Volker Heun

E-Mail:	Volker.Heun * at * bio.ifi.lmu.de
Phone:	+49-89-2180-4341
Fax:	+49-89-2180-99-4341
Address:	Binformatics Institut für Informatik, Fakultät 16 Ludwig-Maximilians-Universität München Amalienstr. 17, 80333 Munich, Germany
Office:	A 303 (Front Building, 3rd floor)

Office Hours

*General Office Hours*	Monday 11am-12pm or by appointment
No regular Office Hours on: 05/20 (Pentecost), 06/03

*Student Advisory*	Thursday 2pm-3pm or by appointment
No regular Office Hours on: 05/23, 05/30 (Corpus Christi), 06/06, 06/13

Research

see Research Algorithmic Bioinformatics

Teaching

SS 2013	Algorithmen auf Sequenzen
WS 2012/13	Algorithmische Bioinformatik II
WS 2012/13	Proseminar Bioinformatik
WS 2012/13	Programmierpraktikum Bioinformatik

Teaching Overview

Lecture Notes and Books

Volker Heun: Algorithmische Bioinformatik I & II. Manuscript (in German)
- 1st edition: xii+378, 2002;
- 2nd edition: xii+457, 2006;
- 3rd edition: xii+468, 2009.
- 4th edition: xii+498, 2011.
- 5th edition: xiv+504, 2013.
Volker Heun: Algorithmische Bioinformatik: Bäume und Graphen. Manuscript (in German)
- 1st edition: vi+136, 2003;
- 2nd edition: vi+226, 2004;
- 3rd edition: vi+233, 2006;
- 4th edition: viii+241, 2009.
- 5th edition: viii+~250, 2011.
Volker Heun: Algorithmen auf Sequenzen. Manuscript (in German)
- 1st edition: x+272 2005;
- 2nd edition: x+294, 2007;
- 3rd edition: x+308, 2008.
- 4th edition: x+316, 2010.
Volker Heun: Efficient Embeddings of Treelike Graphs into Hypercubes, Reihe Informatik, Shaker-Verlag, Aachen, ISBN 978-3-8265-1901-7, 1996. [Link]
Volker Heun: Grundlegende Algorithmen — Einführung in den Entwurf und die Analyse effizienter Algorithmen, Vieweg Verlag,
- 1st edition: xii+346, ISBN 978-3-528-03140-9, 2000. [Link]
- 2nd edition xiv+370, ISBN 978-3-528-13140-1, 2003. [Link]

Publications

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.

BibTex

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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2009

Papers

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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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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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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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.

BibTex

2006

Papers

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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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, 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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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

BibTex

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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Volker Heun, Ernst W. Mayr. Efficient Embeddings into Hypercube-Like Topologies. The Computer Journal, vol 46, no. 6, pp. 632-644, 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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2002

Papers

Volker Heun, Ernst W. Mayr. Embedding Graphs with Bounded Treewidth into Optimal Hypercubes. Journal of Algorithms, vol 43, no. 1, pp. 51-84, 2002.

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Volker Heun, Ernst W. Mayr. Efficient Dynamic Embeddings of Arbitrary Binary Trees into Hypercubes. Journal of Algorithms, vol 43, no. 1, pp. 51-84, 2002.

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Jens Ernst, Volker Heun, Ulrich Voll. Generalized Clustering of Gene Expression Profiles - A Spectral Approach. Proceedings of the International Conference of Bioinformatics (INCOB'02), Bangkok, Thailand, February 06-08, 2002, 2002.

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2001

Papers

Volker Heun, Ernst W. Mayr. Optimal Dynamic Embeddings of Complete Binary Trees into Hypercubes. Journal of Parallel and Distributed Computing, vol 61, no. 8, pp. 1110-1125, 2001.

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2000

Books

Volker Heun. Grundlegende Algorithmen - Einführung in den Entwurf und die Analyse effizienter Algorithmen. 1st edition, Vieweg Verlag, 2000.

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1999

Papers

Volker Heun. Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices. Jaroslav Nesetril (ed.): Proceedings of the 7th Annual European Symposium on Algorithms (ESA'99), Prague, Czech Republic, July 16-18, 1999, Lecture Notes in Computer Science, vol 1643, pp. 212-223, Springer-Verlag, 1999.

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1998

Papers

Volker Heun. Effiziente Einbettungen baumartiger Graphen in den Hyperwürfel. W. Bibel, H. Fiedler, W. Grass, P. Gorny, G. Hotz, I. Kerner, R. Reischuk, F. Roithmayr (eds.): Ausgezeichnete Informatikdissertationen 1996 / im Auftrag der Gesellschaft für Informatik e.V. herausgegeben durch den Nominierungsausschuß, pp. 29-45, Teubner-Verlag, 1998.

Teubner

BibTex

Volker Heun, Wolfgang Merkle, Ulrich Weigand. Proving the PCP-Theorem. Ernst W. Mayr, Angelika Stager, Hans Jürgen Prömel (eds.): Lectures on Proof Verification and Approximation Algorithms, Lecture Notes in Computer Science, vol 1367, pp. 83-160, Springer-Verlag, 1998.

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Volker Heun, Ernst W. Mayr. Optimal Dynamic Embeddings of Complete Binary Trees into Hypercubes. Technical Report, no. ICSI-TR-98-022, International Computer Science Institute, Berkeley, CA, August 1998.

icsi-tr-98-022.pdf

BibTex

Volker Heun, Ernst W. Mayr. Efficient Dynamic Embeddings of Arbitrary Binary Trees into Hypercubes. Technical Report, no. ICSI-TR-98-023, International Computer Science Institute, Berkeley, CA, August 1998.

icsi-tr-98-023.pdf

BibTex

Volker Heun. Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices. Technical Report, no. ICSI-TR-98-029, International Computer Science Institute, Berkeley, CA, December 1998.

icsi-tr-98-029.pdf

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1997

Papers

Volker Heun, Ernst W. Mayr. Optimal Dynamic Edge-Disjoint Embeddings of Complete Binary Trees into Hypercubes. Friedel Hoßfeld, Erik Maehle, Ernst W. Mayr (eds.): Proceedings of the 4th International Workshop on Parallel Systems and Algorithms (PASA'96), Jülich, Germany, April 10-12, 1996, pp. 195-209, World Scientific Publishing, 1997.

BibTex

1996

Papers

Volker Heun, Ernst W. Mayr. A New Efficient Algorithm for Embedding an Arbitrary Binary Tree into Its Optimal Hypercube. Journal of Algorithms, vol 20, no. 2, pp. 375-399, 1996.

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Volker Heun, Ernst W. Mayr. Embedding Graphs with Bounded Treewidth into Optimal Hypercubes. Ernst W. Mayr, Claude Puech (eds.): Proceedings of the 13th Annual Symposium on Theoretical Aspects of Computer Science (STACS'96), Grenoble, France, February 22-24, 1996, Lecture Notes in Computer Science , vol 1046, pp. 157-168, Springer-Verlag, 1996.

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Volker Heun, Ernst W. Mayr. Efficient Dynamic Embeddings of Arbitrary Binary Trees into Hypercubes. Afonso Ferreira, José D.P. Rolim, Yousef Saad, Tao Yang (eds.): Proceedings of the 3rd International Workshop on Parallel Algorithms for Irregularly Structured Problems (IRREGULAR'96), Santa Barbara, CA, USA, August 19-21, 1996, Lecture Notes in Computer Science, vol 1117, pp. 287-298, Springer-Verlag, 1996.

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Volker Heun, Ernst W. Mayr. A General Method for Efficient Embeddings of Graphs into Optimal Hypercubes (Distinguished Paper). Luc Bougé, Pierre Fraigniaud, Anne Mignotte, Yves Robert (eds.): Proceedings of the 2nd International Euro-Par Conference on Parallel Processing (Euro-Par'96), Lyon, France, August 26-29, 1996, Lecture Notes in Computer Science, vol 1123, pp. 222-233, Springer-Verlag, 1996.

BibTex

Volker Heun, Ernst W. Mayr. Optimal Dynamic Edge-Disjoint Embeddings of Complete Binary Trees into Hypercubes. Technical Report, no. TUM-I9607, Institut für Informatik der Technischen Universität München, January 1996.

tum-i9607.pdf

BibTex

Books

Volker Heun. Efficient Embeddings of Treelike Graphs into Hypercubes. Reihe Informatik, Shaker-Verlag, Aachen, 1996.

Link

BibTex

1995

Papers

Volker Heun, Ernst W. Mayr. Embedding Graphs with Bounded Treewidth into Optimal Hypercubes. Technical Report, no. TUM-I9539 , Institut für Informatik der Technischen Universität München, December 1995.

tum-i9539.pdf

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1993

Papers

Volker Heun, Ernst W. Mayr. A New Efficient Algorithm for Embedding an Arbitrary Binary Tree into Its Optimal Hypercube. Technical Report, no. TUM-I9321, Institut für Informatik der TU München, 1993.

tum-i9321.pdf

BibTex

Volker Heun, Ernst W. Mayr. A New Efficient Algorithm for Embedding an Arbitrary Binary Tree into Its Optimal Hypercube. Proceedings of the 3rd Workshop on Parallel Systems and Algorithms (PASA'93), Bonn, Germany, April 1-2, 1993, Mitteilungen - Gesellschaft für Informatik e.V., Parallel-Algorithmen und Rechnerstrukturen, ISSN 0177-0454, vol 11, pp. 7-11, Gesellschaft für Informatik e.V., 1993.

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Supervised PhDs

2009

Theses

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

E-Dissertation

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2008

Theses

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

E-Dissertation

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2007

Theses

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

E-Dissertation

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Open Postions

Within the DFG-funded International Research Training Group Regulation and Evolution of Cellular Systems (RECESS) there are still PhD scholarships available. Applicants for these positions need to have the equivalent of the German University Diploma (e.g., M.Sc.) in Bioinformatics, Computer Science or Mathematics. We are looking in particular for candidates with a strong background in algorithmics, graph theory, and network theory. For more information about RCESESS please visit the RECESS Web-site. For application please visit the application server.

Short Curriculum Vitae

1984–1991	Studies of Computer Science and Mathematics Johann Wolfgang Goethe-Universität Frankfurt
1991–1993	Research Assistant (Wiss. Angestellter) Computer Science Department Johann Wolfgang Goethe-Universität Frankfurt
1993–1996	Research Assistant (Wiss. Angestellter) Computer Science Department Technische Universität München
1996	Doctorate at the Computer Science Department Technische Universität München
1996–2003	Research Associate (Wiss. Assistent) Computer Science Department Technische Universität München
1997–1998	Research Fellow at the International Computer Science Institute University of California at Berkeley
2001	Assistant Professor (Wiss. Oberassistent) Department of Mathematics and Computer Science Universität Passau
2003–	Associate Professor of Bioinformatics Fakultät für Mathematik, Informatik und Statistik Ludwig-Maximilians-Universität München
2004–2007	Vice Dean Fakultät für Mathematik, Informatik und Statistik Ludwig-Maximilians-Universität München
2011–	Dean Fakultät für Mathematik, Informatik und Statistik Ludwig-Maximilians-Universität München

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