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Jens Stoye: [Publications] [Author Rank by year] [Co-authors] [Prefers] [Cites] [Cited by]

Publications of Author

  1. Klaus-Bernd Schürmann, Jens Stoye
    An Incomplex Algorithm for Fast Suffix Array Construction. [Citation Graph (0, 0)][DBLP]
    ALENEX/ANALCO, 2005, pp:78-85 [Conf]
  2. Anne Bergeron, Jens Stoye
    On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. [Citation Graph (0, 0)][DBLP]
    COCOON, 2003, pp:68-79 [Conf]
  3. Constantin Bannert, Jens Stoye
    Protein Annotation by Secondary Structure Based Alignments (PASSTA). [Citation Graph (0, 0)][DBLP]
    CompLife, 2005, pp:79-90 [Conf]
  4. Anne Bergeron, Julia Mixtacki, Jens Stoye
    Reversal Distance without Hurdles and Fortresses. [Citation Graph (0, 0)][DBLP]
    CPM, 2004, pp:388-399 [Conf]
  5. Gerth Stølting Brodal, Rune B. Lyngsø, Christian N. S. Pedersen, Jens Stoye
    Finding Maximal Pairs with Bounded Gap. [Citation Graph (0, 0)][DBLP]
    CPM, 1999, pp:134-149 [Conf]
  6. Steffen Heber, Jens Stoye
    Finding All Common Intervals of k Permutations. [Citation Graph (0, 0)][DBLP]
    CPM, 2001, pp:207-218 [Conf]
  7. Thomas Schmidt, Jens Stoye
    Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences. [Citation Graph (0, 0)][DBLP]
    CPM, 2004, pp:347-358 [Conf]
  8. Jens Stoye, Dan Gusfield
    Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version). [Citation Graph (0, 0)][DBLP]
    CPM, 1998, pp:140-152 [Conf]
  9. Anne Bergeron, Steffen Heber, Jens Stoye
    Common intervals and sorting by reversals: a marriage of necessity. [Citation Graph (0, 0)][DBLP]
    ECCB, 2002, pp:54-63 [Conf]
  10. Michael Sammeth, Burkhard Morgenstern, Jens Stoye
    Divide-and-conquer multiple alignment with segment-based constraints. [Citation Graph (0, 0)][DBLP]
    ECCB, 2003, pp:189-195 [Conf]
  11. Constantin Bannert, Marc Rehmsmeier, Rainer Spang, Jens Stoye
    Sequence Database Search Using Jumping Alignments. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2001, pp:142- [Conf]
  12. Constantin Bannert, Jens Stoye
    Evaluation of the Jumping Alignment algorithm with artificial and biological data. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2003, pp:21-25 [Conf]
  13. Knut Reinert, Jens Stoye, Torsten Will
    Combining Divide-and-Conquer, the A*-Algorithm, and Successive Realignment Approaches to Speed Multiple Sequence Alignment. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 1999, pp:17-24 [Conf]
  14. Jens Stoye
    Index Structures for Large Sequence Data: Suffix Trees and Affix Trees. [Citation Graph (0, 0)][DBLP]
    GI Jahrestagung (Ergänzungsband), 2002, pp:67-71 [Conf]
  15. Mark Cieliebak, Thomas Erlebach, Zsuzsanna Lipták, Jens Stoye, Emo Welzl
    Algorithmic Complexity of Protein Identification: Searching in Weighted Strings. [Citation Graph (0, 0)][DBLP]
    IFIP TCS, 2002, pp:143-156 [Conf]
  16. 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. [Citation Graph (0, 0)][DBLP]
    ISMB (Supplement of Bioinformatics), 2006, pp:281-289 [Conf]
  17. Stefan Kurtz, Enno Ohlebusch, Chris Schleiermacher, Jens Stoye, Robert Giegerich
    Computation and Visualization of Degenerate Repeats in Complete Genomes. [Citation Graph (0, 0)][DBLP]
    ISMB, 2000, pp:228-238 [Conf]
  18. Rainer Spang, Marc Rehmsmeier, Jens Stoye
    Sequence Database Search Using Jumping Alignments. [Citation Graph (0, 0)][DBLP]
    ISMB, 2000, pp:367-375 [Conf]
  19. Jens Stoye, Dirk Evers, Folker Meyer
    Generating Benchmarks for Multiple Sequence Alignments and Phylogenic Reconstructions. [Citation Graph (0, 0)][DBLP]
    ISMB, 1997, pp:303-306 [Conf]
  20. Anne Bergeron, Julia Mixtacki, Jens Stoye
    On Sorting by Translocations. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2005, pp:615-629 [Conf]
  21. Steffen Heber, Jens Stoye, Jörg D. Hoheisel, Martin Vingron
    Contig selection in physical mapping. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2000, pp:155-164 [Conf]
  22. Kim R. Rasmussen, Jens Stoye, Eugene W. Myers
    Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2005, pp:189-203 [Conf]
  23. Klaus-Bernd Schürmann, Jens Stoye
    Counting Suffix Arrays and Strings. [Citation Graph (0, 0)][DBLP]
    SPIRE, 2005, pp:55-66 [Conf]
  24. Morris Michael, Christoph Dieterich, Jens Stoye
    Suboptimal Local Alignments Across Multiple Scoring Schemes. [Citation Graph (0, 0)][DBLP]
    WABI, 2004, pp:99-110 [Conf]
  25. Anne Bergeron, Julia Mixtacki, Jens Stoye
    A Unifying View of Genome Rearrangements. [Citation Graph (0, 0)][DBLP]
    WABI, 2006, pp:163-173 [Conf]
  26. Steffen Heber, Jens Stoye
    Algorithms for Finding Gene Clusters. [Citation Graph (0, 0)][DBLP]
    WABI, 2001, pp:252-263 [Conf]
  27. Michael Sammeth, Thomas Weniger, Dag Harmsen, Jens Stoye
    Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). [Citation Graph (0, 0)][DBLP]
    WABI, 2005, pp:276-290 [Conf]
  28. Robert Giegerich, Stefan Kurtz, Jens Stoye
    Efficient Implementation of Lazy Suffix Trees. [Citation Graph (0, 0)][DBLP]
    Algorithm Engineering, 1999, pp:30-42 [Conf]
  29. Daniela Bartels, Sebastian Kespohl, Stefan 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. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2005, v:21, n:7, pp:853-859 [Journal]
  30. Knut Reinert, Jens Stoye, Torsten Will
    An iterative method for faster sum-of-pairs multiple sequence alignment. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2000, v:16, n:9, pp:808-814 [Journal]
  31. Michael Sammeth, Thasso Griebel, Felix Tille, Jens Stoye
    Panta rhei (QAlign2): an open graphical environment for sequence analysis. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:7, pp:889-890 [Journal]
  32. Michael Sammeth, Jörg Rothgänger, W. Esser, Jürgen Albert, Jens Stoye, Dag Harmsen
    Digital extractor: analysis of digital differential display output. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2003, v:19, n:12, pp:1592-1593 [Journal]
  33. Jens Stoye, Dirk Evers, Folker Meyer
    Rose: generating sequence families. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 1998, v:14, n:2, pp:157-163 [Journal]
  34. Jens Stoye, Vincent Moulton, Andreas W. M. Dress
    DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment. [Citation Graph (0, 0)][DBLP]
    Computer Applications in the Biosciences, 1997, v:13, n:6, pp:625-626 [Journal]
  35. Antje Krause, Jens Stoye, Martin Vingron
    Large scale hierarchical clustering of protein sequences. [Citation Graph (0, 0)][DBLP]
    BMC Bioinformatics, 2005, v:6, n:, pp:15- [Journal]
  36. Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen
    Benchmarking tools for the alignment of functional noncoding DNA. [Citation Graph (0, 0)][DBLP]
    BMC Bioinformatics, 2004, v:5, n:, pp:6- [Journal]
  37. Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen
    Correction: Benchmarking tools for the alignment of functional noncodingDNA. [Citation Graph (0, 0)][DBLP]
    BMC Bioinformatics, 2004, v:5, n:, pp:73- [Journal]
  38. Mark Cieliebak, Thomas Erlebach, Zsuzsanna Lipták, Jens Stoye, Emo Welzl
    Algorithmic complexity of protein identification: combinatorics of weighted strings. [Citation Graph (0, 0)][DBLP]
    Discrete Applied Mathematics, 2004, v:137, n:1, pp:27-46 [Journal]
  39. Steffen Heber, Jens Stoye, Marcus Frohme, Jörg D. Hoheisel, Martin Vingron
    Contig Selection in Physical Mapping. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 2000, v:7, n:3-4, pp:395-408 [Journal]
  40. Rainer Spang, Marc Rehmsmeier, Jens Stoye
    A Novel Approach to Remote Homology Detection: Jumping Alignments. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 2002, v:9, n:5, pp:747-760 [Journal]
  41. Dan Gusfield, Jens Stoye
    Linear time algorithms for finding and representing all the tandem repeats in a string. [Citation Graph (0, 0)][DBLP]
    J. Comput. Syst. Sci., 2004, v:69, n:4, pp:525-546 [Journal]
  42. Gilles Didier, Thomas Schmidt, Jens Stoye, Dekel Tsur
    Character sets of strings. [Citation Graph (0, 0)][DBLP]
    J. Discrete Algorithms, 2007, v:5, n:2, pp:330-340 [Journal]
  43. Gunnar Brinkmann, Andreas W. M. Dress, Sören Perrey, Jens Stoye
    Two applications of the Divide&Conquer principle in the molecular sciences. [Citation Graph (0, 0)][DBLP]
    Math. Program., 1997, v:79, n:, pp:71-97 [Journal]
  44. Antje Krause, Jens Stoye, Martin Vingron
    The SYSTERS protein sequence cluster set. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2000, v:28, n:1, pp:270-272 [Journal]
  45. Robert Giegerich, Stefan Kurtz, Jens Stoye
    Efficient implementation of lazy suffix trees. [Citation Graph (0, 0)][DBLP]
    Softw., Pract. Exper., 2003, v:33, n:11, pp:1035-1049 [Journal]
  46. Klaus-Bernd Schürmann, Jens Stoye
    An incomplex algorithm for fast suffix array construction. [Citation Graph (0, 0)][DBLP]
    Softw., Pract. Exper., 2007, v:37, n:3, pp:309-329 [Journal]
  47. Michael Sammeth, Jens Stoye
    Comparing Tandem Repeats with Duplications and Excisions of Variable Degree. [Citation Graph (0, 0)][DBLP]
    IEEE/ACM Trans. Comput. Biology Bioinform., 2006, v:3, n:4, pp:395-407 [Journal]
  48. Jens Stoye, Dan Gusfield
    Simple and flexible detection of contiguous repeats using a suffix tree. [Citation Graph (0, 0)][DBLP]
    Theor. Comput. Sci., 2002, v:270, n:1-2, pp:843-856 [Journal]

  49. Indexing and Searching a Mass Spectrometry Database. [Citation Graph (, )][DBLP]


  50. HP Distance Via Double Cut and Join Distance. [Citation Graph (, )][DBLP]


  51. Computation of Median Gene Clusters. [Citation Graph (, )][DBLP]


  52. On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios. [Citation Graph (, )][DBLP]


  53. Counting All DCJ Sorting Scenarios. [Citation Graph (, )][DBLP]


  54. Finding Nested Common Intervals Efficiently. [Citation Graph (, )][DBLP]


  55. Rearrangement Models and Single-Cut Operations. [Citation Graph (, )][DBLP]


  56. Detecting Repeat Families in Incompletely Sequenced Genomes. [Citation Graph (, )][DBLP]


  57. Phylogenetic Comparative Assembly. [Citation Graph (, )][DBLP]


  58. Swiftly Computing Center Strings. [Citation Graph (, )][DBLP]


  59. Genomic Distance with DCJ and Indels. [Citation Graph (, )][DBLP]


  60. MeltDB: a software platform for the analysis and integration of metabolomics experiment data. [Citation Graph (, )][DBLP]


  61. ChromA: signal-based retention time alignment for chromatography-mass spectrometry data. [Citation Graph (, )][DBLP]


  62. A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). [Citation Graph (, )][DBLP]


  63. r2cat: synteny plots and comparative assembly. [Citation Graph (, )][DBLP]


  64. WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. [Citation Graph (, )][DBLP]


  65. Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance [Citation Graph (, )][DBLP]


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