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, L.; Garrison, E.; Stoye, J.; Marschall, T.; Doerr, D. (2024): Panacus: fast and exact pangenome growth and core size estimation Bioinformatics
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [237]
    2024 | Conference Paper | Published | PUB-ID: 2992085
    Bohnenkämper, L.; Stoye, J.; Dörr, D. (2024): Reconstructing Rearrangement Phylogenies of Natural Genomes LIPIcs,312:12
    PUB | DOI
     
  • [236]
    2024 | Journal Article | Published | PUB-ID: 2988749
    Parmigiani, L.; Wittler, R.; Stoye, J. (2024): Revisiting pangenome openness with k-mers Peer Community Journal,4:e47
    PUB | DOI | WoS
     
  • [235]
    2024 | Journal Article | Published | PUB-ID: 2990552
    Frolova, D.; Lima, L.; Roberts, L.; Bohnenkämper, L.; Wittler, R.; Stoye, J.; Iqbal, Z. (2024): Applying rearrangement distances to enable plasmid epidemiology with pling Microbial Genomics ,10:(10):001300
    PUB | DOI | PubMed | Europe PMC | Preprint
     
  • [234]
    2024 | Book (Editor) | Published | PUB-ID: 2990269
    João Carlos Setubal; Peter F. Stadler; Jens Stoye (Hrsg.) (2024): Comparative Genomics. Methods and Protocols. 2. New York, NY: Humana.
    PUB | DOI
     
  • [233]
    2024 | Book Chapter | Published | PUB-ID: 2990270
    Dias Vieira Braga, M.; Doerr, D.; Rubert, D. P.; Stoye, J. (2024): Family-Free Genome Comparison. In: João Carlos Setubal; Peter F. Stadler; Jens Stoye (Hrsg.): Comparative Genomics. Methods and Protocols. 2. New York, NY: Humana. (Methods in Molecular Biology, 2802). S. 57-72.
    PUB | DOI
     
  • [232]
    2024 | Book Chapter | Published | PUB-ID: 2990271
    Schulz, T.; Parmigiani, L.; Rempel, A.; Stoye, J. (2024): Methods for Pangenomic Core Detection. In: João Carlos Setubal; Peter F. Stadler; Jens Stoye (Hrsg.): Comparative Genomics. Methods and Protocols. New York, NY: Humana. (Methods in Molecular Biology, 2802). S. 73-106.
    PUB | DOI
     
  • [231]
    2024 | Journal Article | Published | PUB-ID: 2985702 OA
    Dias Vieira Braga, M.; Brockmann, L. R.; Klerx, K.; Stoye, J. (2024): Investigating the complexity of the double distance problems Algorithms for Molecular Biology,19:1
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  • [230]
    2023 | Conference Paper | Published | PUB-ID: 2981606
    Dias Vieira Braga, M.; Brockmann, L. R.; Klerx, K.; Stoye, J. (2023): On the Class of Double Distance Problems. In: Katharina Jahn; Tomáš Vinař (Hrsg.): Comparative Genomics. 20th International Conference, RECOMB-CG 2023, Istanbul, Turkey, April 14–15, 2023, Proceedings. Cham: Springer Nature . (Lecture Notes in Computer Science, 13883). S. 35-50.
    PUB | DOI | WoS
     
  • [229]
    2023 | Journal Article | Published | PUB-ID: 2984551
    Förstner, K. U.; Becker, A.; Blom, J.; Bork, P.; Clavel, T.; Dieckmann, M.; Goesmann, A.; Götz, B.; Gübitz, T.; Hufsky, F.; Jünemann, S.; Körner, M. - L.; Marz, M.; Da Rocha, U. N.; Overmann, J.; Pühler, A.; Rebholz-Schuhmann, D.; Sczyrba, A.; Stoye, J.; Vandendorpe, J.; Van Rossum, T.; McHardy, A. (2023): NFDI4Microbiota – national research data infrastructure for microbiota research Research Ideas and Outcomes,9
    PUB | DOI
     
  • [228]
    2023 | Journal Article | Published | PUB-ID: 2969065
    Kirsch-Gerweck, B.; Bohnenkämper, L.; Henrichs, M. T.; Alanko, J. N.; Bannai, H.; Cazaux, B.; Peterlongo, P.; Burger, J.; Stoye, J.; Diekmann, Y. (2023): HaploBlocks: efficient detection of positive selection in large population genomic datasets Molecular Biology and Evolution,40:(3):msad027
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [227]
    2022 | Preprint | Published | PUB-ID: 2967089
    Parmigiani, L.; Wittler, R.; Stoye, J. (2022): Revisiting pangenome openness with k-mers bioRxiv
    PUB | DOI
     
  • [226]
    2022 | Conference Paper | Published | PUB-ID: 2965398
    Dias Vieira Braga, M.; Brockmann, L. R.; Klerx, K.; Stoye, J. (2022): A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance. In: Christina Boucher; Sven Rahmann (Hrsg.): 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. (Leibniz International Proceedings in Informatics. LIPIcs, 242). S. 13:1-13:16.
    PUB | DOI
     
  • [225]
    2022 | Journal Article | Published | PUB-ID: 2963777
    Bonizzoni, P.; Costantini, M.; De Felice, C.; Petescia, A.; Pirola, Y.; Previtali, M.; Rizzi, R.; Stoye, J.; Zaccagnino, R.; Zizza, R. (2022): Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches Information Sciences,607: 458-476.
    PUB | DOI | WoS
     
  • [224]
    2022 | Journal Article | Published | PUB-ID: 2963659 OA
    Schulz, T.; Wittler, R.; Stoye, J. (2022): Sequence-based pangenomic core detection iScience,25:(6):104413
    PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [223]
    2021 | Book (Editor) | Published | PUB-ID: 2959449 OA
    Jens Stoye; Roland Wittler (Hrsg.) (2021): The Bielefeld Institute for Bioinformatics Infrastructure. Bielefeld: Universität Bielefeld, Techn. Fakultät.
    PUB | PDF | DOI
     
  • [222]
    2021 | Journal Article | Published | PUB-ID: 2942686
    Willing, E.; Stoye, J.; Dias Vieira Braga, M. (2021): Computing the Inversion-Indel Distance IEEE/ACM Transactions on Computational Biology and Bioinformatics,18:(6): 2314-2326.
    PUB | DOI | WoS | PubMed | Europe PMC | arXiv
     
  • [221]
    2021 | Journal Article | Published | PUB-ID: 2950825 OA
    Schulz, T.; Wittler, R.; Rahmann, S.; Hach, F.; Stoye, J. (2021): Detecting High Scoring Local Alignments in Pangenome Graphs Bioinformatics,37:(16): 2266-2274.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [220]
    2021 | Conference Paper | Published | PUB-ID: 2952705
    Bonizzoni, P.; De Felice, C.; Petescia, A.; Pirola, Y.; Rizzi, R.; Stoye, J.; Zaccagnino, R.; Zizza, R. (2021): Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning. In: Proceedings of AlCoB 2021. (LNBI, 12715). S. 16-28.
    PUB
     
  • [219]
    2021 | Journal Article | Published | PUB-ID: 2946303
    Bohnenkämper, L.; Dias Vieira Braga, M.; Dörr, D.; Stoye, J. (2021): Computing the rearrangement distance of natural genomes Journal of Computational Biology,28:(4): 410-431.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [218]
    2021 | Journal Article | Published | PUB-ID: 2945991
    Sundermann, L. K.; Wintersinger, J.; Rätsch, G.; Stoye, J.; Morris, Q. (2021): Reconstructing Tumor Evolutionary Histories and Clone Trees in Polynomial-time with SubMARine PLOS Computational Biology,17:(1):e1008400
    PUB | DOI | WoS | PubMed | Europe PMC | Preprint
     
  • [217]
    2021 | Special Issue | Published | PUB-ID: 2949108
    João C. Setubal; Jens Stoye; Bas E. Dutilh (Hrsg.) (2021): Computational Methods for Microbiome Analysis, In: João C. Setubal; Jens Stoye; Bas E. Dutilh (Hrsg.), Frontiers in Genetics,Research Topic
    PUB | DOI | Download (ext.)
     
  • [216]
    2020 | Preprint | Published | PUB-ID: 2943670
    Rubert, D.; Araujo, E.; Stefanes, M. A.; Stoye, J.; Martinez, F. V. (2020): On motifs in colored graphs arXiv:2005.13634
    PUB | Download (ext.) | arXiv
     
  • [215]
    2020 | Journal Article | Published | PUB-ID: 2942995
    Rubert, D.; Araujo, E.; Stefanes, M. A.; Stoye, J.; Martinez, F. (2020): Searching and Inferring Colorful Topological Motifs in Vertex-Colored Graphs Journal of Combinatorial Optimization,40: 379–411.
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  • [214]
    2020 | Journal Article | Published | PUB-ID: 2937712 OA
    Rubert, D.; Martinez, F. H. V.; Stoye, J.; Dörr, D. (2020): Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants BMC Genomics,21:(Suppl. 2):273
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  • [213]
    2020 | Journal Article | Published | PUB-ID: 2953267
    Schulte-Schrepping, J.; Reusch, N.; Paclik, D.; Baßler, K.; Schlickeiser, S.; Zhang, B.; Krämer, B.; Krammer, T.; Brumhard, S.; Bonaguro, L.; De Domenico, E.; Wendisch, D.; Grasshoff, M.; Kapellos, T. S.; Beckstette, M.; Pecht, T.; Saglam, A.; Dietrich, O.; Mei, H. E.; Schulz, A. R.; Conrad, C.; Kunkel, D.; Vafadarnejad, E.; Xu, C. - J.; Horne, A.; Herbert, M.; Drews, A.; Thibeault, C.; Pfeiffer, M.; Hippenstiel, S.; Hocke, A.; Müller-Redetzky, H.; Heim, K. - M.; Machleidt, F.; Uhrig, A.; Bosquillon de Jarcy, L.; Jürgens, L.; Stegemann, M.; Glösenkamp, C. R.; Volk, H. - D.; Goffinet, C.; Landthaler, M.; Wyler, E.; Georg, P.; Schneider, M.; Dang-Heine, C.; Neuwinger, N.; Kappert, K.; Tauber, R.; Corman, V.; Raabe, J.; Kaiser, K. M.; Vinh, M. T.; Rieke, G.; Meisel, C.; Ulas, T.; Becker, M.; Geffers, R.; Witzenrath, M.; Drosten, C.; Suttorp, N.; von Kalle, C.; Kurth, F.; Händler, K.; Schultze, J. L.; Aschenbrenner, A. C.; Li, Y.; Nattermann, J.; Sawitzki, B.; Saliba, A. - E.; Sander, L. E.; Angelov, A.; Bals, R.; Bartholomäus, A.; Becker, A.; Bezdan, D.; Bonifacio, E.; Bork, P.; Clavel, T.; Colome-Tatche, M.; Diefenbach, A.; Dilthey, A.; Fischer, N.; Förstner, K.; Frick, J. - S.; Gagneur, J.; Goesmann, A.; Hain, T.; Hummel, M.; Janssen, S.; Kalinowski, J.; Kallies, R.; Kehr, B.; Keller, A.; Kim-Hellmuth, S.; Klein, C.; Kohlbacher, O.; Korbel, J. O.; Kurth, I.; Landthaler, M.; Li, Y.; Ludwig, K.; Makarewicz, O.; Marz, M.; McHardy, A.; Mertes, C.; Nöthen, M.; Nürnberg, P.; Ohler, U.; Ossowski, S.; Overmann, J.; Peter, S.; Pfeffer, K.; Poetsch, A. R.; Pühler, A.; Rajewsky, N.; Ralser, M.; Rieß, O.; Ripke, S.; Nunes da Rocha, U.; Rosenstiel, P.; Saliba, A. - E.; Sander, L. E.; Sawitzki, B.; Schiffer, P.; Schulte, E. - C.; Schultze, J. L.; Sczyrba, A.; Stegle, O.; Stoye, J.; Theis, F.; Vehreschild, J.; Vogel, J.; von Kleist, M.; Walker, A.; Walter, J.; Wieczorek, D.; Ziebuhr, J. (2020): Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment Cell,182:(6): 1419-1440.e23.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [212]
    2020 | Report | PUB-ID: 2944669
    Glöckner, F. O.; Diepenbroek, M.; Felden, J.; Güntsch, A.; Stoye, J.; Overmann, J.; Wimmers, K.; Kostadinov, I.; Yahyapour, R.; Müller, W.; Scholz, U.; Triebel, D.; Frenzel, M.; Gemeinholzer, B.; Goesmann, A.; König-Ries, B.; Bonn, A.; Seeger, B. (2020): NFDI4BioDiversity - A Consortium for the National Research Data Infrastructure (NFDI) : Proposal. Zenodo.
    PUB | DOI
     
  • [211]
    2020 | Journal Article | Published | PUB-ID: 2948972
    Setubal, J. C.; Stoye, J.; Dutilh, B. E. (2020): Editorial: Computational Methods for Microbiome Analysis Frontiers in Genetics,11:623897
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [210]
    2020 | Preprint | Published | PUB-ID: 2940602
    Haghshenas, E.; Asghari, H.; Stoye, J.; Chauve, C.; Hach, F. (2020): HASLR: Fast Hybrid Assembly of Long Reads bioRxiv
    PUB | DOI | Download (ext.) | Preprint
     
  • [209]
    2020 | Preprint | Published | PUB-ID: 2945720
    Schulz, T.; Wittler, R.; Rahmann, S.; Hach, F.; Stoye, J. (2020): Detecting High Scoring Local Alignments in Pangenome Graphs bioRxiv
    PUB | DOI | Preprint
     
  • [208]
    2020 | Journal Article | Published | PUB-ID: 2939618 OA
    Alanko, J.; Bannai, H.; Cazaux, B.; Peterlongo, P.; Stoye, J. (2020): Finding all maximal perfect haplotype blocks in linear time Algorithms for Molecular Biology,15:2
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  • [207]
    2020 | Journal Article | Published | PUB-ID: 2945430
    Haghshenas, E.; Asghari, H.; Stoye, J.; Chauve, C.; Hach, F. (2020): HASLR: Fast Hybrid Assembly of Long Reads iScience,23:(8):101389
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [206]
    2020 | Journal Article | Published | PUB-ID: 2939598
    Sevillya, G.; Dörr, D.; Lerner, Y.; Stoye, J.; Steel, M.; Snir, S. (2020): Horizontal Gene Transfer Phylogenetics: A Random Walk Approach Molecular Biology and Evolution,37:(5): 1470–1479.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [205]
    2020 | Preprint | Published | PUB-ID: 2939861
    Bohnenkämper, L.; Dias Vieira Braga, M.; Dörr, D.; Stoye, J. (2020): Computing the rearrangement distance of natural genomes arXiv:2001.02139
    PUB | Download (ext.) | arXiv
     
  • [204]
    2020 | Conference Paper | Published | PUB-ID: 2939729
    Bohnenkämper, L.; Dias Vieira Braga, M.; Dörr, D.; Stoye, J. (2020): Computing the rearrangement distance of natural genomes. In: Proceedings of RECOMB 2020. (LNBI, 12074). S. 3-18.
    PUB | DOI
     
  • [203]
    2019 | Journal Article | Published | PUB-ID: 2932884
    Oey, H.; Zakrzewski, M.; Gravermann, K.; Young, N. D.; Korhonen, P. K.; Gobert, G. N.; Nawaratna, S.; Hasan, S.; Martínez, D. M.; You, H.; Lavin, M.; Jones, M.; Ragan, M. A.; Stoye, J.; Oleaga, A.; Emery, A. M.; Webster, B.; Rollinson, D.; Gasser, R. B.; McManus, D. P.; Krause, L. (2019): Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium PLOS Pathogens,15:(1):e1007513
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [202]
    2019 | Report | Published | PUB-ID: 2939260
    Gagie, T.; Manzini, G.; Navarro, G.; Stoye, J. (2019): 25 Years of the Burrows-Wheeler Transform. Report from Dagstuhl Seminar 19241. Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik.
    PUB | DOI
     
  • [201]
    2019 | Conference Paper | Published | PUB-ID: 2937148
    Alanko, J.; Bannai, H.; Cazaux, B.; Peterlongo, P.; Stoye, J. (2019): Finding All Maximal Perfect Haplotype Blocks in Linear Time. In: Proceedings of WABI 2019. Dagstuhl: Schloss Dagstuhl, Leibniz-Zentrum für Informatik . (Leibniz International Proceedings in Informatics. LIPIcs, 143). S. 8:1-8:9.
    PUB | DOI
     
  • [200]
    2019 | Book Chapter | Published | PUB-ID: 2932883
    Dörr, D.; Stoye, J. (2019): A Perspective on Comparative and Functional Genomics. In: Tandy Warnow (Hrsg.): Bioinformatics and Phylogenetics. Cham: Springer . (Computational Biology, 29). S. 361-372.
    PUB | DOI
     
  • [199]
    2018 | Journal Article | Published | PUB-ID: 2919006 OA
    Rubert, D.; Hoshino, E. A.; Dias Vieira Braga, M.; Stoye, J.; Martinez, F. H. V. (2018): Computing the family-free DCJ similarity BMC Bioinformatics,19:(Suppl. 6):152
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  • [198]
    2018 | Journal Article | Published | PUB-ID: 2919012
    Jaenicke, S.; Albaum, S.; Blumenkamp, P.; Linke, B.; Stoye, J.; Goesmann, A. (2018): Flexible metagenome analysis using the MGX framework Microbiome,6:(1):76
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [197]
    2018 | Journal Article | Published | PUB-ID: 2919005 OA
    Schulz, T.; Stoye, J.; Dörr, D. (2018): GraphTeams. A method for discovering spatial gene clusters in Hi-C sequencing data BMC Genomics,19:(Suppl. 5):308
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [196]
    2018 | Journal Article | Published | PUB-ID: 2930268
    Holley, G.; Wittler, R.; Stoye, J.; Hach, F. (2018): Dynamic Alignment-Free and Reference-Free Read Compression JOURNAL OF COMPUTATIONAL BIOLOGY,25:(7): 825-836.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [195]
    2018 | Book Chapter | Published | PUB-ID: 2913921
    Zekic, T.; Holley, G.; Stoye, J. (2018): Pan-genome Storage and Analysis Techniques. In: João C. Setubal; Peter Stadler; Jens Stoye (Hrsg.): Comparative Genomics. Methods and Protocols. New York: Springer Verlag. (Methods in Molecular Biology, 1704). S. 29-53.
    PUB | DOI
     
  • [194]
    2018 | Book Chapter | Published | PUB-ID: 2913922
    Dörr, D.; Feijão, P.; Stoye, J. (2018): Family-Free Genome Comparison. In: João C. Setubal; Peter Stadler; Jens Stoye (Hrsg.): Comparative Genomics: Methods and Protocols. New York: Springer Verlag. (Methods in Molecular Biology, 1704). S. 331-342.
    PUB | DOI
     
  • [193]
    2018 | Book (Editor) | Published | PUB-ID: 2913920
    João C Setubal; Peter Stadler; Jens Stoye (Hrsg.) (2018): Comparative Genomics: Methods and Protocols. New York: Springer Verlag.
    PUB | DOI
     
  • [192]
    2018 | Journal Article | Published | PUB-ID: 2918481
    Luhmann, N.; Chauve, C.; Stoye, J.; Wittler, R. (2018): Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework IEEE/ACM Transactions on Computational Biology and Bioinformatics,15:(6): 2094-2100.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [191]
    2018 | Conference Paper | Published | PUB-ID: 2930445
    Cunha, L.; Diekmann, Y.; Kowada, L.; Stoye, J. (2018): Identifying Maximal Perfect Haplotype Blocks. In: Proceedings of BSB 2018. Springer Verlag. (LNBI, 11228). S. 26-37.
    PUB | DOI
     
  • [190]
    2017 | Conference Paper | Published | PUB-ID: 2913015
    Rubert, D.; Medeiros, G. L.; Hoshino, E. A.; Dias Vieira Braga, M.; Stoye, J.; Martinez, F. H. V. (2017): Algorithms for Computing the Family-Free Genomic Similarity under DCJ. In: Joao Meidanis; Luay Nakhleh (Hrsg.): Comparative Genomics. RECOMB-CG 2017. Cham: Springer Verlag. (Lecture Notes in Bioinformatics, 10562). S. 76-100.
    PUB | DOI
     
  • [189]
    2017 | Journal Article | Published | PUB-ID: 2909057 OA
    Rubert, D.; Feijão, P.; Dias Vieira Braga, M.; Stoye, J.; Martinez, F. H. V. (2017): Approximating the DCJ distance of balanced genomes in linear time Algorithms for Molecular Biology,12:(1):3
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  • [188]
    2017 | Preprint | Published | PUB-ID: 2908521
    Cunha, L.; Dantas, S.; Gagie, T.; Wittler, R.; Kowada, L.; Stoye, J. (2017): Faster Jumbled Indexing for Binary Run-Length Encoded Strings arXiv: 1702.01280
    PUB | Download (ext.) | arXiv
     
  • [187]
    2017 | Conference Paper | Published | PUB-ID: 2909409
    Cunha, L.; Dantas, S.; Gagie, T.; Wittler, R.; Kowada, L.; Stoye, J. (2017): Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings. In: Proceedings of CPM 2017. (LIPIcs, 78). S. 19:1-19:9.
    PUB | DOI
     
  • [186]
    2017 | Journal Article | Published | PUB-ID: 2913556
    Jünemann, S.; Kleinbölting, N.; Jaenicke, S.; Henke, C.; Hassa, J.; Nelkner, J.; Stolze, Y.; Albaum, S.; Schlüter, A.; Goesmann, A.; Sczyrba, A.; Stoye, J. (2017): Bioinformatics for NGS-based metagenomics and the application to biogas research Journal of Biotechnology,261:(SI): 10-23.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [185]
    2017 | Conference Paper | Published | PUB-ID: 2907587
    Holley, G.; Wittler, R.; Stoye, J.; Hach, F. (2017): Dynamic Alignment-Free and Reference-Free Read Compression. In: Proceedings of RECOMB 2017. (Lecture Notes in Bioinformatics, 10229). S. 50-65.
    PUB | DOI
     
  • [184]
    2017 | Conference Paper | Published | PUB-ID: 2913016
    Schulz, T.; Stoye, J.; Dörr, D. (2017): Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery. In: Proceedings of RECOMB-CG 2017. Berlin: Springer Verlag. (Lecture Notes in Bioinformatics, 1704). S. 197-212.
    PUB | DOI
     
  • [183]
    2017 | Journal Article | Published | PUB-ID: 2909967
    Dörr, D.; Kowada, L. A. B.; Soares de Araujo, F. E.; Deshpande, S.; Dantas, S.; Moret, B. M. E.; Stoye, J. (2017): New Genome Similarity Measures based on Conserved Gene Adjacencies Journal of Computational Biology,24:(6): 616-634.
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  • [182]
    2016 | Conference Paper | Published | PUB-ID: 2903708
    Rubert, D.; Feijão, P.; Dias Vieira Braga, M.; Stoye, J.; Martinez, F. H. V. (2016): A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates. In: Martin Frith; Christian Nørgaard Storm Pedersen (Hrsg.): Algorithms in Bioinformatics. WABI 2016. Cham: Springer. (Lecture Notes in Bioinformatics, 9838). S. 293-306.
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  • [181]
    2016 | Journal Article | Published | PUB-ID: 2905930
    Winter, S.; Jahn, K.; Wehner, S.; Kuchenbecker, L.; Marz, M.; Stoye, J.; Böcker, S. (2016): Finding approximate gene clusters with GECKO 3 Nucleic Acids Research,44:(20): 9600-9610.
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  • [180]
    2016 | Journal Article | Published | PUB-ID: 2900421
    Krause, L.; Nones, K.; Loffler, K. A.; Nancarrow, D.; Oey, H.; Tang, Y. H.; Wayte, N. J.; Patch, A. M.; Patel, K.; Brosda, S.; Manning, S.; Lampe, G.; Clouston, A.; Thomas, J.; Stoye, J.; Hussey, D. J.; Watson, D. I.; Lord, R. V.; Phillips, W. A.; Gotley, D.; Smithers, B. M.; Whiteman, D. C.; Hayward, N. K.; Grimmond, S. M.; Waddell, N.; Barbour, A. P. (2016): 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): 356-365.
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  • [179]
    2016 | Journal Article | Published | PUB-ID: 2900129 OA
    Holley, G.; Wittler, R.; Stoye, J. (2016): Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage Algorithms for Molecular Biology,11:(1):3
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  • [178]
    2016 | Conference Paper | Published | PUB-ID: 2900111
    Kowada, L. A. B.; Doerr, D.; Dantas, S.; Stoye, J. (2016): New Genome Similarity Measures based on Conserved Gene Adjacencies. In: Mona Singh (Hrsg.): Research in Computational Molecular Biology. RECOMB 2016. Springer. (Lecture Notes in Bioinformatics (LNBI), 9649). S. 204-224.
    PUB | DOI
     
  • [177]
    2015 | Conference Paper | Published | PUB-ID: 2757497
    Holley, G.; Wittler, R.; Stoye, J. (2015): Bloom Filter Trie - a data structure for pan-genome storage. In: Mihai Pop; Hélène Touzet (Hrsg.): Algorithms in Bioinformatics. WABI 2015. Proceedings. Berlin, Heidelberg: Springer. ( Lecture Notes in Computer Science , 9289). S. 217-230.
    PUB | DOI
     
  • [176]
    2015 | Journal Article | Published | PUB-ID: 2726366 OA
    Viduani Martinez, F. H.; Feijão, P.; Dias Vieira Braga, M.; Stoye, J. (2015): On the family-free DCJ distance and similarity Algorithms for Molecular Biology,10:(1):13
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [175]
    2015 | Journal Article | Published | PUB-ID: 2677844
    Dias Vieira Braga, M.; Stoye, J. (2015): Sorting linear genomes with rearrangements and indels IEEE/ACM Transactions on Computational Biology and Bioinformatics,12:(3): 500-506.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [174]
    2015 | Conference (Editor) | Published | PUB-ID: 2780229
    Joao Meidanis; Jens Stoye (Hrsg.) (2015): Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Bioinformatics, In: Joao Meidanis; Jens Stoye (Hrsg.), BMC Bioinformatics,16:(Supplement 14)
    PUB | Download (ext.)
     
  • [173]
    2015 | Conference (Editor) | Published | PUB-ID: 2780232
    Joao Meidanis; Jens Stoye (Hrsg.) (2015): Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Genomics, In: Joao Meidanis; Jens Stoye (Hrsg.), BMC Genomics,16:(Supplement 10)
    PUB | Download (ext.)
     
  • [172]
    2014 | Journal Article | Published | PUB-ID: 2689773
    Jünemann, S.; Prior, K.; Albersmeier, A.; Albaum, S.; Kalinowski, J.; Goesmann, A.; Stoye, J.; Harmsen, D. (2014): GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers PLOS ONE,9:(9):e107014
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [171]
    2014 | Journal Article | Published | PUB-ID: 2685362 OA
    Lechner, M.; Hernandez-Rosales, M.; Dörr, D.; Wieseke, N.; Thévenin, A.; Stoye, J.; Hartmann, R. K.; Prohaska, S. J.; Stadler, P. F. (2014): Orthology Detection Combining Clustering and Synteny for Very Large Datasets PLoS ONE,9:(8):e105015
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [170]
    2014 | Conference Paper | Published | PUB-ID: 2684241
    Viduani Martinez, F. H.; Feijão, P.; Dias Vieira Braga, M.; Stoye, J. (2014): On the family-free DCJ distance. In: Dan Brown; Burkhard Morgenstern (Hrsg.): Algorithms in Bioinformatics. WABI 2014. Berlin ; Heidelberg: Springer Verlag. (Lecture Notes in Bioinformatics, 8701). S. 174-186.
    PUB | DOI
     
  • [169]
    2014 | Journal Article | Published | PUB-ID: 2687033 OA
    Dörr, D.; Stoye, J.; Böcker, S.; Jahn, K. (2014): Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings BMC Genomics,15:(Suppl. 6: Proc. of RECOMB-CG 2014):S2
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [168]
    2014 | Journal Article | Published | PUB-ID: 2674387
    Hilker, R.; Stadermann, K. B.; Doppmeier, D.; Kalinowski, J.; Stoye, J.; Straube, J.; Winnebald, J.; Goesmann, A. (2014): ReadXplorer - Visualization and Analysis of Mapped Sequences Bioinformatics,30:(16): 2247-2254.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [167]
    2014 | Journal Article | Published | PUB-ID: 2665038
    Schwientek, P.; Neshat, A.; Kalinowski, J.; Klein, A.; Rückert, C.; Schneiker-Bekel, S.; Wendler, S.; Stoye, J.; Pühler, A. (2014): Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts Journal of Biotechnology,190: 85-95.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [166]
    2014 | Journal Article | Published | PUB-ID: 2685988
    Jakobi, T.; Brinkrolf, K.; Tauch, A.; Noll, T.; Stoye, J.; Pühler, A.; Goesmann, A. (2014): Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing Journal of Biotechnology,190: 64-75.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [165]
    2014 | Conference Paper | Published | PUB-ID: 2690122
    Luhmann, N.; Chauve, C.; Stoye, J.; Wittler, R. (2014): Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. In: Campos Sérgio (Hrsg.): Proc. of BSB 2014. Springer Verlag. (LNBI, 8826). S. 135-143.
    PUB | DOI
     
  • [164]
    2014 | Encyclopedia Article | Published | PUB-ID: 2693552
    Stoye, J. (2014): Suffix Tree Construction. In: M.-Y. Kao (Hrsg.): Encyclopedia of Algorithms. Springer Verlag.
    PUB | DOI
     
  • [163]
    2014 | Journal Article | Published | PUB-ID: 2693409
    Fredrich, E.; Ander, C.; Stoye, J.; Brune, I.; Tauch, A. (2014): Metatranskriptomik der Mikrobiota aus der menschlichen Achselhöhle BIOspektrum,20:(5): 294-296.
    PUB | DOI
     
  • [162]
    2014 | Journal Article | Published | PUB-ID: 2643941
    Hoffmann, N.; Wilhelm, M.; Doebbe, A.; Niehaus, K.; Stoye, J. (2014): BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry Bioinformatics,30:(7): 988-995.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [161]
    2014 | Journal Article | Published | PUB-ID: 2665333
    Henrich, B.; Rumming, M.; Sczyrba, A.; Velleuer, E.; Dietrich, R.; Gerlach, W.; Gombert, M.; Rahn, S.; Stoye, J.; Borkhardt, A.; Fischer, U. (2014): Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma PLoS ONE,9:(3):e92297
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [160]
    2013 | Journal Article | Published | PUB-ID: 2575011
    Ander, C.; Schulz-Trieglaff, O. B.; Stoye, J.; Cox, A. J. (2013): metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences BMC Bioinformatics,14:(Suppl 5: Proc. of RECOMB-Seq 2013):S2
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [159]
    2013 | Encyclopedia Article | Published | PUB-ID: 2577323
    Gerlach, W.; Stoye, J. (2013): Taxonomic classification of metagenomic shotgun sequences with CARMA3. In: Karen E. Nelson (Hrsg.): Encyclopedia of Metagenomics. Springer Verlag.
    PUB | DOI
     
  • [158]
    2013 | Journal Article | Published | PUB-ID: 2611630 OA
    Willing, E.; Zaccaria, S.; Dias Vieira Braga, M.; Stoye, J. (2013): On the Inversion-Indel Distance BMC Bioinformatics,14:(Suppl 15: Proc. of RECOMB-CG 2013):S3
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [157]
    2013 | Conference Paper | Published | PUB-ID: 2611641
    Dias Vieira Braga, M.; Stoye, J. (2013): Restricted DCJ-Indel Model Revisited. In: João C. Setubal; Nalvo F. Almeida (Hrsg.): Advances in Bioinformatics and Computational Biology. BSB 2013. Cham: Springer Verlag. (Lecture Notes in Bioinformatics, 8213). S. 36-46.
    PUB | DOI
     
  • [156]
    2013 | Book Chapter | Published | PUB-ID: 2611648
    Dias Vieira Braga, M.; Chauve, C.; Dörr, D.; Jahn, K.; Stoye, J.; Thévenin, A.; Wittler, R. (2013): The Potential of Family-Free Genome Comparison. In: Cedric Chauve; Nadia El-Mabrouk; Eric Tannier (Hrsg.): Models and Algorithms for Genome Evolution. London: Springer Verlag. (Computational Biology Series, 19). S. 287-307.
    PUB | DOI
     
  • [155]
    2013 | Journal Article | Published | PUB-ID: 2641228
    Jünemann, S.; Sedlazeck, F. J.; Prior, K.; Albersmeier, A.; John, U.; Kalinowski, J.; Mellmann, A.; Goesmann, A.; von Haeseler, A.; Stoye, J.; Harmsen, D. (2013): Corrigendum: Updating benchtop sequencing performance comparison Nature biotechnology,31:(12): 1148.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [154]
    2013 | Book Chapter | Published | PUB-ID: 2611643
    Bergeron, A.; Stoye, J. (2013): The Genesis of the DCJ Formula. In: Cedric Chauve; Nadia El-Mabrouk; Eric Tannier (Hrsg.): Models and Algorithms for Genome Evolution. London: Springer Verlag. (Computational Biology Series, 19). S. 63-81.
    PUB | DOI
     
  • [153]
    2013 | Journal Article | Published | PUB-ID: 2575361
    Krell, P.; Reuther, S.; Fischer, U.; Keller, T.; Weber, S.; Gombert, M.; Schuster, F. R.; Asang, C.; Stepensky, P.; Strahm, B.; Meisel, R.; Stoye, J.; Borkhardt, A. (2013): 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): 1388-1396.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [152]
    2013 | Journal Article | Published | PUB-ID: 2566922
    Jünemann, S.; Sedlazeck, F. J.; Prior, K.; Albersmeier, A.; John, U.; Kalinowski, J.; Mellmann, A.; Goesmann, A.; von Haeseler, A.; Stoye, J.; Harmsen, D. (2013): Updating benchtop sequencing performance comparison Nature Biotechnology,31:(4): 294-296.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [151]
    2013 | Conference (Editor) | Published | PUB-ID: 2616537
    Aaron Darling; Jens Stoye (Hrsg.) (2013): Algorithms in Bioinformatics, In: Aaron Darling; Jens Stoye (Hrsg.), Lecture Notes in Bioinformatics,8126
    PUB | DOI
     
  • [150]
    2013 | Journal Article | Published | PUB-ID: 2611633 OA
    Jahn, K.; Winter, S.; Stoye, J.; Böcker, S. (2013): Statistics for approximate gene clusters BMC Bioinformatics,14:(Suppl 15: Proc. of RECOMB-CG 2013):S14
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [149]
    2013 | Journal Article | Published | PUB-ID: 2548236
    Schwientek, P.; Wendler, S.; Neshat, A.; Eirich, C.; Rückert, C.; Klein, A.; Wehmeier, U. F.; Kalinowski, J.; Stoye, J.; Pühler, A. (2013): Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media Journal of Biotechnology,167:(2): 166-177.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [148]
    2013 | Journal Article | Published | PUB-ID: 2529202
    Zakrzewski, M.; Bekel, T.; Ander, C.; Pühler, A.; Rupp, O.; Stoye, J.; Schlüter, A.; Goesmann, A. (2013): MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets Journal of Biotechnology,167:(2): 156-165.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [147]
    2012 | Journal Article | Published | PUB-ID: 2517230
    Jünemann, S.; Prior, K.; Szczepanowski, R.; Harks, I.; Ehmke, B.; Goesmann, A.; Stoye, J.; Harmsen, D. (2012): Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing PLoS ONE,7:(8):e41606
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [146]
    2012 | Journal Article | Published | PUB-ID: 2512642 OA
    Dörr, D.; Thévenin, A.; Stoye, J. (2012): Gene family assignment-free comparative genomics BMC Bioinformatics,13:(Suppl 19: Proc. of RECOMB-CG 2012):S3
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [145]
    2012 | Journal Article | Published | PUB-ID: 2517239 OA
    Hoffmann, N.; Keck, M.; Neuweger, H.; Wilhelm, M.; Högy, P.; Niehaus, K.; Stoye, J. (2012): Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets BMC Bioinformatics,13:(1):21
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [144]
    2012 | Journal Article | Published | PUB-ID: 2512644 OA
    Jahn, K.; Sudek, H.; Stoye, J. (2012): Multiple genome comparison based on overlap regions of pairwise local alignments BMC Bioinformatics,13:(Suppl. 19: Proc. of RECOMB-CG 2012):S7
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [143]
    2012 | Journal Article | Published | PUB-ID: 2486060 OA
    Schwientek, P.; Szczepanowski, R.; Rückert, C.; Kalinowski, J.; Klein, A.; Selber, K.; Wehmeier, U. F.; Stoye, J.; Pühler, A. (2012): The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110 BMC Genomics,13:(1):112
    PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [142]
    2012 | Conference (Editor) | Published | PUB-ID: 2510416
    Juha Kärkkäinen; Jens Stoye (Hrsg.) (2012): Combinatorial Pattern Matching, In: Juha Kärkkäinen; Jens Stoye (Hrsg.), Lecture Notes in Computer Science,7354
    PUB | DOI
     
  • [141]
    2012 | Book Chapter | Published | PUB-ID: 2468382 OA
    Hoffmann, N.; Stoye, J. (2012): Generic Software Frameworks for GC-MS Based Metabolomics. In: Ute Roessner (Hrsg.): Metabolomics. InTech. S. 73-98.
    PUB | PDF | DOI | Download (ext.)
     
  • [140]
    2012 | Journal Article | Published | PUB-ID: 2510984
    Hilker, R.; Sickinger, C.; Pedersen, C. N. S.; Stoye, J. (2012): UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ Bioinformatics,28:(19): 2509-2511.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [139]
    2011 | Journal Article | Published | PUB-ID: 2091779
    Hufsky, F.; Kuchenbecker, L.; Jahn, K.; Stoye, J.; Böcker, S. (2011): Swiftly Computing Center Strings BMC Bioinformatics,12:(1):106
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [138]
    2011 | Journal Article | Published | PUB-ID: 2396509 OA
    Dias Vieira Braga, M.; Machado, R.; Ribeiro, L. C.; Stoye, J. (2011): Genomic distance under gene substitutions BMC Bioinformatics,12:(Suppl 9: Proc. of RECOMB-CG 2011):S8
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [137]
    2011 | Journal Article | Published | PUB-ID: 2396558 OA
    Dias Vieira Braga, M.; Machado, R.; Ribeiro, L. C.; Stoye, J. (2011): On the weight of indels in genomic distances BMC Bioinformatics,12:(Suppl 9: RECOMB-CG 2011):S13
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [136]
    2011 | Journal Article | Published | PUB-ID: 1897974
    Erdős, P. L.; Soukup, L.; Stoye, J. (2011): Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance Applied Mathematics Letters,24:(1): 82-86.
    PUB | DOI | WoS | arXiv
     
  • [135]
    2011 | Journal Article | Published | PUB-ID: 2091794
    Dias Vieira Braga, M.; Willing, E.; Stoye, J. (2011): Double Cut and Join with Insertions and Deletions Journal of Computational Biology,18:(9): 1167-1184.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [134]
    2011 | Journal Article | Published | PUB-ID: 2091790
    Kovac, J.; Warren, R.; Dias Vieira Braga, M.; Stoye, J. (2011): Restricted DCJ Model. Rearrangement Problems with Chromosome Reincorporation Journal of Computational Biology,18:(9): 1231-1241.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [133]
    2011 | Journal Article | Published | PUB-ID: 2354746
    Schwientek, P.; Szczepanowski, R.; Rückert, C.; Stoye, J.; Pühler, A. (2011): Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology Journal of Biotechnology,155:(1): 68-77.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [132]
    2011 | Journal Article | Published | PUB-ID: 2289952
    Blom, J.; Jakobi, T.; Doppmeier, D.; Jaenicke, S.; Kalinowski, J.; Stoye, J.; Goesmann, A. (2011): Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming Bioinformatics,27:(10): 1351-1358.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [131]
    2011 | Journal Article | Published | PUB-ID: 1918550
    Heber, S.; Mayr, R.; Stoye, J. (2011): Common Intervals of Multiple Permutations Algorithmica,60:(2): 175-206.
    PUB | DOI | WoS
     
  • [130]
    2011 | Journal Article | Published | PUB-ID: 2298170 OA
    Gerlach, W.; Stoye, J. (2011): Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res,39:(14): e91.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [129]
    2011 | Journal Article | Published | PUB-ID: 2091787
    Wittler, R.; Maňuch, J.; Patterson, M.; Stoye, J. (2011): Consistency of Sequence-Based Gene Clusters Journal of Computational Biology,18:(9): 1023-1039.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [128]
    2010 | Conference Paper | Published | PUB-ID: 1919211
    Hufsky, F.; Kuchenbecker, L.; Jahn, K.; Stoye, J.; Böcker, S. (2010): Swiftly Computing Center Strings. In: Proc. of WABI 2010. (LNBI, 6293). S. 325-336.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [127]
    2010 | Journal Article | Published | PUB-ID: 1966439
    Trost, E.; Ott, L.; Schneider, J.; Schröder, J.; Jaenicke, S.; Goesmann, A.; Husemann, P.; Stoye, J.; Alves Dorella, F.; Souza Rocha, F.; de Castro Soares, S.; D'Afonseca, V.; Miyoshi, A.; Ruiz, J.; Silva, A.; Azevedo, V.; Burkovski, A.; Guiso, N.; Join-Lambert, O. F.; Kayal, S.; Tauch, A. (2010): 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):728
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [126]
    2010 | Conference Abstract / Poster | Published | PUB-ID: 2445157
    Bergeron, A.; Mixtacki, J.; Stoye, J. (2010): Computing the Genomic Distance in Linear Time. In: Alberto Apostolico; Andreas Dress; Laxmi Parida (Hrsg.): Dagstuhl Seminar Proceedings: 10231 Abstracts Collection : Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. (10231). S. 18.
    PUB | Download (ext.)
     
  • [125]
    2010 | Conference Abstract / Poster | Published | PUB-ID: 2907492
    Bergeron, A.; Mixtacki, J.; Stoye, J. (2010): A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance. In: Alberto Apostolico; Andreas Dress; Laxmi Parida; Schloss Dagstuhl, Leibniz-Zentrum für Informatik (Hrsg.): Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany. (Dagstuhl Seminar Proceedings, 10231). S. Online-Ressource.
    PUB | Download (ext.)
     
  • [124]
    2010 | Journal Article | Published | PUB-ID: 1893893 OA
    Husemann, P.; Stoye, J. (2010): Phylogenetic Comparative Assembly Algorithms for Molecular Biology,5:(1):3
    PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [123]
    2010 | Book Chapter | Published | PUB-ID: 1918836
    Besenbacher, S.; Schwikowski, B.; Stoye, J. (2010): Indexing and Searching a Mass Spectrometry Database. In: Tapio Elomaa; Heikki Mannila; Pekka Orponen (Hrsg.): Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday. Berlin, Heidelberg: Springer Berlin Heidelberg. (LNCS, 6060). S. 62-76.
    PUB | DOI
     
  • [122]
    2010 | Journal Article | Published | PUB-ID: 1795670
    Wittkop, T.; Emig, D.; Lange, S. J.; Rahmann, S.; Albrecht, M.; Morris, J. H.; Böcker, S.; Stoye, J.; Baumbach, J. (2010): Partitioning Biological Data with Transitivity Clustering Nature Methods,7:(6): 419-420.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [121]
    2010 | Journal Article | Published | PUB-ID: 1898012
    Blin, G.; Faye, D.; Stoye, J. (2010): Finding Nested Common Intervals Efficiently Journal of Computational Biology,17:(9): 1183-1194.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [120]
    2010 | Conference Paper | Published | PUB-ID: 1919217
    Wittler, R.; Stoye, J. (2010): Consistency of Sequence-based Gene Clusters. In: Proc. of Recomb-CG 2010. Springer Verlag. (LNBI, 6398). S. 252-263.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [119]
    2010 | Conference Paper | Published | PUB-ID: 1893890
    Husemann, P.; Stoye, J. (2010): Repeat-aware Comparative Genome Assembly. In: Proc. of GCB 2010. (LNI, P-173). S. 61-70.
    PUB | Download (ext.)
     
  • [118]
    2010 | Journal Article | Published | PUB-ID: 1588556
    Husemann, P.; Stoye, J. (2010): r2cat: Synteny Plots and Comparative Assembly Bioinformatics,26:(4): 570-571.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [117]
    2010 | Journal Article | Published | PUB-ID: 1897997
    Bergeron, A.; Medvedev, P.; Stoye, J. (2010): Rearrangement Models and Single-Cut Operations Journal of Computational Biology,17:(9): 1213-1225.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [116]
    2010 | Conference Paper | Published | PUB-ID: 1919216
    Kovac, J.; Dias Vieira Braga, M.; Stoye, J. (2010): The Problem of Chromosome Reincorporation in DCJ Sorting and Halving. In: Proc. of Recomb-CG 2010. (LNBI, 6398). S. 13-24.
    PUB | DOI
     
  • [115]
    2010 | Journal Article | Published | PUB-ID: 1898025
    Dias Vieira Braga, M.; Stoye, J. (2010): The Solution Space of Sorting by DCJ Journal of Computational Biology,17:(9): 1145-1165.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [114]
    2010 | Conference Paper | Published | PUB-ID: 1919215
    Dias Vieira Braga, M.; Willing, E.; Stoye, J. (2010): Genomic Distance with DCJ and Indels. In: Proc. of WABI 2010. (LNBI, 6293). S. 90-101.
    PUB | DOI
     
  • [113]
    2009 | Conference Paper | Published | PUB-ID: 1893884
    Husemann, P.; Stoye, J. (2009): Phylogenetic Comparative Assembly. In: Proc. of WABI 2009. (LNBI, 5724). S. 145-156.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [112]
    2009 | Journal Article | Published | PUB-ID: 1589663
    Bergeron, A.; Mixtacki, J.; Stoye, J. (2009): A New Linear Time Algorithm to Compute the Genomic Distance via the Double Cut and Join Distance Theoretical Computer Science,410:(51): 5300-5316.
    PUB | DOI | WoS
     
  • [111]
    2009 | Conference Paper | Published | PUB-ID: 1919206
    Dias Vieira Braga, M.; Stoye, J. (2009): Counting All DCJ Sorting Scenarios. In: Proc. of Recomb-CG 2009. (LNBI, 5817). S. 36-47.
    PUB | DOI
     
  • [110]
    2009 | Conference Paper | Published | PUB-ID: 1919207
    Blin, G.; Stoye, J. (2009): Finding Nested Common Intervals Efficiently. In: Proc. of Recomb-CG 2009. (LNBI, 5817). S. 59-69.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [109]
    2009 | Journal Article | Published | PUB-ID: 1898137
    Jahn, K.; Stoye, J. (2009): Approximative Gencluster und ihre Anwendung in der komparativen Genomik Informatik-Spektrum,32:(4): 288-300.
    PUB | DOI
     
  • [108]
    2009 | Journal Article | Published | PUB-ID: 1591507
    Stoye, J.; Wittler, R. (2009): A Unified Approach for Reconstructing Ancient Gene Clusters IEEE/ACM Transactions on Computational Biology and Bioinformatics,6:(3): 387-400.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [107]
    2009 | Journal Article | Published | PUB-ID: 1590204
    Brudno, M.; Medvedev, P.; Stoye, J.; De La Vega, F. M. (2009): A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG) BIOINFORMATICS,25:(21): 2863-2864.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [106]
    2009 | Journal Article | Published | PUB-ID: 1589098 OA
    Gerlach, W.; Jünemann, S.; Tille, F.; Goesmann, A.; Stoye, J. (2009): WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads BMC Bioinformatics,10:(1): 430.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [105]
    2009 | Journal Article | Published | PUB-ID: 1898105
    Böcker, S.; Jahn, K.; Mixtacki, J.; Stoye, J. (2009): Computation of Median Gene Clusters Journal of Computational Biology,16:(8): 1085-1099.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [104]
    2009 | Journal Article | Published | PUB-ID: 1591319
    Hoffmann, N.; Stoye, J. (2009): ChromA: signal-based retention time alignment for chromatography-mass spectrometry data Bioinformatics,25:(16): 2080-2081.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [103]
    2009 | Conference Paper | Published | PUB-ID: 1919209
    Medvedev, P.; Stoye, J. (2009): Rearrangement Models and Single-Cut Operations. In: Comparative Genomics : International Workshop, RECOMB-CG 2009, Budapest, Hungary, September 27-29, 2009. Proceedings. Berlin, Heidelberg: Springer. (Lecture Notes in Computer Science, 5817). S. 84-97.
    PUB | DOI
     
  • [102]
    2009 | Conference Abstract / Poster | Published | PUB-ID: 1918945
    Stoye, J. (2009): Computational Short Read Metagenomics. S. 3-4.
    PUB
     
  • [101]
    2009 | Journal Article | Published | PUB-ID: 1634447
    Bekel, T.; Henckel, K.; Küster, H.; Meyer, F.; Mittard-Runte, V.; Neuweger, H.; Paarmann, D.; Rupp, O.; Zakrzewski, M.; Pühler, A.; Stoye, J.; Goesmann, A. (2009): 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): 3-12.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [100]
    2008 | Conference Paper | Published | PUB-ID: 1919198
    Quitzau, J. A. A.; Stoye, J. (2008): Detecting Repeat Families in Incompletely Sequenced Genomes. In: Proc. of WABI 2008. (LNBI, 5251). S. 342-353.
    PUB | DOI
     
  • [99]
    2008 | Report | PUB-ID: 1970459 OA
    Quitzau, J. A. A.; Stoye, J. (2008): A space efficient representation for sparse de Bruijn subgraphs. Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [98]
    2008 | Report | PUB-ID: 1970461 OA
    Ejaz, T.; Rahmann, S.; Stoye, J. (2008): Online Abelian Pattern Matching. Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [97]
    2008 | Journal Article | Published | PUB-ID: 1636699
    Neuweger, H.; Albaum, S.; Dondrup, M.; Persicke, M.; Watt, T.; Niehaus, K.; Stoye, J.; Goesmann, A. (2008): MeltDB: a software platform for the analysis and integration of metabolomics experiment data Bioinformatics,24:(23): 2726-2732.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [96]
    2008 | Encyclopedia Article | Published | PUB-ID: 1918834
    Stoye, J. (2008): Suffix Tree Construction in RAM (1997; Farach-Colton). In: Ming-Yang Kao (Hrsg.): Encyclopedia of Algorithms. Springer Verlag. S. 925-928.
    PUB | DOI
     
  • [95]
    2008 | Conference Paper | Published | PUB-ID: 1919192
    Böcker, S.; Jahn, K.; Mixtacki, J.; Stoye, J. (2008): Computation of Median Gene Clusters. In: Proc. of RECOMB 2008. (LNBI, 4955). S. 331-345.
    PUB | DOI
     
  • [94]
    2008 | Conference Paper | Published | PUB-ID: 1919200
    Bergeron, A.; Mixtacki, J.; Stoye, J. (2008): On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios. In: Proc. of Recomb-CG 2008. (LNBI, 5267). S. 226-240.
    PUB | DOI
     
  • [93]
    2008 | Journal Article | Published | PUB-ID: 1587078
    Schürmann, K. - B.; Stoye, J. (2008): Counting suffix arrays and strings THEORETICAL COMPUTER SCIENCE,395:(2-3): 220-234.
    PUB | DOI | WoS
     
  • [92]
    2008 | Journal Article | Published | PUB-ID: 1586009
    Krause, L.; Diaz, N. N.; Edwards, R. A.; Gartemann, K. - H.; Krömeke, H.; Neuweger, H.; Pühler, A.; Runte, K. J.; Schlüter, A.; Stoye, J.; Szczepanowski, R.; Tauch, A.; Goesmann, A. (2008): Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor JOURNAL OF BIOTECHNOLOGY,136:(1-2): 91-101.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [91]
    2008 | Journal Article | Published | PUB-ID: 1586785 OA
    Oehm, S.; Gilbert, D.; Tauch, A.; Stoye, J.; Goesmann, A. (2008): Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms NUCLEIC ACIDS RESEARCH,36:(Web Server): W433-W437.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [90]
    2008 | Journal Article | Published | PUB-ID: 1783364 OA
    Krause, L.; Diaz, N. N.; Goesmann, A.; Kelley, S.; Nattkemper, T. W.; Rohwer, F.; Edwards, R. A.; Stoye, J. (2008): Phylogenetic classification of short environmental DNA fragments Nucleic Acids Research,36:(7): 2230-2239.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [89]
    2008 | Conference Paper | Published | PUB-ID: 1919195
    Bergeron, A.; Mixtacki, J.; Stoye, J. (2008): HP Distance via Double Cut and Join Distance. In: Combinatorial Pattern Matching. 19th Annual Symposium, CPM 2008, Pisa, Italy, June 18-20, 2008 Proceedings. (Lecture Notes in Computer Science, 5029, ). S. 56-68.
    PUB | DOI
     
  • [88]
    2007 | Journal Article | Published | PUB-ID: 1630781
    Mellmann, A.; Weniger, T.; Berssenbrügge, C.; Rothgänger, J.; Sammeth, M.; Stoye, J.; Harmsen, D. (2007): 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): 98.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [87]
    2007 | Book Chapter | Published | PUB-ID: 1918828
    Schmidt, T.; Stoye, J. (2007): Chapter 12: Gecko and GhostFam - Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes. In: Nicholas H. Bergman (Hrsg.): Comparative Genomics, Volume 2. Totowa, NJ: Humana Press Inc. (Methods in Molecular Biology, 396). S. 165-182.
    PUB | DOI | PubMed | Europe PMC
     
  • [86]
    2007 | Journal Article | Published | PUB-ID: 1918432
    Didier, G.; Schmidt, T.; Stoye, J.; Tsur, D. (2007): Character Sets of Strings Journal of Discrete Algorithms,5:(2): 330-340.
    PUB | DOI
     
  • [85]
    2007 | Journal Article | Published | PUB-ID: 1595253
    Schürmann, K. - B.; Stoye, J. (2007): An incomplex algorithm for fast suffix array construction SOFTWARE-PRACTICE & EXPERIENCE,37:(3): 309-329.
    PUB | DOI | WoS
     
  • [84]
    2007 | Journal Article | Published | PUB-ID: 1783345 OA
    Krause, L.; McHardy, A. C.; Nattkemper, T. W.; Pühler, A.; Stoye, J.; Meyer, F. (2007): GISMO - gene identification using a support vector machine for ORF classification Nucleic Acids Research,35:(2): 540-549.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [83]
    2006 | Journal Article | Published | PUB-ID: 1599943
    Sammeth, M.; Griebel, T.; Tille, F.; Stoye, J. (2006): Panta rhei (QAlign2): an open graphical environment for sequence analysis BIOINFORMATICS,22:(7): 889-890.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [82]
    2006 | Journal Article | Published | PUB-ID: 1599570
    Rasmussen, K. R.; Stoye, J.; Myers, E. W. (2006): Efficient q-gram filters for finding all epsilon-matches over a given length JOURNAL OF COMPUTATIONAL BIOLOGY,13:(2): 296-308.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [81]
    2006 | Journal Article | Published | PUB-ID: 1599574
    Bergeron, A.; Mixtacki, J.; Stoye, J. (2006): On sorting by translocations JOURNAL OF COMPUTATIONAL BIOLOGY,13:(2): 567-578.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [80]
    2006 | Conference Paper | Published | PUB-ID: 1596811
    Bergeron, A.; Mixtacki, J.; Stoye, J. (2006): A Unifying View of Genome Rearrangements. In: Proc. of WABI 2006. SPRINGER-VERLAG BERLIN. (LNBI, 4175). S. 163-173.
    PUB | DOI | WoS
     
  • [79]
    2006 | Journal Article | Published | PUB-ID: 1597213
    Sammeth, M.; Stoye, J. (2006): Comparing tandem repeats with duplications and excisions of variable degree IEEE/ACM Transactions on Computational Biology and Bioinformatics,3:(4): 395-407.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [78]
    2006 | Journal Article | Published | PUB-ID: 1597313
    Bergeron, A.; Stoye, J. (2006): On the similarity of sets of permutations and its applications to genome comparison JOURNAL OF COMPUTATIONAL BIOLOGY,13:(7): 1340-1354.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [77]
    2006 | Conference Abstract / Poster | Published | PUB-ID: 1918946
    Stoye, J. (2006): Index Structures in Biological Sequence Analysis: From Simplicity to Complexity and Back. S. 3-3.
    PUB
     
  • [76]
    2006 | Report | PUB-ID: 1970464 OA
    Chauve, C.; Diekmann, Y.; Heber, S.; Mixtacki, J.; Rahmann, S.; Stoye, J. (2006): On Common Intervals with Errors. Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [75]
    2006 | Journal Article | Published | PUB-ID: 1631957
    Krause, L.; Diaz, N. N.; Bartels, D.; Edwards, R. A.; Pühler, A.; Rohwer, F.; Meyer, F.; Stoye, J. (2006): Finding novel genes in bacterial communities isolated from the environment BIOINFORMATICS,22:(14): e281-e289.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [74]
    2005 | Report | PUB-ID: 1970470 OA
    Sammeth, M.; Stoye, J. (2005): Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF | DOI
     
  • [73]
    2005 | Conference Paper | Published | PUB-ID: 1919012
    Schürmann, K. - B.; Stoye, J. (2005): An Incomplex Algorithm for Fast Suffix Array Construction. In: Proc. of ALENEX/ANALCO 2005. S. 77-85.
    PUB
     
  • [72]
    2005 | Book Chapter | Published | PUB-ID: 1918824
    Bergeron, A.; Mixtacki, J.; Stoye, J. (2005): Chapter 10: The Inversion Distance Problem. In: Olivier Gascuel (Hrsg.): Mathematics of Evolution and Phylogeny. Oxford University Press. S. 262-290.
    PUB
     
  • [71]
    2005 | Conference Paper | Published | PUB-ID: 1603220
    Bergeron, A.; Mixtacki, J.; Stoye, J. (2005): On Sorting by Translocations. In: Proc. of RECOMB 2005. SPRINGER-VERLAG BERLIN. (LNBI, 3500). S. 615-629.
    PUB | DOI | WoS
     
  • [70]
    2005 | Journal Article | Published | PUB-ID: 1775168 OA
    Krause, A.; Stoye, J.; Vingron, M. (2005): Large scale hierarchical clustering of protein sequences BMC Bioinformatics,6:(1):15
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [69]
    2005 | Journal Article | Published | PUB-ID: 1773302 OA
    Bartels, D.; Kespohl, S.; Albaum, S.; Drüke, T.; Goesmann, A.; Herold, J.; Kaiser, O.; Pühler, A.; Pfeiffer, F.; Raddatz, G.; Stoye, J.; Meyer, F.; Schuster, S. C. (2005): BACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison Bioinformatics,21:(7): 853-859.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [68]
    2005 | Journal Article | Published | PUB-ID: 1918947
    Böcker, S.; Stoye, J. (2005): Informatische Methoden zur Protein-Identifikation LaborPraxis,29:(10): 24-26.
    PUB
     
  • [67]
    2005 | Conference Paper | Published | PUB-ID: 1601348
    Bannert, C.; Stoye, J. (2005): Protein Annotation by Secondary Structure Based Alignments (PASSTA). In: Proc. of CompLife 2005. Springer-Verlag. (LNBI, 3695). S. 79-90.
    PUB | DOI | WoS
     
  • [66]
    2005 | Conference Paper | Published | PUB-ID: 1601361
    Sammeth, M.; Weniger, T.; Harmsen, D.; Stoye, J. (2005): Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). In: Proc. of WABI 2005. SPRINGER-VERLAG BERLIN. (LNBI, 3692). S. 276-290.
    PUB | DOI | WoS
     
  • [65]
    2005 | Conference Paper | Published | PUB-ID: 1603216
    Rasmussen, K. R.; Stoye, J.; Myers, E. W. (2005): Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length. In: Proc. of RECOMB 2005. SPRINGER-VERLAG BERLIN. (LNBI, 3500). S. 189-203.
    PUB | DOI | WoS
     
  • [64]
    2005 | Conference Paper | Published | PUB-ID: 1919026
    Schürmann, K. - B.; Stoye, J. (2005): Counting Suffix Arrays and Strings. In: Proc. of SPIRE 2005. (LNCS, 3772). S. 55-66.
    PUB | DOI
     
  • [63]
    2005 | Report | PUB-ID: 1970472 OA
    Schürmann, K. - B.; Stoye, J. (2005): Counting Suffix Arrays and Strings. Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [62]
    2004 | Conference (Editor) | Published | PUB-ID: 1918823
    Robert Giegerich; Jens Stoye (Hrsg.) (2004): Proceedings of the German Conference on Bioinformatics, GCB 2004, In: Robert Giegerich; Jens Stoye (Hrsg.), Lecture Notes in Informatics,P-53: 234.
    PUB
     
  • [61]
    2004 | Conference Paper | Published | PUB-ID: 1607260
    Schmidt, T.; Stoye, J. (2004): Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences. In: Proc. of CPM 2004. (LNCS, 3109). S. 347-358.
    PUB | DOI | WoS
     
  • [60]
    2004 | Conference Paper | Published | PUB-ID: 1606286
    Michael, M.; Dieterich, C.; Stoye, J. (2004): Suboptimal Local Alignments across Multiple Scoring Schemes. In: Proc. of WABI 2004. SPRINGER-VERLAG BERLIN. (LNBI, 3240). S. 99-110.
    PUB | DOI | WoS
     
  • [59]
    2004 | Journal Article | Published | PUB-ID: 1773554 OA
    Pollard, D. A.; Bergman, C. M.; Stoye, J.; Celniker, S. E.; Eisen, M. B. (2004): Correction: Benchmarking tools for the alignment of functional noncoding DNA BMC Bioinformatics,5:(1):73
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [58]
    2004 | Journal Article | Published | PUB-ID: 1773560 OA
    Cieliebak, M.; Erlebach, T.; Lipták, Z.; Stoye, J.; Welzl, E. (2004): Algorithmic complexity of protein identification: combinatorics of weighted strings Discrete Applied Mathematics,137:(1): 27-46.
    PUB | PDF | DOI | WoS
     
  • [57]
    2004 | Journal Article | Published | PUB-ID: 1773312 OA
    Pollard, D. A.; Bergman, C. M.; Stoye, J.; Celniker, S. E.; Eisen, M. B. (2004): Benchmarking tools for the alignment of functional noncoding DNA BMC Bioinformatics,5:(1):6
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [56]
    2004 | Journal Article | Published | PUB-ID: 1773569 OA
    Gusfield, D.; Stoye, J. (2004): Linear time algorithms for finding and representing all the tandem repeats in a string Journal of computer and system sciences,69:(4): 525-546.
    PUB | PDF | DOI | WoS
     
  • [55]
    2004 | Conference Paper | Published | PUB-ID: 1607263
    Bergeron, A.; Mixtacki, J.; Stoye, J. (2004): Reversal Distance without Hurdles and Fortresses. In: Proc. of CPM 2004. SPRINGER-VERLAG BERLIN. (LNCS, 3109). S. 388-399.
    PUB | DOI | WoS
     
  • [54]
    2003 | Report | PUB-ID: 1970475 OA
    Schürmann, K. - B.; Stoye, J. (2003): Suffix Tree Construction and Storage with Limited Main Memory. Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [53]
    2003 | Journal Article | Published | PUB-ID: 1612664
    Heber, S.; Stoye, J. (2003): The European Conference on Computational Biology Drug Discovery Today,8:(3): 113-114.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [52]
    2003 | Journal Article | Published | PUB-ID: 1918949
    Giegerich, R.; Stoye, J. (2003): Finden, fast ohne zu suchen: Indexstrukturen in der Bioinformatik Forschung an der Universität Bielefeld,26: 63-68.
    PUB
     
  • [51]
    2003 | Conference Paper | Published | PUB-ID: 1919005
    Bannert, C.; Stoye, J. (2003): Evaluation of the Jumping Alignment Algorithm with Artificial and Biological Data. In: Proc. of GCB 2003. S. 21-25.
    PUB
     
  • [50]
    2003 | Journal Article | Published | PUB-ID: 1610397 OA
    Giegerich, R.; Kurtz, S.; Stoye, J. (2003): Efficient implementation of lazy suffix trees SOFTWARE-PRACTICE & EXPERIENCE,33:(11): 1035-1049.
    PUB | PDF | DOI | WoS
     
  • [49]
    2003 | Journal Article | Published | PUB-ID: 1609403 OA
    Sammeth, M.; Morgenstern, B.; Stoye, J. (2003): Divide-and-conquer multiple alignment with segment-based constraints BIOINFORMATICS,19:(Suppl 2): ii189-ii195.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [48]
    2003 | Conference Paper | Published | PUB-ID: 1610433
    Bergeron, A.; Stoye, J. (2003): On the similarity of sets of permutations and its applications to genome comparison. In: Proc. of COCOON 2003. (LNCS, 2697). S. 68-79.
    PUB | DOI | WoS
     
  • [47]
    2003 | Journal Article | Published | PUB-ID: 1610503 OA
    Sammeth, M.; Rothgänger, J.; Esser, W.; Albert, J.; Stoye, J.; Harmsen, D. (2003): QAlign: quality-based multiple alignments with dynamic phylogenetic analysis BIOINFORMATICS,19:(12): 1592-1593.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [46]
    2003 | Report | PUB-ID: 1970477 OA
    Bergeron, A.; Stoye, J. (2003): On the Similarity of Sets of Permutations and its Applications to Genome Comparison. Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [45]
    2002 | Conference Abstract / Poster | Published | PUB-ID: 1918951
    Stoye, J. (2002): Index Structures for Large Sequence Data: Suffix Trees and Affix Trees. In: Sigrid Schubert; Bernd Reusch; Norbert Jesse (Hrsg.): Lecture Notes in Informatics. (P-20). S. 67-67.
    PUB
     
  • [44]
    2002 | Conference Paper | Published | PUB-ID: 1919000
    Cieliebak, M.; Lipták, Z.; Welzl, E.; Erlebach, T.; Stoye, J. (2002): Algorithmic Complexity of Protein Identification: Searching in Weighted Strings. In: Proc. of IFIP TCS 2002. S. 143-156.
    PUB
     
  • [43]
    2002 | Journal Article | Published | PUB-ID: 1773578 OA
    Spang, R.; Rehmsmeier, M.; Stoye, J. (2002): A novel approach to remote homology detection: jumping alignments Journal of Computational Biology,9:(5): 747-760.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [42]
    2002 | Journal Article | Published | PUB-ID: 1773332 OA
    Stoye, J.; Gusfield, D. (2002): Simple and flexible detection of contiguous repeats using a suffix tree Theoretical Computer Science,270:(1-2): 843-856.
    PUB | PDF | DOI | WoS
     
  • [41]
    2002 | Journal Article | Published | PUB-ID: 1773329 OA
    Bergeron, A.; Heber, S.; Stoye, J. (2002): Common intervals and sorting by reversals: a marriage of necessity Bioinformatics,18:(Suppl 2): S54-S63.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [40]
    2002 | Conference Paper | Published | PUB-ID: 1918995
    Heber, S.; Stoye, J.; Frohme, M.; Hoheisel, J.; Vingron, M. (2002): Resampling Methods in Physical Mapping. In: Proc. of GfKl 2000. S. 437-444.
    PUB
     
  • [39]
    2001 | Journal Article | Published | PUB-ID: 1773335 OA
    Kurtz, S.; Choudhuri, J. V.; Ohlebusch, E.; Schleiermacher, C.; Stoye, J.; Giegerich, R. (2001): REPuter: the manifold applications of repeat analysis on a genomic scale Nucleic Acids Research,29:(22): 4633-4642.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [38]
    2001 | Conference Paper | Published | PUB-ID: 1918992
    Heber, S.; Stoye, J. (2001): Finding all Common Intervals of k Permutations. In: Proc. of CPM 2001. (LNCS, 2089). S. 207-218.
    PUB | DOI
     
  • [37]
    2001 | Conference Paper | Published | PUB-ID: 1880197
    Heber, S.; Stoye, J. (2001): Algorithms for Finding Gene Clusters. In: Proc. of WABI 2001. Berlin: Sppringer. (LNCS, 2149). S. 252-263.
    PUB | DOI
     
  • [36]
    2001 | Report | PUB-ID: 1970479
    Cieliebak, M.; Erlebach, T.; Lipták, Z.; Stoye, J.; Welzl, E. (2001): Algorithmic Complexity of Protein Identification: Combinatorics of Weighted Strings. ETH Zürich, Dept. of Computer Science.
    PUB
     
  • [35]
    2000 | Conference Paper | Published | PUB-ID: 1918981
    Heber, S.; Stoye, J.; Hoheisel, J.; Vingron, M. (2000): Contig Selection in Physical Mapping. In: Proc. of RECOMB 2000. S. 155-164.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [34]
    2000 | Book Chapter | Published | PUB-ID: 1918817
    Brodal, G. S.; Lyngsø, R. B.; Pedersen, C. N. S.; Stoye, J. (2000): Finding Maximal Pairs with Bounded Gap. In: Maxime Crochemore; Leszek Gąsieniec (Hrsg.): Matching Patterns (Journal of Discrete Algorithms). S. 77-104.
    PUB
     
  • [33]
    2000 | Journal Article | Published | PUB-ID: 1773345 OA
    Krause, A.; Stoye, J.; Vingron, M. (2000): The SYSTERS protein sequence cluster set Nucleic Acids Research,28:(1): 270-272.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [32]
    2000 | Journal Article | Published | PUB-ID: 1773572 OA
    Heber, S.; Stoye, J.; Frohme, M.; Hoheisel, J.; Vingron, M. (2000): Contig selection in physical mapping Journal of Computational Biology,7:(3-4): 395-408.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [31]
    2000 | Conference Paper | Published | PUB-ID: 1918985
    Spang, R.; Rehmsmeier, M.; Stoye, J. (2000): Sequence Database Search Using Jumping Alignments. In: Proc. of ISMB 2000. S. 367-375.
    PUB | PubMed | Europe PMC
     
  • [30]
    2000 | Report | PUB-ID: 1970490 OA
    Stoye, J. (2000): Affix Trees. Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [29]
    2000 | Journal Article | Published | PUB-ID: 1773341 OA
    Reinert, K.; Stoye, J.; Will, T. (2000): An iterative method for faster sum-of-pairs multiple sequence alignment Bioinformatics,16:(9): 808-814.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [28]
    2000 | Conference Paper | Published | PUB-ID: 1918988
    Kurtz, S.; Ohlebusch, E.; Schleiermacher, C.; Stoye, J.; Giegerich, R. (2000): Computation and Visualization of Degenerate Repeats in Complete Genomes. In: Proc. of ISMB 2000. S. 228-238.
    PUB | PubMed | Europe PMC
     
  • [27]
    2000 | Conference (Editor) | Published | PUB-ID: 1918813
    Erich Bornberg-Bauer; Ursula Rost; Jens Stoye; Martin Vingron (Hrsg.) (2000): Proceedings of the German Conference on Bioinformatics, GCB 2000. Berlin: Logos Verlag.
    PUB
     
  • [26]
    1999 | Conference Paper | Published | PUB-ID: 1620435
    Giegerich, R.; Kurtz, S.; Stoye, J. (1999): Efficient implementation of lazy suffix trees. In: Algorithm Engineering. 3rd International Workshop, WAE’99 London, UK, July 19–21, 1999 Proceedings. (LNCS, 1668). S. 30-42.
    PUB | DOI | WoS
     
  • [25]
    1999 | Conference Paper | Published | PUB-ID: 1918978
    Reinert, K.; Will, T.; Stoye, J. (1999): Combining Divide-and-Conquer, the A*-Algorithm, and Successive Realignment Approaches to Speed up Multiple Sequence Alignment. In: Proc. of GCB 1999. S. 17-24.
    PUB | Download (ext.)
     
  • [24]
    1999 | Report | PUB-ID: 1970495
    Morgenstern, B.; Stoye, J.; Dress, A. (1999): Consistent Equivalence Relations: A Set-Theoretical Framework for Multiple Sequence Alignment. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
  • [23]
    1999 | Report | PUB-ID: 1970509
    Brodal, G. S.; Lyngsø, R. B.; Pedersen, C. N. S.; Stoye, J. (1999): Finding Maximal Pairs with Bounded Gap. BRICS, Department of Computer Science, University of Aarhus.
    PUB
     
  • [22]
    1999 | Conference Paper | Published | PUB-ID: 1918971
    Brodal, G. S.; Lyngsø, R. B.; Pedersen, C. N. S.; Stoye, J. (1999): Finding Maximal Pairs with Bounded Gap. In: Proc. of CPM 1999. (LNCS, 1645). S. 134-149.
    PUB | DOI
     
  • [21]
    1998 | Journal Article | Published | PUB-ID: 2488102
    Dress, A.; Morgenstern, B.; Stoye, J. (1998): The Number of Standard and of Effective Multiple Alignments Appl. Math. Lett.,11:(4): 43-49.
    PUB
     
  • [20]
    1998 | Journal Article | Published | PUB-ID: 1918538
    Hildebrand, M.; Stoye, J. (1998): Die Bedeutung der Zusammenarbeit der Disziplinen in der Anwendung - erläutert anhand von Beispielen Der Mathematikunterricht,44:(6): 34-53.
    PUB
     
  • [19]
    1998 | Journal Article | Published | PUB-ID: 1667771 OA
    Stoye, J. (1998): Multiple sequence alignment with the Divide-and-Conquer method. Gene,211:(2): GC45-GC56.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [18]
    1998 | Journal Article | Published | PUB-ID: 1625402 OA
    Stoye, J.; Evers, D.; Meyer, F. (1998): Rose: generating sequence families BIOINFORMATICS,14:(2): 157-163.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [17]
    1998 | Report | PUB-ID: 1970515
    Stoye, J.; Gusfield, D. (1998): Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree. Department of Computer Science, University of California, Davis.
    PUB
     
  • [16]
    1998 | Conference Paper | Published | PUB-ID: 1918964
    Stoye, J.; Gusfield, D. (1998): Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version). In: Proc. of CPM 1998. (LNCS, 1448). S. 140-152.
    PUB | DOI
     
  • [15]
    1998 | Report | PUB-ID: 1970513
    Gusfield, D.; Stoye, J. (1998): Linear Time Algorithms for Finding and Representing all the Tandem Repeats in a String. Department of Computer Science, University of California, Davis.
    PUB
     
  • [14]
    1997 | Journal Article | Published | PUB-ID: 1773358
    Brinkmann, G.; Dress, A.; Perrey, S. W.; Stoye, J. (1997): Two applications of the Divide & Conquer principle in the molecular sciences Mathematical programming,79:(1-3): 71-97.
    PUB | DOI | WoS
     
  • [13]
    1997 | Journal Article | Published | PUB-ID: 2488107
    Stoye, J.; Moulton, V.; Dress, A. (1997): DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment CABIOS,13:(6): 625-626.
    PUB
     
  • [12]
    1997 | Report | PUB-ID: 1970526
    Perrey, S. W.; Stoye, J.; Moulton, V.; Dress, A. (1997): On Simultaneous versus Iterative Multiple Sequence Alignment. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
  • [11]
    1997 | Report | PUB-ID: 1970517
    Stoye, J.; Evers, D.; Meyer, F. (1997): Rose: Generating Sequence Families. Technische Fakultät der Universität Bielefeld.
    PUB
     
  • [10]
    1997 | Report | PUB-ID: 1970529
    Brinkmann, G.; Dress, A.; Perrey, S. W.; Stoye, J. (1997): Two Applications of the Divide & Conquer Principle in the Molecular Sciences. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
  • [9]
    1997 | Conference Paper | Published | PUB-ID: 1667885
    Stoye, J.; Evers, D.; Meyer, F. (1997): Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions. In: Proc. of ISMB 1997. S. 303-306.
    PUB | PubMed | Europe PMC
     
  • [8]
    1997 | Journal Article | Published | PUB-ID: 1773355 OA
    Stoye, J.; Perrey, S. W.; Dress, A. (1997): Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment Applied mathematics letters,10:(2): 67-73.
    PUB | PDF | DOI | WoS
     
  • [7]
    1997 | Report | PUB-ID: 1970523
    Dress, A.; Morgenstern, B.; Stoye, J. (1997): On the Number of Standard and Effective Multiple Alignments. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
  • [6]
    1997 | Report | PUB-ID: 1970520
    Perrey, S. W.; Stoye, J.; Moulton, V. (1997): FDCA: Fast and Accurate Approximation to Sum-of-Pairs Score Optimal Multiple Sequence Alignment. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
  • [5]
    1997 | Report | PUB-ID: 1970532
    Stoye, J. (1997): Divide-and-Conquer Multiple Sequence Alignment. Technische Fakultät der Universität Bielefeld.
    PUB
     
  • [4]
    1996 | Report | PUB-ID: 1970533
    Perrey, S. W.; Stoye, J. (1996): Fast Approximation to the NP-hard Problem of Multiple Sequence Alignment. Dept. of Mathematics, Massey University, Palmerston North, New Zealand.
    PUB
     
  • [3]
    1996 | Journal Article | Published | PUB-ID: 1773351
    Tönges, U.; Perrey, S. W.; Stoye, J.; Dress, A. (1996): A general method for fast multiple sequence alignment Gene,172:(1): GC33-GC41.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [2]
    1996 | Report | PUB-ID: 1970535
    Stoye, J.; Dress, A.; Perrey, S. W. (1996): Improving the Divide-and-Conquer Approach to Sum-of-Pairs Multiple Sequence Alignment. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
  • [1]
    1996 | Report | PUB-ID: 1970537
    Tönges, U.; Perrey, S. W.; Stoye, J.; Dress, A. (1996): A General Method for Fast Multiple Sequence Alignment. Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
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