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., et al., 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., 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., et al., 2023. On the Class of Double Distance Problems. In K. Jahn & T. Vinař, eds. Comparative Genomics. 20th International Conference, RECOMB-CG 2023, Istanbul, Turkey, April 14–15, 2023, Proceedings. Lecture Notes in Computer Science. no.13883 Cham: Springer Nature , pp. 35-50.
    PUB | DOI
     
  • [228]
    2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2969065
    Kirsch-Gerweck, B., et al., 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 | Veröffentlicht | PUB-ID: 2967089
    Parmigiani, L., Wittler, R., & Stoye, J., 2022. Revisiting pangenome openness with k-mers. bioRxiv.
    PUB | DOI
     
  • [226]
    2022 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2965398
    Dias Vieira Braga, M., et al., 2022. A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance. In C. Boucher & S. Rahmann, eds. 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics. LIPIcs. no.242 Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 13:1-13:16.
    PUB | DOI
     
  • [225]
    2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2963777
    Bonizzoni, P., et al., 2022. Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches. Information Sciences, 607, p 458-476.
    PUB | DOI | WoS
     
  • [224]
    2022 | Zeitschriftenaufsatz | Veröffentlicht | 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 | Herausgeber*in Sammelwerk | Veröffentlicht | PUB-ID: 2959449 OA
    J. Stoye & R. Wittler, 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., & Dias Vieira Braga, M., 2021. Computing the Inversion-Indel Distance. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 18(6), p 2314-2326.
    PUB | DOI | WoS | PubMed | Europe PMC | arXiv
     
  • [221]
    2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2950825 OA
    Schulz, T., et al., 2021. Detecting High Scoring Local Alignments in Pangenome Graphs. Bioinformatics, 37(16), p 2266-2274.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [220]
    2021 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2952705
    Bonizzoni, P., et al., 2021. Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning. In Proceedings of AlCoB 2021. LNBI. no.12715 pp. 16-28.
    PUB
     
  • [219]
    2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2946303
    Bohnenkämper, L., et al., 2021. Computing the rearrangement distance of natural genomes. Journal of Computational Biology, 28(4), p 410-431.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [218]
    2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2945991
    Sundermann, L.K., et al., 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 | Sonderausgabe Zeitschrift | Veröffentlicht | PUB-ID: 2949108
    J. C. Setubal, J. Stoye, & B. E. Dutilh, 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., et al., 2020. On motifs in colored graphs. arXiv:2005.13634.
    PUB | Download (ext.) | arXiv
     
  • [215]
    2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2942995
    Rubert, D., et al., 2020. Searching and Inferring Colorful Topological Motifs in Vertex-Colored Graphs. Journal of Combinatorial Optimization, 40, p 379–411.
    PUB | DOI | WoS
     
  • [214]
    2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2937712 OA
    Rubert, D., et al., 2020. Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants. BMC Genomics, 21(Suppl. 2): 273.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [213]
    2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2953267
    Schulte-Schrepping, J., et al., 2020. Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment. Cell, 182(6), p 1419-1440.e23.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [212]
    2020 | Report | PUB-ID: 2944669
    Glöckner, F.O., 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., & 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., et al., 2020. HASLR: Fast Hybrid Assembly of Long Reads. bioRxiv.
    PUB | DOI | Download (ext.) | Preprint
     
  • [209]
    2020 | Preprint | Veröffentlicht | PUB-ID: 2945720
    Schulz, T., et al., 2020. Detecting High Scoring Local Alignments in Pangenome Graphs. bioRxiv.
    PUB | DOI | Preprint
     
  • [208]
    2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2939618 OA
    Alanko, J., et al., 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., et al., 2020. HASLR: Fast Hybrid Assembly of Long Reads. iScience, 23(8): 101389.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [206]
    2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2939598
    Sevillya, G., et al., 2020. Horizontal Gene Transfer Phylogenetics: A Random Walk Approach. Molecular Biology and Evolution, 37(5), p 1470–1479.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [205]
    2020 | Preprint | Veröffentlicht | PUB-ID: 2939861
    Bohnenkämper, L., et al., 2020. Computing the rearrangement distance of natural genomes. arXiv:2001.02139.
    PUB | Download (ext.) | arXiv
     
  • [204]
    2020 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2939729
    Bohnenkämper, L., et al., 2020. Computing the rearrangement distance of natural genomes. In Proceedings of RECOMB 2020. LNBI. no.12074 pp. 3-18.
    PUB | DOI
     
  • [203]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2932884
    Oey, H., et al., 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 | Veröffentlicht | PUB-ID: 2939260
    Gagie, T., et al., 2019. 25 Years of the Burrows-Wheeler Transform. Report from Dagstuhl Seminar 19241, Dagstuhl Reports, no.9(6), Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik.
    PUB | DOI
     
  • [201]
    2019 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2937148
    Alanko, J., et al., 2019. Finding All Maximal Perfect Haplotype Blocks in Linear Time. In Proceedings of WABI 2019. Leibniz International Proceedings in Informatics. LIPIcs. no.143 Dagstuhl: Schloss Dagstuhl, Leibniz-Zentrum für Informatik , pp. 8:1-8:9.
    PUB | DOI
     
  • [200]
    2019 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2932883
    Dörr, D., & Stoye, J., 2019. A Perspective on Comparative and Functional Genomics. In T. Warnow, ed. Bioinformatics and Phylogenetics. Computational Biology. no.29 Cham: Springer , pp. 361-372.
    PUB | DOI
     
  • [199]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919006 OA
    Rubert, D., et al., 2018. Computing the family-free DCJ similarity. BMC Bioinformatics, 19(Suppl. 6): 152.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [198]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919012
    Jaenicke, S., et al., 2018. Flexible metagenome analysis using the MGX framework. Microbiome, 6(1): 76.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [197]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | 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 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930268
    Holley, G., et al., 2018. Dynamic Alignment-Free and Reference-Free Read Compression. JOURNAL OF COMPUTATIONAL BIOLOGY, 25(7), p 825-836.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [195]
    2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913921
    Zekic, T., Holley, G., & Stoye, J., 2018. Pan-genome Storage and Analysis Techniques. In J. C. Setubal, P. Stadler, & J. Stoye, eds. Comparative Genomics. Methods and Protocols. Methods in Molecular Biology. no.1704 New York: Springer Verlag, pp. 29-53.
    PUB | DOI
     
  • [194]
    2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913922
    Dörr, D., Feijão, P., & Stoye, J., 2018. Family-Free Genome Comparison. In J. C. Setubal, P. Stadler, & J. Stoye, eds. Comparative Genomics: Methods and Protocols. Methods in Molecular Biology. no.1704 New York: Springer Verlag, pp. 331-342.
    PUB | DOI
     
  • [193]
    2018 | Herausgeber*in Sammelwerk | Veröffentlicht | PUB-ID: 2913920
    J. C. Setubal, P. Stadler, & J. Stoye, eds., 2018. Comparative Genomics: Methods and Protocols, Methods in Molecular Biology, no.1704, New York: Springer Verlag.
    PUB | DOI
     
  • [192]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918481
    Luhmann, N., et al., 2018. Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15(6), p 2094-2100.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [191]
    2018 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2930445
    Cunha, L., et al., 2018. Identifying Maximal Perfect Haplotype Blocks. In Proceedings of BSB 2018. LNBI. no.11228 Springer Verlag, pp. 26-37.
    PUB | DOI
     
  • [190]
    2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913015
    Rubert, D., et al., 2017. Algorithms for Computing the Family-Free Genomic Similarity under DCJ. In J. Meidanis & L. Nakhleh, eds. Comparative Genomics. RECOMB-CG 2017. Lecture Notes in Bioinformatics. no.10562 Cham: Springer Verlag, pp. 76-100.
    PUB | DOI
     
  • [189]
    2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909057 OA
    Rubert, D., et al., 2017. Approximating the DCJ distance of balanced genomes in linear time. Algorithms for Molecular Biology, 12(1): 3.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [188]
    2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2909409
    Cunha, L., et al., 2017. Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings. In Proceedings of CPM 2017. LIPIcs. no.78 pp. 19:1-19:9.
    PUB | DOI
     
  • [187]
    2017 | Preprint | Veröffentlicht | PUB-ID: 2908521
    Cunha, L., et al., 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., et al., 2017. Bioinformatics for NGS-based metagenomics and the application to biogas research. Journal of Biotechnology, 261(SI), p 10-23.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [185]
    2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2907587
    Holley, G., et al., 2017. Dynamic Alignment-Free and Reference-Free Read Compression. In Proceedings of RECOMB 2017. Lecture Notes in Bioinformatics. no.10229 pp. 50-65.
    PUB | DOI
     
  • [184]
    2017 | Konferenzbeitrag | Veröffentlicht | 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. Lecture Notes in Bioinformatics. no.1704 Berlin: Springer Verlag, pp. 197-212.
    PUB | DOI
     
  • [183]
    2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909967
    Dörr, D., et al., 2017. New Genome Similarity Measures based on Conserved Gene Adjacencies. Journal of Computational Biology, 24(6), p 616-634.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [182]
    2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2903708
    Rubert, D., et al., 2016. A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates. In M. Frith & C. N. Storm Pedersen, eds. Algorithms in Bioinformatics. WABI 2016. Lecture Notes in Bioinformatics. no.9838 Cham: Springer, pp. 293-306.
    PUB | DOI
     
  • [181]
    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905930
    Winter, S., et al., 2016. Finding approximate gene clusters with GECKO 3. Nucleic Acids Research, 44(20), p 9600-9610.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [180]
    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900421
    Krause, L., 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(4), p 356-365.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [179]
    2016 | Zeitschriftenaufsatz | Veröffentlicht | 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.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [178]
    2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2900111
    Kowada, L.A.B., et al., 2016. New Genome Similarity Measures based on Conserved Gene Adjacencies. In M. Singh, ed. Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Bioinformatics (LNBI). no.9649 Springer, pp. 204-224.
    PUB | DOI
     
  • [177]
    2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2757497
    Holley, G., Wittler, R., & Stoye, J., 2015. Bloom Filter Trie - a data structure for pan-genome storage. In M. Pop & H. Touzet, eds. Algorithms in Bioinformatics. WABI 2015. Proceedings. Lecture Notes in Computer Science . no.9289 Berlin, Heidelberg: Springer, pp. 217-230.
    PUB | DOI
     
  • [176]
    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726366 OA
    Viduani Martinez, F.H., et al., 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 | Zeitschriftenaufsatz | Veröffentlicht | 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), p 500-506.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [174]
    2015 | Konferenzband | Veröffentlicht | PUB-ID: 2780229
    J. Meidanis & J. Stoye, eds., 2015. Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Bioinformatics. BMC Bioinformatics, 16(Supplement 14).
    PUB | Download (ext.)
     
  • [173]
    2015 | Konferenzband | Veröffentlicht | PUB-ID: 2780232
    J. Meidanis & J. Stoye, eds., 2015. Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Genomics. BMC Genomics, 16(Supplement 10).
    PUB | Download (ext.)
     
  • [172]
    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2689773
    Jünemann, S., et al., 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 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685362 OA
    Lechner, M., et al., 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 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2684241
    Viduani Martinez, F.H., et al., 2014. On the family-free DCJ distance. In D. Brown & B. Morgenstern, eds. Algorithms in Bioinformatics. WABI 2014. Lecture Notes in Bioinformatics. no.8701 Berlin ; Heidelberg: Springer Verlag, pp. 174-186.
    PUB | DOI
     
  • [169]
    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2687033 OA
    Dörr, D., et al., 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 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2674387
    Hilker, R., et al., 2014. ReadXplorer - Visualization and Analysis of Mapped Sequences. Bioinformatics, 30(16), p 2247-2254.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [167]
    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665038
    Schwientek, P., et al., 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, p 85-95.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [166]
    2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2690122
    Luhmann, N., et al., 2014. Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. In C. Sérgio, ed. Proc. of BSB 2014. LNBI. no.8826 Springer Verlag, pp. 135-143.
    PUB | DOI
     
  • [165]
    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685988
    Jakobi, T., et al., 2014. Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. Journal of Biotechnology, 190, p 64-75.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [164]
    2014 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2693552
    Stoye, J., 2014. Suffix Tree Construction. In M. - Y. Kao, ed. Encyclopedia of Algorithms. Springer Verlag.
    PUB | DOI
     
  • [163]
    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2643941
    Hoffmann, N., et al., 2014. BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry. Bioinformatics, 30(7), p 988-995.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [162]
    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2693409
    Fredrich, E., et al., 2014. Metatranskriptomik der Mikrobiota aus der menschlichen Achselhöhle. BIOspektrum, 20(5), p 294-296.
    PUB | DOI
     
  • [161]
    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333
    Henrich, B., et al., 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 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575011
    Ander, C., et al., 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 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2577323
    Gerlach, W., & Stoye, J., 2013. Taxonomic classification of metagenomic shotgun sequences with CARMA3. In K. E. Nelson, ed. Encyclopedia of Metagenomics. Springer Verlag.
    PUB | DOI
     
  • [158]
    2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611630 OA
    Willing, E., et al., 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 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2611641
    Dias Vieira Braga, M., & Stoye, J., 2013. Restricted DCJ-Indel Model Revisited. In J. C. Setubal & N. F. Almeida, eds. Advances in Bioinformatics and Computational Biology. BSB 2013. Lecture Notes in Bioinformatics. no.8213 Cham: Springer Verlag, pp. 36-46.
    PUB | DOI
     
  • [156]
    2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611648
    Dias Vieira Braga, M., et al., 2013. The Potential of Family-Free Genome Comparison. In C. Chauve, N. El-Mabrouk, & E. Tannier, eds. Models and Algorithms for Genome Evolution. Computational Biology Series. no.19 London: Springer Verlag, pp. 287-307.
    PUB | DOI
     
  • [155]
    2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641228
    Jünemann, S., et al., 2013. Corrigendum: Updating benchtop sequencing performance comparison. Nature biotechnology, 31(12), p 1148.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [154]
    2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611643
    Bergeron, A., & Stoye, J., 2013. The Genesis of the DCJ Formula. In C. Chauve, N. El-Mabrouk, & E. Tannier, eds. Models and Algorithms for Genome Evolution. Computational Biology Series. no.19 London: Springer Verlag, pp. 63-81.
    PUB | DOI
     
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    2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575361
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    2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517230
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    2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512642 OA
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    2012 | Konferenzband | Veröffentlicht | PUB-ID: 2510416
    J. Kärkkäinen & J. Stoye, eds., 2012. Combinatorial Pattern Matching. Lecture Notes in Computer Science, 7354.
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    2012 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2468382 OA
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    Husemann, P., & Stoye, J., 2010. r2cat: Synteny Plots and Comparative Assembly. Bioinformatics, 26(4), p 570-571.
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    Hoffmann, N., & Stoye, J., 2009. ChromA: signal-based retention time alignment for chromatography-mass spectrometry data. Bioinformatics, 25(16), p 2080-2081.
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    Quitzau, J.A.A., & 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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    Ejaz, T., Rahmann, S., & 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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    Stoye, J., 2008. Suffix Tree Construction in RAM (1997; Farach-Colton). In M. - Y. Kao, ed. Encyclopedia of Algorithms. Springer Verlag, pp. 925-928.
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    Schürmann, K.-B., & Stoye, J., 2008. Counting suffix arrays and strings. THEORETICAL COMPUTER SCIENCE, 395(2-3), p 220-234.
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    Schmidt, T., & Stoye, J., 2007. Chapter 12: Gecko and GhostFam - Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes. In N. H. Bergman, ed. Comparative Genomics, Volume 2. Methods in Molecular Biology. no.396 Totowa, NJ: Humana Press Inc., pp. 165-182.
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    Sammeth, M., et al., 2006. Panta rhei (QAlign2): an open graphical environment for sequence analysis. BIOINFORMATICS, 22(7), p 889-890.
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    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), p 296-308.
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    Bergeron, A., Mixtacki, J., & Stoye, J., 2006. On sorting by translocations. JOURNAL OF COMPUTATIONAL BIOLOGY, 13(2), p 567-578.
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    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), p 395-407.
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    2006 | Report | PUB-ID: 1970464 OA
    Chauve, C., et al., 2006. On Common Intervals with Errors, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
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    2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1631957
    Krause, L., et al., 2006. Finding novel genes in bacterial communities isolated from the environment. BIOINFORMATICS, 22(14), p 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), Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF | DOI
     
  • [73]
    2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919012
    Schürmann, K.-B., & Stoye, J., 2005. An Incomplex Algorithm for Fast Suffix Array Construction. In Proc. of ALENEX/ANALCO 2005. pp. 77-85.
    PUB
     
  • [72]
    2005 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918824
    Bergeron, A., Mixtacki, J., & Stoye, J., 2005. Chapter 10: The Inversion Distance Problem. In O. Gascuel, ed. Mathematics of Evolution and Phylogeny. Oxford University Press, pp. 262-290.
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  • [71]
    2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1603220
    Bergeron, A., Mixtacki, J., & Stoye, J., 2005. On Sorting by Translocations. In Proc. of RECOMB 2005. LNBI. no.3500 SPRINGER-VERLAG BERLIN, pp. 615-629.
    PUB | DOI | WoS
     
  • [70]
    2005 | Zeitschriftenaufsatz | Veröffentlicht | 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 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773302 OA
    Bartels, D., et al., 2005. BACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics, 21(7), p 853-859.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [68]
    2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918947
    Böcker, S., & Stoye, J., 2005. Informatische Methoden zur Protein-Identifikation. LaborPraxis, 29(10), p 24-26.
    PUB
     
  • [67]
    2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1601348
    Bannert, C., & Stoye, J., 2005. Protein Annotation by Secondary Structure Based Alignments (PASSTA). In Proc. of CompLife 2005. LNBI. no.3695 Springer-Verlag, pp. 79-90.
    PUB | DOI | WoS
     
  • [66]
    2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1601361
    Sammeth, M., et al., 2005. Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). In Proc. of WABI 2005. LNBI. no.3692 SPRINGER-VERLAG BERLIN, pp. 276-290.
    PUB | DOI | WoS
     
  • [65]
    2005 | Konferenzbeitrag | Veröffentlicht | 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. LNBI. no.3500 SPRINGER-VERLAG BERLIN, pp. 189-203.
    PUB | DOI | WoS
     
  • [64]
    2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919026
    Schürmann, K.-B., & Stoye, J., 2005. Counting Suffix Arrays and Strings. In Proc. of SPIRE 2005. LNCS. no.3772 pp. 55-66.
    PUB | DOI
     
  • [63]
    2005 | Report | PUB-ID: 1970472 OA
    Schürmann, K.-B., & Stoye, J., 2005. Counting Suffix Arrays and Strings, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [62]
    2004 | Konferenzband | Veröffentlicht | PUB-ID: 1918823
    R. Giegerich & J. Stoye, eds., 2004. Proceedings of the German Conference on Bioinformatics, GCB 2004. Lecture Notes in Informatics, P-53, p 234.
    PUB
     
  • [61]
    2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1606286
    Michael, M., Dieterich, C., & Stoye, J., 2004. Suboptimal Local Alignments across Multiple Scoring Schemes. In Proc. of WABI 2004. LNBI. no.3240 SPRINGER-VERLAG BERLIN, pp. 99-110.
    PUB | DOI | WoS
     
  • [60]
    2004 | Konferenzbeitrag | Veröffentlicht | 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. no.3109 pp. 347-358.
    PUB | DOI | WoS
     
  • [59]
    2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773554 OA
    Pollard, D.A., et al., 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 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773560 OA
    Cieliebak, M., et al., 2004. Algorithmic complexity of protein identification: combinatorics of weighted strings. Discrete Applied Mathematics, 137(1), p 27-46.
    PUB | PDF | DOI | WoS
     
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    2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773312 OA
    Pollard, D.A., et al., 2004. Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics, 5(1): 6.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [56]
    2004 | Zeitschriftenaufsatz | Veröffentlicht | 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), p 525-546.
    PUB | PDF | DOI | WoS
     
  • [55]
    2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1607263
    Bergeron, A., Mixtacki, J., & Stoye, J., 2004. Reversal Distance without Hurdles and Fortresses. In Proc. of CPM 2004. LNCS. no.3109 SPRINGER-VERLAG BERLIN, pp. 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, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [53]
    2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1612664
    Heber, S., & Stoye, J., 2003. The European Conference on Computational Biology. Drug Discovery Today, 8(3), p 113-114.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [52]
    2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918949
    Giegerich, R., & Stoye, J., 2003. Finden, fast ohne zu suchen: Indexstrukturen in der Bioinformatik. Forschung an der Universität Bielefeld, 26, p 63-68.
    PUB
     
  • [51]
    2003 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919005
    Bannert, C., & Stoye, J., 2003. Evaluation of the Jumping Alignment Algorithm with Artificial and Biological Data. In Proc. of GCB 2003. pp. 21-25.
    PUB
     
  • [50]
    2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1610397 OA
    Giegerich, R., Kurtz, S., & Stoye, J., 2003. Efficient implementation of lazy suffix trees. SOFTWARE-PRACTICE & EXPERIENCE, 33(11), p 1035-1049.
    PUB | PDF | DOI | WoS
     
  • [49]
    2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1609403 OA
    Sammeth, M., Morgenstern, B., & Stoye, J., 2003. Divide-and-conquer multiple alignment with segment-based constraints. BIOINFORMATICS, 19(Suppl 2), p ii189-ii195.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [48]
    2003 | Konferenzbeitrag | Veröffentlicht | 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. no.2697 pp. 68-79.
    PUB | DOI | WoS
     
  • [47]
    2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1610503 OA
    Sammeth, M., et al., 2003. QAlign: quality-based multiple alignments with dynamic phylogenetic analysis. BIOINFORMATICS, 19(12), p 1592-1593.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
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    2003 | Report | PUB-ID: 1970477 OA
    Bergeron, A., & Stoye, J., 2003. On the Similarity of Sets of Permutations and its Applications to Genome Comparison, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [45]
    2002 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918951
    Stoye, J., 2002. Index Structures for Large Sequence Data: Suffix Trees and Affix Trees. In S. Schubert, B. Reusch, & N. Jesse, eds. Lecture Notes in Informatics. no.P-20 pp. 67-67.
    PUB
     
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    2002 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919000
    Cieliebak, M., et al., 2002. Algorithmic Complexity of Protein Identification: Searching in Weighted Strings. In Proc. of IFIP TCS 2002. pp. 143-156.
    PUB
     
  • [43]
    2002 | Zeitschriftenaufsatz | Veröffentlicht | 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), p 747-760.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [42]
    2002 | Zeitschriftenaufsatz | Veröffentlicht | 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), p 843-856.
    PUB | PDF | DOI | WoS
     
  • [41]
    2002 | Zeitschriftenaufsatz | Veröffentlicht | 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), p S54-S63.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [40]
    2002 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918995
    Heber, S., et al., 2002. Resampling Methods in Physical Mapping. In Proc. of GfKl 2000. pp. 437-444.
    PUB
     
  • [39]
    2001 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773335 OA
    Kurtz, S., et al., 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research, 29(22), p 4633-4642.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [38]
    2001 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918992
    Heber, S., & Stoye, J., 2001. Finding all Common Intervals of k Permutations. In Proc. of CPM 2001. LNCS. no.2089 pp. 207-218.
    PUB | DOI
     
  • [37]
    2001 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1880197
    Heber, S., & Stoye, J., 2001. Algorithms for Finding Gene Clusters. In Proc. of WABI 2001. LNCS. no.2149 Berlin: Sppringer, pp. 252-263.
    PUB | DOI
     
  • [36]
    2001 | Report | PUB-ID: 1970479
    Cieliebak, M., et al., 2001. Algorithmic Complexity of Protein Identification: Combinatorics of Weighted Strings, Technical Report, ETH Zürich, Dept. of Computer Science.
    PUB
     
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    2000 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918981
    Heber, S., et al., 2000. Contig Selection in Physical Mapping. In Proc. of RECOMB 2000. pp. 155-164.
    PUB | DOI | WoS | PubMed | Europe PMC
     
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    2000 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918817
    Brodal, G.S., et al., 2000. Finding Maximal Pairs with Bounded Gap. In M. Crochemore & L. Gąsieniec, eds. Matching Patterns (Journal of Discrete Algorithms). pp. 77-104.
    PUB
     
  • [33]
    2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773345 OA
    Krause, A., Stoye, J., & Vingron, M., 2000. The SYSTERS protein sequence cluster set. Nucleic Acids Research, 28(1), p 270-272.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [32]
    2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773572 OA
    Heber, S., et al., 2000. Contig selection in physical mapping. Journal of Computational Biology, 7(3-4), p 395-408.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [31]
    2000 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918985
    Spang, R., Rehmsmeier, M., & Stoye, J., 2000. Sequence Database Search Using Jumping Alignments. In Proc. of ISMB 2000. pp. 367-375.
    PUB | PubMed | Europe PMC
     
  • [30]
    2000 | Report | PUB-ID: 1970490 OA
    Stoye, J., 2000. Affix Trees, Forschungsberichte, Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [29]
    2000 | Zeitschriftenaufsatz | Veröffentlicht | 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), p 808-814.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [28]
    2000 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918988
    Kurtz, S., et al., 2000. Computation and Visualization of Degenerate Repeats in Complete Genomes. In Proc. of ISMB 2000. pp. 228-238.
    PUB | PubMed | Europe PMC
     
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    2000 | Konferenzband | Veröffentlicht | PUB-ID: 1918813
    E. Bornberg-Bauer, et al., eds., 2000. Proceedings of the German Conference on Bioinformatics, GCB 2000, Berlin: Logos Verlag.
    PUB
     
  • [26]
    1999 | Konferenzbeitrag | Veröffentlicht | 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. no.1668 pp. 30-42.
    PUB | DOI | WoS
     
  • [25]
    1999 | Konferenzbeitrag | Veröffentlicht | 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. pp. 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, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
  • [23]
    1999 | Report | PUB-ID: 1970509
    Brodal, G.S., et al., 1999. Finding Maximal Pairs with Bounded Gap, Report, BRICS, Department of Computer Science, University of Aarhus.
    PUB
     
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    1999 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918971
    Brodal, G.S., et al., 1999. Finding Maximal Pairs with Bounded Gap. In Proc. of CPM 1999. LNCS. no.1645 pp. 134-149.
    PUB | DOI
     
  • [21]
    1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2488102
    Dress, A., Morgenstern, B., & Stoye, J., 1998. The Number of Standard and of Effective Multiple Alignments. Appl. Math. Lett., 11(4), p 43-49.
    PUB
     
  • [20]
    1998 | Zeitschriftenaufsatz | Veröffentlicht | 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), p 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(2), p GC45-GC56.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [18]
    1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1625402 OA
    Stoye, J., Evers, D., & Meyer, F., 1998. Rose: generating sequence families. BIOINFORMATICS, 14(2), p 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, Report, Department of Computer Science, University of California, Davis.
    PUB
     
  • [16]
    1998 | Konferenzbeitrag | Veröffentlicht | 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. no.1448 pp. 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, Report, Department of Computer Science, University of California, Davis.
    PUB
     
  • [14]
    1997 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773358
    Brinkmann, G., et al., 1997. Two applications of the Divide & Conquer principle in the molecular sciences. Mathematical programming, 79(1-3), p 71-97.
    PUB | DOI | WoS
     
  • [13]
    1997 | Zeitschriftenaufsatz | Veröffentlicht | 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), p 625-626.
    PUB
     
  • [12]
    1997 | Report | PUB-ID: 1970526
    Perrey, S.W., et al., 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., & Meyer, F., 1997. Rose: Generating Sequence Families, Forschungsberichte, Technische Fakultät der Universität Bielefeld.
    PUB
     
  • [10]
    1997 | Report | PUB-ID: 1970529
    Brinkmann, G., et al., 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., & Meyer, F., 1997. Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions. In Proc. of ISMB 1997. pp. 303-306.
    PUB | PubMed | Europe PMC
     
  • [8]
    1997 | Zeitschriftenaufsatz | Veröffentlicht | 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), p 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, Materialien/Preprints, 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, 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., & 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., et al., 1996. A general method for fast multiple sequence alignment. Gene, 172(1), p 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, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
  • [1]
    1996 | Report | PUB-ID: 1970537
    Tönges, U., et al., 1996. A General Method for Fast Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
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