Research Groups

German Tischler

Research Interests

  • algorithms on strings (full text  indexing, pattern matching)
  • algorithms in bio-informatics (assembly and mapping)

Software

Curriculum vitae

Education

8/2002 - 7/2008
PhD (Dr rer nat) in Computer Science, University of Würzburg, Germany, supervised by Prof. Dr. Jürgen Albert (Thesis: Theory and Applications of Parametric Weighted Finite Automata)
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10/1997-7/2002
Diploma in Computer Science University of Würzburg, Germany

Positions previously held

8/2014-4/2015
Staff scientist at the Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
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8/2011-7/2014
Postdoctoral Fellow at the Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK with Dr. Zemin Ning
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8/2008-2/2009 and 3/2011-8/2011
Akademischer Rat at the Department of Computer Science, University of Würzburg, Germany
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Postdoctoral Fellow at King's College London, Department of Computer Science with Prof. Dr. Maxime Crochemore (Newton International Fellowship)
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8/2002-8/2008
Wissenschaftlicher Mitarbeiter at the Department of Computer Science, University of Würzburg, Germany 

Selected publications

Articles in peer reviewed journals:

German Tischler: Faster Average Case Low Memory Semi-External Construction of the Burrows-Wheeler Transform, Mathematics in Computer Science, accepted

German Tischler, Steven Leonard: biobambam: tools for read pair collation based algorithms on BAM files Source Code for Biology and Medicine, 9/13, June 2014

Tomas Flouri, Kimon Frousios, Costas S. Iliopoulos, Kunsoo Park, Solon P. Pissis, German Tischler: GapMis: a Tool for Pairwise Sequence Alignment with a Single Gap (Recent Patents on DNA & Gene Sequences 7/2 (12), 84-95, 2013)

Kimon Frousios, Costas S. Iliopoulos, German Tischler, Sophia Kossida, Solon P. Pissis, Stilianos Arhondakis: Transcriptome map of mouse isochores in embryonic and neonatal cortex (Genomics 101/2, pp. 120-124, 2013)

Joseph Henson, German Tischler, Zemin Ning: Next-generation sequencing and large genome assemblies (Pharmacogenomics 13/8, pp. 901-915, 2012)

Tomas Flouri, Costas S. Iliopoulos, Solon P. Pissis, German Tischler: Mapping Short Reads to a Genomic Sequence with Circular Structure (International Journal of Systems Biology and Biomedical Technologies 1/1, pp. 26-34, 2012)

Maxime Crochemore, Costas S. Iliopoulos, Marcin Kubica, M. Sohel Rahman, German Tischler, Tomasz Walen: Improved algorithms for the range next value problem and applications (Theoretical Computer Science 434, pp. 23-34, 2012)

Anisa Al-Hafeedh, Maxime Crochemore, Lucian Ilie, Evguenia Kopylova, William F. Smyth, German Tischler, Munina Yusufu: A comparison of Lempel-Ziv factorization algorithms (ACM Computing Surveys 45/1, 5, 2012)

Stilianos Arhondakis, Kimon Frousios, Costas S. Iliopoulos, Solon Pissis, German Tischler, Sophia Kossida: Transcriptome map of mouse isochores (BMC Genomics 12/1, pp. 511, 2011)

Maxime Crochemore, German Tischler: Computing Longest Previous non-overlapping Factors (Information Processing Letters 111/6, pp.~291-295, 2011)

German Tischler, Jürgen Wolff von Gudenberg: Solving Decidability Problems with Interval Arithmetic (Reliable Computing 15, 279-289, 2011)

Marc Ebner, German Tischler, Jürgen Albert: Integrating Color Constancy Into JPEG 2000 (IEEE Transactions on Image Processing 16/11, pp. 2697-2706, 2007)

Michael Lerch, German Tischler, Jürgen Wolff von Gudenberg, Werner Hofschuster, Walter Krämer: FILIB++, A Fast Interval Library Supporting Containment Computations (ACM Transactions on Mathematical Software 32/2, pp. 299-324, 2006)

Articles in conference proceedings:

German Tischler: Faster Average Case Low Memory Semi-External Construction of the Burrows-Wheeler Transform (in Alessio Langiu, Costas Iliopoulos (editors): Proceedings of the 2nd International Conference on Algorithms for Big Data (ICABD 2014), CEUR-WS Proceedings 1146, pp. 61-68, 2014)

Juha Käarkkäinen, German Tischler: Near in Place Linear Time Minimum Redundancy Coding (in Ali Bilgin, Michael W. Marcellin, Joan Serri-Sagrista, James A. Storer (editors): Data Compression Conference (DCC) 2013, IEEE, pp. 411-420, 2013)

Luis M. S. Russo, German Tischler: Succinct Gapped Suffix Arrays (in Roberto Grossi, Fabrizio Sebastiani, Fabrizio Silvestri (editors): 18th International Symposium on String Processing and Information Retrieval (SPIRE 2011), Springer-Verlag, Lecture Notes in Computer Science 7024, pp. 290-294, 2011)

German Tischler: On Wavelet Tree Construction (in Raffaele Giancarlo, Giovanni Manzini (editors): 22nd Annual Symposium on Combinatorial Pattern Matching (CPM 2011), Springer-Verlag, Lecture Notes in Computer Science 6661, pp. 208--218, 2011)

Maxime Crochemore, German Tischler: The Gapped Suffix Array: a New Index Structure for Fast Approximate Matching (in Edgar Chavez, Stefano Lonardi (editors): 17th International Symposium on String Processing and Information Retrieval (SPIRE 2010), Springer-Verlag, Lecture Notes in Computer Science 6393, pp. 359-364, 2010)

Maxime Crochemore, Costas S. Iliopoulos, Solon P. Pissis, German Tischler: Cover array string reconstruction (in Amihood Amir and Laxmi Parida (editors): Proceedings of the 21st Annual Symposium on Combinatorial Pattern Matching (CPM 2010), Springer-Verlag, Lecture Notes in Computer Science 6129, pp. 251-259, 2010)

Kimon Frousios, Costas S. Iliopoulos, Laurent Mouchard, Solon P. Pissis, German Tischler: REAL: An efficient REad ALigner for next generation sequencing reads (in Aidong Zhang, Mark Borodovsky, Gultekin Özsoyoglu, Armin R. Mikler (editors): Proceedings of the 1st ACM International Conference on Bioinformatics and Computational Biology (ACM BCB 2010), Association of Computing Machinery, pp. 154-159, 2010)

Costas S. Iliopoulos, T. A. Okanlawon, Solon P. Pissis, German Tischler: Mapping short reads to a genomic sequence with circular structure (in 10th IEEE International Conference on Information Technology and Applications in Biomedicine (ITAB 2010), IEEE, pp. 1-4, 2010)