Forschungsgruppe Algorithmische Bioinformatik

The research group for Algorithmic Bioinformatics was established in April 2003 and is part of the Teaching and Research Unit for Practical Computer Science and Bioinformatics at the Institute for Informatics of the Ludwig-Maximilians-Universität München.
The research group for Algorithmic Bioinformatics was funded by the by the German Research Foundation (DFG, Bioinformatics Initiative) in the period 2003-2008.

People

Volker Heun

Alumni

Teaching

cf. Teaching Overview

Research

cf. Research Overview of the TRU Bioinformatik

Publications

2015

Papers

Benjamin Albrecht. Computing all hybridization networks for multiple binary phylogenetic input trees. BMC Bioinformatics, vol 16, no. 236, pp. 439-441, July 2015.

DOI
http://www.biomedcentral.com/1471-2105/16/236

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Theses

Katharina Schmid. Efficient Construction of de Bruijn Graphs Using Suffix Arrays. Bachelor Thesis, LFE Bioinformatik / LMU München, September 2015.

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2014

Papers

Benjamin Albrecht. Computing Hybridization Networks for Multiple Rooted Binary Phylogenetic Trees by Maximum Acyclic Agreement Forests. arXiv:1408.3044, 2014.

arxiv

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Theses

Laura Schiller. Efficient computation of hybridization networks. Master Thesis, LFE Bioinformatik / LMU München, June 2014.

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Matthias Danner. Implementierung und Evaluierung einer fehlertoleranten Textsuche basierend auf Suffix-Arrays. Bachelor Thesis, LFE Bioinformatik / LMU München, November 2014.

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2012

Papers

Benjamin Albrecht, Volker Heun. Space Efficient Modifications to Structator - a Fast Index-Based Search Tool for RNA Sequence-Structure Patterns. Ralf Klasing (ed.): Proceedings of the 11th International Symposium on Experimental Algorithms (SEA 2012), Bordeaux, France, June 7-9, 2012, Lecture Notes in Computer Science, vol 7276, pp. 27-38, Springer Verlag, 2012.

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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.

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2010

Papers

Johannes Fischer, Volker Heun. Finding Range Minima in the Middle: Approximations and Applications. Mathematics in Computer Science, vol 3, no. 1, pp. 17-30, March 2010.

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Johannes Fischer, Volker Heun. Range Median of Minima Queries, Super-Cartesian Trees, and Text Indexing. Mirka Miller, Koichi Wada (eds.): Proceedings of the International Workshop on Combinatorial Algorithms (IWOCA'08), September 13-15, 2008, Nagoya, Japan, Texts in Algorithmics, vol 12, pp. 239-252, College Publications, January 2010.

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Theses

Markus Meier. Visualisierung von Repeats im Genom. Bachelor Thesis, LFE Bioinformatik, LMU München, November 2010.

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2009

Papers

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, March 2009.

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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, August 2009.

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Luca Chiarabini. Automatic Synthesis of an Efficient Algorithm for the Similarity of Strings Problem. H. Saidi, N. Shankar (eds.): Proceedings of the 4th Workshop on Automated Formal Methods (AFM'09), Grenoble, France, June 27, 2009, pp. 23-30, 2009.

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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.

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Theses

Jeremias Weihmann. Genome-Rearrangements: Sortieren mit erweiterten Transreversals. Diploma Thesis, LFE Bioinformatik / LMU München, August 2009.

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Luca Chiarabini. Program Development by Proof Transformation. PhD Thesis, LMU München, December 2009.

E-Dissertation

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2008

Papers

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.

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Johannes Fischer, Volker Heun, Horst Martin Stühler. Practical Entropy-Bounded Schemes for O(1)-Range Minimum Queries. J.A. Storer, M.W. Marcellin (eds.): Proceedings of the 2008 Data Compression Conference (DCC'08), Snowbird, Utah, U.S.A., March 25-27, 2008, pp. 272-281, IEEE Computer Society, 2008.

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Johannes Fischer, Volker Heun. Range Median of Minima Queries, Super-Cartesian Trees, and Text Indexing. Mirka Miller, Koichi Wada (eds.): Local Proceedings of the 19th International Workshop on Combinatorial Algorithms (IWOCA'08), Nagoya, Japan, September 13-15, 2008, pp. 239-252, 2008.

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Luca Chiarabini. Extraction of Efficient Programs from Proofs: The Case of Structural Induction over Natural Numbers. A. Beckmann, C. Dimitracopoulos, B. Löwe (eds.): Local Proceedings of the Fourth Conference on Computability in Europe: Logic and Theory of Algorithms (CiE'08), Athens, Greece, June 15-20, 2008, pp. 64-76, 2008.

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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, Short Talk, 2008.

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Theses

Simon W. Ginzinger. Bioinformatics Methods for NMR Chemical Shift Data. PhD Thesis, LMU München, February 2008.

E-Dissertation

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Marko Skocibusic. Improving CheckShift. Diploma Thesis, LFE Bioinformatik, LMU München, June 2008.

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Annabelle Teresa Klarl. Konstruktion und Anwendung von Affixarrays. Bachelor Thesis, LFE Bioinformatik, LMU München, August 2008.

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2007

Papers

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, September 2007.

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Simon W. Ginzinger, Thomas Gräupl, Volker Heun. SimShiftDB: Chemical-Shift-Based Homology Modeling. Sepp Hochreiter, Roland Wagner (eds.): Proceedings of the First International Conference on Bioinformatics Research and Development (BIRD'07), Berlin, Germany, March 12-14, Lecture Notes in Bioinformatics, vol 4414, pp. 357-370, Springer, 2007.

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Johannes Fischer, Volker Heun. A New Succinct Representation of RMQ-Information and Improvements in the Enhanced Suffix Array. Bo Chen, Mike Paterson, Guochuan Zhang (eds.): Proceedings of the International Symposium on Combinatorics, Algorithms, Probabilistic and Experimental Methodologies (ESCAPE'07), Hangzhou, China, April 7-9, 2007, Lecture Notes in Computer Science, vol 4614, pp. 459-470, Springer-Verlag, 2007.

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Paolo Ferragina, Johannes Fischer. Suffix Arrays on Words. Bin Ma, Kaizhong Zhang (eds.): Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM'07), London, Ontario, July 9-11, 2007, Lecture Notes in Computer Science, vol 4580, pp. 328-339, Springer-Verlag, 2007.

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Amihood Amir, Johannes Fischer, Moshe Lewenstein. Two-Dimensional Range Minimum Queries. Bin Ma, Kaizhong Zhang (eds.): Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM'07),, London, Ontario, July 9-11, 2007, Lecture Notes in Computer Science, vol 4580, pp. 286-294, Springer-Verlag, 2007.

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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., PLoS Track Talk and Poster, 2007.

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Theses

Alois Huber. OBMASS: Entwicklung eines linearen Algorithmus zur Berechnung des Bounded Maximum Average Scoring Subsequence Problems. Diploma Thesis, LFE Bioinformatik, LMU München, January 2007.

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Horst Martin Stühler. Practical Performance of Preprocessing Schemes for Range Minimum Queries. Diploma Thesis, LFE Bioinformatik, LMU München, October 2007.

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Johannes Fischer. Data Structures for Efficient String Algorithms. PhD Thesis, LMU München, October 2007.

E-Dissertation

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2006

Papers

Simon W. Ginzinger, Johannes Fischer. SimShift: Identifying structural similarities from NMR chemical shifts. Bioinformatics, vol 22, no. 4, pp. 460-465, 2006.

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Johannes Fischer, Volker Heun. Theoretical and Practical Improvements on the RMQ-Problem with Applications to LCA and LCE. Moshe Lewenstein, Gabriel Valiente (eds.): Proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching (CPM'06), Barcelona, Spain, July 5-7, 2006, Lecture Notes in Computer Science, vol 4009, pp. 36-48, Springer-Verlag, 2006.

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Johannes Fischer, Volker Heun, Stefan Kramer. Optimal String Mining Under Frequency Constraints. J. Fürnkranz, T. Scheffer, M. Spiliopoulou (eds.): Proceedings of the 10th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD'06), Berlin, Germany, September 18-22, 2006, Lecture Notes in Computer Science, vol 4213, pp. 139-150, Springer-Verlag, 2006.

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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, May 2006.

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Sebastian Bauer. Vergleich und Visualisierung von Algorithmen zur Konstruktion von Suffix-Arrays anhand sehr langer Texte. Bachelor Thesis, LFE Bioinformatik, LMU München, May 2006.

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Fabian Gerick. Identification and Correction of Errors in NMR-Chemical Shift Data. Master Thesis, LFE Bioinformatik, LMU München, June 2006.

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2005

Papers

Johannes Fischer, Volker Heun, Stefan Kramer. Fast Frequent String Mining Using Suffix Arrays. Technical Report, no. TUM-I0512, Institut für Informatik der Technischen Universität München, November 2005.

tum-i0512.pdf

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Johannes Fischer, Simon W. Ginzinger. A 2-Approximation Algorithm for Sorting by Prefix Reversals. Gerth Stølting Brodal, Stefano Leonardi (eds.): Proceedings of the 13th Annual European Symposium on Algorithms (ESA'05), Mallorca, Spain, October 3-6, 2005, Lecture Notes in Computer Science, vol 3669, pp. 415-425,, Springer-Verlag, 2005.

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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), Houston, TX, USA, November 27-30, 2005, pp. 609-612, IEEE Computer Society, 2005.

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Simon W. Ginzinger, Johannes Fischer. SimShift: Identifying Structural Similarities from NMR Chemical Shifts. European Conference on Computational Biology (ECCB05) , Poster, 2005.

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Theses

Alexander Kohn. Quantitative Analyse von Protein-Massenspektren. Diploma Thesis, LFE Bioinformatik, LMU München, October 2005.

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2003

Papers

Volker Heun. Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices. S. Istrail, P. Pevzner, R. Shamir (eds.): Computational Molecular Biology, Topics in Discrete Mathematics, vol 12, North Holland, 2003.

Link

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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.

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Books

Volker Heun. Grundlegende Algorithmen - Einführung in den Entwurf und die Analyse effizienter Algorithmen. 2nd edition, Vieweg Verlag, May 2003.

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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.

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Conferences

German Conference on Bioinformatics (GCB'03) October 12–14, 2003, Neuherberg/Garching near Munich, Germany
2nd International Conference on High Performance Computing and Communications (HPCC'06), September 13–15, 2006, Munich, Germany
Bioinformatics Munich: From Genomes to Systems Biology, Workshop, November 9–10, 2006, Munich Germany
2nd International Conference on Bioinformatics Research and Development (BIRD'08), July 7–9, 2008, Vienna, Austria
Workshop on Bioinformatics and Biotechnology within the 38th Symposium of the Gesellschaft für Informatik, September 9, 2008, Munich, Germany
1st International Conference on Information Technology in Bio- and Medical Informatics (ITBAM'10), August 30 – September 3, 2010, Bilbao, Spain
2nd International Conference on Information Technology in Bio- and Medical Informatics (ITBAM'11), August 29–September 2, 2011, Bilbao, Spain
German Conference on Bioinformatics (GCB'11), September 7–9, 2011, Weihenstephan/Freising near Munich, Germany
3rd International Conference on Information Technology in Bio- and Medical Informatics (ITBAM'12), September 3–7, 2012, Vienna, Austria
4th International Conference on Information Technology in Bio- and Medical Informatics (ITBAM'13), August 26–30, 2013, Prague, Czech Republic
German Conference on Bioinformatics (GCB'13), September 10–13, 2013, Göttingen, Germany
5th International Conference on Information Technology in Bio- and Medical Informatics (ITBAM'14), September 1–5, 2014, Munich, Germany
German Conference on Bioinformatics (GCB'14), September 28–October 1, 2014, Bielefeld, Germany
6th International Conference on Information Technology in Bio- and Medical Informatics (ITBAM'15), September 3–4, 2015, Valencia, Spain
Studierendenkonferenz Informatik (SKILL 2015) im Rahmen der 45. Jahrestagung der Gesellschaft für Informatik (INFORMATIK 2015), October 1–2, 2015, Cottbus, Germany
7th International Conference on Information Technology in Bio- and Medical Informatics (ITBAM'16), September 5–8, 2016, Porto, Portugal

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