Jens Stoye

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

PEVZ-ID
65864

231 Publikationen

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