201 Publikationen

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[201]
2019 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2932883
Dörr, Daniel, and Stoye, Jens. “A Perspective on Comparative and Functional Genomics”. Bioinformatics and Phylogenetics. Ed. Tandy Warnow. Cham: Springer , 2019.Vol. 29. Computational Biology. 361-372.
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[200]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2932884
Oey, Harald, Zakrzewski, Martha, Gravermann, Kerstin, Young, Neil D., Korhonen, Pasi K., Gobert, Geoffrey N., Nawaratna, Sujeevi, Hasan, Shibab, Martínez, David M., You, Hong, Lavin, Martin, Jones, Malcolm, Ragan, Mark A., Stoye, Jens, Oleaga, Ana, Emery, Aidan M., Webster, Bonnie, Rollinson, David, Gasser, Robin B., McManus, Donald P., and Krause, Lutz. “Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium”. PLOS Pathogens 15.1 (2019): e1007513.
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[199]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919005
Schulz, Tizian, Stoye, Jens, and Dörr, Daniel. “GraphTeams. A method for discovering spatial gene clusters in Hi-C sequencing data”. BMC Genomics 19.Suppl. 5 (2018): 308.
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[198]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919006
Rubert, Diego, Hoshino, Edna A., Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. “Computing the family-free DCJ similarity”. BMC Bioinformatics 19.Suppl. 6 (2018): 152.
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[197]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918481
Luhmann, Nina, Chauve, Cedric, Stoye, Jens, and Wittler, Roland. “Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 15.6 (2018): 2094-2100.
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[196]
2018 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2930445
Cunha, Luís, Diekmann, Yoan, Kowada, Luis, and Stoye, Jens. “Identifying Maximal Perfect Haplotype Blocks”. Proceedings of BSB 2018. Springer Verlag, 2018.Vol. 11228. LNBI. 26-37.
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[195]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930268
Holley, Guillaume, Wittler, Roland, Stoye, Jens, and Hach, Faraz. “Dynamic Alignment-Free and Reference-Free Read Compression”. JOURNAL OF COMPUTATIONAL BIOLOGY 25.7 (2018): 825-836.
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[194]
2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913921
Zekic, Tina, Holley, Guillaume, and Stoye, Jens. “Pan-genome Storage and Analysis Techniques”. Comparative Genomics. Methods and Protocols. Ed. João C. Setubal, Peter Stadler, and Jens Stoye. New York: Springer Verlag, 2018.Vol. 1704. Methods in Molecular Biology. 29-53.
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[193]
2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913922
Dörr, Daniel, Feijão, Pedro, and Stoye, Jens. “Family-Free Genome Comparison”. Comparative Genomics: Methods and Protocols. Ed. João C. Setubal, Peter Stadler, and Jens Stoye. New York: Springer Verlag, 2018.Vol. 1704. Methods in Molecular Biology. 331-342.
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[192]
2018 | Herausgeber Sammelwerk | Veröffentlicht | PUB-ID: 2913920
João C Setubal, Peter Stadler, and Jens Stoye, eds. Comparative Genomics: Methods and Protocols. New York: Springer Verlag, 2018. Methods in Molecular Biology. 1704.
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[191]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919012
Jaenicke, Sebastian, Albaum, Stefan, Blumenkamp, Patrick, Linke, Burkhard, Stoye, Jens, and Goesmann, Alexander. “Flexible metagenome analysis using the MGX framework”. Microbiome 6 (2018): 76.
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[190]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556
Jünemann, Sebastian, Kleinbölting, Nils, Jaenicke, Sebastian, Henke, Christian, Hassa, Julia, Nelkner, Johanna, Stolze, Yvonne, Albaum, Stefan, Schlüter, Andreas, Goesmann, Alexander, Sczyrba, Alexander, and Stoye, Jens. “Bioinformatics for NGS-based metagenomics and the application to biogas research”. Journal of Biotechnology 261.SI (2017): 10-23.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[189]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913015
Rubert, Diego, Medeiros, Gabriel L., Hoshino, Edna A., Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. “Algorithms for Computing the Family-Free Genomic Similarity under DCJ”. Comparative Genomics. RECOMB-CG 2017. Ed. Joao Meidanis and Luay Nakhleh. Cham: Springer Verlag, 2017.Vol. 10562. Lecture Notes in Bioinformatics. 76-100.
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[188]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909057
Rubert, Diego, Feijão, Pedro, Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. “Approximating the DCJ distance of balanced genomes in linear time”. Algorithms for Molecular Biology 12 (2017): 3.
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[187]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2909409
Cunha, Luis, Dantas, Simone, Gagie, Travis, Wittler, Roland, Kowada, Luis, and Stoye, Jens. “Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings”. Proceedings of CPM 2017. 2017.Vol. 78. LIPIcs. 19:1-19:9.
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[186]
2017 | Preprint | Veröffentlicht | PUB-ID: 2908521
Cunha, Luís, Dantas, Simone, Gagie, Travis, Wittler, Roland, Kowada, Luis, and Stoye, Jens. “Faster Jumbled Indexing for Binary Run-Length Encoded Strings”. arXiv: 1702.01280 (2017).
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[185]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2907587
Holley, Guillaume, Wittler, Roland, Stoye, Jens, and Hach, Faraz. “Dynamic Alignment-Free and Reference-Free Read Compression”. Proceedings of RECOMB 2017. 2017.Vol. 10229. Lecture Notes in Bioinformatics. 50-65.
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[184]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913016
Schulz, Tizian, Stoye, Jens, and Dörr, Daniel. “Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery”. Proceedings of RECOMB-CG 2017. Berlin: Springer Verlag, 2017.Vol. 1704. Lecture Notes in Bioinformatics. 197-212.
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[183]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909967
Dörr, Daniel, Kowada, Luis Antonio B., Soares de Araujo, Francisco Eloi, Deshpande, Shachi, Dantas, Simone, Moret, Bernard M. E., and Stoye, Jens. “New Genome Similarity Measures based on Conserved Gene Adjacencies”. Journal of Computational Biology 24.6 (2017): 616-634.
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[182]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905930
Winter, Sascha, Jahn, Katharina, Wehner, Stefanie, Kuchenbecker, Leon, Marz, Manja, Stoye, Jens, and Böcker, Sebastian. “Finding approximate gene clusters with GECKO 3”. Nucleic Acids Research 44.20 (2016): 9600-9610.
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[181]
2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2903708
Rubert, Diego, Feijão, Pedro, Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. “A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates”. Algorithms in Bioinformatics. WABI 2016. Ed. Martin Frith and Christian Nørgaard Storm Pedersen. Cham: Springer, 2016.Vol. 9838. Lecture Notes in Bioinformatics. 293-306.
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[180]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900129
Holley, Guillaume, Wittler, Roland, and Stoye, Jens. “Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage”. Algorithms for Molecular Biology 11 (2016): 3.
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[179]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900421
Krause, Lutz, Nones, Katia, Loffler, Kelly A., Nancarrow, Derek, Oey, Harald, Tang, Yup Hang, Wayte, Nicola J., Patch, Ann Marie, Patel, Kalpana, Brosda, Sandra, Manning, Suzanne, Lampe, Guy, Clouston, Andrew, Thomas, Janine, Stoye, Jens, Hussey, Damian J., Watson, David I., Lord, Reginald V., Phillips, Wayne A., Gotley, David, Smithers, B. Mark, Whiteman, David C., Hayward, Nicholas K., Grimmond, Sean M., Waddell, Nicola, and Barbour, Andrew P. “Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma”. Carcinogenesis 37.4 (2016): 356-365.
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[178]
2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2900111
Kowada, Luis Antonio B., Doerr, Daniel, Dantas, Simone, and Stoye, Jens. “New Genome Similarity Measures based on Conserved Gene Adjacencies”. Research in Computational Molecular Biology. RECOMB 2016. Ed. Mona Singh. Springer, 2016.Vol. 9649. Lecture Notes in Bioinformatics (LNBI). 204-224.
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[177]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2677844
Dias Vieira Braga, Marília, and Stoye, Jens. “Sorting linear genomes with rearrangements and indels”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 12.3 (2015): 500-506.
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[176]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726366
Viduani Martinez, Fábio Henrique, Feijão, Pedro, Dias Vieira Braga, Marília, and Stoye, Jens. “On the family-free DCJ distance and similarity”. Algorithms for Molecular Biology 10 (2015): 13.
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[175]
2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2757497
Holley, Guillaume, Wittler, Roland, and Stoye, Jens. “Bloom Filter Trie - a data structure for pan-genome storage”. Proceedings of WABI 2015. 2015.Vol. 9289. LNBI. 217-230.
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[174]
2015 | Konferenzband | Veröffentlicht | PUB-ID: 2780229
Joao Meidanis and Jens Stoye, eds. “Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Bioinformatics”. BMC Bioinformatics 16.Supplement 14 (2015).
PUB | Download (ext.)
 
[173]
2015 | Konferenzband | Veröffentlicht | PUB-ID: 2780232
Joao Meidanis and Jens Stoye, eds. “Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Genomics”. BMC Genomics 16.Supplement 10 (2015).
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[172]
2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2684241
Viduani Martinez, Fábio Henrique, Feijão, Pedro, Dias Vieira Braga, Marília, and Stoye, Jens. “On the family-free DCJ distance”. Algorithms in Bioinformatics. WABI 2014. Ed. Dan Brown and Burkhard Morgenstern. Berlin ; Heidelberg: Springer Verlag, 2014.Vol. 8701. Lecture Notes in Bioinformatics. 174-186.
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[171]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2687033
Dörr, Daniel, Stoye, Jens, Böcker, Sebastian, and Jahn, Katharina. “Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings”. BMC Genomics 15.Suppl. 6: Proc. of RECOMB-CG 2014 (2014): S2.
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[170]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685362
Lechner, Marcus, Hernandez-Rosales, Maribel, Dörr, Daniel, Wieseke, Nicolas, Thévenin, Annelyse, Stoye, Jens, Hartmann, Roland K., Prohaska, Sonja J., and Stadler, Peter F. “Orthology Detection Combining Clustering and Synteny for Very Large Datasets”. PLoS ONE 9.8 (2014): e105015.
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[169]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2689773
Jünemann, Sebastian, Prior, Karola, Albersmeier, Andreas, Albaum, Stefan, Kalinowski, Jörn, Goesmann, Alexander, Stoye, Jens, and Harmsen, Dag. “GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers”. PLOS ONE 9.9 (2014): e107014.
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[168]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2674387
Hilker, Rolf, Stadermann, Kai Bernd, Doppmeier, Daniel, Kalinowski, Jörn, Stoye, Jens, Straube, Jasmin, Winnebald, Jörn, and Goesmann, Alexander. “ReadXplorer - Visualization and Analysis of Mapped Sequences”. Bioinformatics 30.16 (2014): 2247-2254.
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[167]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665038
Schwientek, Patrick, Neshat, Armin, Kalinowski, Jörn, Klein, Andreas, Rückert, Christian, Schneiker-Bekel, Susanne, Wendler, Sergej, Stoye, Jens, and Pühler, Alfred. “Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts”. Journal of Biotechnology 190 (2014): 85-95.
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[166]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685988
Jakobi, Tobias, Brinkrolf, Karina, Tauch, Andreas, Noll, Thomas, Stoye, Jens, Pühler, Alfred, and Goesmann, Alexander. “Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing”. Journal of Biotechnology 190 (2014): 64-75.
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[165]
2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2690122
Luhmann, Nina, Chauve, Cedric, Stoye, Jens, and Wittler, Roland. “Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework”. Proc. of BSB 2014. Ed. Campos Sérgio. Springer Verlag, 2014.Vol. 8826. LNBI. 135-143.
PUB | DOI
 
[164]
2014 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2693552
Stoye, Jens. “Suffix Tree Construction”. Encyclopedia of Algorithms. Ed. M.-Y. Kao. Springer Verlag, 2014.
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[163]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2643941
Hoffmann, Nils, Wilhelm, Mathias, Doebbe, Anja, Niehaus, Karsten, and Stoye, Jens. “BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry”. Bioinformatics 30.7 (2014): 988-995.
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[162]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2693409
Fredrich, Eugenie, Ander, Christina, Stoye, Jens, Brune, Iris, and Tauch, Andreas. “Metatranskriptomik der Mikrobiota aus der menschlichen Achselhöhle”. BIOspektrum 20.5 (2014): 294-296.
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[161]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333
Henrich, Birgit, Rumming, Madis, Sczyrba, Alexander, Velleuer, Eunike, Dietrich, Ralf, Gerlach, Wolfgang, Gombert, Michael, Rahn, Sebastian, Stoye, Jens, Borkhardt, Arndt, and Fischer, Ute. “Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma”. PLoS ONE 9.3 (2014): e92297.
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[160]
2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2611641
Dias Vieira Braga, Marília, and Stoye, Jens. “Restricted DCJ-Indel Model Revisited”. Advances in Bioinformatics and Computational Biology. BSB 2013. Ed. João C. Setubal and Nalvo F. Almeida. Cham: Springer Verlag, 2013.Vol. 8213. Lecture Notes in Bioinformatics. 36-46.
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[159]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611630
Willing, Eyla, Zaccaria, Simone, Dias Vieira Braga, Marília, and Stoye, Jens. “On the Inversion-Indel Distance”. BMC Bioinformatics 14.Suppl 15: Proc. of RECOMB-CG 2013 (2013): S3.
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[158]
2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611648
Dias Vieira Braga, Marília, Chauve, Cedric, Dörr, Daniel, Jahn, Katharina, Stoye, Jens, Thévenin, Annelyse, and Wittler, Roland. “The Potential of Family-Free Genome Comparison”. Models and Algorithms for Genome Evolution. Ed. Cedric Chauve, Nadia El-Mabrouk, and Eric Tannier. Springer Verlag, 2013.Vol. 19. Computational Biology Series. 287-307.
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[157]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575011
Ander, Christina, Schulz-Trieglaff, Ole B., Stoye, Jens, and Cox, Anthony J. “metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences”. BMC Bioinformatics 14.Suppl 5: Proc. of RECOMB-Seq 2013 (2013): S2.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[156]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641228
Jünemann, Sebastian, Sedlazeck, Fritz Joachim, Prior, Karola, Albersmeier, Andreas, John, Uwe, Kalinowski, Jörn, Mellmann, Alexander, Goesmann, Alexander, von Haeseler, Arndt, Stoye, Jens, and Harmsen, Dag. “Corrigendum: Updating benchtop sequencing performance comparison”. Nature biotechnology 31.12 (2013): 1148.
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[155]
2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611643
Bergeron, Anne, and Stoye, Jens. “The Genesis of the DCJ Formula”. Models and Algorithms for Genome Evolution. Ed. Cedric Chauve, Nadia El-Mabrouk, and Eric Tannier. Springer Verlag, 2013.Vol. 19. Computational Biology Series. 63-81.
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[154]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575361
Krell, Pina, Reuther, Susanne, Fischer, Ute, Keller, Thomas, Weber, Stephan, Gombert, Michael, Schuster, Friedhelm R., Asang, Corinna, Stepensky, Polina, Strahm, Birgit, Meisel, Roland, Stoye, Jens, and Borkhardt, Arndt. “Next-generation-sequencing-spectratyping reveals public T-cell receptor repertoires in pediatric very severe aplastic anemia and identifies a beta chain CDR3 sequence associated with hepatitis-induced pathogenesis”. Haematologica 98.9 (2013): 1388-1396.
PUB | DOI | WoS | PubMed | Europe PMC
 
[153]
2013 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2577323
Gerlach, Wolfgang, and Stoye, Jens. “Taxonomic classification of metagenomic shotgun sequences with CARMA3”. Encyclopedia of Metagenomics. Ed. Karen E. Nelson. Springer Verlag, 2013.
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[152]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2566922
Jünemann, Sebastian, Sedlazeck, Fritz Joachim, Prior, Karola, Albersmeier, Andreas, John, Uwe, Kalinowski, Jörn, Mellmann, Alexander, Goesmann, Alexander, von Haeseler, Arndt, Stoye, Jens, and Harmsen, Dag. “Updating benchtop sequencing performance comparison”. Nature Biotechnology 31.4 (2013): 294-296.
PUB | DOI | WoS | PubMed | Europe PMC
 
[151]
2013 | Konferenzband | Veröffentlicht | PUB-ID: 2616537
Aaron Darling and Jens Stoye, eds. “Algorithms in Bioinformatics”. Lecture Notes in Bioinformatics 8126 (2013).
PUB | DOI
 
[150]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611633
Jahn, Katharina, Winter, Sascha, Stoye, Jens, and Böcker, Sebastian. “Statistics for approximate gene clusters”. BMC Bioinformatics 14.Suppl 15: Proc. of RECOMB-CG 2013 (2013): S14.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[149]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2548236
Schwientek, Patrick, Wendler, Sergej, Neshat, Armin, Eirich, Christina, Rückert, Christian, Klein, Andreas, Wehmeier, Udo F, Kalinowski, Jörn, Stoye, Jens, and Pühler, Alfred. “Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media”. Journal of Biotechnology 167.2 (2013): 166-177.
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[148]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2529202
Zakrzewski, Martha, Bekel, Thomas, Ander, Christina, Pühler, Alfred, Rupp, Oliver, Stoye, Jens, Schlüter, Andreas, and Goesmann, Alexander. “MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets”. Journal of Biotechnology 167.2 (2013): 156-165.
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[147]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512642
Dörr, Daniel, Thévenin, Annelyse, and Stoye, Jens. “Gene family assignment-free comparative genomics”. BMC Bioinformatics 13.Suppl 19: Proc. of RECOMB-CG 2012 (2012): S3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[146]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517239
Hoffmann, Nils, Keck, Matthias, Neuweger, Heiko, Wilhelm, Mathias, Högy, Petra, Niehaus, Karsten, and Stoye, Jens. “Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets”. BMC Bioinformatics 13.1 (2012): 21.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[145]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512644
Jahn, Katharina, Sudek, Henner, and Stoye, Jens. “Multiple genome comparison based on overlap regions of pairwise local alignments”. BMC Bioinformatics 13.Suppl. 19: Proc. of RECOMB-CG 2012 (2012): S7.
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[144]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2486060
Schwientek, Patrick, Szczepanowski, Rafael, Rückert, Christian, Kalinowski, Jörn, Klein, Andreas, Selber, Klaus, Wehmeier, Udo F., Stoye, Jens, and Pühler, Alfred. “The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110”. BMC Genomics 13.1 (2012): 112.
PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[143]
2012 | Konferenzband | Veröffentlicht | PUB-ID: 2510416
Juha Kärkkäinen and Jens Stoye, eds. “Combinatorial Pattern Matching”. Lecture Notes in Computer Science 7354 (2012).
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[142]
2012 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2468382
Hoffmann, Nils, and Stoye, Jens. “Generic Software Frameworks for GC-MS Based Metabolomics”. Metabolomics. Ed. Ute Roessner. InTech, 2012. 73-98.
PUB | PDF | DOI | Download (ext.)
 
[141]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2510984
Hilker, Rolf, Sickinger, Corinna, Pedersen, Christian N. S., and Stoye, Jens. “UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ”. Bioinformatics 28.19 (2012): 2509-2511.
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[140]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517230
Jünemann, Sebastian, Prior, Karola, Szczepanowski, Rafael, Harks, Inga, Ehmke, Benjamin, Goesmann, Alexander, Stoye, Jens, and Harmsen, Dag. “Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing”. PLoS ONE 7.8 (2012): e41606.
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[139]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396558
Dias Vieira Braga, Marília, Machado, Raphael, Ribeiro, Leonardo C., and Stoye, Jens. “On the weight of indels in genomic distances”. BMC Bioinformatics 12.Suppl 9: RECOMB-CG 2011 (2011): S13.
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[138]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396509
Dias Vieira Braga, Marília, Machado, Raphael, Ribeiro, Leonardo C., and Stoye, Jens. “Genomic distance under gene substitutions”. BMC Bioinformatics 12.Suppl 9: Proc. of RECOMB-CG 2011 (2011): S8.
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[137]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091794
Dias Vieira Braga, Marília, Willing, Eyla, and Stoye, Jens. “Double Cut and Join with Insertions and Deletions”. Journal of Computational Biology 18.9 (2011): 1167-1184.
PUB | DOI | WoS | PubMed | Europe PMC
 
[136]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091790
Kovac, Jakub, Warren, Robert, Dias Vieira Braga, Marília, and Stoye, Jens. “Restricted DCJ Model. Rearrangement Problems with Chromosome Reincorporation”. Journal of Computational Biology 18.9 (2011): 1231-1241.
PUB | DOI | WoS | PubMed | Europe PMC
 
[135]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2354746
Schwientek, Patrick, Szczepanowski, Rafael, Rückert, Christian, Stoye, Jens, and Pühler, Alfred. “Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology”. Journal of Biotechnology 155.1 (2011): 68-77.
PUB | DOI | WoS | PubMed | Europe PMC
 
[134]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2289952
Blom, Jochen, Jakobi, Tobias, Doppmeier, Daniel, Jaenicke, Sebastian, Kalinowski, Jörn, Stoye, Jens, and Goesmann, Alexander. “Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming”. Bioinformatics 27.10 (2011): 1351-1358.
PUB | DOI | WoS | PubMed | Europe PMC
 
[133]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918550
Heber, Steffen, Mayr, Richard, and Stoye, Jens. “Common Intervals of Multiple Permutations”. Algorithmica 60.2 (2011): 175-206.
PUB | DOI | WoS
 
[132]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2298170
Gerlach, Wolfgang, and Stoye, Jens. “Taxonomic classification of metagenomic shotgun sequences with CARMA3.”. Nucleic Acids Res 39.14 (2011): e91.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[131]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897974
Erdős, Péter L., Soukup, Lajos, and Stoye, Jens. “Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance”. Applied Mathematics Letters 24.1 (2011): 82-86.
PUB | DOI | WoS
 
[130]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091787
Wittler, Roland, Maňuch, Ján, Patterson, Murray, and Stoye, Jens. “Consistency of Sequence-Based Gene Clusters”. Journal of Computational Biology 18.9 (2011): 1023-1039.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[129]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091779
Hufsky, Franziska, Kuchenbecker, Leon, Jahn, Katharina, Stoye, Jens, and Böcker, Sebastian. “Swiftly Computing Center Strings”. BMC Bioinformatics 12.1 (2011): 106.
PUB | DOI | WoS | PubMed | Europe PMC
 
[128]
2010 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2445157
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “Computing the Genomic Distance in Linear Time”. Dagstuhl Seminar Proceedings: 10231 Abstracts Collection : Structure Discovery in Biology: Motifs, Networks & Phylogenies. Ed. Alberto Apostolico, Andreas Dress, and Laxmi Parida. Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010.Vol. 10231. 18.
PUB | Download (ext.)
 
[127]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1893893
Husemann, Peter, and Stoye, Jens. “Phylogenetic Comparative Assembly”. Algorithms for Molecular Biology 5.1 (2010): 3.
PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[126]
2010 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918836
Besenbacher, Søren, Schwikowski, Benno, and Stoye, Jens. “Indexing and Searching a Mass Spectrometry Database”. Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday. Ed. Tapio Elomaa, Heikki Mannila, and Pekka Orponen. 2010.Vol. 6060. LNCS. 62-76.
PUB | DOI
 
[125]
2010 | Report | Veröffentlicht | PUB-ID: 1966434
Erdős, Péter L., Soukup, Lajos, and Stoye, Jens. Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance. 2010.
PUB | arXiv
 
[124]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1966439
Trost, Eva, Ott, Lisa, Schneider, Jessica, Schröder, Jasmin, Jaenicke, Sebastian, Goesmann, Alexander, Husemann, Peter, Stoye, Jens, Alves Dorella, Fernanda, Souza Rocha, Flavia, de Castro Soares, Siomar, D'Afonseca, Vivian, Miyoshi, Anderson, Ruiz, Jeronimo, Silva, Artur, Azevedo, Vasco, Burkovski, Andreas, Guiso, Nicole, Join-Lambert, Olivier F., Kayal, Samer, and Tauch, Andreas. “The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence”. BMC Genomics 11.1 (2010): 728.
PUB | DOI | WoS | PubMed | Europe PMC
 
[123]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1795670
Wittkop, Tobias, Emig, Dorothea, Lange, Sita J., Rahmann, Sven, Albrecht, Mario, Morris, John H., Böcker, Sebastian, Stoye, Jens, and Baumbach, Jan. “Partitioning Biological Data with Transitivity Clustering”. Nature Methods 7.6 (2010): 419-420.
PUB | DOI | WoS | PubMed | Europe PMC
 
[122]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898012
Blin, Guillaume, Faye, David, and Stoye, Jens. “Finding Nested Common Intervals Efficiently”. Journal of Computational Biology 17.9 (2010): 1183-1194.
PUB | DOI | WoS | PubMed | Europe PMC
 
[121]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919217
Wittler, Roland, and Stoye, Jens. “Consistency of Sequence-based Gene Clusters”. Proc. of Recomb-CG 2010. Springer Verlag, 2010.Vol. 6398. LNBI. 252-263.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[120]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1893890
Husemann, Peter, and Stoye, Jens. “Repeat-aware Comparative Genome Assembly”. Proc. of GCB 2010. 2010.Vol. P-173. LNI. 61-70.
PUB | Download (ext.)
 
[119]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588556
Husemann, Peter, and Stoye, Jens. “r2cat: Synteny Plots and Comparative Assembly”. Bioinformatics 26.4 (2010): 570-571.
PUB | DOI | WoS | PubMed | Europe PMC
 
[118]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897997
Bergeron, Anne, Medvedev, Paul, and Stoye, Jens. “Rearrangement Models and Single-Cut Operations”. Journal of Computational Biology 17.9 (2010): 1213-1225.
PUB | DOI | WoS | PubMed | Europe PMC
 
[117]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919211
Hufsky, Franziska, Kuchenbecker, Leon, Jahn, Katharina, Stoye, Jens, and Böcker, Sebastian. “Swiftly Computing Center Strings”. Proc. of WABI 2010. 2010.Vol. 6293. LNBI. 325-336.
PUB | DOI | WoS | PubMed | Europe PMC
 
[116]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919216
Kovac, Jakub, Dias Vieira Braga, Marília, and Stoye, Jens. “The Problem of Chromosome Reincorporation in DCJ Sorting and Halving”. Proc. of Recomb-CG 2010. 2010.Vol. 6398. LNBI. 13-24.
PUB | DOI
 
[115]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898025
Dias Vieira Braga, Marília, and Stoye, Jens. “The Solution Space of Sorting by DCJ”. Journal of Computational Biology 17.9 (2010): 1145-1165.
PUB | DOI | WoS | PubMed | Europe PMC
 
[114]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919215
Dias Vieira Braga, Marília, Willing, Eyla, and Stoye, Jens. “Genomic Distance with DCJ and Indels”. Proc. of WABI 2010. 2010.Vol. 6293. LNBI. 90-101.
PUB | DOI
 
[113]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919206
Dias Vieira Braga, Marília, and Stoye, Jens. “Counting All DCJ Sorting Scenarios”. Proc. of Recomb-CG 2009. 2009.Vol. 5817. LNBI. 36-47.
PUB | DOI
 
[112]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919207
Blin, Guillaume, and Stoye, Jens. “Finding Nested Common Intervals Efficiently”. Proc. of Recomb-CG 2009. 2009.Vol. 5817. LNBI. 59-69.
PUB | DOI | WoS | PubMed | Europe PMC
 
[111]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898137
Jahn, Katharina, and Stoye, Jens. “Approximative Gencluster und ihre Anwendung in der komparativen Genomik”. Informatik-Spektrum 32.4 (2009): 288-300.
PUB | DOI
 
[110]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1893884
Husemann, Peter, and Stoye, Jens. “Phylogenetic Comparative Assembly”. Proc. of WABI 2009. 2009.Vol. 5724. LNBI. 145-156.
PUB | DOI | WoS | PubMed | Europe PMC
 
[109]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1591507
Stoye, Jens, and Wittler, Roland. “A Unified Approach for Reconstructing Ancient Gene Clusters”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 6.3 (2009): 387-400.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[108]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589098
Gerlach, Wolfgang, Jünemann, Sebastian, Tille, Felix, Goesmann, Alexander, and Stoye, Jens. “WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads”. BMC Bioinformatics 10.1 (2009): 430.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[107]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589663
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “A New Linear Time Algorithm to Compute the Genomic Distance via the Double Cut and Join Distance”. Theoretical Computer Science 410.51 (2009): 5300-5316.
PUB | DOI | WoS
 
[106]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1590204
Brudno, Michael, Medvedev, Paul, Stoye, Jens, and De La Vega, Francisco M. “A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)”. BIOINFORMATICS 25.21 (2009): 2863-2864.
PUB | DOI | WoS | PubMed | Europe PMC
 
[105]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898105
Böcker, Sebastian, Jahn, Katharina, Mixtacki, Julia, and Stoye, Jens. “Computation of Median Gene Clusters”. Journal of Computational Biology 16.8 (2009): 1085-1099.
PUB | DOI | WoS | PubMed | Europe PMC
 
[104]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1591319
Hoffmann, Nils, and Stoye, Jens. “ChromA: signal-based retention time alignment for chromatography-mass spectrometry data”. Bioinformatics 25.16 (2009): 2080-2081.
PUB | DOI | WoS | PubMed | Europe PMC
 
[103]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919209
Medvedev, Paul, and Stoye, Jens. “Rearrangement Models and Single-Cut Operations”. Comparative Genomics : International Workshop, RECOMB-CG 2009, Budapest, Hungary, September 27-29, 2009. Proceedings. Berlin, Heidelberg: Springer, 2009.Vol. 5817. Lecture Notes in Computer Science. 84-97.
PUB | DOI
 
[102]
2009 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918945
Stoye, Jens. “Computational Short Read Metagenomics”. Presented at the JOBIM 2009, Nantes, France, 2009.
PUB
 
[101]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1634447
Bekel, Thomas, Henckel, Kolja, Küster, Helge, Meyer, Folker, Mittard-Runte, Virginie, Neuweger, Heiko, Paarmann, Daniel, Rupp, Oliver, Zakrzewski, Martha, Pühler, Alfred, Stoye, Jens, and Goesmann, Alexander. “The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies”. Journal of Biotechnology 140.1-2 (2009): 3-12.
PUB | DOI | WoS | PubMed | Europe PMC
 
[100]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919198
Quitzau, José Augusto Amgarten, and Stoye, Jens. “Detecting Repeat Families in Incompletely Sequenced Genomes”. Proc. of WABI 2008. 2008.Vol. 5251. LNBI. 342-353.
PUB | DOI
 
[99]
2008 | Report | PUB-ID: 1970459
Quitzau, José Augusto Amgarten, and Stoye, Jens. A space efficient representation for sparse de Bruijn subgraphs. Bielefeld: Technische Fakultät der Universität Bielefeld, 2008. Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld.
PUB | PDF
 
[98]
2008 | Report | PUB-ID: 1970461
Ejaz, Tahir, Rahmann, Sven, and Stoye, Jens. Online Abelian Pattern Matching. Bielefeld: Technische Fakultät der Universität Bielefeld, 2008. Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld.
PUB | PDF
 
[97]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1636699
Neuweger, Heiko, Albaum, Stefan, Dondrup, Michael, Persicke, Marcus, Watt, Tony, Niehaus, Karsten, Stoye, Jens, and Goesmann, Alexander. “MeltDB: a software platform for the analysis and integration of metabolomics experiment data”. Bioinformatics 24.23 (2008): 2726-2732.
PUB | DOI | WoS | PubMed | Europe PMC
 
[96]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919192
Böcker, Sebastian, Jahn, Katharina, Mixtacki, Julia, and Stoye, Jens. “Computation of Median Gene Clusters”. Proc. of RECOMB 2008. 2008.Vol. 4955. LNBI. 331-345.
PUB | DOI
 
[95]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919200
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios”. Proc. of Recomb-CG 2008. 2008.Vol. 5267. LNBI. 226-240.
PUB | DOI
 
[94]
2008 | Lexikoneintrag | Veröffentlicht | PUB-ID: 1918834
Stoye, Jens. “Suffix Tree Construction in RAM (1997; Farach-Colton)”. Encyclopedia of Algorithms. Ed. Ming-Yang Kao. Springer Verlag, 2008. 925-928.
PUB | DOI
 
[93]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1587078
Schürmann, Klaus-Bernd, and Stoye, Jens. “Counting suffix arrays and strings”. THEORETICAL COMPUTER SCIENCE 395.2-3 (2008): 220-234.
PUB | DOI | WoS
 
[92]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1586009
Krause, Lutz, Diaz, Naryttza N., Edwards, Robert A., Gartemann, Karl-Heinz, Krömeke, Holger, Neuweger, Heiko, Pühler, Alfred, Runte, Kai J., Schlüter, Andreas, Stoye, Jens, Szczepanowski, Rafael, Tauch, Andreas, and Goesmann, Alexander. “Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor”. JOURNAL OF BIOTECHNOLOGY 136.1-2 (2008): 91-101.
PUB | DOI | WoS | PubMed | Europe PMC
 
[91]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1586785
Oehm, Sebastian, Gilbert, David, Tauch, Andreas, Stoye, Jens, and Goesmann, Alexander. “Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms”. NUCLEIC ACIDS RESEARCH 36.Web Server (2008): W433-W437.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[90]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783364
Krause, Lutz, Diaz, Naryttza N., Goesmann, Alexander, Kelley, Scott, Nattkemper, Tim Wilhelm, Rohwer, Forest, Edwards, Robert A., and Stoye, Jens. “Phylogenetic classification of short environmental DNA fragments”. Nucleic Acids Research 36.7 (2008): 2230-2239.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[89]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919195
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “HP Distance via Double Cut and Join Distance”. Combinatorial Pattern Matching. 19th Annual Symposium, CPM 2008, Pisa, Italy, June 18-20, 2008 Proceedings. 2008. Lecture Notes in Computer Science, 5029. 56-68.
PUB | DOI
 
[88]
2007 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918828
Schmidt, Thomas, and Stoye, Jens. “Chapter 12: Gecko and GhostFam - Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes”. Comparative Genomics, Volume 2. Ed. Nicholas H. Bergman. Totowa, NJ: Humana Press Inc., 2007.Vol. 396. Methods in Molecular Biology. 165-182.
PUB | DOI | PubMed | Europe PMC
 
[87]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918432
Didier, Gilles, Schmidt, Thomas, Stoye, Jens, and Tsur, Dekel. “Character Sets of Strings”. Journal of Discrete Algorithms 5.2 (2007): 330-340.
PUB | DOI
 
[86]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1595253
Schürmann, Klaus-Bernd, and Stoye, Jens. “An incomplex algorithm for fast suffix array construction”. SOFTWARE-PRACTICE & EXPERIENCE 37.3 (2007): 309-329.
PUB | DOI | WoS
 
[85]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783345
Krause, Lutz, McHardy, Alice C., Nattkemper, Tim Wilhelm, Pühler, Alfred, Stoye, Jens, and Meyer, Folker. “GISMO - gene identification using a support vector machine for ORF classification”. Nucleic Acids Research 35.2 (2007): 540-549.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[84]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1630781
Mellmann, Alexander, Weniger, Thomas, Berssenbrügge, Christoph, Rothgänger, Jörg, Sammeth, Michael, Stoye, Jens, and Harmsen, Dag. “Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms”. BMC MICROBIOLOGY 7.1 (2007): 98.
PUB | DOI | WoS | PubMed | Europe PMC
 
[83]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599943
Sammeth, Michael, Griebel, Thasso, Tille, Felix, and Stoye, Jens. “Panta rhei (QAlign2): an open graphical environment for sequence analysis”. BIOINFORMATICS 22.7 (2006): 889-890.
PUB | DOI | WoS | PubMed | Europe PMC
 
[82]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599570
Rasmussen, Kim R., Stoye, Jens, and Myers, Eugene W. “Efficient q-gram filters for finding all epsilon-matches over a given length”. JOURNAL OF COMPUTATIONAL BIOLOGY 13.2 (2006): 296-308.
PUB | DOI | WoS | PubMed | Europe PMC
 
[81]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599574
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “On sorting by translocations”. JOURNAL OF COMPUTATIONAL BIOLOGY 13.2 (2006): 567-578.
PUB | DOI | WoS | PubMed | Europe PMC
 
[80]
2006 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1596811
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “A Unifying View of Genome Rearrangements”. Proc. of WABI 2006. SPRINGER-VERLAG BERLIN, 2006.Vol. 4175. LNBI. 163-173.
PUB | DOI | WoS
 
[79]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1597213
Sammeth, Michael, and Stoye, Jens. “Comparing tandem repeats with duplications and excisions of variable degree”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 3.4 (2006): 395-407.
PUB | DOI | WoS | PubMed | Europe PMC
 
[78]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1597313
Bergeron, Anne, and Stoye, Jens. “On the similarity of sets of permutations and its applications to genome comparison”. JOURNAL OF COMPUTATIONAL BIOLOGY 13.7 (2006): 1340-1354.
PUB | DOI | WoS | PubMed | Europe PMC
 
[77]
2006 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918946
Stoye, Jens. “Index Structures in Biological Sequence Analysis: From Simplicity to Complexity and Back”. Presented at the JOBIM 2006, Bordeaux, France, 2006.
PUB
 
[76]
2006 | Report | PUB-ID: 1970464
Chauve, Cedric, Diekmann, Yoan, Heber, Steffen, Mixtacki, Julia, Rahmann, Sven, and Stoye, Jens. On Common Intervals with Errors. Bielefeld: Technische Fakultät der Universität Bielefeld, 2006. Forschungsberichte.
PUB | PDF
 
[75]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1631957
Krause, Lutz, Diaz, Naryttza N., Bartels, Daniela, Edwards, Robert A., Pühler, Alfred, Rohwer, Forest, Meyer, Folker, and Stoye, Jens. “Finding novel genes in bacterial communities isolated from the environment”. BIOINFORMATICS 22.14 (2006): e281-e289.
PUB | DOI | WoS | PubMed | Europe PMC
 
[74]
2005 | Report | PUB-ID: 1970470
Sammeth, Michael, and Stoye, Jens. Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). Bielefeld: Technische Fakultät der Universität Bielefeld, 2005. Forschungsberichte.
PUB | PDF | DOI
 
[73]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919012
Schürmann, Klaus-Bernd, and Stoye, Jens. “An Incomplex Algorithm for Fast Suffix Array Construction”. Proc. of ALENEX/ANALCO 2005. 2005. 77-85.
PUB
 
[72]
2005 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918824
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “Chapter 10: The Inversion Distance Problem”. Mathematics of Evolution and Phylogeny. Ed. Olivier Gascuel. Oxford University Press, 2005. 262-290.
PUB
 
[71]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1603220
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “On Sorting by Translocations”. Proc. of RECOMB 2005. SPRINGER-VERLAG BERLIN, 2005.Vol. 3500. LNBI. 615-629.
PUB | DOI | WoS
 
[70]
2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1775168
Krause, Antje, Stoye, Jens, and Vingron, Martin. “Large scale hierarchical clustering of protein sequences”. BMC Bioinformatics 6.1 (2005): 15.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[69]
2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773302
Bartels, Daniela, Kespohl, Sebastian, Albaum, Stefan, Drüke, Tanja, Goesmann, Alexander, Herold, Julia, Kaiser, Olaf, Pühler, Alfred, Pfeiffer, Friedhelm, Raddatz, Günter, Stoye, Jens, Meyer, Folker, and Schuster, Stephan C. “BACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison”. Bioinformatics 21.7 (2005): 853-859.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[68]
2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918947
Böcker, Sebastian, and Stoye, Jens. “Informatische Methoden zur Protein-Identifikation”. LaborPraxis 29.10 (2005): 24-26.
PUB
 
[67]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1601348
Bannert, Constantin, and Stoye, Jens. “Protein Annotation by Secondary Structure Based Alignments (PASSTA)”. Proc. of CompLife 2005. Springer-Verlag, 2005.Vol. 3695. LNBI. 79-90.
PUB | DOI | WoS
 
[66]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1601361
Sammeth, Michael, Weniger, Thomas, Harmsen, Dag, and Stoye, Jens. “Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)”. Proc. of WABI 2005. SPRINGER-VERLAG BERLIN, 2005.Vol. 3692. LNBI. 276-290.
PUB | DOI | WoS
 
[65]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1603216
Rasmussen, Kim R., Stoye, Jens, and Myers, Eugene W. “Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length”. Proc. of RECOMB 2005. SPRINGER-VERLAG BERLIN, 2005.Vol. 3500. LNBI. 189-203.
PUB | DOI | WoS
 
[64]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919026
Schürmann, Klaus-Bernd, and Stoye, Jens. “Counting Suffix Arrays and Strings”. Proc. of SPIRE 2005. 2005.Vol. 3772. LNCS. 55-66.
PUB | DOI
 
[63]
2005 | Report | PUB-ID: 1970472
Schürmann, Klaus-Bernd, and Stoye, Jens. Counting Suffix Arrays and Strings. Bielefeld: Technische Fakultät der Universität Bielefeld, 2005. Forschungsberichte.
PUB | PDF
 
[62]
2004 | Konferenzband | Veröffentlicht | PUB-ID: 1918823
Robert Giegerich and Jens Stoye, eds. “Proceedings of the German Conference on Bioinformatics, GCB 2004”. Lecture Notes in Informatics P-53 (2004).
PUB
 
[61]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1606286
Michael, Morris, Dieterich, Christoph, and Stoye, Jens. “Suboptimal Local Alignments across Multiple Scoring Schemes”. Proc. of WABI 2004. SPRINGER-VERLAG BERLIN, 2004.Vol. 3240. LNBI. 99-110.
PUB | DOI | WoS
 
[60]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1607260
Schmidt, Thomas, and Stoye, Jens. “Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences”. Proc. of CPM 2004. 2004.Vol. 3109. LNCS. 347-358.
PUB | DOI | WoS
 
[59]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773554
Pollard, Daniel A., Bergman, Casey M., Stoye, Jens, Celniker, Susan E., and Eisen, Michael B. “Correction: Benchmarking tools for the alignment of functional noncoding DNA”. BMC Bioinformatics 5.1 (2004): 73.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[58]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773560
Cieliebak, Mark, Erlebach, Thomas, Lipták, Zsuzsanna, Stoye, Jens, and Welzl, Emo. “Algorithmic complexity of protein identification: combinatorics of weighted strings”. Discrete Applied Mathematics 137.1 (2004): 27-46.
PUB | PDF | DOI | WoS
 
[57]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773312
Pollard, Daniel A., Bergman, Casey M., Stoye, Jens, Celniker, Susan E., and Eisen, Michael B. “Benchmarking tools for the alignment of functional noncoding DNA”. BMC Bioinformatics 5.1 (2004): 6.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[56]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773569
Gusfield, Dan, and Stoye, Jens. “Linear time algorithms for finding and representing all the tandem repeats in a string”. Journal of computer and system sciences 69.4 (2004): 525-546.
PUB | PDF | DOI | WoS
 
[55]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1607263
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “Reversal Distance without Hurdles and Fortresses”. Proc. of CPM 2004. SPRINGER-VERLAG BERLIN, 2004.Vol. 3109. LNCS. 388-399.
PUB | DOI | WoS
 
[54]
2003 | Report | PUB-ID: 1970475
Schürmann, Klaus-Bernd, and Stoye, Jens. Suffix Tree Construction and Storage with Limited Main Memory. Bielefeld: Technische Fakultät der Universität Bielefeld, 2003. Forschungsberichte.
PUB | PDF
 
[53]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1612664
Heber, Steffen, and Stoye, Jens. “The European Conference on Computational Biology”. Drug Discovery Today 8.3 (2003): 113-114.
PUB | DOI | WoS | PubMed | Europe PMC
 
[52]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918949
Giegerich, Robert, and Stoye, Jens. “Finden, fast ohne zu suchen: Indexstrukturen in der Bioinformatik”. Forschung an der Universität Bielefeld 26 (2003): 63-68.
PUB
 
[51]
2003 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919005
Bannert, Constantin, and Stoye, Jens. “Evaluation of the Jumping Alignment Algorithm with Artificial and Biological Data”. Proc. of GCB 2003. 2003. 21-25.
PUB
 
[50]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1610397
Giegerich, Robert, Kurtz, Stefan, and Stoye, Jens. “Efficient implementation of lazy suffix trees”. SOFTWARE-PRACTICE & EXPERIENCE 33.11 (2003): 1035-1049.
PUB | PDF | DOI | WoS
 
[49]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1609403
Sammeth, Michael, Morgenstern, Burkhard, and Stoye, Jens. “Divide-and-conquer multiple alignment with segment-based constraints”. BIOINFORMATICS 19.Suppl 2 (2003): ii189-ii195.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[48]
2003 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1610433
Bergeron, Anne, and Stoye, Jens. “On the similarity of sets of permutations and its applications to genome comparison”. Proc. of COCOON 2003. 2003.Vol. 2697. LNCS. 68-79.
PUB | DOI | WoS
 
[47]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1610503
Sammeth, Michael, Rothgänger, Jörg, Esser, Wolfram, Albert, Jürgen, Stoye, Jens, and Harmsen, Dag. “QAlign: quality-based multiple alignments with dynamic phylogenetic analysis”. BIOINFORMATICS 19.12 (2003): 1592-1593.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[46]
2003 | Report | PUB-ID: 1970477
Bergeron, Anne, and Stoye, Jens. On the Similarity of Sets of Permutations and its Applications to Genome Comparison. Bielefeld: Technische Fakultät der Universität Bielefeld, 2003. Forschungsberichte.
PUB | PDF
 
[45]
2002 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918951
Stoye, Jens. “Index Structures for Large Sequence Data: Suffix Trees and Affix Trees”. Lecture Notes in Informatics. Ed. Sigrid Schubert, Bernd Reusch, and Norbert Jesse. 2002.Vol. P-20. 67-67.
PUB
 
[44]
2002 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919000
Cieliebak, Marc, Lipták, Zsuzsanna, Welzl, Emo, Erlebach, Thomas, and Stoye, Jens. “Algorithmic Complexity of Protein Identification: Searching in Weighted Strings”. Proc. of IFIP TCS 2002. 2002. 143-156.
PUB
 
[43]
2002 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773578
Spang, Rainer, Rehmsmeier, Marc, and Stoye, Jens. “A novel approach to remote homology detection: jumping alignments”. Journal of Computational Biology 9.5 (2002): 747-760.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[42]
2002 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773332
Stoye, Jens, and Gusfield, Dan. “Simple and flexible detection of contiguous repeats using a suffix tree”. Theoretical Computer Science 270.1-2 (2002): 843-856.
PUB | PDF | DOI | WoS
 
[41]
2002 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773329
Bergeron, Anne, Heber, Steffen, and Stoye, Jens. “Common intervals and sorting by reversals: a marriage of necessity”. Bioinformatics 18.Suppl 2 (2002): S54-S63.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[40]
2002 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918995
Heber, Steffen, Stoye, Jens, Frohme, Marcus, Hoheisel, Jörg, and Vingron, Martin. “Resampling Methods in Physical Mapping”. Proc. of GfKl 2000. 2002. 437-444.
PUB
 
[39]
2001 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773335
Kurtz, Stefan, Choudhuri, Jomuna V., Ohlebusch, Enno, Schleiermacher, Chris, Stoye, Jens, and Giegerich, Robert. “REPuter: the manifold applications of repeat analysis on a genomic scale”. Nucleic Acids Research 29.22 (2001): 4633-4642.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[38]
2001 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918992
Heber, Steffen, and Stoye, Jens. “Finding all Common Intervals of k Permutations”. Proc. of CPM 2001. 2001.Vol. 2089. LNCS. 207-218.
PUB | DOI
 
[37]
2001 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1880197
Heber, Steffen, and Stoye, Jens. “Algorithms for Finding Gene Clusters”. Proc. of WABI 2001. Berlin: Sppringer, 2001.Vol. 2149. LNCS. 252-263.
PUB | DOI
 
[36]
2001 | Report | PUB-ID: 1970479
Cieliebak, Marc, Erlebach, Thomas, Lipták, Zsuzsanna, Stoye, Jens, and Welzl, Emo. Algorithmic Complexity of Protein Identification: Combinatorics of Weighted Strings. ETH Zürich, Dept. of Computer Science, 2001. Technical Report.
PUB
 
[35]
2000 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918981
Heber, Steffen, Stoye, Jens, Hoheisel, Jörg, and Vingron, Martin. “Contig Selection in Physical Mapping”. Proc. of RECOMB 2000. 2000. 155-164.
PUB | DOI | WoS | PubMed | Europe PMC
 
[34]
2000 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918817
Brodal, Gerth S., Lyngsø, Rune B., Pedersen, Christian N. S., and Stoye, Jens. “Finding Maximal Pairs with Bounded Gap”. Matching Patterns (Journal of Discrete Algorithms). Ed. Maxime Crochemore and Leszek Gąsieniec. 2000. 77-104.
PUB
 
[33]
2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773345
Krause, Antje, Stoye, Jens, and Vingron, Martin. “The SYSTERS protein sequence cluster set”. Nucleic Acids Research 28.1 (2000): 270-272.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[32]
2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773572
Heber, Steffen, Stoye, Jens, Frohme, Marcus, Hoheisel, Jörg, and Vingron, Martin. “Contig selection in physical mapping”. Journal of Computational Biology 7.3-4 (2000): 395-408.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[31]
2000 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918985
Spang, Rainer, Rehmsmeier, Marc, and Stoye, Jens. “Sequence Database Search Using Jumping Alignments”. Proc. of ISMB 2000. 2000. 367-375.
PUB | PubMed | Europe PMC
 
[30]
2000 | Report | PUB-ID: 1970490
Stoye, Jens. Affix Trees. Technische Fakultät der Universität Bielefeld, 2000. Forschungsberichte.
PUB | PDF
 
[29]
2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773341
Reinert, Knut, Stoye, Jens, and Will, Torsten. “An iterative method for faster sum-of-pairs multiple sequence alignment”. Bioinformatics 16.9 (2000): 808-814.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[28]
2000 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918988
Kurtz, Stefan, Ohlebusch, Enno, Schleiermacher, Chris, Stoye, Jens, and Giegerich, Robert. “Computation and Visualization of Degenerate Repeats in Complete Genomes”. Proc. of ISMB 2000. 2000. 228-238.
PUB | PubMed | Europe PMC
 
[27]
2000 | Konferenzband | Veröffentlicht | PUB-ID: 1918813
Erich Bornberg-Bauer, Ursula Rost, Jens Stoye, and Martin Vingron, eds. Proceedings of the German Conference on Bioinformatics, GCB 2000. Berlin: Logos Verlag, 2000.
PUB
 
[26]
1999 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1620435
Giegerich, Robert, Kurtz, Stefan, and Stoye, Jens. “Efficient implementation of lazy suffix trees”. Algorithm Engineering. 3rd International Workshop, WAE’99 London, UK, July 19–21, 1999 Proceedings. 1999.Vol. 1668. LNCS. 30-42.
PUB | DOI | WoS
 
[25]
1999 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918978
Reinert, Knut, Will, Torsten, and Stoye, Jens. “Combining Divide-and-Conquer, the A*-Algorithm, and Successive Realignment Approaches to Speed up Multiple Sequence Alignment”. Proc. of GCB 1999. 1999. 17-24.
PUB | Download (ext.)
 
[24]
1999 | Report | PUB-ID: 1970495
Morgenstern, Burkhard, Stoye, Jens, and Dress, Andreas. Consistent Equivalence Relations: A Set-Theoretical Framework for Multiple Sequence Alignment. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1999. Materialien/Preprints.
PUB
 
[23]
1999 | Report | PUB-ID: 1970509
Brodal, Gerth S., Lyngsø, Rune B., Pedersen, Christian N. S., and Stoye, Jens. Finding Maximal Pairs with Bounded Gap. BRICS, Department of Computer Science, University of Aarhus, 1999. Report.
PUB
 
[22]
1999 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918971
Brodal, Gerth S., Lyngsø, Rune B., Pedersen, Christian N. S., and Stoye, Jens. “Finding Maximal Pairs with Bounded Gap”. Proc. of CPM 1999. 1999.Vol. 1645. LNCS. 134-149.
PUB | DOI
 
[21]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2488102
Dress, Andreas, Morgenstern, Burkhard, and Stoye, Jens. “The Number of Standard and of Effective Multiple Alignments”. Appl. Math. Lett. 11.4 (1998): 43-49.
PUB
 
[20]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918538
Hildebrand, Martin, and Stoye, Jens. “Die Bedeutung der Zusammenarbeit der Disziplinen in der Anwendung - erläutert anhand von Beispielen”. Der Mathematikunterricht 44.6 (1998): 34-53.
PUB
 
[19]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1667771
Stoye, Jens. “Multiple sequence alignment with the Divide-and-Conquer method.”. Gene 211.2 (1998): GC45-GC56.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[18]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1625402
Stoye, Jens, Evers, Dirk, and Meyer, Folker. “Rose: generating sequence families”. BIOINFORMATICS 14.2 (1998): 157-163.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[17]
1998 | Report | PUB-ID: 1970515
Stoye, Jens, and Gusfield, Dan. Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree. Department of Computer Science, University of California, Davis, 1998. Report.
PUB
 
[16]
1998 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918964
Stoye, Jens, and Gusfield, Dan. “Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version)”. Proc. of CPM 1998. 1998.Vol. 1448. LNCS. 140-152.
PUB | DOI
 
[15]
1998 | Report | PUB-ID: 1970513
Gusfield, Dan, and Stoye, Jens. Linear Time Algorithms for Finding and Representing all the Tandem Repeats in a String. Department of Computer Science, University of California, Davis, 1998. Report.
PUB
 
[14]
1997 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2488107
Stoye, Jens, Moulton, Vincent, and Dress, Andreas. “DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment”. CABIOS 13.6 (1997): 625-626.
PUB
 
[13]
1997 | Report | PUB-ID: 1970526
Perrey, Sören W., Stoye, Jens, Moulton, Vincent, and Dress, Andreas. On Simultaneous versus Iterative Multiple Sequence Alignment. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1997. Materialien/Preprints.
PUB
 
[12]
1997 | Report | PUB-ID: 1970517
Stoye, Jens, Evers, Dirk, and Meyer, Folker. Rose: Generating Sequence Families. Technische Fakultät der Universität Bielefeld, 1997. Forschungsberichte.
PUB
 
[11]
1997 | Report | PUB-ID: 1970529
Brinkmann, Gunnar, Dress, Andreas, Perrey, Sören W., and Stoye, Jens. Two Applications of the Divide & Conquer Principle in the Molecular Sciences. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1997. Materialien/Preprints.
PUB
 
[10]
1997 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1667885
Stoye, Jens, Evers, Dirk, and Meyer, Folker. “Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions”. Proc. of ISMB 1997. 1997. 303-306.
PUB | PubMed | Europe PMC
 
[9]
1997 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773355
Stoye, Jens, Perrey, Sören W., and Dress, Andreas. “Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment”. Applied mathematics letters 10.2 (1997): 67-73.
PUB | PDF | DOI | WoS
 
[8]
1997 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773358
Brinkmann, Gunnar, Dress, Andreas, Perrey, Sören W., and Stoye, Jens. “Two applications of the Divide & Conquer principle in the molecular sciences”. Mathematical programming 79.1-3 (1997): 71-97.
PUB | DOI | WoS
 
[7]
1997 | Report | PUB-ID: 1970523
Dress, Andreas, Morgenstern, Burkhard, and Stoye, Jens. On the Number of Standard and Effective Multiple Alignments. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1997. Materialien/Preprints.
PUB
 
[6]
1997 | Report | PUB-ID: 1970520
Perrey, Sören W., Stoye, Jens, and Moulton, Vincent. FDCA: Fast and Accurate Approximation to Sum-of-Pairs Score Optimal Multiple Sequence Alignment. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1997. Materialien/Preprints.
PUB
 
[5]
1997 | Report | PUB-ID: 1970532
Stoye, Jens. Divide-and-Conquer Multiple Sequence Alignment. Technische Fakultät der Universität Bielefeld, 1997. Forschungsberichte.
PUB
 
[4]
1996 | Report | PUB-ID: 1970533
Perrey, Sören W., and Stoye, Jens. Fast Approximation to the NP-hard Problem of Multiple Sequence Alignment. Dept. of Mathematics, Massey University, Palmerston North, New Zealand, 1996. Information and Mathematical Sciences Reports, Series B.
PUB
 
[3]
1996 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773351
Tönges, Udo, Perrey, Sören W., Stoye, Jens, and Dress, Andreas. “A general method for fast multiple sequence alignment”. Gene 172.1 (1996): GC33-GC41.
PUB | DOI | WoS | PubMed | Europe PMC
 
[2]
1996 | Report | PUB-ID: 1970535
Stoye, Jens, Dress, Andreas, and Perrey, Sören W. Improving the Divide-and-Conquer Approach to Sum-of-Pairs Multiple Sequence Alignment. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1996. Materialien/Preprints.
PUB
 
[1]
1996 | Report | PUB-ID: 1970537
Tönges, Udo, Perrey, Sören W., Stoye, Jens, and Dress, Andreas. A General Method for Fast Multiple Sequence Alignment. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1996. Materialien/Preprints.
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[201]
2019 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2932883
Dörr, Daniel, and Stoye, Jens. “A Perspective on Comparative and Functional Genomics”. Bioinformatics and Phylogenetics. Ed. Tandy Warnow. Cham: Springer , 2019.Vol. 29. Computational Biology. 361-372.
PUB | DOI
 
[200]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2932884
Oey, Harald, Zakrzewski, Martha, Gravermann, Kerstin, Young, Neil D., Korhonen, Pasi K., Gobert, Geoffrey N., Nawaratna, Sujeevi, Hasan, Shibab, Martínez, David M., You, Hong, Lavin, Martin, Jones, Malcolm, Ragan, Mark A., Stoye, Jens, Oleaga, Ana, Emery, Aidan M., Webster, Bonnie, Rollinson, David, Gasser, Robin B., McManus, Donald P., and Krause, Lutz. “Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium”. PLOS Pathogens 15.1 (2019): e1007513.
PUB | DOI | WoS | PubMed | Europe PMC
 
[199]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919005
Schulz, Tizian, Stoye, Jens, and Dörr, Daniel. “GraphTeams. A method for discovering spatial gene clusters in Hi-C sequencing data”. BMC Genomics 19.Suppl. 5 (2018): 308.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[198]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919006
Rubert, Diego, Hoshino, Edna A., Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. “Computing the family-free DCJ similarity”. BMC Bioinformatics 19.Suppl. 6 (2018): 152.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[197]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918481
Luhmann, Nina, Chauve, Cedric, Stoye, Jens, and Wittler, Roland. “Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 15.6 (2018): 2094-2100.
PUB | DOI | WoS | PubMed | Europe PMC
 
[196]
2018 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2930445
Cunha, Luís, Diekmann, Yoan, Kowada, Luis, and Stoye, Jens. “Identifying Maximal Perfect Haplotype Blocks”. Proceedings of BSB 2018. Springer Verlag, 2018.Vol. 11228. LNBI. 26-37.
PUB | DOI
 
[195]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930268
Holley, Guillaume, Wittler, Roland, Stoye, Jens, and Hach, Faraz. “Dynamic Alignment-Free and Reference-Free Read Compression”. JOURNAL OF COMPUTATIONAL BIOLOGY 25.7 (2018): 825-836.
PUB | DOI | WoS | PubMed | Europe PMC
 
[194]
2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913921
Zekic, Tina, Holley, Guillaume, and Stoye, Jens. “Pan-genome Storage and Analysis Techniques”. Comparative Genomics. Methods and Protocols. Ed. João C. Setubal, Peter Stadler, and Jens Stoye. New York: Springer Verlag, 2018.Vol. 1704. Methods in Molecular Biology. 29-53.
PUB
 
[193]
2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913922
Dörr, Daniel, Feijão, Pedro, and Stoye, Jens. “Family-Free Genome Comparison”. Comparative Genomics: Methods and Protocols. Ed. João C. Setubal, Peter Stadler, and Jens Stoye. New York: Springer Verlag, 2018.Vol. 1704. Methods in Molecular Biology. 331-342.
PUB
 
[192]
2018 | Herausgeber Sammelwerk | Veröffentlicht | PUB-ID: 2913920
João C Setubal, Peter Stadler, and Jens Stoye, eds. Comparative Genomics: Methods and Protocols. New York: Springer Verlag, 2018. Methods in Molecular Biology. 1704.
PUB
 
[191]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919012
Jaenicke, Sebastian, Albaum, Stefan, Blumenkamp, Patrick, Linke, Burkhard, Stoye, Jens, and Goesmann, Alexander. “Flexible metagenome analysis using the MGX framework”. Microbiome 6 (2018): 76.
PUB | DOI | WoS | PubMed | Europe PMC
 
[190]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556
Jünemann, Sebastian, Kleinbölting, Nils, Jaenicke, Sebastian, Henke, Christian, Hassa, Julia, Nelkner, Johanna, Stolze, Yvonne, Albaum, Stefan, Schlüter, Andreas, Goesmann, Alexander, Sczyrba, Alexander, and Stoye, Jens. “Bioinformatics for NGS-based metagenomics and the application to biogas research”. Journal of Biotechnology 261.SI (2017): 10-23.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[189]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913015
Rubert, Diego, Medeiros, Gabriel L., Hoshino, Edna A., Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. “Algorithms for Computing the Family-Free Genomic Similarity under DCJ”. Comparative Genomics. RECOMB-CG 2017. Ed. Joao Meidanis and Luay Nakhleh. Cham: Springer Verlag, 2017.Vol. 10562. Lecture Notes in Bioinformatics. 76-100.
PUB | DOI
 
[188]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909057
Rubert, Diego, Feijão, Pedro, Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. “Approximating the DCJ distance of balanced genomes in linear time”. Algorithms for Molecular Biology 12 (2017): 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[187]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2909409
Cunha, Luis, Dantas, Simone, Gagie, Travis, Wittler, Roland, Kowada, Luis, and Stoye, Jens. “Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings”. Proceedings of CPM 2017. 2017.Vol. 78. LIPIcs. 19:1-19:9.
PUB | DOI
 
[186]
2017 | Preprint | Veröffentlicht | PUB-ID: 2908521
Cunha, Luís, Dantas, Simone, Gagie, Travis, Wittler, Roland, Kowada, Luis, and Stoye, Jens. “Faster Jumbled Indexing for Binary Run-Length Encoded Strings”. arXiv: 1702.01280 (2017).
PUB
 
[185]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2907587
Holley, Guillaume, Wittler, Roland, Stoye, Jens, and Hach, Faraz. “Dynamic Alignment-Free and Reference-Free Read Compression”. Proceedings of RECOMB 2017. 2017.Vol. 10229. Lecture Notes in Bioinformatics. 50-65.
PUB | DOI
 
[184]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913016
Schulz, Tizian, Stoye, Jens, and Dörr, Daniel. “Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery”. Proceedings of RECOMB-CG 2017. Berlin: Springer Verlag, 2017.Vol. 1704. Lecture Notes in Bioinformatics. 197-212.
PUB | DOI
 
[183]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909967
Dörr, Daniel, Kowada, Luis Antonio B., Soares de Araujo, Francisco Eloi, Deshpande, Shachi, Dantas, Simone, Moret, Bernard M. E., and Stoye, Jens. “New Genome Similarity Measures based on Conserved Gene Adjacencies”. Journal of Computational Biology 24.6 (2017): 616-634.
PUB | DOI | WoS | PubMed | Europe PMC
 
[182]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905930
Winter, Sascha, Jahn, Katharina, Wehner, Stefanie, Kuchenbecker, Leon, Marz, Manja, Stoye, Jens, and Böcker, Sebastian. “Finding approximate gene clusters with GECKO 3”. Nucleic Acids Research 44.20 (2016): 9600-9610.
PUB | DOI | WoS | PubMed | Europe PMC
 
[181]
2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2903708
Rubert, Diego, Feijão, Pedro, Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. “A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates”. Algorithms in Bioinformatics. WABI 2016. Ed. Martin Frith and Christian Nørgaard Storm Pedersen. Cham: Springer, 2016.Vol. 9838. Lecture Notes in Bioinformatics. 293-306.
PUB | DOI
 
[180]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900129
Holley, Guillaume, Wittler, Roland, and Stoye, Jens. “Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage”. Algorithms for Molecular Biology 11 (2016): 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[179]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900421
Krause, Lutz, Nones, Katia, Loffler, Kelly A., Nancarrow, Derek, Oey, Harald, Tang, Yup Hang, Wayte, Nicola J., Patch, Ann Marie, Patel, Kalpana, Brosda, Sandra, Manning, Suzanne, Lampe, Guy, Clouston, Andrew, Thomas, Janine, Stoye, Jens, Hussey, Damian J., Watson, David I., Lord, Reginald V., Phillips, Wayne A., Gotley, David, Smithers, B. Mark, Whiteman, David C., Hayward, Nicholas K., Grimmond, Sean M., Waddell, Nicola, and Barbour, Andrew P. “Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma”. Carcinogenesis 37.4 (2016): 356-365.
PUB | DOI | WoS | PubMed | Europe PMC
 
[178]
2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2900111
Kowada, Luis Antonio B., Doerr, Daniel, Dantas, Simone, and Stoye, Jens. “New Genome Similarity Measures based on Conserved Gene Adjacencies”. Research in Computational Molecular Biology. RECOMB 2016. Ed. Mona Singh. Springer, 2016.Vol. 9649. Lecture Notes in Bioinformatics (LNBI). 204-224.
PUB | DOI
 
[177]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2677844
Dias Vieira Braga, Marília, and Stoye, Jens. “Sorting linear genomes with rearrangements and indels”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 12.3 (2015): 500-506.
PUB | DOI | WoS | PubMed | Europe PMC
 
[176]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726366
Viduani Martinez, Fábio Henrique, Feijão, Pedro, Dias Vieira Braga, Marília, and Stoye, Jens. “On the family-free DCJ distance and similarity”. Algorithms for Molecular Biology 10 (2015): 13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[175]
2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2757497
Holley, Guillaume, Wittler, Roland, and Stoye, Jens. “Bloom Filter Trie - a data structure for pan-genome storage”. Proceedings of WABI 2015. 2015.Vol. 9289. LNBI. 217-230.
PUB
 
[174]
2015 | Konferenzband | Veröffentlicht | PUB-ID: 2780229
Joao Meidanis and Jens Stoye, eds. “Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Bioinformatics”. BMC Bioinformatics 16.Supplement 14 (2015).
PUB | Download (ext.)
 
[173]
2015 | Konferenzband | Veröffentlicht | PUB-ID: 2780232
Joao Meidanis and Jens Stoye, eds. “Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Genomics”. BMC Genomics 16.Supplement 10 (2015).
PUB | Download (ext.)
 
[172]
2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2684241
Viduani Martinez, Fábio Henrique, Feijão, Pedro, Dias Vieira Braga, Marília, and Stoye, Jens. “On the family-free DCJ distance”. Algorithms in Bioinformatics. WABI 2014. Ed. Dan Brown and Burkhard Morgenstern. Berlin ; Heidelberg: Springer Verlag, 2014.Vol. 8701. Lecture Notes in Bioinformatics. 174-186.
PUB | DOI
 
[171]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2687033
Dörr, Daniel, Stoye, Jens, Böcker, Sebastian, and Jahn, Katharina. “Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings”. BMC Genomics 15.Suppl. 6: Proc. of RECOMB-CG 2014 (2014): S2.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[170]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685362
Lechner, Marcus, Hernandez-Rosales, Maribel, Dörr, Daniel, Wieseke, Nicolas, Thévenin, Annelyse, Stoye, Jens, Hartmann, Roland K., Prohaska, Sonja J., and Stadler, Peter F. “Orthology Detection Combining Clustering and Synteny for Very Large Datasets”. PLoS ONE 9.8 (2014): e105015.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[169]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2689773
Jünemann, Sebastian, Prior, Karola, Albersmeier, Andreas, Albaum, Stefan, Kalinowski, Jörn, Goesmann, Alexander, Stoye, Jens, and Harmsen, Dag. “GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers”. PLOS ONE 9.9 (2014): e107014.
PUB | DOI | WoS | PubMed | Europe PMC
 
[168]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2674387
Hilker, Rolf, Stadermann, Kai Bernd, Doppmeier, Daniel, Kalinowski, Jörn, Stoye, Jens, Straube, Jasmin, Winnebald, Jörn, and Goesmann, Alexander. “ReadXplorer - Visualization and Analysis of Mapped Sequences”. Bioinformatics 30.16 (2014): 2247-2254.
PUB | DOI | WoS | PubMed | Europe PMC
 
[167]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665038
Schwientek, Patrick, Neshat, Armin, Kalinowski, Jörn, Klein, Andreas, Rückert, Christian, Schneiker-Bekel, Susanne, Wendler, Sergej, Stoye, Jens, and Pühler, Alfred. “Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts”. Journal of Biotechnology 190 (2014): 85-95.
PUB | DOI | WoS | PubMed | Europe PMC
 
[166]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685988
Jakobi, Tobias, Brinkrolf, Karina, Tauch, Andreas, Noll, Thomas, Stoye, Jens, Pühler, Alfred, and Goesmann, Alexander. “Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing”. Journal of Biotechnology 190 (2014): 64-75.
PUB | DOI | WoS | PubMed | Europe PMC
 
[165]
2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2690122
Luhmann, Nina, Chauve, Cedric, Stoye, Jens, and Wittler, Roland. “Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework”. Proc. of BSB 2014. Ed. Campos Sérgio. Springer Verlag, 2014.Vol. 8826. LNBI. 135-143.
PUB | DOI
 
[164]
2014 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2693552
Stoye, Jens. “Suffix Tree Construction”. Encyclopedia of Algorithms. Ed. M.-Y. Kao. Springer Verlag, 2014.
PUB | DOI
 
[163]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2643941
Hoffmann, Nils, Wilhelm, Mathias, Doebbe, Anja, Niehaus, Karsten, and Stoye, Jens. “BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry”. Bioinformatics 30.7 (2014): 988-995.
PUB | DOI | WoS | PubMed | Europe PMC
 
[162]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2693409
Fredrich, Eugenie, Ander, Christina, Stoye, Jens, Brune, Iris, and Tauch, Andreas. “Metatranskriptomik der Mikrobiota aus der menschlichen Achselhöhle”. BIOspektrum 20.5 (2014): 294-296.
PUB | DOI
 
[161]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333
Henrich, Birgit, Rumming, Madis, Sczyrba, Alexander, Velleuer, Eunike, Dietrich, Ralf, Gerlach, Wolfgang, Gombert, Michael, Rahn, Sebastian, Stoye, Jens, Borkhardt, Arndt, and Fischer, Ute. “Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma”. PLoS ONE 9.3 (2014): e92297.
PUB | DOI | WoS | PubMed | Europe PMC
 
[160]
2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2611641
Dias Vieira Braga, Marília, and Stoye, Jens. “Restricted DCJ-Indel Model Revisited”. Advances in Bioinformatics and Computational Biology. BSB 2013. Ed. João C. Setubal and Nalvo F. Almeida. Cham: Springer Verlag, 2013.Vol. 8213. Lecture Notes in Bioinformatics. 36-46.
PUB | DOI
 
[159]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611630
Willing, Eyla, Zaccaria, Simone, Dias Vieira Braga, Marília, and Stoye, Jens. “On the Inversion-Indel Distance”. BMC Bioinformatics 14.Suppl 15: Proc. of RECOMB-CG 2013 (2013): S3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[158]
2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611648
Dias Vieira Braga, Marília, Chauve, Cedric, Dörr, Daniel, Jahn, Katharina, Stoye, Jens, Thévenin, Annelyse, and Wittler, Roland. “The Potential of Family-Free Genome Comparison”. Models and Algorithms for Genome Evolution. Ed. Cedric Chauve, Nadia El-Mabrouk, and Eric Tannier. Springer Verlag, 2013.Vol. 19. Computational Biology Series. 287-307.
PUB | DOI
 
[157]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575011
Ander, Christina, Schulz-Trieglaff, Ole B., Stoye, Jens, and Cox, Anthony J. “metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences”. BMC Bioinformatics 14.Suppl 5: Proc. of RECOMB-Seq 2013 (2013): S2.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[156]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641228
Jünemann, Sebastian, Sedlazeck, Fritz Joachim, Prior, Karola, Albersmeier, Andreas, John, Uwe, Kalinowski, Jörn, Mellmann, Alexander, Goesmann, Alexander, von Haeseler, Arndt, Stoye, Jens, and Harmsen, Dag. “Corrigendum: Updating benchtop sequencing performance comparison”. Nature biotechnology 31.12 (2013): 1148.
PUB | DOI | WoS | PubMed | Europe PMC
 
[155]
2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611643
Bergeron, Anne, and Stoye, Jens. “The Genesis of the DCJ Formula”. Models and Algorithms for Genome Evolution. Ed. Cedric Chauve, Nadia El-Mabrouk, and Eric Tannier. Springer Verlag, 2013.Vol. 19. Computational Biology Series. 63-81.
PUB | DOI
 
[154]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575361
Krell, Pina, Reuther, Susanne, Fischer, Ute, Keller, Thomas, Weber, Stephan, Gombert, Michael, Schuster, Friedhelm R., Asang, Corinna, Stepensky, Polina, Strahm, Birgit, Meisel, Roland, Stoye, Jens, and Borkhardt, Arndt. “Next-generation-sequencing-spectratyping reveals public T-cell receptor repertoires in pediatric very severe aplastic anemia and identifies a beta chain CDR3 sequence associated with hepatitis-induced pathogenesis”. Haematologica 98.9 (2013): 1388-1396.
PUB | DOI | WoS | PubMed | Europe PMC
 
[153]
2013 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2577323
Gerlach, Wolfgang, and Stoye, Jens. “Taxonomic classification of metagenomic shotgun sequences with CARMA3”. Encyclopedia of Metagenomics. Ed. Karen E. Nelson. Springer Verlag, 2013.
PUB | DOI
 
[152]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2566922
Jünemann, Sebastian, Sedlazeck, Fritz Joachim, Prior, Karola, Albersmeier, Andreas, John, Uwe, Kalinowski, Jörn, Mellmann, Alexander, Goesmann, Alexander, von Haeseler, Arndt, Stoye, Jens, and Harmsen, Dag. “Updating benchtop sequencing performance comparison”. Nature Biotechnology 31.4 (2013): 294-296.
PUB | DOI | WoS | PubMed | Europe PMC
 
[151]
2013 | Konferenzband | Veröffentlicht | PUB-ID: 2616537
Aaron Darling and Jens Stoye, eds. “Algorithms in Bioinformatics”. Lecture Notes in Bioinformatics 8126 (2013).
PUB | DOI
 
[150]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611633
Jahn, Katharina, Winter, Sascha, Stoye, Jens, and Böcker, Sebastian. “Statistics for approximate gene clusters”. BMC Bioinformatics 14.Suppl 15: Proc. of RECOMB-CG 2013 (2013): S14.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[149]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2548236
Schwientek, Patrick, Wendler, Sergej, Neshat, Armin, Eirich, Christina, Rückert, Christian, Klein, Andreas, Wehmeier, Udo F, Kalinowski, Jörn, Stoye, Jens, and Pühler, Alfred. “Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media”. Journal of Biotechnology 167.2 (2013): 166-177.
PUB | DOI | WoS | PubMed | Europe PMC
 
[148]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2529202
Zakrzewski, Martha, Bekel, Thomas, Ander, Christina, Pühler, Alfred, Rupp, Oliver, Stoye, Jens, Schlüter, Andreas, and Goesmann, Alexander. “MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets”. Journal of Biotechnology 167.2 (2013): 156-165.
PUB | DOI | WoS | PubMed | Europe PMC
 
[147]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512642
Dörr, Daniel, Thévenin, Annelyse, and Stoye, Jens. “Gene family assignment-free comparative genomics”. BMC Bioinformatics 13.Suppl 19: Proc. of RECOMB-CG 2012 (2012): S3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[146]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517239
Hoffmann, Nils, Keck, Matthias, Neuweger, Heiko, Wilhelm, Mathias, Högy, Petra, Niehaus, Karsten, and Stoye, Jens. “Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets”. BMC Bioinformatics 13.1 (2012): 21.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[145]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512644
Jahn, Katharina, Sudek, Henner, and Stoye, Jens. “Multiple genome comparison based on overlap regions of pairwise local alignments”. BMC Bioinformatics 13.Suppl. 19: Proc. of RECOMB-CG 2012 (2012): S7.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[144]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2486060
Schwientek, Patrick, Szczepanowski, Rafael, Rückert, Christian, Kalinowski, Jörn, Klein, Andreas, Selber, Klaus, Wehmeier, Udo F., Stoye, Jens, and Pühler, Alfred. “The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110”. BMC Genomics 13.1 (2012): 112.
PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[143]
2012 | Konferenzband | Veröffentlicht | PUB-ID: 2510416
Juha Kärkkäinen and Jens Stoye, eds. “Combinatorial Pattern Matching”. Lecture Notes in Computer Science 7354 (2012).
PUB | DOI
 
[142]
2012 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2468382
Hoffmann, Nils, and Stoye, Jens. “Generic Software Frameworks for GC-MS Based Metabolomics”. Metabolomics. Ed. Ute Roessner. InTech, 2012. 73-98.
PUB | PDF | DOI | Download (ext.)
 
[141]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2510984
Hilker, Rolf, Sickinger, Corinna, Pedersen, Christian N. S., and Stoye, Jens. “UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ”. Bioinformatics 28.19 (2012): 2509-2511.
PUB | DOI | WoS | PubMed | Europe PMC
 
[140]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517230
Jünemann, Sebastian, Prior, Karola, Szczepanowski, Rafael, Harks, Inga, Ehmke, Benjamin, Goesmann, Alexander, Stoye, Jens, and Harmsen, Dag. “Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing”. PLoS ONE 7.8 (2012): e41606.
PUB | DOI | WoS | PubMed | Europe PMC
 
[139]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396558
Dias Vieira Braga, Marília, Machado, Raphael, Ribeiro, Leonardo C., and Stoye, Jens. “On the weight of indels in genomic distances”. BMC Bioinformatics 12.Suppl 9: RECOMB-CG 2011 (2011): S13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[138]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396509
Dias Vieira Braga, Marília, Machado, Raphael, Ribeiro, Leonardo C., and Stoye, Jens. “Genomic distance under gene substitutions”. BMC Bioinformatics 12.Suppl 9: Proc. of RECOMB-CG 2011 (2011): S8.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[137]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091794
Dias Vieira Braga, Marília, Willing, Eyla, and Stoye, Jens. “Double Cut and Join with Insertions and Deletions”. Journal of Computational Biology 18.9 (2011): 1167-1184.
PUB | DOI | WoS | PubMed | Europe PMC
 
[136]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091790
Kovac, Jakub, Warren, Robert, Dias Vieira Braga, Marília, and Stoye, Jens. “Restricted DCJ Model. Rearrangement Problems with Chromosome Reincorporation”. Journal of Computational Biology 18.9 (2011): 1231-1241.
PUB | DOI | WoS | PubMed | Europe PMC
 
[135]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2354746
Schwientek, Patrick, Szczepanowski, Rafael, Rückert, Christian, Stoye, Jens, and Pühler, Alfred. “Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology”. Journal of Biotechnology 155.1 (2011): 68-77.
PUB | DOI | WoS | PubMed | Europe PMC
 
[134]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2289952
Blom, Jochen, Jakobi, Tobias, Doppmeier, Daniel, Jaenicke, Sebastian, Kalinowski, Jörn, Stoye, Jens, and Goesmann, Alexander. “Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming”. Bioinformatics 27.10 (2011): 1351-1358.
PUB | DOI | WoS | PubMed | Europe PMC
 
[133]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918550
Heber, Steffen, Mayr, Richard, and Stoye, Jens. “Common Intervals of Multiple Permutations”. Algorithmica 60.2 (2011): 175-206.
PUB | DOI | WoS
 
[132]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2298170
Gerlach, Wolfgang, and Stoye, Jens. “Taxonomic classification of metagenomic shotgun sequences with CARMA3.”. Nucleic Acids Res 39.14 (2011): e91.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[131]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897974
Erdős, Péter L., Soukup, Lajos, and Stoye, Jens. “Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance”. Applied Mathematics Letters 24.1 (2011): 82-86.
PUB | DOI | WoS
 
[130]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091787
Wittler, Roland, Maňuch, Ján, Patterson, Murray, and Stoye, Jens. “Consistency of Sequence-Based Gene Clusters”. Journal of Computational Biology 18.9 (2011): 1023-1039.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[129]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091779
Hufsky, Franziska, Kuchenbecker, Leon, Jahn, Katharina, Stoye, Jens, and Böcker, Sebastian. “Swiftly Computing Center Strings”. BMC Bioinformatics 12.1 (2011): 106.
PUB | DOI | WoS | PubMed | Europe PMC
 
[128]
2010 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2445157
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “Computing the Genomic Distance in Linear Time”. Dagstuhl Seminar Proceedings: 10231 Abstracts Collection : Structure Discovery in Biology: Motifs, Networks & Phylogenies. Ed. Alberto Apostolico, Andreas Dress, and Laxmi Parida. Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010.Vol. 10231. 18.
PUB | Download (ext.)
 
[127]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1893893
Husemann, Peter, and Stoye, Jens. “Phylogenetic Comparative Assembly”. Algorithms for Molecular Biology 5.1 (2010): 3.
PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[126]
2010 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918836
Besenbacher, Søren, Schwikowski, Benno, and Stoye, Jens. “Indexing and Searching a Mass Spectrometry Database”. Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday. Ed. Tapio Elomaa, Heikki Mannila, and Pekka Orponen. 2010.Vol. 6060. LNCS. 62-76.
PUB | DOI
 
[125]
2010 | Report | Veröffentlicht | PUB-ID: 1966434
Erdős, Péter L., Soukup, Lajos, and Stoye, Jens. Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance. 2010.
PUB | arXiv
 
[124]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1966439
Trost, Eva, Ott, Lisa, Schneider, Jessica, Schröder, Jasmin, Jaenicke, Sebastian, Goesmann, Alexander, Husemann, Peter, Stoye, Jens, Alves Dorella, Fernanda, Souza Rocha, Flavia, de Castro Soares, Siomar, D'Afonseca, Vivian, Miyoshi, Anderson, Ruiz, Jeronimo, Silva, Artur, Azevedo, Vasco, Burkovski, Andreas, Guiso, Nicole, Join-Lambert, Olivier F., Kayal, Samer, and Tauch, Andreas. “The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence”. BMC Genomics 11.1 (2010): 728.
PUB | DOI | WoS | PubMed | Europe PMC
 
[123]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1795670
Wittkop, Tobias, Emig, Dorothea, Lange, Sita J., Rahmann, Sven, Albrecht, Mario, Morris, John H., Böcker, Sebastian, Stoye, Jens, and Baumbach, Jan. “Partitioning Biological Data with Transitivity Clustering”. Nature Methods 7.6 (2010): 419-420.
PUB | DOI | WoS | PubMed | Europe PMC
 
[122]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898012
Blin, Guillaume, Faye, David, and Stoye, Jens. “Finding Nested Common Intervals Efficiently”. Journal of Computational Biology 17.9 (2010): 1183-1194.
PUB | DOI | WoS | PubMed | Europe PMC
 
[121]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919217
Wittler, Roland, and Stoye, Jens. “Consistency of Sequence-based Gene Clusters”. Proc. of Recomb-CG 2010. Springer Verlag, 2010.Vol. 6398. LNBI. 252-263.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[120]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1893890
Husemann, Peter, and Stoye, Jens. “Repeat-aware Comparative Genome Assembly”. Proc. of GCB 2010. 2010.Vol. P-173. LNI. 61-70.
PUB | Download (ext.)
 
[119]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588556
Husemann, Peter, and Stoye, Jens. “r2cat: Synteny Plots and Comparative Assembly”. Bioinformatics 26.4 (2010): 570-571.
PUB | DOI | WoS | PubMed | Europe PMC
 
[118]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897997
Bergeron, Anne, Medvedev, Paul, and Stoye, Jens. “Rearrangement Models and Single-Cut Operations”. Journal of Computational Biology 17.9 (2010): 1213-1225.
PUB | DOI | WoS | PubMed | Europe PMC
 
[117]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919211
Hufsky, Franziska, Kuchenbecker, Leon, Jahn, Katharina, Stoye, Jens, and Böcker, Sebastian. “Swiftly Computing Center Strings”. Proc. of WABI 2010. 2010.Vol. 6293. LNBI. 325-336.
PUB | DOI | WoS | PubMed | Europe PMC
 
[116]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919216
Kovac, Jakub, Dias Vieira Braga, Marília, and Stoye, Jens. “The Problem of Chromosome Reincorporation in DCJ Sorting and Halving”. Proc. of Recomb-CG 2010. 2010.Vol. 6398. LNBI. 13-24.
PUB | DOI
 
[115]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898025
Dias Vieira Braga, Marília, and Stoye, Jens. “The Solution Space of Sorting by DCJ”. Journal of Computational Biology 17.9 (2010): 1145-1165.
PUB | DOI | WoS | PubMed | Europe PMC
 
[114]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919215
Dias Vieira Braga, Marília, Willing, Eyla, and Stoye, Jens. “Genomic Distance with DCJ and Indels”. Proc. of WABI 2010. 2010.Vol. 6293. LNBI. 90-101.
PUB | DOI
 
[113]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919206
Dias Vieira Braga, Marília, and Stoye, Jens. “Counting All DCJ Sorting Scenarios”. Proc. of Recomb-CG 2009. 2009.Vol. 5817. LNBI. 36-47.
PUB | DOI
 
[112]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919207
Blin, Guillaume, and Stoye, Jens. “Finding Nested Common Intervals Efficiently”. Proc. of Recomb-CG 2009. 2009.Vol. 5817. LNBI. 59-69.
PUB | DOI | WoS | PubMed | Europe PMC
 
[111]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898137
Jahn, Katharina, and Stoye, Jens. “Approximative Gencluster und ihre Anwendung in der komparativen Genomik”. Informatik-Spektrum 32.4 (2009): 288-300.
PUB | DOI
 
[110]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1893884
Husemann, Peter, and Stoye, Jens. “Phylogenetic Comparative Assembly”. Proc. of WABI 2009. 2009.Vol. 5724. LNBI. 145-156.
PUB | DOI | WoS | PubMed | Europe PMC
 
[109]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1591507
Stoye, Jens, and Wittler, Roland. “A Unified Approach for Reconstructing Ancient Gene Clusters”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 6.3 (2009): 387-400.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[108]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589098
Gerlach, Wolfgang, Jünemann, Sebastian, Tille, Felix, Goesmann, Alexander, and Stoye, Jens. “WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads”. BMC Bioinformatics 10.1 (2009): 430.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[107]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589663
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “A New Linear Time Algorithm to Compute the Genomic Distance via the Double Cut and Join Distance”. Theoretical Computer Science 410.51 (2009): 5300-5316.
PUB | DOI | WoS
 
[106]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1590204
Brudno, Michael, Medvedev, Paul, Stoye, Jens, and De La Vega, Francisco M. “A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)”. BIOINFORMATICS 25.21 (2009): 2863-2864.
PUB | DOI | WoS | PubMed | Europe PMC
 
[105]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898105
Böcker, Sebastian, Jahn, Katharina, Mixtacki, Julia, and Stoye, Jens. “Computation of Median Gene Clusters”. Journal of Computational Biology 16.8 (2009): 1085-1099.
PUB | DOI | WoS | PubMed | Europe PMC
 
[104]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1591319
Hoffmann, Nils, and Stoye, Jens. “ChromA: signal-based retention time alignment for chromatography-mass spectrometry data”. Bioinformatics 25.16 (2009): 2080-2081.
PUB | DOI | WoS | PubMed | Europe PMC
 
[103]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919209
Medvedev, Paul, and Stoye, Jens. “Rearrangement Models and Single-Cut Operations”. Comparative Genomics : International Workshop, RECOMB-CG 2009, Budapest, Hungary, September 27-29, 2009. Proceedings. Berlin, Heidelberg: Springer, 2009.Vol. 5817. Lecture Notes in Computer Science. 84-97.
PUB | DOI
 
[102]
2009 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918945
Stoye, Jens. “Computational Short Read Metagenomics”. Presented at the JOBIM 2009, Nantes, France, 2009.
PUB
 
[101]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1634447
Bekel, Thomas, Henckel, Kolja, Küster, Helge, Meyer, Folker, Mittard-Runte, Virginie, Neuweger, Heiko, Paarmann, Daniel, Rupp, Oliver, Zakrzewski, Martha, Pühler, Alfred, Stoye, Jens, and Goesmann, Alexander. “The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies”. Journal of Biotechnology 140.1-2 (2009): 3-12.
PUB | DOI | WoS | PubMed | Europe PMC
 
[100]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919198
Quitzau, José Augusto Amgarten, and Stoye, Jens. “Detecting Repeat Families in Incompletely Sequenced Genomes”. Proc. of WABI 2008. 2008.Vol. 5251. LNBI. 342-353.
PUB | DOI
 
[99]
2008 | Report | PUB-ID: 1970459
Quitzau, José Augusto Amgarten, and Stoye, Jens. A space efficient representation for sparse de Bruijn subgraphs. Bielefeld: Technische Fakultät der Universität Bielefeld, 2008. Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld.
PUB | PDF
 
[98]
2008 | Report | PUB-ID: 1970461
Ejaz, Tahir, Rahmann, Sven, and Stoye, Jens. Online Abelian Pattern Matching. Bielefeld: Technische Fakultät der Universität Bielefeld, 2008. Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld.
PUB | PDF
 
[97]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1636699
Neuweger, Heiko, Albaum, Stefan, Dondrup, Michael, Persicke, Marcus, Watt, Tony, Niehaus, Karsten, Stoye, Jens, and Goesmann, Alexander. “MeltDB: a software platform for the analysis and integration of metabolomics experiment data”. Bioinformatics 24.23 (2008): 2726-2732.
PUB | DOI | WoS | PubMed | Europe PMC
 
[96]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919192
Böcker, Sebastian, Jahn, Katharina, Mixtacki, Julia, and Stoye, Jens. “Computation of Median Gene Clusters”. Proc. of RECOMB 2008. 2008.Vol. 4955. LNBI. 331-345.
PUB | DOI
 
[95]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919200
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios”. Proc. of Recomb-CG 2008. 2008.Vol. 5267. LNBI. 226-240.
PUB | DOI
 
[94]
2008 | Lexikoneintrag | Veröffentlicht | PUB-ID: 1918834
Stoye, Jens. “Suffix Tree Construction in RAM (1997; Farach-Colton)”. Encyclopedia of Algorithms. Ed. Ming-Yang Kao. Springer Verlag, 2008. 925-928.
PUB | DOI
 
[93]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1587078
Schürmann, Klaus-Bernd, and Stoye, Jens. “Counting suffix arrays and strings”. THEORETICAL COMPUTER SCIENCE 395.2-3 (2008): 220-234.
PUB | DOI | WoS
 
[92]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1586009
Krause, Lutz, Diaz, Naryttza N., Edwards, Robert A., Gartemann, Karl-Heinz, Krömeke, Holger, Neuweger, Heiko, Pühler, Alfred, Runte, Kai J., Schlüter, Andreas, Stoye, Jens, Szczepanowski, Rafael, Tauch, Andreas, and Goesmann, Alexander. “Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor”. JOURNAL OF BIOTECHNOLOGY 136.1-2 (2008): 91-101.
PUB | DOI | WoS | PubMed | Europe PMC
 
[91]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1586785
Oehm, Sebastian, Gilbert, David, Tauch, Andreas, Stoye, Jens, and Goesmann, Alexander. “Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms”. NUCLEIC ACIDS RESEARCH 36.Web Server (2008): W433-W437.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[90]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783364
Krause, Lutz, Diaz, Naryttza N., Goesmann, Alexander, Kelley, Scott, Nattkemper, Tim Wilhelm, Rohwer, Forest, Edwards, Robert A., and Stoye, Jens. “Phylogenetic classification of short environmental DNA fragments”. Nucleic Acids Research 36.7 (2008): 2230-2239.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[89]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919195
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “HP Distance via Double Cut and Join Distance”. Combinatorial Pattern Matching. 19th Annual Symposium, CPM 2008, Pisa, Italy, June 18-20, 2008 Proceedings. 2008. Lecture Notes in Computer Science, 5029. 56-68.
PUB | DOI
 
[88]
2007 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918828
Schmidt, Thomas, and Stoye, Jens. “Chapter 12: Gecko and GhostFam - Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes”. Comparative Genomics, Volume 2. Ed. Nicholas H. Bergman. Totowa, NJ: Humana Press Inc., 2007.Vol. 396. Methods in Molecular Biology. 165-182.
PUB | DOI | PubMed | Europe PMC
 
[87]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918432
Didier, Gilles, Schmidt, Thomas, Stoye, Jens, and Tsur, Dekel. “Character Sets of Strings”. Journal of Discrete Algorithms 5.2 (2007): 330-340.
PUB | DOI
 
[86]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1595253
Schürmann, Klaus-Bernd, and Stoye, Jens. “An incomplex algorithm for fast suffix array construction”. SOFTWARE-PRACTICE & EXPERIENCE 37.3 (2007): 309-329.
PUB | DOI | WoS
 
[85]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783345
Krause, Lutz, McHardy, Alice C., Nattkemper, Tim Wilhelm, Pühler, Alfred, Stoye, Jens, and Meyer, Folker. “GISMO - gene identification using a support vector machine for ORF classification”. Nucleic Acids Research 35.2 (2007): 540-549.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[84]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1630781
Mellmann, Alexander, Weniger, Thomas, Berssenbrügge, Christoph, Rothgänger, Jörg, Sammeth, Michael, Stoye, Jens, and Harmsen, Dag. “Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms”. BMC MICROBIOLOGY 7.1 (2007): 98.
PUB | DOI | WoS | PubMed | Europe PMC
 
[83]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599943
Sammeth, Michael, Griebel, Thasso, Tille, Felix, and Stoye, Jens. “Panta rhei (QAlign2): an open graphical environment for sequence analysis”. BIOINFORMATICS 22.7 (2006): 889-890.
PUB | DOI | WoS | PubMed | Europe PMC
 
[82]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599570
Rasmussen, Kim R., Stoye, Jens, and Myers, Eugene W. “Efficient q-gram filters for finding all epsilon-matches over a given length”. JOURNAL OF COMPUTATIONAL BIOLOGY 13.2 (2006): 296-308.
PUB | DOI | WoS | PubMed | Europe PMC
 
[81]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599574
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “On sorting by translocations”. JOURNAL OF COMPUTATIONAL BIOLOGY 13.2 (2006): 567-578.
PUB | DOI | WoS | PubMed | Europe PMC
 
[80]
2006 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1596811
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “A Unifying View of Genome Rearrangements”. Proc. of WABI 2006. SPRINGER-VERLAG BERLIN, 2006.Vol. 4175. LNBI. 163-173.
PUB | DOI | WoS
 
[79]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1597213
Sammeth, Michael, and Stoye, Jens. “Comparing tandem repeats with duplications and excisions of variable degree”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 3.4 (2006): 395-407.
PUB | DOI | WoS | PubMed | Europe PMC
 
[78]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1597313
Bergeron, Anne, and Stoye, Jens. “On the similarity of sets of permutations and its applications to genome comparison”. JOURNAL OF COMPUTATIONAL BIOLOGY 13.7 (2006): 1340-1354.
PUB | DOI | WoS | PubMed | Europe PMC
 
[77]
2006 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918946
Stoye, Jens. “Index Structures in Biological Sequence Analysis: From Simplicity to Complexity and Back”. Presented at the JOBIM 2006, Bordeaux, France, 2006.
PUB
 
[76]
2006 | Report | PUB-ID: 1970464
Chauve, Cedric, Diekmann, Yoan, Heber, Steffen, Mixtacki, Julia, Rahmann, Sven, and Stoye, Jens. On Common Intervals with Errors. Bielefeld: Technische Fakultät der Universität Bielefeld, 2006. Forschungsberichte.
PUB | PDF
 
[75]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1631957
Krause, Lutz, Diaz, Naryttza N., Bartels, Daniela, Edwards, Robert A., Pühler, Alfred, Rohwer, Forest, Meyer, Folker, and Stoye, Jens. “Finding novel genes in bacterial communities isolated from the environment”. BIOINFORMATICS 22.14 (2006): e281-e289.
PUB | DOI | WoS | PubMed | Europe PMC
 
[74]
2005 | Report | PUB-ID: 1970470
Sammeth, Michael, and Stoye, Jens. Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). Bielefeld: Technische Fakultät der Universität Bielefeld, 2005. Forschungsberichte.
PUB | PDF | DOI
 
[73]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919012
Schürmann, Klaus-Bernd, and Stoye, Jens. “An Incomplex Algorithm for Fast Suffix Array Construction”. Proc. of ALENEX/ANALCO 2005. 2005. 77-85.
PUB
 
[72]
2005 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918824
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “Chapter 10: The Inversion Distance Problem”. Mathematics of Evolution and Phylogeny. Ed. Olivier Gascuel. Oxford University Press, 2005. 262-290.
PUB
 
[71]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1603220
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “On Sorting by Translocations”. Proc. of RECOMB 2005. SPRINGER-VERLAG BERLIN, 2005.Vol. 3500. LNBI. 615-629.
PUB | DOI | WoS
 
[70]
2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1775168
Krause, Antje, Stoye, Jens, and Vingron, Martin. “Large scale hierarchical clustering of protein sequences”. BMC Bioinformatics 6.1 (2005): 15.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[69]
2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773302
Bartels, Daniela, Kespohl, Sebastian, Albaum, Stefan, Drüke, Tanja, Goesmann, Alexander, Herold, Julia, Kaiser, Olaf, Pühler, Alfred, Pfeiffer, Friedhelm, Raddatz, Günter, Stoye, Jens, Meyer, Folker, and Schuster, Stephan C. “BACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison”. Bioinformatics 21.7 (2005): 853-859.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[68]
2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918947
Böcker, Sebastian, and Stoye, Jens. “Informatische Methoden zur Protein-Identifikation”. LaborPraxis 29.10 (2005): 24-26.
PUB
 
[67]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1601348
Bannert, Constantin, and Stoye, Jens. “Protein Annotation by Secondary Structure Based Alignments (PASSTA)”. Proc. of CompLife 2005. Springer-Verlag, 2005.Vol. 3695. LNBI. 79-90.
PUB | DOI | WoS
 
[66]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1601361
Sammeth, Michael, Weniger, Thomas, Harmsen, Dag, and Stoye, Jens. “Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)”. Proc. of WABI 2005. SPRINGER-VERLAG BERLIN, 2005.Vol. 3692. LNBI. 276-290.
PUB | DOI | WoS
 
[65]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1603216
Rasmussen, Kim R., Stoye, Jens, and Myers, Eugene W. “Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length”. Proc. of RECOMB 2005. SPRINGER-VERLAG BERLIN, 2005.Vol. 3500. LNBI. 189-203.
PUB | DOI | WoS
 
[64]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919026
Schürmann, Klaus-Bernd, and Stoye, Jens. “Counting Suffix Arrays and Strings”. Proc. of SPIRE 2005. 2005.Vol. 3772. LNCS. 55-66.
PUB | DOI
 
[63]
2005 | Report | PUB-ID: 1970472
Schürmann, Klaus-Bernd, and Stoye, Jens. Counting Suffix Arrays and Strings. Bielefeld: Technische Fakultät der Universität Bielefeld, 2005. Forschungsberichte.
PUB | PDF
 
[62]
2004 | Konferenzband | Veröffentlicht | PUB-ID: 1918823
Robert Giegerich and Jens Stoye, eds. “Proceedings of the German Conference on Bioinformatics, GCB 2004”. Lecture Notes in Informatics P-53 (2004).
PUB
 
[61]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1606286
Michael, Morris, Dieterich, Christoph, and Stoye, Jens. “Suboptimal Local Alignments across Multiple Scoring Schemes”. Proc. of WABI 2004. SPRINGER-VERLAG BERLIN, 2004.Vol. 3240. LNBI. 99-110.
PUB | DOI | WoS
 
[60]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1607260
Schmidt, Thomas, and Stoye, Jens. “Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences”. Proc. of CPM 2004. 2004.Vol. 3109. LNCS. 347-358.
PUB | DOI | WoS
 
[59]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773554
Pollard, Daniel A., Bergman, Casey M., Stoye, Jens, Celniker, Susan E., and Eisen, Michael B. “Correction: Benchmarking tools for the alignment of functional noncoding DNA”. BMC Bioinformatics 5.1 (2004): 73.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[58]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773560
Cieliebak, Mark, Erlebach, Thomas, Lipták, Zsuzsanna, Stoye, Jens, and Welzl, Emo. “Algorithmic complexity of protein identification: combinatorics of weighted strings”. Discrete Applied Mathematics 137.1 (2004): 27-46.
PUB | PDF | DOI | WoS
 
[57]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773312
Pollard, Daniel A., Bergman, Casey M., Stoye, Jens, Celniker, Susan E., and Eisen, Michael B. “Benchmarking tools for the alignment of functional noncoding DNA”. BMC Bioinformatics 5.1 (2004): 6.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[56]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773569
Gusfield, Dan, and Stoye, Jens. “Linear time algorithms for finding and representing all the tandem repeats in a string”. Journal of computer and system sciences 69.4 (2004): 525-546.
PUB | PDF | DOI | WoS
 
[55]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1607263
Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “Reversal Distance without Hurdles and Fortresses”. Proc. of CPM 2004. SPRINGER-VERLAG BERLIN, 2004.Vol. 3109. LNCS. 388-399.
PUB | DOI | WoS
 
[54]
2003 | Report | PUB-ID: 1970475
Schürmann, Klaus-Bernd, and Stoye, Jens. Suffix Tree Construction and Storage with Limited Main Memory. Bielefeld: Technische Fakultät der Universität Bielefeld, 2003. Forschungsberichte.
PUB | PDF
 
[53]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1612664
Heber, Steffen, and Stoye, Jens. “The European Conference on Computational Biology”. Drug Discovery Today 8.3 (2003): 113-114.
PUB | DOI | WoS | PubMed | Europe PMC
 
[52]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918949
Giegerich, Robert, and Stoye, Jens. “Finden, fast ohne zu suchen: Indexstrukturen in der Bioinformatik”. Forschung an der Universität Bielefeld 26 (2003): 63-68.
PUB
 
[51]
2003 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919005
Bannert, Constantin, and Stoye, Jens. “Evaluation of the Jumping Alignment Algorithm with Artificial and Biological Data”. Proc. of GCB 2003. 2003. 21-25.
PUB
 
[50]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1610397
Giegerich, Robert, Kurtz, Stefan, and Stoye, Jens. “Efficient implementation of lazy suffix trees”. SOFTWARE-PRACTICE & EXPERIENCE 33.11 (2003): 1035-1049.
PUB | PDF | DOI | WoS
 
[49]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1609403
Sammeth, Michael, Morgenstern, Burkhard, and Stoye, Jens. “Divide-and-conquer multiple alignment with segment-based constraints”. BIOINFORMATICS 19.Suppl 2 (2003): ii189-ii195.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[48]
2003 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1610433
Bergeron, Anne, and Stoye, Jens. “On the similarity of sets of permutations and its applications to genome comparison”. Proc. of COCOON 2003. 2003.Vol. 2697. LNCS. 68-79.
PUB | DOI | WoS
 
[47]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1610503
Sammeth, Michael, Rothgänger, Jörg, Esser, Wolfram, Albert, Jürgen, Stoye, Jens, and Harmsen, Dag. “QAlign: quality-based multiple alignments with dynamic phylogenetic analysis”. BIOINFORMATICS 19.12 (2003): 1592-1593.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[46]
2003 | Report | PUB-ID: 1970477
Bergeron, Anne, and Stoye, Jens. On the Similarity of Sets of Permutations and its Applications to Genome Comparison. Bielefeld: Technische Fakultät der Universität Bielefeld, 2003. Forschungsberichte.
PUB | PDF
 
[45]
2002 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918951
Stoye, Jens. “Index Structures for Large Sequence Data: Suffix Trees and Affix Trees”. Lecture Notes in Informatics. Ed. Sigrid Schubert, Bernd Reusch, and Norbert Jesse. 2002.Vol. P-20. 67-67.
PUB
 
[44]
2002 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919000
Cieliebak, Marc, Lipták, Zsuzsanna, Welzl, Emo, Erlebach, Thomas, and Stoye, Jens. “Algorithmic Complexity of Protein Identification: Searching in Weighted Strings”. Proc. of IFIP TCS 2002. 2002. 143-156.
PUB
 
[43]
2002 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773578
Spang, Rainer, Rehmsmeier, Marc, and Stoye, Jens. “A novel approach to remote homology detection: jumping alignments”. Journal of Computational Biology 9.5 (2002): 747-760.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[42]
2002 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773332
Stoye, Jens, and Gusfield, Dan. “Simple and flexible detection of contiguous repeats using a suffix tree”. Theoretical Computer Science 270.1-2 (2002): 843-856.
PUB | PDF | DOI | WoS
 
[41]
2002 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773329
Bergeron, Anne, Heber, Steffen, and Stoye, Jens. “Common intervals and sorting by reversals: a marriage of necessity”. Bioinformatics 18.Suppl 2 (2002): S54-S63.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[40]
2002 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918995
Heber, Steffen, Stoye, Jens, Frohme, Marcus, Hoheisel, Jörg, and Vingron, Martin. “Resampling Methods in Physical Mapping”. Proc. of GfKl 2000. 2002. 437-444.
PUB
 
[39]
2001 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773335
Kurtz, Stefan, Choudhuri, Jomuna V., Ohlebusch, Enno, Schleiermacher, Chris, Stoye, Jens, and Giegerich, Robert. “REPuter: the manifold applications of repeat analysis on a genomic scale”. Nucleic Acids Research 29.22 (2001): 4633-4642.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[38]
2001 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918992
Heber, Steffen, and Stoye, Jens. “Finding all Common Intervals of k Permutations”. Proc. of CPM 2001. 2001.Vol. 2089. LNCS. 207-218.
PUB | DOI
 
[37]
2001 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1880197
Heber, Steffen, and Stoye, Jens. “Algorithms for Finding Gene Clusters”. Proc. of WABI 2001. Berlin: Sppringer, 2001.Vol. 2149. LNCS. 252-263.
PUB | DOI
 
[36]
2001 | Report | PUB-ID: 1970479
Cieliebak, Marc, Erlebach, Thomas, Lipták, Zsuzsanna, Stoye, Jens, and Welzl, Emo. Algorithmic Complexity of Protein Identification: Combinatorics of Weighted Strings. ETH Zürich, Dept. of Computer Science, 2001. Technical Report.
PUB
 
[35]
2000 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918981
Heber, Steffen, Stoye, Jens, Hoheisel, Jörg, and Vingron, Martin. “Contig Selection in Physical Mapping”. Proc. of RECOMB 2000. 2000. 155-164.
PUB | DOI | WoS | PubMed | Europe PMC
 
[34]
2000 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918817
Brodal, Gerth S., Lyngsø, Rune B., Pedersen, Christian N. S., and Stoye, Jens. “Finding Maximal Pairs with Bounded Gap”. Matching Patterns (Journal of Discrete Algorithms). Ed. Maxime Crochemore and Leszek Gąsieniec. 2000. 77-104.
PUB
 
[33]
2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773345
Krause, Antje, Stoye, Jens, and Vingron, Martin. “The SYSTERS protein sequence cluster set”. Nucleic Acids Research 28.1 (2000): 270-272.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[32]
2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773572
Heber, Steffen, Stoye, Jens, Frohme, Marcus, Hoheisel, Jörg, and Vingron, Martin. “Contig selection in physical mapping”. Journal of Computational Biology 7.3-4 (2000): 395-408.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[31]
2000 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918985
Spang, Rainer, Rehmsmeier, Marc, and Stoye, Jens. “Sequence Database Search Using Jumping Alignments”. Proc. of ISMB 2000. 2000. 367-375.
PUB | PubMed | Europe PMC
 
[30]
2000 | Report | PUB-ID: 1970490
Stoye, Jens. Affix Trees. Technische Fakultät der Universität Bielefeld, 2000. Forschungsberichte.
PUB | PDF
 
[29]
2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773341
Reinert, Knut, Stoye, Jens, and Will, Torsten. “An iterative method for faster sum-of-pairs multiple sequence alignment”. Bioinformatics 16.9 (2000): 808-814.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[28]
2000 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918988
Kurtz, Stefan, Ohlebusch, Enno, Schleiermacher, Chris, Stoye, Jens, and Giegerich, Robert. “Computation and Visualization of Degenerate Repeats in Complete Genomes”. Proc. of ISMB 2000. 2000. 228-238.
PUB | PubMed | Europe PMC
 
[27]
2000 | Konferenzband | Veröffentlicht | PUB-ID: 1918813
Erich Bornberg-Bauer, Ursula Rost, Jens Stoye, and Martin Vingron, eds. Proceedings of the German Conference on Bioinformatics, GCB 2000. Berlin: Logos Verlag, 2000.
PUB
 
[26]
1999 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1620435
Giegerich, Robert, Kurtz, Stefan, and Stoye, Jens. “Efficient implementation of lazy suffix trees”. Algorithm Engineering. 3rd International Workshop, WAE’99 London, UK, July 19–21, 1999 Proceedings. 1999.Vol. 1668. LNCS. 30-42.
PUB | DOI | WoS
 
[25]
1999 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918978
Reinert, Knut, Will, Torsten, and Stoye, Jens. “Combining Divide-and-Conquer, the A*-Algorithm, and Successive Realignment Approaches to Speed up Multiple Sequence Alignment”. Proc. of GCB 1999. 1999. 17-24.
PUB | Download (ext.)
 
[24]
1999 | Report | PUB-ID: 1970495
Morgenstern, Burkhard, Stoye, Jens, and Dress, Andreas. Consistent Equivalence Relations: A Set-Theoretical Framework for Multiple Sequence Alignment. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1999. Materialien/Preprints.
PUB
 
[23]
1999 | Report | PUB-ID: 1970509
Brodal, Gerth S., Lyngsø, Rune B., Pedersen, Christian N. S., and Stoye, Jens. Finding Maximal Pairs with Bounded Gap. BRICS, Department of Computer Science, University of Aarhus, 1999. Report.
PUB
 
[22]
1999 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918971
Brodal, Gerth S., Lyngsø, Rune B., Pedersen, Christian N. S., and Stoye, Jens. “Finding Maximal Pairs with Bounded Gap”. Proc. of CPM 1999. 1999.Vol. 1645. LNCS. 134-149.
PUB | DOI
 
[21]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2488102
Dress, Andreas, Morgenstern, Burkhard, and Stoye, Jens. “The Number of Standard and of Effective Multiple Alignments”. Appl. Math. Lett. 11.4 (1998): 43-49.
PUB
 
[20]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918538
Hildebrand, Martin, and Stoye, Jens. “Die Bedeutung der Zusammenarbeit der Disziplinen in der Anwendung - erläutert anhand von Beispielen”. Der Mathematikunterricht 44.6 (1998): 34-53.
PUB
 
[19]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1667771
Stoye, Jens. “Multiple sequence alignment with the Divide-and-Conquer method.”. Gene 211.2 (1998): GC45-GC56.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[18]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1625402
Stoye, Jens, Evers, Dirk, and Meyer, Folker. “Rose: generating sequence families”. BIOINFORMATICS 14.2 (1998): 157-163.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[17]
1998 | Report | PUB-ID: 1970515
Stoye, Jens, and Gusfield, Dan. Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree. Department of Computer Science, University of California, Davis, 1998. Report.
PUB
 
[16]
1998 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918964
Stoye, Jens, and Gusfield, Dan. “Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version)”. Proc. of CPM 1998. 1998.Vol. 1448. LNCS. 140-152.
PUB | DOI
 
[15]
1998 | Report | PUB-ID: 1970513
Gusfield, Dan, and Stoye, Jens. Linear Time Algorithms for Finding and Representing all the Tandem Repeats in a String. Department of Computer Science, University of California, Davis, 1998. Report.
PUB
 
[14]
1997 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2488107
Stoye, Jens, Moulton, Vincent, and Dress, Andreas. “DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment”. CABIOS 13.6 (1997): 625-626.
PUB
 
[13]
1997 | Report | PUB-ID: 1970526
Perrey, Sören W., Stoye, Jens, Moulton, Vincent, and Dress, Andreas. On Simultaneous versus Iterative Multiple Sequence Alignment. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1997. Materialien/Preprints.
PUB
 
[12]
1997 | Report | PUB-ID: 1970517
Stoye, Jens, Evers, Dirk, and Meyer, Folker. Rose: Generating Sequence Families. Technische Fakultät der Universität Bielefeld, 1997. Forschungsberichte.
PUB
 
[11]
1997 | Report | PUB-ID: 1970529
Brinkmann, Gunnar, Dress, Andreas, Perrey, Sören W., and Stoye, Jens. Two Applications of the Divide & Conquer Principle in the Molecular Sciences. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1997. Materialien/Preprints.
PUB
 
[10]
1997 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1667885
Stoye, Jens, Evers, Dirk, and Meyer, Folker. “Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions”. Proc. of ISMB 1997. 1997. 303-306.
PUB | PubMed | Europe PMC
 
[9]
1997 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773355
Stoye, Jens, Perrey, Sören W., and Dress, Andreas. “Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment”. Applied mathematics letters 10.2 (1997): 67-73.
PUB | PDF | DOI | WoS
 
[8]
1997 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773358
Brinkmann, Gunnar, Dress, Andreas, Perrey, Sören W., and Stoye, Jens. “Two applications of the Divide & Conquer principle in the molecular sciences”. Mathematical programming 79.1-3 (1997): 71-97.
PUB | DOI | WoS
 
[7]
1997 | Report | PUB-ID: 1970523
Dress, Andreas, Morgenstern, Burkhard, and Stoye, Jens. On the Number of Standard and Effective Multiple Alignments. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1997. Materialien/Preprints.
PUB
 
[6]
1997 | Report | PUB-ID: 1970520
Perrey, Sören W., Stoye, Jens, and Moulton, Vincent. FDCA: Fast and Accurate Approximation to Sum-of-Pairs Score Optimal Multiple Sequence Alignment. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1997. Materialien/Preprints.
PUB
 
[5]
1997 | Report | PUB-ID: 1970532
Stoye, Jens. Divide-and-Conquer Multiple Sequence Alignment. Technische Fakultät der Universität Bielefeld, 1997. Forschungsberichte.
PUB
 
[4]
1996 | Report | PUB-ID: 1970533
Perrey, Sören W., and Stoye, Jens. Fast Approximation to the NP-hard Problem of Multiple Sequence Alignment. Dept. of Mathematics, Massey University, Palmerston North, New Zealand, 1996. Information and Mathematical Sciences Reports, Series B.
PUB
 
[3]
1996 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773351
Tönges, Udo, Perrey, Sören W., Stoye, Jens, and Dress, Andreas. “A general method for fast multiple sequence alignment”. Gene 172.1 (1996): GC33-GC41.
PUB | DOI | WoS | PubMed | Europe PMC
 
[2]
1996 | Report | PUB-ID: 1970535
Stoye, Jens, Dress, Andreas, and Perrey, Sören W. Improving the Divide-and-Conquer Approach to Sum-of-Pairs Multiple Sequence Alignment. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1996. Materialien/Preprints.
PUB
 
[1]
1996 | Report | PUB-ID: 1970537
Tönges, Udo, Perrey, Sören W., Stoye, Jens, and Dress, Andreas. A General Method for Fast Multiple Sequence Alignment. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1996. Materialien/Preprints.
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