| * | 2009 |
|---|
| 67 | EE | Marília D. V. Braga,
Jens Stoye:
Counting All DCJ Sorting Scenarios.
RECOMB-CG 2009: 36-47 |
| 66 | EE | Guillaume Blin,
Jens Stoye:
Finding Nested Common Intervals Efficiently.
RECOMB-CG 2009: 59-69 |
| 65 | EE | Paul Medvedev,
Jens Stoye:
Rearrangement Models and Single-Cut Operations.
RECOMB-CG 2009: 84-97 |
| 64 | EE | Peter Husemann,
Jens Stoye:
Phylogenetic Comparative Assembly.
WABI 2009: 145-156 |
| 63 | EE | Nils Hoffmann,
Jens Stoye:
ChromA: signal-based retention time alignment for chromatography-mass spectrometry data.
Bioinformatics 25(16): 2080-2081 (2009) |
| 62 | EE | Jens Stoye,
Roland Wittler:
A Unified Approach for Reconstructing Ancient Gene Clusters.
IEEE/ACM Trans. Comput. Biology Bioinform. 6(3): 387-400 (2009) |
| 2008 |
|---|
| 61 | EE | Anne Bergeron,
Julia Mixtacki,
Jens Stoye:
HP Distance Via Double Cut and Join Distance.
CPM 2008: 56-68 |
| 60 | EE | Sebastian Böcker,
Katharina Jahn,
Julia Mixtacki,
Jens Stoye:
Computation of Median Gene Clusters.
RECOMB 2008: 331-345 |
| 59 | EE | Anne Bergeron,
Julia Mixtacki,
Jens Stoye:
On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios.
RECOMB-CG 2008: 226-240 |
| 58 | EE | José Augusto Amgarten Quitzau,
Jens Stoye:
Detecting Repeat Families in Incompletely Sequenced Genomes.
WABI 2008: 342-353 |
| 57 | EE | Jens Stoye:
Suffix Tree Construction in RAM.
Encyclopedia of Algorithms 2008 |
| 56 | EE | 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) |
| 55 | EE | 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) |
| 54 | EE | Klaus-Bernd Schürmann,
Jens Stoye:
Counting suffix arrays and strings.
Theor. Comput. Sci. 395(2-3): 220-234 (2008) |
| 2007 |
|---|
| 53 | EE | Gilles Didier,
Thomas Schmidt,
Jens Stoye,
Dekel Tsur:
Character sets of strings.
J. Discrete Algorithms 5(2): 330-340 (2007) |
| 52 | EE | Klaus-Bernd Schürmann,
Jens Stoye:
An incomplex algorithm for fast suffix array construction.
Softw., Pract. Exper. 37(3): 309-329 (2007) |
| 2006 |
|---|
| 51 | EE | 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 |
| 50 | EE | Anne Bergeron,
Julia Mixtacki,
Jens Stoye:
A Unifying View of Genome Rearrangements.
WABI 2006: 163-173 |
| 49 | EE | Michael Sammeth,
Thasso Griebel,
Felix Tille,
Jens Stoye:
Panta rhei (QAlign2): an open graphical environment for sequence analysis.
Bioinformatics 22(7): 889-890 (2006) |
| 48 | EE | 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) |
| 47 | EE | 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) |
| 46 | EE | Anne Bergeron,
Julia Mixtacki,
Jens Stoye:
On Sorting by Translocations.
Journal of Computational Biology 13(2): 567-578 (2006) |
| 45 | EE | 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) |
| 2005 |
|---|
| 44 | EE | Klaus-Bernd Schürmann,
Jens Stoye:
An Incomplex Algorithm for Fast Suffix Array Construction.
ALENEX/ANALCO 2005: 78-85 |
| 43 | EE | Constantin Bannert,
Jens Stoye:
Protein Annotation by Secondary Structure Based Alignments (PASSTA).
CompLife 2005: 79-90 |
| 42 | EE | 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 |
| 41 | EE | Anne Bergeron,
Julia Mixtacki,
Jens Stoye:
On Sorting by Translocations.
RECOMB 2005: 615-629 |
| 40 | EE | Klaus-Bernd Schürmann,
Jens Stoye:
Counting Suffix Arrays and Strings.
SPIRE 2005: 55-66 |
| 39 | EE | Michael Sammeth,
Thomas Weniger,
Dag Harmsen,
Jens Stoye:
Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI).
WABI 2005: 276-290 |
| 38 | EE | Antje Krause,
Jens Stoye,
Martin Vingron:
Large scale hierarchical clustering of protein sequences.
BMC Bioinformatics 6: 15 (2005) |
| 37 | EE | 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) |
| 2004 |
|---|
| 36 | | Robert Giegerich,
Jens Stoye:
Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, Germany, October 4-6, 2004
GI 2004 |
| 35 | EE | Thomas Schmidt,
Jens Stoye:
Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences.
CPM 2004: 347-358 |
| 34 | EE | Anne Bergeron,
Julia Mixtacki,
Jens Stoye:
Reversal Distance without Hurdles and Fortresses.
CPM 2004: 388-399 |
| 33 | EE | Morris Michael,
Christoph Dieterich,
Jens Stoye:
Suboptimal Local Alignments Across Multiple Scoring Schemes.
WABI 2004: 99-110 |
| 32 | EE | 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) |
| 31 | EE | 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) |
| 30 | EE | 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) |
| 29 | EE | 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) |
| 2003 |
|---|
| 28 | EE | Anne Bergeron,
Jens Stoye:
On the Similarity of Sets of Permutations and Its Applications to Genome Comparison.
COCOON 2003: 68-79 |
| 27 | | Michael Sammeth,
Burkhard Morgenstern,
Jens Stoye:
Divide-and-conquer multiple alignment with segment-based constraints.
ECCB 2003: 189-195 |
| 26 | | Constantin Bannert,
Jens Stoye:
Evaluation of the Jumping Alignment algorithm with artificial and biological data.
German Conference on Bioinformatics 2003: 21-25 |
| 25 | | 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) |
| 24 | EE | Robert Giegerich,
Stefan Kurtz,
Jens Stoye:
Efficient implementation of lazy suffix trees.
Softw., Pract. Exper. 33(11): 1035-1049 (2003) |
| 2002 |
|---|
| 23 | | Anne Bergeron,
Steffen Heber,
Jens Stoye:
Common intervals and sorting by reversals: a marriage of necessity.
ECCB 2002: 54-63 |
| 22 | | Jens Stoye:
Index Structures for Large Sequence Data: Suffix Trees and Affix Trees.
GI Jahrestagung (Ergänzungsband) 2002: 67-71 |
| 21 | | Mark Cieliebak,
Thomas Erlebach,
Zsuzsanna Lipták,
Jens Stoye,
Emo Welzl:
Algorithmic Complexity of Protein Identification: Searching in Weighted Strings.
IFIP TCS 2002: 143-156 |
| 20 | | Rainer Spang,
Marc Rehmsmeier,
Jens Stoye:
A Novel Approach to Remote Homology Detection: Jumping Alignments.
Journal of Computational Biology 9(5): 747-760 (2002) |
| 19 | EE | Jens Stoye,
Dan Gusfield:
Simple and flexible detection of contiguous repeats using a suffix tree.
Theor. Comput. Sci. 270(1-2): 843-856 (2002) |
| 2001 |
|---|
| 18 | EE | Steffen Heber,
Jens Stoye:
Finding All Common Intervals of k Permutations.
CPM 2001: 207-218 |
| 17 | | Constantin Bannert,
Marc Rehmsmeier,
Rainer Spang,
Jens Stoye:
Sequence Database Search Using Jumping Alignments.
German Conference on Bioinformatics 2001: 142 |
| 16 | EE | Steffen Heber,
Jens Stoye:
Algorithms for Finding Gene Clusters.
WABI 2001: 252-263 |
| 2000 |
|---|
| 15 | | Erich Bornberg-Bauer,
Ursula Rost,
Jens Stoye:
Proceedings of the German Conference on Bioinformatics (GCB 2000), Heidelberg, October 5-7, 2000
Logos Verlag 2000 |
| 14 | | Stefan Kurtz,
Enno Ohlebusch,
Chris Schleiermacher,
Jens Stoye,
Robert Giegerich:
Computation and Visualization of Degenerate Repeats in Complete Genomes.
ISMB 2000: 228-238 |
| 13 | | Rainer Spang,
Marc Rehmsmeier,
Jens Stoye:
Sequence Database Search Using Jumping Alignments.
ISMB 2000: 367-375 |
| 12 | EE | Steffen Heber,
Jens Stoye,
Jörg D. Hoheisel,
Martin Vingron:
Contig selection in physical mapping.
RECOMB 2000: 155-164 |
| 11 | | Knut Reinert,
Jens Stoye,
Torsten Will:
An iterative method for faster sum-of-pairs multiple sequence alignment.
Bioinformatics 16(9): 808-814 (2000) |
| 10 | | 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) |
| 9 | | Antje Krause,
Jens Stoye,
Martin Vingron:
The SYSTERS protein sequence cluster set.
Nucleic Acids Research 28(1): 270-272 (2000) |
| 1999 |
|---|
| 8 | EE | Robert Giegerich,
Stefan Kurtz,
Jens Stoye:
Efficient Implementation of Lazy Suffix Trees.
Algorithm Engineering 1999: 30-42 |
| 7 | EE | Gerth Stølting Brodal,
Rune B. Lyngsø,
Christian N. S. Pedersen,
Jens Stoye:
Finding Maximal Pairs with Bounded Gap.
CPM 1999: 134-149 |
| 6 | | 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 |
| 1998 |
|---|
| 5 | | Jens Stoye,
Dan Gusfield:
Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version).
CPM 1998: 140-152 |
| 4 | | Jens Stoye,
Dirk Evers,
Folker Meyer:
Rose: generating sequence families.
Bioinformatics 14(2): 157-163 (1998) |
| 1997 |
|---|
| 3 | | Jens Stoye,
Dirk Evers,
Folker Meyer:
Generating Benchmarks for Multiple Sequence Alignments and Phylogenic Reconstructions.
ISMB 1997: 303-306 |
| 2 | | 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) |
| 1 | | 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) |
