Jens Stoye

	2009
70		Marília D. V. Braga, Jens Stoye: Counting All DCJ Sorting Scenarios. RECOMB-CG 2009: 36-47
69		Guillaume Blin, Jens Stoye: Finding Nested Common Intervals Efficiently. RECOMB-CG 2009: 59-69
68		Paul Medvedev, Jens Stoye: Rearrangement Models and Single-Cut Operations. RECOMB-CG 2009: 84-97
67		Peter Husemann, Jens Stoye: Phylogenetic Comparative Assembly. WABI 2009: 145-156
66		Nils Hoffmann, Jens Stoye: ChromA: signal-based retention time alignment for chromatography-mass spectrometry data. Bioinformatics 25(16): 2080-2081 (2009)
65		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)
64		Jens Stoye, Roland Wittler: A Unified Approach for Reconstructing Ancient Gene Clusters. IEEE/ACM Trans. Comput. Biology Bioinform. 6(3): 387-400 (2009)
63		Katharina Jahn, Jens Stoye: Approximative Gencluster und ihre Anwendung in der komparativen Genomik. Informatik Spektrum 32(4): 288-300 (2009)
62		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)
	2008
61		Anne Bergeron, Julia Mixtacki, Jens Stoye: HP Distance Via Double Cut and Join Distance. CPM 2008: 56-68
60		Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye: Computation of Median Gene Clusters. RECOMB 2008: 331-345
59		Anne Bergeron, Julia Mixtacki, Jens Stoye: On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios. RECOMB-CG 2008: 226-240
58		José Augusto Amgarten Quitzau, Jens Stoye: Detecting Repeat Families in Incompletely Sequenced Genomes. WABI 2008: 342-353
57		Jens Stoye: Suffix Tree Construction in RAM. Encyclopedia of Algorithms 2008
56		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		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		Klaus-Bernd Schürmann, Jens Stoye: Counting suffix arrays and strings. Theor. Comput. Sci. 395(2-3): 220-234 (2008)
	2007
53		Gilles Didier, Thomas Schmidt, Jens Stoye, Dekel Tsur: Character sets of strings. J. Discrete Algorithms 5(2): 330-340 (2007)
52		Klaus-Bernd Schürmann, Jens Stoye: An incomplex algorithm for fast suffix array construction. Softw., Pract. Exper. 37(3): 309-329 (2007)
	2006
51		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		Anne Bergeron, Julia Mixtacki, Jens Stoye: A Unifying View of Genome Rearrangements. WABI 2006: 163-173
49		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		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		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		Anne Bergeron, Julia Mixtacki, Jens Stoye: On Sorting by Translocations. Journal of Computational Biology 13(2): 567-578 (2006)
45		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		Klaus-Bernd Schürmann, Jens Stoye: An Incomplex Algorithm for Fast Suffix Array Construction. ALENEX/ANALCO 2005: 78-85
43		Constantin Bannert, Jens Stoye: Protein Annotation by Secondary Structure Based Alignments (PASSTA). CompLife 2005: 79-90
42		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		Anne Bergeron, Julia Mixtacki, Jens Stoye: On Sorting by Translocations. RECOMB 2005: 615-629
40		Klaus-Bernd Schürmann, Jens Stoye: Counting Suffix Arrays and Strings. SPIRE 2005: 55-66
39		Michael Sammeth, Thomas Weniger, Dag Harmsen, Jens Stoye: Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). WABI 2005: 276-290
38		Antje Krause, Jens Stoye, Martin Vingron: Large scale hierarchical clustering of protein sequences. BMC Bioinformatics 6: 15 (2005)
37		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		Thomas Schmidt, Jens Stoye: Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences. CPM 2004: 347-358
34		Anne Bergeron, Julia Mixtacki, Jens Stoye: Reversal Distance without Hurdles and Fortresses. CPM 2004: 388-399
33		Morris Michael, Christoph Dieterich, Jens Stoye: Suboptimal Local Alignments Across Multiple Scoring Schemes. WABI 2004: 99-110
32		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		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		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		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		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		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		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		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		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		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		Robert Giegerich, Stefan Kurtz, Jens Stoye: Efficient Implementation of Lazy Suffix Trees. Algorithm Engineering 1999: 30-42
7		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)

Coauthor Index

1	Stefan P. Albaum	[37] [56]
2	Jürgen Albert	[25]
3	Constantin Bannert	[17] [26] [43]
4	Daniela Bartels	[37] [51]
5	Anne Bergeron	[23] [28] [34] [41] [45] [46] [50] [59] [61] [62]
6	Casey M. Bergman	[31] [32]
7	Guillaume Blin	[69]
8	Sebastian Böcker	[60]
9	Erich Bornberg-Bauer	[15]
10	Marília D. V. Braga	[70]
11	Gunnar Brinkmann	[1]
12	Gerth Stølting Brodal	[7]
13	Michael Brudno	[65]
14	Susan E. Celniker	[31] [32]
15	Mark Cieliebak	[21] [30]
16	Naryttza N. Diaz	[51]
17	Gilles Didier	[53]
18	Christoph Dieterich	[33]
19	Michael Dondrup	[56]
20	Andreas W. M. Dress	[1] [2]
21	Tanja Drüke	[37]
22	Robert A. Edwards	[51]
23	Michael B. Eisen	[31] [32]
24	Thomas Erlebach	[21] [30]
25	W. Esser	[25]
26	Dirk Evers	[3] [4]
27	Marcus Frohme	[10]
28	Robert Giegerich	[8] [14] [24] [36]
29	David Gilbert (David R. Gilbert)	[55]
30	Alexander Goesmann	[37] [55] [56]
31	Thasso Griebel	[49]
32	Dan Gusfield	[5] [19] [29]
33	Dag Harmsen	[25] [39]
34	Steffen Heber	[10] [12] [16] [18] [23]
35	Julia Herold	[37]
36	Nils Hoffmann	[66]
37	Jörg D. Hoheisel	[10] [12]
38	Peter Husemann	[67]
39	Katharina Jahn	[60] [63]
40	Olaf Kaiser	[37]
41	Sebastian Kespohl	[37]
42	Antje Krause	[9] [38]
43	Lutz Krause	[51]
44	Stefan Kurtz	[8] [14] [24]
45	Zsuzsanna Lipták	[21] [30]
46	Rune B. Lyngsø	[7]
47	Paul Medvedev	[65] [68]
48	Folker Meyer	[3] [4] [37] [51]
49	Morris Michael	[33]
50	Julia Mixtacki	[34] [41] [46] [50] [59] [60] [61] [62]
51	Burkhard Morgenstern	[27]
52	Vincent Moulton	[2]
53	Eugene W. Myers (Gene Myers)	[42] [47]
54	Heiko Neuweger	[56]
55	Karsten Niehaus	[56]
56	Sebastian Oehm	[55]
57	Enno Ohlebusch	[14]
58	Christian N. S. Pedersen	[7]
59	Sören Perrey	[1]
60	Marcus Persicke	[56]
61	Friedhelm Pfeiffer	[37]
62	Daniel A. Pollard	[31] [32]
63	Alfred Pühler	[37] [51]
64	José Augusto Amgarten Quitzau	[58]
65	Günter Raddatz	[37]
66	Kim R. Rasmussen	[42] [47]
67	Marc Rehmsmeier	[13] [17] [20]
68	Knut Reinert	[6] [11]
69	Forest Rohwer	[51]
70	Ursula Rost	[15]
71	Jörg Rothgänger	[25]
72	Michael Sammeth	[25] [27] [39] [48] [49]
73	Chris Schleiermacher	[14]
74	Thomas Schmidt	[35] [53]
75	Klaus-Bernd Schürmann	[40] [44] [52] [54]
76	Stephan C. Schuster	[37]
77	Rainer Spang	[13] [17] [20]
78	Andreas Tauch	[55]
79	Felix Tille	[49]
80	Dekel Tsur	[53]
81	Francisco M. de la Vega	[65]
82	Martin Vingron	[9] [10] [12] [38]
83	Tony Watt	[56]
84	Emo Welzl	[21] [30]
85	Thomas Weniger	[39]
86	Torsten Will	[6] [11]
87	Roland Wittler	[64]

Colors in the list of coauthors