2017
Theses
Stefan Weber,
Enhanced Suffix Arrays: Analysis of Efficient Implementations in Java, Master Thesis, LFE Bioinformatik, LMU München, 2017.
2016
Theses
Daniel Schmitz,
Algorithmische Erzeugung von NGS-Panels sowie Berechnung von Allelfrequenzen in der molekulargenetischen Diagnostik, Bachelor Thesis, LFE Bioinformatik, LMU München, 2016.
Benjamin Albrecht,
Computing Hybridization Networks Using Agreement Forests, PhD Thesis, Ludwig-Maximilians-Universität München, 2016.
Marco Lombardi,
Implementation and Evaluation of Algorithms for Approximate Tandem Repeats, Master Thesis, LFE Bioinformatik, LMU München, 2016.
2015
Papers
Benjamin Albrecht,
Computing all hybridization networks for multiple binary phylogenetic input trees, BMC Bioinformatics, vol. 16, no. 236, pp. 439-441, 2015.
Theses
Katharina Schmid,
Efficient Construction of de Bruijn Graphs Using Suffix Arrays, Bachelor Thesis, LFE Bioinformatik / LMU München, 2015.
2014
Papers
Benjamin Albrecht,
Computing Hybridization Networks for Multiple Rooted Binary Phylogenetic Trees by Maximum Acyclic Agreement Forests, arXiv:1408.3044, 2014.
Theses
Laura Schiller,
Efficient computation of hybridization networks, Master Thesis, LFE Bioinformatik / LMU München, 2014.
Matthias Danner,
Implementierung und Evaluierung einer fehlertoleranten Textsuche basierend auf Suffix-Arrays, Bachelor Thesis, LFE Bioinformatik / LMU München, 2014.
2012
Papers
Benjamin Albrecht,
Volker Heun,
Space Efficient Modifications to Structator - a Fast Index-Based Search Tool for RNA Sequence-Structure Patterns, Proceedings of the 11th International Symposium on Experimental Algorithms (SEA 2012) (Ralf Klasing, ed.), Springer Verlag, vol. 7276, Bordeaux, France, June 7-9, 2012, pp. 27-38, 2012.
2011
Papers
Johannes Fischer,
Volker Heun,
Space-Efficient Preprocessing Schemes for Range Minimum Queries on Static Arrays, SIAM Journal on Computing, vol. 40, no. 2, pp. 465-492, 2011.
2010
Papers
Johannes Fischer,
Volker Heun,
Range Median of Minima Queries, Super-Cartesian Trees, and Text Indexing, Proceedings of the International Workshop on Combinatorial Algorithms (IWOCA’08) (Mirka Miller, Koichi Wada, eds.), College Publications, vol. 12, September 13-15, 2008, Nagoya, Japan, pp. 239-252, 2010.
Johannes Fischer,
Volker Heun,
Finding Range Minima in the Middle: Approximations and Applications, Mathematics in Computer Science, vol. 3, no. 1, pp. 17-30, 2010.
Theses
Markus Meier,
Visualisierung von Repeats im Genom, Bachelor Thesis, LFE Bioinformatik, LMU München, 2010.
2009
Papers
Luca Chiarabini,
Automatic Synthesis of an Efficient Algorithm for the Similarity of Strings Problem, Proceedings of the 4th Workshop on Automated Formal Methods (AFM’09) (H. Saidi, N. Shankar, eds.), Grenoble, France, June 27, 2009, pp. 23-30, 2009.
Philippe Audebaud,
Luca Chiarabini,
New Development in Extracting Tail Recursive Programs from Proofs, Pre-Proceedings of the 19th International Symposium on Logic-Based Program Synthesis and Transformation (LOPSTR’09), Coimbra, Portugal, September 9-11, 2009, 2009.
Simon W. Ginzinger, Murray Coles,
SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database, Journal of Biomolecular NMR, vol. 43, no. 3, pp. 179-185, 2009.
Simon W. Ginzinger, Marko Skocibusic,
Volker Heun,
CheckShift Improved: Fast Chemical Shift Reference Correction with High Accuracy, Journal of Biomolecular NMR, vol. 44, no. 4, pp. 207-211, 2009.
Theses
Jeremias Weihmann,
Genome-Rearrangements: Sortieren mit erweiterten Transreversals, Diploma Thesis, LFE Bioinformatik / LMU München, 2009.
Luca Chiarabini,
Program Development by Proof Transformation, PhD Thesis, LMU München, 2009.
2008
Papers
Johannes Fischer,
Volker Heun,
Range Median of Minima Queries, Super-Cartesian Trees, and Text Indexing, Local Proceedings of the 19th International Workshop on Combinatorial Algorithms (IWOCA’08) (Mirka Miller, Koichi Wada, eds.), Nagoya, Japan, September 13-15, 2008, pp. 239-252, 2008.
Johannes Fischer,
Volker Heun, Horst Martin Stühler,
Practical Entropy-Bounded Schemes for O(1)-Range Minimum Queries, Proceedings of the 2008 Data Compression Conference (DCC’08) (J.A. Storer, M.W. Marcellin, eds.), IEEE Computer Society, Snowbird, Utah, U.S.A., March 25-27, 2008, pp. 272-281, 2008.
Volker Heun,
Analysis of a Modification of Gusfield’s Recursive Algorithm for Reconstructing Ultrametric Trees, Information Processing Letters, vol. 108, no. 4, pp. 222-225, 2008.
Luca Chiarabini,
Extraction of Efficient Programs from Proofs: The Case of Structural Induction over Natural Numbers, Local Proceedings of the Fourth Conference on Computability in Europe: Logic and Theory of Algorithms (CiE’08) (A. Beckmann, C. Dimitracopoulos, B. Löwe, eds.), Athens, Greece, June 15-20, 2008, pp. 64-76, 2008.
Luca Chiarabini,
Program Development by Proof Transformation: Recent Evolutions, 15th International Conferences on Logic for Programming, Artificial Intelligence and Reasoning (LPAR’08), Doha, Qatar, November 22-27, 2008, 2008.
Theses
Simon W. Ginzinger,
Bioinformatics Methods for NMR Chemical Shift Data, PhD Thesis, LMU München, 2008.
Marko Skocibusic,
Improving CheckShift, Diploma Thesis, LFE Bioinformatik, LMU München, 2008.
Annabelle Teresa Klarl,
Konstruktion und Anwendung von Affixarrays, Bachelor Thesis, LFE Bioinformatik, LMU München, 2008.
2007
Papers
Amihood Amir,
Johannes Fischer, Moshe Lewenstein,
Two-Dimensional Range Minimum Queries, Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM’07), (Bin Ma, Kaizhong Zhang, eds.), Springer-Verlag, vol. 4580, London, Ontario, July 9-11, 2007, pp. 286-294, 2007.
Paolo Ferragina,
Johannes Fischer,
Suffix Arrays on Words, Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM’07) (Bin Ma, Kaizhong Zhang, eds.), Springer-Verlag, vol. 4580, London, Ontario, July 9-11, 2007, pp. 328-339, 2007.
Johannes Fischer,
Volker Heun,
A New Succinct Representation of RMQ-Information and Improvements in the Enhanced Suffix Array, Proceedings of the International Symposium on Combinatorics, Algorithms, Probabilistic and Experimental Methodologies (ESCAPE’07) (Bo Chen, Mike Paterson, Guochuan Zhang, eds.), Springer-Verlag, vol. 4614, Hangzhou, China, April 7-9, 2007, pp. 459-470, 2007.
Simon W. Ginzinger, Thomas Gräupl,
Volker Heun,
SimShiftDB: Chemical-Shift-Based Homology Modeling, Proceedings of the First International Conference on Bioinformatics Research and Development (BIRD’07) (Sepp Hochreiter, Roland Wagner, eds.), Springer, vol. 4414, Berlin, Germany, March 12-14, pp. 357-370, 2007.
Simon W. Ginzinger,
Volker Heun,
SimShiftDB: Chemical-Shift-Based Homology Modeling, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), Vienna, Austria., 2007.
Simon W. Ginzinger, Fabian Gerick, Murray Coles,
Volker Heun,
CheckShift: Automatic Correction of Inconsistent Chemical Shift Referencing, Journal of Biomolecular NMR, vol. 39, no. 3, pp. 223-227, 2007.
Theses
Alois Huber,
OBMASS: Entwicklung eines linearen Algorithmus zur Berechnung des Bounded Maximum Average Scoring Subsequence Problems, Diploma Thesis, LFE Bioinformatik, LMU München, 2007.
Horst Martin Stühler,
Practical Performance of Preprocessing Schemes for Range Minimum Queries, Diploma Thesis, LFE Bioinformatik, LMU München, 2007.
Johannes Fischer,
Data Structures for Efficient String Algorithms, PhD Thesis, LMU München, 2007.
2006
Papers
Johannes Fischer,
Volker Heun,
Theoretical and Practical Improvements on the RMQ-Problem with Applications to LCA and LCE, Proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching (CPM’06) (Moshe Lewenstein, Gabriel Valiente, eds.), Springer-Verlag, vol. 4009, Barcelona, Spain, July 5-7, 2006, pp. 36-48, 2006.
Johannes Fischer,
Volker Heun, Stefan Kramer,
Optimal String Mining Under Frequency Constraints, Proceedings of the 10th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD’06) (J. Fürnkranz, T. Scheffer, M. Spiliopoulou, eds.), Springer-Verlag, vol. 4213, Berlin, Germany, September 18-22, 2006, pp. 139-150, 2006.
Simon W. Ginzinger,
Johannes Fischer,
SimShift: Identifying structural similarities from NMR chemical shifts, Bioinformatics, vol. 22, no. 4, pp. 460-465, 2006.
Theses
Julia Sellmeier,
Analysis of Available Bioinformatic Tools for Exploration of Microarray Data using Gene Ontology and Design of a Bioinformatic Tool with a Graphical User Interface for Interactive Exploration of Gene Networks Predicted from Microarray Data, Diploma Thesis, LFE Bioinformatik, LMU München, 2006.
Sebastian Bauer,
Vergleich und Visualisierung von Algorithmen zur Konstruktion von Suffix-Arrays anhand sehr langer Texte, Bachelor Thesis, LFE Bioinformatik, LMU München, 2006.
Fabian Gerick,
Identification and Correction of Errors in NMR-Chemical Shift Data, Master Thesis, LFE Bioinformatik, LMU München, 2006.
2005
Papers
Johannes Fischer, Simon W. Ginzinger,
A 2-Approximation Algorithm for Sorting by Prefix Reversals, Proceedings of the 13th Annual European Symposium on Algorithms (ESA’05) (Gerth Stølting Brodal, Stefano Leonardi, eds.), Springer-Verlag, vol. 3669, Mallorca, Spain, October 3-6, 2005, pp. 415-425,, 2005.
Johannes Fischer,
Volker Heun, Stefan Kramer,
Fast Frequent String Mining Using Suffix Arrays, Proceedings of the 5th IEEE International Conference on Data Mining (ICDM’05), IEEE Computer Society, Houston, TX, USA, November 27-30, 2005, pp. 609-612, 2005.
Simon W. Ginzinger,
Johannes Fischer,
SimShift: Identifying Structural Similarities from NMR Chemical Shifts, European Conference on Computational Biology (ECCB05), 2005.
Johannes Fischer,
Volker Heun, Stefan Kramer,
Fast Frequent String Mining Using Suffix Arrays, TUM-I0512, Institut für Informatik der Technischen Universität München, no. TUM-I0512, 2005.
Theses
Alexander Kohn,
Quantitative Analyse von Protein-Massenspektren, Diploma Thesis, LFE Bioinformatik, LMU München, 2005.
2003
Papers
Volker Heun,
Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices, Discrete Applied Mathematics, vol. 127, no. 1, pp. 163-177, 2003.
Volker Heun,
Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices, Computational Molecular Biology (S. Istrail, P. Pevzner, R. Shamir, eds.), North Holland, vol. 12, 2003.
Books
Werner Mewes, Dmitrij Frishman,
Volker Heun, Stefan Kramer,
Proceedings of the German Conference on Bioinformatics, GCB 2003 (Neuherberg and Garching, Germany, October 12-14, 2003), belleville Verlag München, 2003.
Volker Heun,
Grundlegende Algorithmen - Einführung in den Entwurf und die Analyse effizienter Algorithmen, Vieweg Verlag, 2003.
