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Jens Stoye
2010 – today
- 2013
[j52]Christina Ander, Ole Schulz-Trieglaff, Jens Stoye, Anthony J. Cox: metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. BMC Bioinformatics 14(S-5): S2 (2013)- 2012
- [j51]Rolf Hilker, Corinna Sickinger, Christian N. S. Pedersen, Jens Stoye: UniMoG - a unifying framework for genomic distance calculation and sorting based on DCJ. Bioinformatics 28(19): 2509-2511 (2012)
- [j50]Nils Hoffmann, Matthias Keck, Heiko Neuweger, Mathias Wilhelm, Petra Högy, Karsten Niehaus, Jens Stoye: Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinformatics 13: 214 (2012)
- [j49]Daniel Doerr, Annelyse Thévenin, Jens Stoye: Gene family assignment-free comparative genomics. BMC Bioinformatics 13(S-19): S3 (2012)
- [j48]Katharina Jahn, Henner Sudek, Jens Stoye: Multiple genome comparison based on overlap regions of pairwise local alignments. BMC Bioinformatics 13(S-19): S7 (2012)
- [e3]Juha Kärkkäinen, Jens Stoye (Eds.): Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Helsinki, Finland, July 3-5, 2012. Proceedings. Lecture Notes in Computer Science 7354, Springer 2012, ISBN 978-3-642-31264-9
- 2011
- [j47]Steffen Heber, Richard Mayr, Jens Stoye: Common Intervals of Multiple Permutations. Algorithmica 60(2): 175-206 (2011)
- [j46]Péter L. Erdös, Lajos Soukup, Jens Stoye: Balanced vertices in trees and a simpler algorithm to compute the genomic distance. Appl. Math. Lett. 24(1): 82-86 (2011)
- [j45]Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jörn Kalinowski, Jens Stoye, Alexander Goesmann: Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics 27(10): 1351-1358 (2011)
- [j44]Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker: Swiftly Computing Center Strings. BMC Bioinformatics 12: 106 (2011)
- [j43]Marília D. V. Braga, Raphael Machado, Leonardo C. Ribeiro, Jens Stoye: On the weight of indels in genomic distances. BMC Bioinformatics 12(S-9): S13 (2011)
- [j42]Marília D. V. Braga, Raphael Machado, Leonardo C. Ribeiro, Jens Stoye: Genomic distance under gene substitutions. BMC Bioinformatics 12(S-9): S8 (2011)
- [j41]Roland Wittler, Ján Manuch, Murray Patterson, Jens Stoye: Consistency of Sequence-Based Gene Clusters. Journal of Computational Biology 18(9): 1023-1039 (2011)
- [j40]Marília D. V. Braga, Eyla Willing, Jens Stoye: Double Cut and Join with Insertions and Deletions. Journal of Computational Biology 18(9): 1167-1184 (2011)
- [j39]Jakub Kovác, Robert Warren, Marília D. V. Braga, Jens Stoye: Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation. Journal of Computational Biology 18(9): 1231-1241 (2011)
- 2010
- [j38]Peter Husemann, Jens Stoye: Phylogenetic comparative assembly. Algorithms for Molecular Biology 5: 3 (2010)
- [j37]Peter Husemann, Jens Stoye: r2cat: synteny plots and comparative assembly. Bioinformatics 26(4): 570-571 (2010)
- [j36]Marília D. V. Braga, Jens Stoye: The Solution Space of Sorting by DCJ. Journal of Computational Biology 17(9): 1145-1165 (2010)
- [j35]Guillaume Blin, David Faye, Jens Stoye: Finding Nested Common Intervals Efficiently. Journal of Computational Biology 17(9): 1183-1194 (2010)
- [j34]Anne Bergeron, Paul Medvedev, Jens Stoye: Rearrangement Models and Single-Cut Operations. Journal of Computational Biology 17(9): 1213-1225 (2010)
- [c42]Søren Besenbacher, Benno Schwikowski, Jens Stoye: Indexing and Searching a Mass Spectrometry Database. Algorithms and Applications 2010: 62-76
- [c41]
- [c40]Jakub Kovác, Marília D. V. Braga, Jens Stoye: The Problem of Chromosome Reincorporation in DCJ Sorting and Halving. RECOMB-CG 2010: 13-24
- [c39]
- [c38]Marília D. V. Braga, Eyla Willing, Jens Stoye: Genomic Distance with DCJ and Indels. WABI 2010: 90-101
- [c37]Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker: Swiftly Computing Center Strings. WABI 2010: 325-336
- [i1]Péter L. Erdös, Lajos Soukup, Jens Stoye: Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance. CoRR abs/1004.2735 (2010)
2000 – 2009
- 2009
- [j33]Nils Hoffmann, Jens Stoye: ChromA: signal-based retention time alignment for chromatography-mass spectrometry data. Bioinformatics 25(16): 2080-2081 (2009)
- [j32]Michael Brudno, Paul Medvedev, Jens Stoye, Francisco M. de la Vega: A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). Bioinformatics 25(21): 2863-2864 (2009)
- [j31]Wolfgang Gerlach, Sebastian Jünemann, Felix Tille, Alexander Goesmann, Jens Stoye: WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics 10: 430 (2009)
- [j30]Katharina Jahn, Jens Stoye: Approximative Gencluster und ihre Anwendung in der komparativen Genomik. Informatik Spektrum 32(4): 288-300 (2009)
- [j29]Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye: Computation of Median Gene Clusters. Journal of Computational Biology 16(8): 1085-1099 (2009)
- [j28]Jens Stoye, Roland Wittler: A Unified Approach for Reconstructing Ancient Gene Clusters. IEEE/ACM Trans. Comput. Biology Bioinform. 6(3): 387-400 (2009)
- [j27]Anne Bergeron, Julia Mixtacki, Jens Stoye: A new linear time algorithm to compute the genomic distance via the double cut and join distance. Theor. Comput. Sci. 410(51): 5300-5316 (2009)
- [c36]
- [c35]
- [c34]
- [c33]
- 2008
- [j26]Heiko Neuweger, Stefan P. Albaum, Michael Dondrup, Marcus Persicke, Tony Watt, Karsten Niehaus, Jens Stoye, Alexander Goesmann: MeltDB: a software platform for the analysis and integration of metabolomics experiment data. Bioinformatics 24(23): 2726-2732 (2008)
- [j25]Sebastian Oehm, David Gilbert, Andreas Tauch, Jens Stoye, Alexander Goesmann: Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic Acids Research 36(Web-Server-Issue): 433-437 (2008)
- [j24]Klaus-Bernd Schürmann, Jens Stoye: Counting suffix arrays and strings. Theor. Comput. Sci. 395(2-3): 220-234 (2008)
- [c32]Anne Bergeron, Julia Mixtacki, Jens Stoye: HP Distance Via Double Cut and Join Distance. CPM 2008: 56-68
- [c31]Anne Bergeron, Julia Mixtacki, Jens Stoye: On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios. RECOMB-CG 2008: 226-240
- [c30]Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye: Computation of Median Gene Clusters. RECOMB 2008: 331-345
- [c29]José Augusto Amgarten Quitzau, Jens Stoye: Detecting Repeat Families in Incompletely Sequenced Genomes. WABI 2008: 342-353
- [r1]
- 2007
- [j23]Gilles Didier, Thomas Schmidt, Jens Stoye, Dekel Tsur: Character sets of strings. J. Discrete Algorithms 5(2): 330-340 (2007)
- [j22]Klaus-Bernd Schürmann, Jens Stoye: An incomplex algorithm for fast suffix array construction. Softw., Pract. Exper. 37(3): 309-329 (2007)
- 2006
- [j21]Michael Sammeth, Thasso Griebel, Felix Tille, Jens Stoye: Panta rhei (QAlign2): an open graphical environment for sequence analysis. Bioinformatics 22(7): 889-890 (2006)
- [j20]Kim R. Rasmussen, Jens Stoye, Eugene W. Myers: Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length. Journal of Computational Biology 13(2): 296-308 (2006)
- [j19]Anne Bergeron, Julia Mixtacki, Jens Stoye: On Sorting by Translocations. Journal of Computational Biology 13(2): 567-578 (2006)
- [j18]Anne Bergeron, Jens Stoye: On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. Journal of Computational Biology 13(7): 1340-1354 (2006)
- [j17]Michael Sammeth, Jens Stoye: Comparing Tandem Repeats with Duplications and Excisions of Variable Degree. IEEE/ACM Trans. Comput. Biology Bioinform. 3(4): 395-407 (2006)
- [c28]Lutz Krause, Naryttza N. Diaz, Daniela Bartels, Robert A. Edwards, Alfred Pühler, Forest Rohwer, Folker Meyer, Jens Stoye: Finding novel genes in bacterial communities isolated from the environment. ISMB (Supplement of Bioinformatics) 2006: 281-289
- [c27]Anne Bergeron, Julia Mixtacki, Jens Stoye: A Unifying View of Genome Rearrangements. WABI 2006: 163-173
- 2005
- [j16]Daniela Bartels, Sebastian Kespohl, Stefan P. Albaum, Tanja Drüke, Alexander Goesmann, Julia Herold, Olaf Kaiser, Alfred Pühler, Friedhelm Pfeiffer, Günter Raddatz, Jens Stoye, Folker Meyer, Stephan C. Schuster: BACCardI-a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics 21(7): 853-859 (2005)
- [j15]Antje Krause, Jens Stoye, Martin Vingron: Large scale hierarchical clustering of protein sequences. BMC Bioinformatics 6: 15 (2005)
- [c26]Klaus-Bernd Schürmann, Jens Stoye: An Incomplex Algorithm for Fast Suffix Array Construction. ALENEX/ANALCO 2005: 78-85
- [c25]Constantin Bannert, Jens Stoye: Protein Annotation by Secondary Structure Based Alignments (PASSTA). CompLife 2005: 79-90
- [c24]Kim R. Rasmussen, Jens Stoye, Eugene W. Myers: Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length. RECOMB 2005: 189-203
- [c23]
- [c22]
- [c21]Michael Sammeth, Thomas Weniger, Dag Harmsen, Jens Stoye: Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). WABI 2005: 276-290
- 2004
- [j14]Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen: Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 5: 6 (2004)
- [j13]Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen: Correction: Benchmarking tools for the alignment of functional noncodingDNA. BMC Bioinformatics 5: 73 (2004)
- [j12]Mark Cieliebak, Thomas Erlebach, Zsuzsanna Lipták, Jens Stoye, Emo Welzl: Algorithmic complexity of protein identification: combinatorics of weighted strings. Discrete Applied Mathematics 137(1): 27-46 (2004)
- [j11]Dan Gusfield, Jens Stoye: Linear time algorithms for finding and representing all the tandem repeats in a string. J. Comput. Syst. Sci. 69(4): 525-546 (2004)
- [c20]Thomas Schmidt, Jens Stoye: Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences. CPM 2004: 347-358
- [c19]Anne Bergeron, Julia Mixtacki, Jens Stoye: Reversal Distance without Hurdles and Fortresses. CPM 2004: 388-399
- [c18]Morris Michael, Christoph Dieterich, Jens Stoye: Suboptimal Local Alignments Across Multiple Scoring Schemes. WABI 2004: 99-110
- [e2]Robert Giegerich, Jens Stoye (Eds.): Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, Germany, October 4-6, 2004. LNI 53, GI 2004, ISBN 3-88579-382-2
- 2003
- [j10]Michael Sammeth, Jörg Rothgänger, W. Esser, Jürgen Albert, Jens Stoye, Dag Harmsen: Digital extractor: analysis of digital differential display output. Bioinformatics 19(12): 1592-1593 (2003)
- [j9]Robert Giegerich, Stefan Kurtz, Jens Stoye: Efficient implementation of lazy suffix trees. Softw., Pract. Exper. 33(11): 1035-1049 (2003)
- [c17]Anne Bergeron, Jens Stoye: On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. COCOON 2003: 68-79
- [c16]Michael Sammeth, Burkhard Morgenstern, Jens Stoye: Divide-and-conquer multiple alignment with segment-based constraints. ECCB 2003: 189-195
- [c15]Constantin Bannert, Jens Stoye: Evaluation of the Jumping Alignment algorithm with artificial and biological data. German Conference on Bioinformatics 2003: 21-25
- 2002
- [j8]Rainer Spang, Marc Rehmsmeier, Jens Stoye: A Novel Approach to Remote Homology Detection: Jumping Alignments. Journal of Computational Biology 9(5): 747-760 (2002)
- [j7]Jens Stoye, Dan Gusfield: Simple and flexible detection of contiguous repeats using a suffix tree. Theor. Comput. Sci. 270(1-2): 843-856 (2002)
- [c14]Anne Bergeron, Steffen Heber, Jens Stoye: Common intervals and sorting by reversals: a marriage of necessity. ECCB 2002: 54-63
- [c13]Jens Stoye: Index Structures for Large Sequence Data: Suffix Trees and Affix Trees. GI Jahrestagung (Ergänzungsband) 2002: 67-71
- [c12]Mark Cieliebak, Thomas Erlebach, Zsuzsanna Lipták, Jens Stoye, Emo Welzl: Algorithmic Complexity of Protein Identification: Searching in Weighted Strings. IFIP TCS 2002: 143-156
- 2001
- [c11]
- [c10]Constantin Bannert, Marc Rehmsmeier, Rainer Spang, Jens Stoye: Sequence Database Search Using Jumping Alignments. German Conference on Bioinformatics 2001: 142
- [c9]
- 2000
- [j6]Knut Reinert, Jens Stoye, Torsten Will: An iterative method for faster sum-of-pairs multiple sequence alignment. Bioinformatics 16(9): 808-814 (2000)
- [j5]Steffen Heber, Jens Stoye, Marcus Frohme, Jörg D. Hoheisel, Martin Vingron: Contig Selection in Physical Mapping. Journal of Computational Biology 7(3-4): 395-408 (2000)
- [j4]Antje Krause, Jens Stoye, Martin Vingron: The SYSTERS protein sequence cluster set. Nucleic Acids Research 28(1): 270-272 (2000)
- [c8]Stefan Kurtz, Enno Ohlebusch, Chris Schleiermacher, Jens Stoye, Robert Giegerich: Computation and Visualization of Degenerate Repeats in Complete Genomes. ISMB 2000: 228-238
- [c7]Rainer Spang, Marc Rehmsmeier, Jens Stoye: Sequence Database Search Using Jumping Alignments. ISMB 2000: 367-375
- [c6]Steffen Heber, Jens Stoye, Jörg D. Hoheisel, Martin Vingron: Contig selection in physical mapping. RECOMB 2000: 155-164
- [e1]Erich Bornberg-Bauer, Ursula Rost, Jens Stoye (Eds.): Proceedings of the German Conference on Bioinformatics (GCB 2000), Heidelberg, October 5-7, 2000. Logos Verlag 2000, ISBN 3-89722-498-4
1990 – 1999
- 1999
- [c5]Gerth Stølting Brodal, Rune B. Lyngsø, Christian N. S. Pedersen, Jens Stoye: Finding Maximal Pairs with Bounded Gap. CPM 1999: 134-149
- [c4]Knut Reinert, Jens Stoye, Torsten Will: Combining Divide-and-Conquer, the A*-Algorithm, and Successive Realignment Approaches to Speed Multiple Sequence Alignment. German Conference on Bioinformatics 1999: 17-24
- [c3]Robert Giegerich, Stefan Kurtz, Jens Stoye: Efficient Implementation of Lazy Suffix Trees. Algorithm Engineering 1999: 30-42
- 1998
- [j3]Jens Stoye, Dirk Evers, Folker Meyer: Rose: generating sequence families. Bioinformatics 14(2): 157-163 (1998)
- [c2]Jens Stoye, Dan Gusfield: Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version). CPM 1998: 140-152
- 1997
- [j2]Jens Stoye, Vincent Moulton, Andreas W. M. Dress: DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment. Computer Applications in the Biosciences 13(6): 625-626 (1997)
- [j1]Gunnar Brinkmann, Andreas W. M. Dress, Sören Perrey, Jens Stoye: Two applications of the Divide&Conquer principle in the molecular sciences. Math. Program. 79: 71-97 (1997)
- [c1]Jens Stoye, Dirk Evers, Folker Meyer: Generating Benchmarks for Multiple Sequence Alignments and Phylogenic Reconstructions. ISMB 1997: 303-306
Coauthor Index
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last updated on 2013-06-11 21:36 CEST by the dblp team