Universität Bielefeld
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Technische Fakultät
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AG Genominformatik
Jens Stoye's Technical Reports
A Space Efficient Representation for Sparse de Bruijn Subgraphs
J. A. A. Quitzau, J. Stoye
Universität Bielefeld,
Forschungsbericht der Technischen Fakultät,
Abteilung Informationstechnik. Report 2008-02, 2008.
(ISSN 0946-7831)
Online Abelian Pattern Matching
T. Ejaz, S. Rahmann, J. Stoye
Universität Bielefeld,
Forschungsbericht der Technischen Fakultät,
Abteilung Informationstechnik. Report 2008-01, 2008.
(ISSN 0946-7831)
On Common Intervals with Errors
C. Chauve, Y. Diekmann, S. Heber, J. Mixtacki, S. Rahmann, J. Stoye
Universität Bielefeld,
Forschungsbericht der Technischen Fakultät,
Abteilung Informationstechnik. Report 2006-02, 2006.
(ISSN 0946-7831)
Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)
M. Sammeth, J. Stoye
Universität Bielefeld,
Forschungsbericht der Technischen Fakultät,
Abteilung Informationstechnik. Report 2005-05, 2005.
(ISSN 0946-7831)
Counting Suffix Arrays and Strings
K.-B. Schürmann, J. Stoye
Universität Bielefeld,
Forschungsbericht der Technischen Fakultät,
Abteilung Informationstechnik. Report 2005-04, 2005.
(ISSN 0946-7831)
Suffix Tree Construction and Storage with Limited Main
Memory
K.-B. Schürmann, J. Stoye
Universität Bielefeld,
Forschungsbericht der Technischen Fakultät,
Abteilung Informationstechnik. Report 2003-06, 2003.
(ISSN 0946-7831)
On the Similarity of Sets of Permutations and its Applications
to Genome Comparison
A. Bergeron, J. Stoye
Universität Bielefeld,
Forschungsbericht der Technischen Fakultät,
Abteilung Informationstechnik. Report 2003-01, 2003.
(ISSN 0946-7831)
Algorithmic Complexity of Protein Identification: Combinatorics of
Weighted Strings
M. Cieliebak, T. Erlebach, Zs. Lipták, J. Stoye, E. Welzl
Technical Report no. 361, ETH Zürich, Dept. of Computer Science,
2001.
Affix Trees
J. Stoye
Diploma thesis.
Universität Bielefeld,
Forschungsbericht der Technischen Fakultät,
Abteilung Informationstechnik. Report 2000-04, 2000.
(ISSN 0946-7831)
English translation. Original title in German:
Affixbäume.
Bielefeld, 1995.
Consistent Equivalence Relations: A Set-Theoretical Framework for
Multiple Sequence Alignment
B. Morgenstern, J. Stoye, A. Dress
Universität Bielefeld,
Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse.
Materialien/Preprints 133,
1999.
Finding Maximal Pairs with Bounded Gap
G. S. Brodal, R. B. Lyngsø, C. N. S. Pedersen, J. Stoye
BRICS, Department of Computer Science, University of Aarhus,
Ny Munkegade, 8000 Århus C, Denmark.
Report RS-99-12, 1999.
Linear Time Algorithms for Finding and Representing all the Tandem
Repeats in a String
D. Gusfield, J. Stoye
Department of Computer Science, University of California, Davis.
Report CSE-98-4, 1998.
Simple and Flexible Detection of Contiguous Repeats Using a Suffix
Tree
J. Stoye, D. Gusfield
Department of Computer Science, University of California, Davis.
Report CSE-98-2, 1998.
Rose: Generating Sequence Families
J. Stoye, D. Evers, F. Meyer
Universität Bielefeld,
Forschungsbericht der Technischen Fakultät,
Abteilung Informationstechnik. Report 97-04, 1997.
(ISSN 0946-7831)
FDCA: Fast and Accurate Approximation to Sum-of-Pairs Score Optimal
Multiple Sequence Alignment
S.W. Perrey, J. Stoye, V. Moulton
Universität Bielefeld,
Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse.
Materialien/Preprints 114,
1997.
On the Number of Standard and Effective Multiple Alignments
A. Dress, B. Morgenstern, J. Stoye
Universität Bielefeld,
Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse.
Materialien/Preprints 112,
1997.
On Simultaneous versus Iterative Multiple Sequence
Alignment
S.W. Perrey, J. Stoye, V. Moulton, A.W.M. Dress
Universität Bielefeld,
Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse.
Materialien/Preprints 111,
1997.
Two Applications of the Divide & Conquer Principle in the Molecular
Sciences
G. Brinkmann, A.W.M. Dress, S.W. Perrey, J. Stoye
Universität Bielefeld,
Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse.
Materialien/Preprints 109,
1997.
(Also appeared as: Research Report 151,
University of Canterbury, Christchurch, New Zealand.
Department of Mathematics and Statistics,
March, 1997.)
Divide-and-Conquer Multiple Sequence Alignment
J. Stoye
Dissertation Thesis.
Universität Bielefeld,
Forschungsbericht der Technischen Fakultät,
Abteilung Informationstechnik. Report 97-02, 1997.
(ISSN 0946-7831)
Fast Approximation to the NP-hard Problem of Multiple Sequence
Alignment
S.W. Perrey, J. Stoye
Information and Mathematical Sciences Reports, Series B:96/06.
Dept. of Mathematics, Massey University, Palmerston North, New Zealand.
May, 1996.
(ISSN 1171-7637)
Improving the Divide-and-Conquer Approach to Sum-of-Pairs
Multiple Sequence Alignment
J. Stoye, A.W.M. Dress, S.W. Perrey
Universität Bielefeld,
Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse.
Materialien/Preprints 102,
1996.
A General Method for Fast Multiple Sequence Alignment
U. Tönges, S.W. Perrey, J. Stoye, A.W.M. Dress
Universität Bielefeld,
Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse.
Materialien/Preprints XCIX,
1996.
Posters
Maltcms - an Application Framework for Processing of Metabolomics-Data
N. Hoffmann, M. Wilhelm, M. Keck, A. Döbbe, K. Niehaus, J. Stoye
Presented at
GCB 2009,
Halle/Saale, Germany, September 28-30, 2009.
Sequence Database Search Using Jumping Alignments
C. Bannert, R. Spang, M. Rehmsmeier, J. Stoye
Presented at
GCB 01,
Braunschweig, Germany, October 7-10, 2001.
On the Number of Standard and of Effective Alignments
A.W.M. Dress, B. Morgenstern, J. Stoye
Presented at
RECOMB 98,
New York, NY, USA, March 22-25, 1998.
Generating Benchmarks for Multiple Sequence Alignments and Phylogenetic
Reconstructions
J. Stoye, D. Evers, F. Meyer
Presented at
ISMB 97,
Halkidiki, Greece, June 21-25, 1997.
Divide-and-Conquer Multiple Sequence Alignment
J. Stoye, S.W. Perrey, A.W.M. Dress
Presented at the Winter Seminar on Molecular Biology and Biophysical
Chemistry of the Cell, Klosters, Switzerland, Jan. 11-25, 1997.
Other
Transforming the Mouse Genome into the Human Genome with only 6 Breakpoint Reuses (high-res version)
A. Bergeron, A. Gués, B. Stoye, F. Stoye, J. Stoye, L. Stoye
Animated video with three kids and 281 post-it notes, 2007.
The original photos can be found
here.
Sorting Leaf-Lists in a Tree
C. N. S. Pedersen, J. Stoye
Unpublished manuscript, 1998.
Statistics for Fragment Comparison - A Biologically Motivated Approach
to Sequence Alignment
S.W. Perrey, J. Stoye, A.W.M. Dress
Presented by S.W. Perrey at the German Conference on Bioinformatics,
Braunschweig, 1995.
Affixbäume (in German)
J. Stoye
Diploma thesis, 1995.
Jens Stoye