks, Proceedings of SEA 2010, LNCS, vol. 6049, pp. 35-46, Springer 2010.


• S. Wolf, S. Schmidt, M. M.-H., and S. Neumann
  In silico fragmentation for computer assisted identification of metabolite mass spectra, BMC Bioinformatics 11:148, 2010.


• M. M.-H. and Siamak Tazari
  A Near Linear Time Approximation Scheme for Steiner Tree among Obstacles in the Plane
  Computational Geometry:Theory and Applications 43, pp. 395–409 (2010). Extended abstract appeared in WADS 2007.


• A. Berger, D. Delling, A. Gebhardt, and M.M.-H.
  Accelerating Time-Dependent Multi-Criteria Timetable Information is Harder Than Expected, proceedings of ATMOS 2009.


• M.M.-H. and M. Schnee
  Efficient Timetable Information in the Presence of Delays, in Robust and Online Large Scale Optimization, LNCS 5868, pp. 249–272, Springer, 2009.


• S. Tazari and M.M.-H.
  Shortest Paths in Linear Time on Minor-Closed Graph Classes with an Application to Steiner Tree Approximation, Discrete Applied Mathematics, volume 157, Issue 4, pp. 673-684, 2009.


• S. Tazari and M.M.-H.
  Dealing with Large Hidden Constants: Engineering a Planar Steiner Tree PTAS, in Proceedings of ALENEX 2009, pp. 120-131, SIAM Philadelphia, 2009.


• L. Frede, M.M.-H., and M. Schnee
  Efficient On-Trip Timetable Information in the Presence of Delays, in Proceedings of ATMOS 2008 - 8th Workshop on Algorithmic Approaches for Transportation Modeling, Optimization, and Systems.


• S. Tazari and M. M.-H.
  A Faster Shortest-Paths Algorithm for Minor-Closed Graph Classes, WG 2008, Lecture Notes in Computer Science 5344. pp.360-371, Springer, 2008.


• Y. Disser, M. M.-H., and M. Schnee
  Multi-Criteria Shortest Paths in Time-Dependent Train Networks, WEA 2008. 7th International Workshop on Experimental Algorithms, Provincetown, MA, USA, Lecture Notes in Computer Science 5038, pp. 347-361, Springer 2008.


• M. M.-H. and A. Sonnikow
  Non-Approximability of Just-in-Time Scheduling
  MAPSP 2007 Special Issue, Journal of Scheduling, vol. 12, pp. 555- 562, 2009.

• T. Gunkel, M. M.-H. and M. Schnee
  Improved Search for Night Train Connections, Networks 57, pp. 19-27, 2011.
  Extended abstract in ATMOS 2007.


• M. M.-H. and Siamak Tazari
  A Near Linear Time Approximation Scheme for Steiner Tree among Obstacles in the Plane
  WADS 2007, 10th Workshop on Algorithms and Data Structures, Halifax, Nova Scotia, Canada, Lecture Notes in Computer Science 4619, Springer, pp. 151-162, 2007.


• M. M.-H. and Anna Schulze
  Hardness and Approximation of Octilinear Steiner Trees
  International Journal of Computational Geometry and Applications (IJCGA), vol. 17 (2007), pp. 231-260.


• M. M.-H., F. Schulz, D. Wagner and C. Zaroliagis
  Timetable Information: Models and Algorithms,
  LNCS Proceedings on Algorithmic Methods for Railway Optimization, Lecture Notes in Computer Science, vol. 4359, pp. 67-89, Springer, 2007.

• M. M.-H. and M. Schnee
  Finding All Attractive Train Connections by Multi-Criteria Pareto Search,
  Proceedings of the 4th Workshop on Algorithmic Methods and Models for Optimization of Railways (ATMOS 2004), Bergen, Norway, Lecture Notes in Computer Science, vol. 4359, pp. 246-263, Springer, 2007.


• M. M.-H. and Anna Schulze
  Approximation of Octilinear Steiner Trees Constrained by Hard and Soft Obstacles, SWAT 2006, 10th Scandinavian Workshop on Algorithm Theory, Lecture Notes in Computer Science 4059, pp. 242-254, Springer, 2006.


• S. Tazari, M. M.-H. and K. Weihe
  Workload Balancing in Multi-Stage Production Processes
  WEA 2006, 5th Int. Workshop on Experimental Algorithms, Lecture Notes in Computer Science 4007, pp. 49-60, Springer, 2006.

• M. M.-H. and M. Schnee
  Paying Less for Train Connections with MOTIS,
  Proceedings of Algorithmic MeThods and Models for Optimization of RailwayS (ATMOS 2005), Palma de Mallorca, Spain, 2005.

• M. M.-H. and K. Weihe
  Moving Policies in Cyclic Assembly-Line Scheduling,
  Theoretical Computer Science, vol. 351, pp. 425-436, 2006
  Extended abstract in Proceedings of the International Workshop on Parameterized and Exact Computation (IWPEC 2004), Bergen, Norway, Lecture Notes in Computer Science 3162, pp. 149-161, Springer, 2004.

• M. M.-H. and Karsten Weihe
  On the Cardinality of the Pareto Set in Bicriteria Shortest Path Problems,
  Annals of Operations Research, vol. 147, pp. 269-286, 2006.

• M. M.-H. and U. Zimmermann
  Slack Optimization of Timing-Critical Nets,
  11th Annual European Symposium on Algorithms (ESA 2003) , Lecture Notes in Computer Science, vol. 2832, pp. 727-739, 2003.

• M. M.-H. and S. Peyer
  Approximation of Rectilinear Steiner Trees with Length Restrictions on Obstacles,
  8th Workshop on Algorithms and Data Structures (WADS 2003), Carleton Univ., Ottawa, Canada, Lecture Notes in Computer Science, vol. 2748, pp. 207-218, 2003

• M. M.-H., M. Schnee, and K. Weihe
  Getting Train Timetables into the Main Storage
  Electronic Notes in Theoretical Computer Science 66.6, Proceedings of Algorithmic MeThods and Models for Optimization of RailwayS (ATMOS 2002).

• M. M.-H., C. Kober, R. Sader, and H.-F. Zeilhofer
  Anisotropic Validation of Hexahedral Meshes for Composite Materials in Biomechanics,
  Proceedings of the 10th International Meshing Roundtable, Newport Beach, CA, pp. 249-260, 2001.

• M. M.-H. and K. Weihe
  Pareto Shortest Paths is Often Feasible in Practice,
  Proceedings of the 5th International Workshop on Algorithm Engineering (WAE 2001), Arhus, Denmark, Lecture Notes in Computer Science, vol. 2141, pp. 185-197, 2001.

• C. Kober and M. M.-H.
  A Case Study in Hexahedral Mesh Generation: Simulation of the Human Mandible,
  Engineering with Computers, vol. 17, pp. 249-260, 2001.

  Extended abstract in Proceedings of the 9th International Meshing Roundtable, New Orleans, Louisiana, Sandia National Laboratories, pp. 423-434, 2000 under the title ``Hexahedral Mesh Generation for the Simulation of the Human Mandible.''

• M. M.-H.
  Quadrilateral Surface Meshes without Self-Intersecting Dual Cycles for Hexahedral Mesh Generation,
  Computational Geometry: Theory and Applications, vol. 22, pp. 75-97, 2002.

  Extended abstract in Proceedings of the 16th Annual ACM Symposium on Computational Geometry (SCG'00), Hong Kong, June 12-14, 2000, pp. 19-28, under the title ``Improving the Surface Cycle Structure for Hexahedral Mesh Generation.''

• K. Weihe, U. Brandes, A. Liebers, M. M.-H., D. Wagner, and T. Willhalm
  Empirical design of geometric algorithms,
  Proceedings of the 15th ACM Symposium on Computational Geometry (SCG'99), 1999, pp. 86-94.

• M. M.-H. and A. Schwartz
  Implementing Weighted b-Matching Algorithms: Insights from a Computational Study,
  ACM Journal of Experimental Algorithmics, Volume 5, Article 8 (24 pages), 2000,

  as part of a special issue dedicated to selected papers from the Workshop on Algorithm Engineering and Experimentation (ALENEX99), Lecture Notes in Computer Science, vol. 1619, pp. 18-36, Springer Verlag, 1999.

• M. M.-H. and A. Schwartz
  Implementing Weighted b-Matching Algorithms: Towards a Flexible Software Design,
  ACM Journal of Experimental Algorithmics, Volume 4, Article 7 (28 pages), 1999,

  as part of a special issue dedicated to selected papers from the Second Workshop on Algorithmic Engineering, held in August 1998 in Saarbrücken, Germany, with guest editor Kurt Mehlhorn.

• M. M.-H.
  Shelling hexahedral complexes for mesh generation in CAD,
  Journal of Graph Algorithms and Applications, vol. 5, no. 5, pp. 59-91, 2001.

• M. M.-H.
  Combinatorics Helps for Hexahedral Mesh Generation in CAD,
  Proceedings of the 10th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'99), Baltimore, Maryland, USA, January 17-19, 1999, pp. 949-950.

• M. M.-H.
  Hexahedral Mesh Generation by Successive Dual Cycle Elimination,
  Engineering with Computers 15, pp. 269-279, 1999.

• M. M.-H. and K. Weihe
  On the Discrete Core of Quadrilateral Mesh Refinement,
  International Journal For Numerical Methods in Engineering (IJNME), vol. 46, no. 4, pp. 593-622, 1999.

• M. M.-H.
  High quality quadrilateral surface meshing without template restrictions: A new approach based on network flow techniques,
  International Journal of Computational Geometry and Applications (IJCGA) 10 (2000), pp. 285-307.

• R. H. Möhring and M. M.-H.
  Complexity and modeling aspects of mesh refinement into quadrilaterals,
  Algorithmica 26 (2000), pp. 148-171,

  extended abstract in Proceedings of the 8th Annual International Symposium on Algorithms and Computation, ISAAC'97, Singapore, Lecture Notes in Computer Science 1350, Springer-Verlag, 1997, pp. 263-273.

• M. M.-H. and K. Weihe
  Improved approximations for minimum cardinality quadrangulations of finite element meshes,
  Proceedings of the 5th Annual European Symposium on Algorithms, ESA'97, Graz, Austria, Lecture Notes in Computer Science 1284, Springer-Verlag, 1997, pp. 364-377.

• M. M.-H. and K. Weihe
  Quadrangular Refinements of Convex Polygons with an Application to Finite-Element Meshes,
  International Journal of Computational Geometry and Applications (IJCGA) 10 (2000), pp. 1-40.

• M. M.-H. and K. Weihe
  Minimum strictly convex quadrangulations of convex polygons,
  Proceedings of the 13th Annual ACM Symposium on Computational Geometry, Nice, France, ACM, 1997, pp. 193-202.

• R. H. Möhring, M. M.-H., and K. Weihe
  Mesh refinement via bidirected flows: Modeling, complexity, and computational results,
  Journal of the ACM 44 (1997), pp. 395-426.

• R. H. Möhring, M. M.-H., and K. Weihe
  Using network flows for surface modeling,
  Proceedings of the Sixth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 95), San Francisco, California, 1995, pp. 350-359.