Jens Stoye

jens.stoye@uni-bielefeld.de
ORCID logo https://orcid.org/0000-0002-4656-7155

PEVZ-ID
65864

238 Publications

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  • [238]
    2024 | Journal Article | Published | PUB-ID: 2999592
    Parmigiani, Luca, Garrison, Erik, Stoye, Jens, Marschall, Tobias, and Doerr, Daniel. “Panacus: fast and exact pangenome growth and core size estimation”. Bioinformatics (2024).
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [237]
    2024 | Conference Paper | Published | PUB-ID: 2992085
    Bohnenkämper, Leonard, Stoye, Jens, and Dörr, Daniel. “Reconstructing Rearrangement Phylogenies of Natural Genomes”. LIPIcs 312 (2024): 12.
    PUB | DOI
     
  • [236]
    2024 | Journal Article | Published | PUB-ID: 2988749
    Parmigiani, Luca, Wittler, Roland, and Stoye, Jens. “Revisiting pangenome openness with k-mers”. Peer Community Journal 4 (2024): e47.
    PUB | DOI | WoS
     
  • [235]
    2024 | Journal Article | Published | PUB-ID: 2990552
    Frolova, Daria, Lima, Leandro, Roberts, Leah, Bohnenkämper, Leonard, Wittler, Roland, Stoye, Jens, and Iqbal, Zamin. “Applying rearrangement distances to enable plasmid epidemiology with pling”. Microbial Genomics 10.10 (2024): 001300.
    PUB | DOI | PubMed | Europe PMC | Preprint
     
  • [234]
    2024 | Book (Editor) | Published | PUB-ID: 2990269
    João Carlos Setubal, Peter F. Stadler, and Jens Stoye, eds. Comparative Genomics. Methods and Protocols. 2nd ed. New York, NY: Humana, 2024. Methods in Molecular Biology. 2802.
    PUB | DOI
     
  • [233]
    2024 | Book Chapter | Published | PUB-ID: 2990270
    Dias Vieira Braga, Marília, Doerr, Daniel, Rubert, Diego P., and Stoye, Jens. “Family-Free Genome Comparison”. Comparative Genomics. Methods and Protocols. Ed. João Carlos Setubal, Peter F. Stadler, and Jens Stoye. 2nd ed. New York, NY: Humana, 2024.Vol. 2802. Methods in Molecular Biology. 57-72.
    PUB | DOI
     
  • [232]
    2024 | Book Chapter | Published | PUB-ID: 2990271
    Schulz, Tizian, Parmigiani, Luca, Rempel, Andreas, and Stoye, Jens. “Methods for Pangenomic Core Detection”. Comparative Genomics. Methods and Protocols. Ed. João Carlos Setubal, Peter F. Stadler, and Jens Stoye. New York, NY: Humana, 2024.Vol. 2802. Methods in Molecular Biology. 73-106.
    PUB | DOI
     
  • [231]
    2024 | Journal Article | Published | PUB-ID: 2985702 OA
    Dias Vieira Braga, Marília, Brockmann, Leonie Ruth, Klerx, Katharina, and Stoye, Jens. “Investigating the complexity of the double distance problems”. Algorithms for Molecular Biology 19 (2024): 1.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [230]
    2023 | Conference Paper | Published | PUB-ID: 2981606
    Dias Vieira Braga, Marília, Brockmann, Leonie Ruth, Klerx, Katharina, and Stoye, Jens. “On the Class of Double Distance Problems”. Comparative Genomics. 20th International Conference, RECOMB-CG 2023, Istanbul, Turkey, April 14–15, 2023, Proceedings. Ed. Katharina Jahn and Tomáš Vinař. Cham: Springer Nature , 2023.Vol. 13883. Lecture Notes in Computer Science. 35-50.
    PUB | DOI | WoS
     
  • [229]
    2023 | Journal Article | Published | PUB-ID: 2984551
    Förstner, Konrad U., Becker, Anke, Blom, Jochen, Bork, Peer, Clavel, Thomas, Dieckmann, Marius, Goesmann, Alexander, Götz, Barbara, Gübitz, Thomas, Hufsky, Franziska, Jünemann, Sebastian, Körner, Marie-Louise, Marz, Manja, Da Rocha, Ulisses Nunes, Overmann, Jörg, Pühler, Alfred, Rebholz-Schuhmann, Dietrich, Sczyrba, Alexander, Stoye, Jens, Vandendorpe, Justine, Van Rossum, Thea, and McHardy, Alice. “NFDI4Microbiota – national research data infrastructure for microbiota research”. Research Ideas and Outcomes 9 (2023).
    PUB | DOI
     
  • [228]
    2023 | Journal Article | Published | PUB-ID: 2969065
    Kirsch-Gerweck, Benedikt, Bohnenkämper, Leonard, Henrichs, Michel Theodor, Alanko, Jarno N, Bannai, Hideo, Cazaux, Bastien, Peterlongo, Pierre, Burger, Joachim, Stoye, Jens, and Diekmann, Yoan. “HaploBlocks: efficient detection of positive selection in large population genomic datasets”. Molecular Biology and Evolution 40.3 (2023): msad027.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [227]
    2022 | Preprint | Published | PUB-ID: 2967089
    Parmigiani, Luca, Wittler, Roland, and Stoye, Jens. “Revisiting pangenome openness with k-mers”. bioRxiv (2022).
    PUB | DOI
     
  • [226]
    2022 | Conference Paper | Published | PUB-ID: 2965398
    Dias Vieira Braga, Marília, Brockmann, Leonie Ruth, Klerx, Katharina, and Stoye, Jens. “A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance”. 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Ed. Christina Boucher and Sven Rahmann. Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.Vol. 242. Leibniz International Proceedings in Informatics. LIPIcs. 13:1-13:16.
    PUB | DOI
     
  • [225]
    2022 | Journal Article | Published | PUB-ID: 2963777
    Bonizzoni, Paola, Costantini, Matteo, De Felice, Clelia, Petescia, Alessia, Pirola, Yuri, Previtali, Marco, Rizzi, Raffaela, Stoye, Jens, Zaccagnino, Rocco, and Zizza, Rosalba. “Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches”. Information Sciences 607 (2022): 458-476.
    PUB | DOI | WoS
     
  • [224]
    2022 | Journal Article | Published | PUB-ID: 2963659 OA
    Schulz, Tizian, Wittler, Roland, and Stoye, Jens. “Sequence-based pangenomic core detection”. iScience 25.6 (2022): 104413.
    PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [223]
    2021 | Book (Editor) | Published | PUB-ID: 2959449 OA
    Jens Stoye and Roland Wittler, eds. The Bielefeld Institute for Bioinformatics Infrastructure. Bielefeld: Universität Bielefeld, Techn. Fakultät, 2021.
    PUB | PDF | DOI
     
  • [222]
    2021 | Journal Article | Published | PUB-ID: 2942686
    Willing, Eyla, Stoye, Jens, and Dias Vieira Braga, Marília. “Computing the Inversion-Indel Distance”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 18.6 (2021): 2314-2326.
    PUB | DOI | WoS | PubMed | Europe PMC | arXiv
     
  • [221]
    2021 | Journal Article | Published | PUB-ID: 2950825 OA
    Schulz, Tizian, Wittler, Roland, Rahmann, Sven, Hach, Faraz, and Stoye, Jens. “Detecting High Scoring Local Alignments in Pangenome Graphs”. Bioinformatics 37.16 (2021): 2266-2274.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [220]
    2021 | Conference Paper | Published | PUB-ID: 2952705
    Bonizzoni, Paola, De Felice, Clelia, Petescia, Alessia, Pirola, Yuri, Rizzi, Raffaela, Stoye, Jens, Zaccagnino, Rocco, and Zizza, Rosalba. “Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning”. Proceedings of AlCoB 2021. 2021.Vol. 12715. LNBI. 16-28.
    PUB
     
  • [219]
    2021 | Journal Article | Published | PUB-ID: 2946303
    Bohnenkämper, Leonard, Dias Vieira Braga, Marília, Dörr, Daniel, and Stoye, Jens. “Computing the rearrangement distance of natural genomes”. Journal of Computational Biology 28.4 (2021): 410-431.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [218]
    2021 | Journal Article | Published | PUB-ID: 2945991
    Sundermann, Linda K., Wintersinger, Jeff, Rätsch, Gunnar, Stoye, Jens, and Morris, Quaid. “Reconstructing Tumor Evolutionary Histories and Clone Trees in Polynomial-time with SubMARine”. PLOS Computational Biology 17.1 (2021): e1008400.
    PUB | DOI | WoS | PubMed | Europe PMC | Preprint
     
  • [217]
    2021 | Special Issue | Published | PUB-ID: 2949108
    João C. Setubal, Jens Stoye, and Bas E. Dutilh, eds. “Computational Methods for Microbiome Analysis”. Frontiers in Genetics Research Topic (2021).
    PUB | DOI | Download (ext.)
     
  • [216]
    2020 | Preprint | Published | PUB-ID: 2943670
    Rubert, Diego, Araujo, Eloi, Stefanes, Marco A., Stoye, Jens, and Martinez, Fábio V. “On motifs in colored graphs”. arXiv:2005.13634 (2020).
    PUB | Download (ext.) | arXiv
     
  • [215]
    2020 | Journal Article | Published | PUB-ID: 2942995
    Rubert, Diego, Araujo, Eloi, Stefanes, Marco A., Stoye, Jens, and Martinez, Fabio. “Searching and Inferring Colorful Topological Motifs in Vertex-Colored Graphs”. Journal of Combinatorial Optimization 40 (2020): 379–411.
    PUB | DOI | WoS
     
  • [214]
    2020 | Journal Article | Published | PUB-ID: 2937712 OA
    Rubert, Diego, Martinez, Fábio Henrique Viduani, Stoye, Jens, and Dörr, Daniel. “Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants”. BMC Genomics 21.Suppl. 2 (2020): 273.
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  • [213]
    2020 | Journal Article | Published | PUB-ID: 2953267
    Schulte-Schrepping, Jonas, Reusch, Nico, Paclik, Daniela, Baßler, Kevin, Schlickeiser, Stephan, Zhang, Bowen, Krämer, Benjamin, Krammer, Tobias, Brumhard, Sophia, Bonaguro, Lorenzo, De Domenico, Elena, Wendisch, Daniel, Grasshoff, Martin, Kapellos, Theodore S., Beckstette, Michael, Pecht, Tal, Saglam, Adem, Dietrich, Oliver, Mei, Henrik E., Schulz, Axel R., Conrad, Claudia, Kunkel, Désirée, Vafadarnejad, Ehsan, Xu, Cheng-Jian, Horne, Arik, Herbert, Miriam, Drews, Anna, Thibeault, Charlotte, Pfeiffer, Moritz, Hippenstiel, Stefan, Hocke, Andreas, Müller-Redetzky, Holger, Heim, Katrin-Moira, Machleidt, Felix, Uhrig, Alexander, Bosquillon de Jarcy, Laure, Jürgens, Linda, Stegemann, Miriam, Glösenkamp, Christoph R., Volk, Hans-Dieter, Goffinet, Christine, Landthaler, Markus, Wyler, Emanuel, Georg, Philipp, Schneider, Maria, Dang-Heine, Chantip, Neuwinger, Nick, Kappert, Kai, Tauber, Rudolf, Corman, Victor, Raabe, Jan, Kaiser, Kim Melanie, Vinh, Michael To, Rieke, Gereon, Meisel, Christian, Ulas, Thomas, Becker, Matthias, Geffers, Robert, Witzenrath, Martin, Drosten, Christian, Suttorp, Norbert, von Kalle, Christof, Kurth, Florian, Händler, Kristian, Schultze, Joachim L., Aschenbrenner, Anna C., Li, Yang, Nattermann, Jacob, Sawitzki, Birgit, Saliba, Antoine-Emmanuel, Sander, Leif Erik, Angelov, Angel, Bals, Robert, Bartholomäus, Alexander, Becker, Anke, Bezdan, Daniela, Bonifacio, Ezio, Bork, Peer, Clavel, Thomas, Colome-Tatche, Maria, Diefenbach, Andreas, Dilthey, Alexander, Fischer, Nicole, Förstner, Konrad, Frick, Julia-Stefanie, Gagneur, Julien, Goesmann, Alexander, Hain, Torsten, Hummel, Michael, Janssen, Stefan, Kalinowski, Jörn, Kallies, René, Kehr, Birte, Keller, Andreas, Kim-Hellmuth, Sarah, Klein, Christoph, Kohlbacher, Oliver, Korbel, Jan O., Kurth, Ingo, Landthaler, Markus, Li, Yang, Ludwig, Kerstin, Makarewicz, Oliwia, Marz, Manja, McHardy, Alice, Mertes, Christian, Nöthen, Markus, Nürnberg, Peter, Ohler, Uwe, Ossowski, Stephan, Overmann, Jörg, Peter, Silke, Pfeffer, Klaus, Poetsch, Anna R., Pühler, Alfred, Rajewsky, Nikolaus, Ralser, Markus, Rieß, Olaf, Ripke, Stephan, Nunes da Rocha, Ulisses, Rosenstiel, Philip, Saliba, Antoine-Emmanuel, Sander, Leif Erik, Sawitzki, Birgit, Schiffer, Philipp, Schulte, Eva-Christina, Schultze, Joachim L., Sczyrba, Alexander, Stegle, Oliver, Stoye, Jens, Theis, Fabian, Vehreschild, Janne, Vogel, Jörg, von Kleist, Max, Walker, Andreas, Walter, Jörn, Wieczorek, Dagmar, and Ziebuhr, John. “Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment”. Cell 182.6 (2020): 1419-1440.e23.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [212]
    2020 | Report | PUB-ID: 2944669
    Glöckner, Frank Oliver, Diepenbroek, Michael, Felden, Janine, Güntsch, Anton, Stoye, Jens, Overmann, Jörg, Wimmers, Klaus, Kostadinov, Ivaylo, Yahyapour, Ramin, Müller, Wolfgang, Scholz, Uwe, Triebel, Dagmar, Frenzel, Mark, Gemeinholzer, Birgit, Goesmann, Alexander, König-Ries, Birgitta, Bonn, Aletta, and Seeger, Bernhard. NFDI4BioDiversity - A Consortium for the National Research Data Infrastructure (NFDI) : Proposal. Zenodo, 2020.
    PUB | DOI
     
  • [211]
    2020 | Journal Article | Published | PUB-ID: 2948972
    Setubal, Joao C., Stoye, Jens, and Dutilh, Bas E. “Editorial: Computational Methods for Microbiome Analysis”. Frontiers in Genetics 11 (2020): 623897.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [210]
    2020 | Preprint | Published | PUB-ID: 2940602
    Haghshenas, Ehsan, Asghari, Hossein, Stoye, Jens, Chauve, Cedric, and Hach, Faraz. “HASLR: Fast Hybrid Assembly of Long Reads”. bioRxiv (2020).
    PUB | DOI | Download (ext.) | Preprint
     
  • [209]
    2020 | Preprint | Published | PUB-ID: 2945720
    Schulz, Tizian, Wittler, Roland, Rahmann, Sven, Hach, Faraz, and Stoye, Jens. “Detecting High Scoring Local Alignments in Pangenome Graphs”. bioRxiv (2020).
    PUB | DOI | Preprint
     
  • [208]
    2020 | Journal Article | Published | PUB-ID: 2939618 OA
    Alanko, Jarno, Bannai, Hideo, Cazaux, Bastien, Peterlongo, Pierre, and Stoye, Jens. “Finding all maximal perfect haplotype blocks in linear time”. Algorithms for Molecular Biology 15 (2020): 2.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [207]
    2020 | Journal Article | Published | PUB-ID: 2945430
    Haghshenas, Ehsan, Asghari, Hossein, Stoye, Jens, Chauve, Cedric, and Hach, Faraz. “HASLR: Fast Hybrid Assembly of Long Reads”. iScience 23.8 (2020): 101389.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [206]
    2020 | Journal Article | Published | PUB-ID: 2939598
    Sevillya, Gur, Dörr, Daniel, Lerner, Yael, Stoye, Jens, Steel, Mike, and Snir, Sagi. “Horizontal Gene Transfer Phylogenetics: A Random Walk Approach”. Molecular Biology and Evolution 37.5 (2020): 1470–1479.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [205]
    2020 | Preprint | Published | PUB-ID: 2939861
    Bohnenkämper, Leonard, Dias Vieira Braga, Marília, Dörr, Daniel, and Stoye, Jens. “Computing the rearrangement distance of natural genomes”. arXiv:2001.02139 (2020).
    PUB | Download (ext.) | arXiv
     
  • [204]
    2020 | Conference Paper | Published | PUB-ID: 2939729
    Bohnenkämper, Leonard, Dias Vieira Braga, Marília, Dörr, Daniel, and Stoye, Jens. “Computing the rearrangement distance of natural genomes”. Proceedings of RECOMB 2020. 2020.Vol. 12074. LNBI. 3-18.
    PUB | DOI
     
  • [203]
    2019 | Journal Article | Published | 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
     
  • [202]
    2019 | Report | Published | PUB-ID: 2939260
    Gagie, Travis, Manzini, Giovanni, Navarro, Gonzalo, and Stoye, Jens. 25 Years of the Burrows-Wheeler Transform. Report from Dagstuhl Seminar 19241. Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, 2019. Dagstuhl Reports. 9(6).
    PUB | DOI
     
  • [201]
    2019 | Conference Paper | Published | PUB-ID: 2937148
    Alanko, Jarno, Bannai, Hideo, Cazaux, Bastien, Peterlongo, Pierre, and Stoye, Jens. “Finding All Maximal Perfect Haplotype Blocks in Linear Time”. Proceedings of WABI 2019. Dagstuhl: Schloss Dagstuhl, Leibniz-Zentrum für Informatik , 2019.Vol. 143. Leibniz International Proceedings in Informatics. LIPIcs. 8:1-8:9.
    PUB | DOI
     
  • [200]
    2019 | Book Chapter | Published | 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
     
  • [199]
    2018 | Journal Article | Published | PUB-ID: 2919006 OA
    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
     
  • [198]
    2018 | Journal Article | Published | PUB-ID: 2919012
    Jaenicke, Sebastian, Albaum, Stefan, Blumenkamp, Patrick, Linke, Burkhard, Stoye, Jens, and Goesmann, Alexander. “Flexible metagenome analysis using the MGX framework”. Microbiome 6.1 (2018): 76.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [197]
    2018 | Journal Article | Published | PUB-ID: 2919005 OA
    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
     
  • [196]
    2018 | Journal Article | Published | 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
     
  • [195]
    2018 | Book Chapter | Published | 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 | DOI
     
  • [194]
    2018 | Book Chapter | Published | 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 | DOI
     
  • [193]
    2018 | Book (Editor) | Published | 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 | DOI
     
  • [192]
    2018 | Journal Article | Published | 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
     
  • [191]
    2018 | Conference Paper | Published | 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
     
  • [190]
    2017 | Conference Paper | Published | 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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  • [189]
    2017 | Journal Article | Published | PUB-ID: 2909057 OA
    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 12.1 (2017): 3.
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  • [188]
    2017 | Preprint | Published | 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 | Download (ext.) | arXiv
     
  • [187]
    2017 | Conference Paper | Published | 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 | Journal Article | Published | 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
     
  • [185]
    2017 | Conference Paper | Published | 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 | Conference Paper | Published | 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 | Journal Article | Published | 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 | Conference Paper | Published | 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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  • [181]
    2016 | Journal Article | Published | 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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  • [180]
    2016 | Journal Article | Published | 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
     
  • [179]
    2016 | Journal Article | Published | PUB-ID: 2900129 OA
    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 11.1 (2016): 3.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [178]
    2016 | Conference Paper | Published | 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 | Conference Paper | Published | PUB-ID: 2757497
    Holley, Guillaume, Wittler, Roland, and Stoye, Jens. “Bloom Filter Trie - a data structure for pan-genome storage”. Algorithms in Bioinformatics. WABI 2015. Proceedings. Ed. Mihai Pop and Hélène Touzet. Berlin, Heidelberg: Springer, 2015.Vol. 9289. Lecture Notes in Computer Science . 217-230.
    PUB | DOI
     
  • [176]
    2015 | Journal Article | Published | PUB-ID: 2726366 OA
    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 10.1 (2015): 13.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [175]
    2015 | Journal Article | Published | 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
     
  • [174]
    2015 | Conference (Editor) | Published | 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 | Conference (Editor) | Published | 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 | Journal Article | Published | 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
     
  • [171]
    2014 | Journal Article | Published | PUB-ID: 2685362 OA
    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
     
  • [170]
    2014 | Conference Paper | Published | 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
     
  • [169]
    2014 | Journal Article | Published | PUB-ID: 2687033 OA
    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
     
  • [168]
    2014 | Journal Article | Published | 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 | Journal Article | Published | 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 | Journal Article | Published | 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 | Conference Paper | Published | 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 | Encyclopedia Article | Published | PUB-ID: 2693552
    Stoye, Jens. “Suffix Tree Construction”. Encyclopedia of Algorithms. Ed. M.-Y. Kao. Springer Verlag, 2014.
    PUB | DOI
     
  • [163]
    2014 | Journal Article | Published | 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
     
  • [162]
    2014 | Journal Article | Published | 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
     
  • [161]
    2014 | Journal Article | Published | 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 | Journal Article | Published | 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
     
  • [159]
    2013 | Encyclopedia Article | Published | 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
     
  • [158]
    2013 | Journal Article | Published | PUB-ID: 2611630 OA
    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
     
  • [157]
    2013 | Conference Paper | Published | 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
     
  • [156]
    2013 | Book Chapter | Published | 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. London: Springer Verlag, 2013.Vol. 19. Computational Biology Series. 287-307.
    PUB | DOI
     
  • [155]
    2013 | Journal Article | Published | 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
     
  • [154]
    2013 | Book Chapter | Published | 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. London: Springer Verlag, 2013.Vol. 19. Computational Biology Series. 63-81.
    PUB | DOI
     
  • [153]
    2013 | Journal Article | Published | 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
     
  • [152]
    2013 | Journal Article | Published | 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 | Conference (Editor) | Published | PUB-ID: 2616537
    Aaron Darling and Jens Stoye, eds. “Algorithms in Bioinformatics”. Lecture Notes in Bioinformatics 8126 (2013).
    PUB | DOI
     
  • [150]
    2013 | Journal Article | Published | PUB-ID: 2611633 OA
    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 | Journal Article | Published | 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 | Journal Article | Published | 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 | Journal Article | Published | 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
     
  • [146]
    2012 | Journal Article | Published | PUB-ID: 2512642 OA
    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
     
  • [145]
    2012 | Journal Article | Published | PUB-ID: 2517239 OA
    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
     
  • [144]
    2012 | Journal Article | Published | PUB-ID: 2512644 OA
    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
     
  • [143]
    2012 | Journal Article | Published | PUB-ID: 2486060 OA
    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
     
  • [142]
    2012 | Conference (Editor) | Published | PUB-ID: 2510416
    Juha Kärkkäinen and Jens Stoye, eds. “Combinatorial Pattern Matching”. Lecture Notes in Computer Science 7354 (2012).
    PUB | DOI
     
  • [141]
    2012 | Book Chapter | Published | PUB-ID: 2468382 OA
    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.)
     
  • [140]
    2012 | Journal Article | Published | 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
     
  • [139]
    2011 | Journal Article | Published | 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
     
  • [138]
    2011 | Journal Article | Published | PUB-ID: 2396509 OA
    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 | Journal Article | Published | PUB-ID: 2396558 OA
    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
     
  • [136]
    2011 | Journal Article | Published | 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 | arXiv
     
  • [135]
    2011 | Journal Article | Published | 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
     
  • [134]
    2011 | Journal Article | Published | 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
     
  • [133]
    2011 | Journal Article | Published | 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
     
  • [132]
    2011 | Journal Article | Published | 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
     
  • [131]
    2011 | Journal Article | Published | PUB-ID: 1918550
    Heber, Steffen, Mayr, Richard, and Stoye, Jens. “Common Intervals of Multiple Permutations”. Algorithmica 60.2 (2011): 175-206.
    PUB | DOI | WoS
     
  • [130]
    2011 | Journal Article | Published | PUB-ID: 2298170 OA
    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
     
  • [129]
    2011 | Journal Article | Published | 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
     
  • [128]
    2010 | Conference Paper | Published | 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
     
  • [127]
    2010 | Journal Article | Published | 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
     
  • [126]
    2010 | Conference Abstract / Poster | Published | 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.)
     
  • [125]
    2010 | Conference Abstract / Poster | Published | PUB-ID: 2907492
    Bergeron, Anne, Mixtacki, Julia, and Stoye, Jens. “A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance”. Structure Discovery in Biology: Motifs, Networks & Phylogenies. Ed. Alberto Apostolico, Andreas Dress, Laxmi Parida, and Schloss Dagstuhl, Leibniz-Zentrum für Informatik. Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, 2010.Vol. 10231. Dagstuhl Seminar Proceedings. Online-Ressource.
    PUB | Download (ext.)
     
  • [124]
    2010 | Journal Article | Published | PUB-ID: 1893893 OA
    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
     
  • [123]
    2010 | Book Chapter | Published | 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. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010.Vol. 6060. LNCS. 62-76.
    PUB | DOI
     
  • [122]
    2010 | Journal Article | Published | 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
     
  • [121]
    2010 | Journal Article | Published | 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
     
  • [120]
    2010 | Conference Paper | Published | 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
     
  • [119]
    2010 | Conference Paper | Published | 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.)
     
  • [118]
    2010 | Journal Article | Published | 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
     
  • [117]
    2010 | Journal Article | Published | 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
     
  • [116]
    2010 | Conference Paper | Published | 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 | Journal Article | Published | 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 | Conference Paper | Published | 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 | Conference Paper | Published | 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
     
  • [112]
    2009 | Journal Article | Published | 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
     
  • [111]
    2009 | Conference Paper | Published | 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
     
  • [110]
    2009 | Conference Paper | Published | 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
     
  • [109]
    2009 | Journal Article | Published | 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
     
  • [108]
    2009 | Journal Article | Published | 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
     
  • [107]
    2009 | Journal Article | Published | 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
     
  • [106]
    2009 | Journal Article | Published | PUB-ID: 1589098 OA
    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
     
  • [105]
    2009 | Journal Article | Published | 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 | Journal Article | Published | 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 | Conference Paper | Published | 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 | Conference Abstract / Poster | Published | PUB-ID: 1918945
    Stoye, Jens. “Computational Short Read Metagenomics”. Presented at the JOBIM 2009, Nantes, France, 2009.
    PUB
     
  • [101]
    2009 | Journal Article | Published | 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 | Conference Paper | Published | 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 OA
    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 OA
    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 | Journal Article | Published | 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 | Encyclopedia Article | Published | 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
     
  • [95]
    2008 | Conference Paper | Published | 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
     
  • [94]
    2008 | Conference Paper | Published | 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
     
  • [93]
    2008 | Journal Article | Published | 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 | Journal Article | Published | 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 | Journal Article | Published | PUB-ID: 1586785 OA
    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 | Journal Article | Published | PUB-ID: 1783364 OA
    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 | Conference Paper | Published | 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 | Journal Article | Published | 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
     
  • [87]
    2007 | Book Chapter | Published | 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
     
  • [86]
    2007 | Journal Article | Published | 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
     
  • [85]
    2007 | Journal Article | Published | 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
     
  • [84]
    2007 | Journal Article | Published | PUB-ID: 1783345 OA
    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
     
  • [83]
    2006 | Journal Article | Published | 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 | Journal Article | Published | 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 | Journal Article | Published | 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 | Conference Paper | Published | 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 | Journal Article | Published | 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 | Journal Article | Published | 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 | Conference Abstract / Poster | Published | 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 OA
    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 | Journal Article | Published | 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 OA
    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 | Conference Paper | Published | 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 | Book Chapter | Published | 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 | Conference Paper | Published | 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 | Journal Article | Published | PUB-ID: 1775168 OA
    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 | Journal Article | Published | PUB-ID: 1773302 OA
    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 | Journal Article | Published | PUB-ID: 1918947
    Böcker, Sebastian, and Stoye, Jens. “Informatische Methoden zur Protein-Identifikation”. LaborPraxis 29.10 (2005): 24-26.
    PUB
     
  • [67]
    2005 | Conference Paper | Published | 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 | Conference Paper | Published | 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 | Conference Paper | Published | 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 | Conference Paper | Published | 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 OA
    Schürmann, Klaus-Bernd, and Stoye, Jens. Counting Suffix Arrays and Strings. Bielefeld: Technische Fakultät der Universität Bielefeld, 2005. Forschungsberichte.
    PUB | PDF
     
  • [62]
    2004 | Conference (Editor) | Published | 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): 234.
    PUB
     
  • [61]
    2004 | Conference Paper | Published | 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
     
  • [60]
    2004 | Conference Paper | Published | 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
     
  • [59]
    2004 | Journal Article | Published | PUB-ID: 1773554 OA
    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 | Journal Article | Published | PUB-ID: 1773560 OA
    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 | Journal Article | Published | PUB-ID: 1773312 OA
    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 | Journal Article | Published | PUB-ID: 1773569 OA
    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 | Conference Paper | Published | 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 OA
    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 | Journal Article | Published | 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 | Journal Article | Published | 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 | Conference Paper | Published | 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 | Journal Article | Published | PUB-ID: 1610397 OA
    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 | Journal Article | Published | PUB-ID: 1609403 OA
    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 | Conference Paper | Published | 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 | Journal Article | Published | PUB-ID: 1610503 OA
    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 OA
    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 | Conference Abstract / Poster | Published | 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 | Conference Paper | Published | 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 | Journal Article | Published | PUB-ID: 1773578 OA
    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 | Journal Article | Published | PUB-ID: 1773332 OA
    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 | Journal Article | Published | PUB-ID: 1773329 OA
    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 | Conference Paper | Published | 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 | Journal Article | Published | PUB-ID: 1773335 OA
    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 | Conference Paper | Published | 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 | Conference Paper | Published | 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 | Conference Paper | Published | 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 | Book Chapter | Published | 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 | Journal Article | Published | PUB-ID: 1773345 OA
    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 | Journal Article | Published | PUB-ID: 1773572 OA
    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 | Conference Paper | Published | 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 OA
    Stoye, Jens. Affix Trees. Technische Fakultät der Universität Bielefeld, 2000. Forschungsberichte.
    PUB | PDF
     
  • [29]
    2000 | Journal Article | Published | PUB-ID: 1773341 OA
    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 | Conference Paper | Published | 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 | Conference (Editor) | Published | 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 | Conference Paper | Published | 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 | Conference Paper | Published | 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 | Conference Paper | Published | 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 | Journal Article | Published | 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 | Journal Article | Published | 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 | Journal Article | Published | PUB-ID: 1667771 OA
    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 | Journal Article | Published | PUB-ID: 1625402 OA
    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 | Conference Paper | Published | 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 | Journal Article | Published | 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
     
  • [13]
    1997 | Journal Article | Published | 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
     
  • [12]
    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
     
  • [11]
    1997 | Report | PUB-ID: 1970517
    Stoye, Jens, Evers, Dirk, and Meyer, Folker. Rose: Generating Sequence Families. Technische Fakultät der Universität Bielefeld, 1997. Forschungsberichte.
    PUB
     
  • [10]
    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
     
  • [9]
    1997 | Conference Paper | Published | 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
     
  • [8]
    1997 | Journal Article | Published | PUB-ID: 1773355 OA
    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
     
  • [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 | Journal Article | Published | 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.
    PUB
     
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