Jens Stoye

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

PEVZ-ID
65864

238 Publications

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  • [238]
    2024 | Journal Article | Published | PUB-ID: 2999592
    L. Parmigiani, et al., “Panacus: fast and exact pangenome growth and core size estimation”, Bioinformatics, 2024.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [237]
    2024 | Conference Paper | Published | PUB-ID: 2992085
    L. Bohnenkämper, J. Stoye, and D. Dörr, “Reconstructing Rearrangement Phylogenies of Natural Genomes”, LIPIcs, vol. 312, 2024, : 12.
    PUB | DOI
     
  • [236]
    2024 | Journal Article | Published | PUB-ID: 2988749
    L. Parmigiani, R. Wittler, and J. Stoye, “Revisiting pangenome openness with k-mers”, Peer Community Journal, vol. 4, 2024, : e47.
    PUB | DOI | WoS
     
  • [235]
    2024 | Journal Article | Published | PUB-ID: 2990552
    D. Frolova, et al., “Applying rearrangement distances to enable plasmid epidemiology with pling”, Microbial Genomics , vol. 10, 2024, : 001300.
    PUB | DOI | PubMed | Europe PMC | Preprint
     
  • [234]
    2024 | Book (Editor) | Published | PUB-ID: 2990269
    J.C. Setubal, P.F. Stadler, and J. Stoye, eds., Comparative Genomics. Methods and Protocols, Methods in Molecular Biology, vol. 2802, 2nd ed., New York, NY: Humana, 2024.
    PUB | DOI
     
  • [233]
    2024 | Book Chapter | Published | PUB-ID: 2990270
    M. Dias Vieira Braga, et al., “Family-Free Genome Comparison”, Comparative Genomics. Methods and Protocols, J.C. Setubal, P.F. Stadler, and J. Stoye, eds., Methods in Molecular Biology, vol. 2802, 2nd ed., New York, NY: Humana, 2024, pp.57-72.
    PUB | DOI
     
  • [232]
    2024 | Book Chapter | Published | PUB-ID: 2990271
    T. Schulz, et al., “Methods for Pangenomic Core Detection”, Comparative Genomics. Methods and Protocols, J.C. Setubal, P.F. Stadler, and J. Stoye, eds., Methods in Molecular Biology, vol. 2802, New York, NY: Humana, 2024, pp.73-106.
    PUB | DOI
     
  • [231]
    2024 | Journal Article | Published | PUB-ID: 2985702 OA
    M. Dias Vieira Braga, et al., “Investigating the complexity of the double distance problems”, Algorithms for Molecular Biology, vol. 19, 2024, : 1.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [230]
    2023 | Conference Paper | Published | PUB-ID: 2981606
    M. Dias Vieira Braga, et al., “On the Class of Double Distance Problems”, Comparative Genomics. 20th International Conference, RECOMB-CG 2023, Istanbul, Turkey, April 14–15, 2023, Proceedings, K. Jahn and T. Vinař, eds., Lecture Notes in Computer Science, vol. 13883, Cham: Springer Nature , 2023, pp.35-50.
    PUB | DOI | WoS
     
  • [229]
    2023 | Journal Article | Published | PUB-ID: 2984551
    K.U. Förstner, et al., “NFDI4Microbiota – national research data infrastructure for microbiota research”, Research Ideas and Outcomes, vol. 9, 2023.
    PUB | DOI
     
  • [228]
    2023 | Journal Article | Published | PUB-ID: 2969065
    B. Kirsch-Gerweck, et al., “HaploBlocks: efficient detection of positive selection in large population genomic datasets”, Molecular Biology and Evolution, vol. 40, 2023, : msad027.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [227]
    2022 | Preprint | Published | PUB-ID: 2967089
    L. Parmigiani, R. Wittler, and J. Stoye, “Revisiting pangenome openness with k-mers”, bioRxiv, 2022.
    PUB | DOI
     
  • [226]
    2022 | Conference Paper | Published | PUB-ID: 2965398
    M. Dias Vieira Braga, et al., “A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance”, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), C. Boucher and S. Rahmann, eds., Leibniz International Proceedings in Informatics. LIPIcs, vol. 242, Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, pp.13:1-13:16.
    PUB | DOI
     
  • [225]
    2022 | Journal Article | Published | PUB-ID: 2963777
    P. Bonizzoni, et al., “Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches”, Information Sciences, vol. 607, 2022, pp. 458-476.
    PUB | DOI | WoS
     
  • [224]
    2022 | Journal Article | Published | PUB-ID: 2963659 OA
    T. Schulz, R. Wittler, and J. Stoye, “Sequence-based pangenomic core detection”, iScience, vol. 25, 2022, : 104413.
    PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [223]
    2021 | Book (Editor) | Published | PUB-ID: 2959449 OA
    J. Stoye and R. Wittler, eds., The Bielefeld Institute for Bioinformatics Infrastructure, Bielefeld: Universität Bielefeld, Techn. Fakultät, 2021.
    PUB | PDF | DOI
     
  • [222]
    2021 | Journal Article | Published | PUB-ID: 2942686
    E. Willing, J. Stoye, and M. Dias Vieira Braga, “Computing the Inversion-Indel Distance”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 18, 2021, pp. 2314-2326.
    PUB | DOI | WoS | PubMed | Europe PMC | arXiv
     
  • [221]
    2021 | Journal Article | Published | PUB-ID: 2950825 OA
    T. Schulz, et al., “Detecting High Scoring Local Alignments in Pangenome Graphs”, Bioinformatics, vol. 37, 2021, pp. 2266-2274.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [220]
    2021 | Conference Paper | Published | PUB-ID: 2952705
    P. Bonizzoni, et al., “Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning”, Proceedings of AlCoB 2021, LNBI, vol. 12715, 2021, pp.16-28.
    PUB
     
  • [219]
    2021 | Journal Article | Published | PUB-ID: 2946303
    L. Bohnenkämper, et al., “Computing the rearrangement distance of natural genomes”, Journal of Computational Biology, vol. 28, 2021, pp. 410-431.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [218]
    2021 | Journal Article | Published | PUB-ID: 2945991
    L.K. Sundermann, et al., “Reconstructing Tumor Evolutionary Histories and Clone Trees in Polynomial-time with SubMARine”, PLOS Computational Biology, vol. 17, 2021, : e1008400.
    PUB | DOI | WoS | PubMed | Europe PMC | Preprint
     
  • [217]
    2021 | Special Issue | Published | PUB-ID: 2949108
    J.C. Setubal, J. Stoye, and B.E. Dutilh, eds., “Computational Methods for Microbiome Analysis”, Frontiers in Genetics, vol. Research Topic, 2021.
    PUB | DOI | Download (ext.)
     
  • [216]
    2020 | Preprint | Published | PUB-ID: 2943670
    D. Rubert, et al., “On motifs in colored graphs”, arXiv:2005.13634, 2020.
    PUB | Download (ext.) | arXiv
     
  • [215]
    2020 | Journal Article | Published | PUB-ID: 2942995
    D. Rubert, et al., “Searching and Inferring Colorful Topological Motifs in Vertex-Colored Graphs”, Journal of Combinatorial Optimization, vol. 40, 2020, pp. 379–411.
    PUB | DOI | WoS
     
  • [214]
    2020 | Journal Article | Published | PUB-ID: 2937712 OA
    D. Rubert, et al., “Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants”, BMC Genomics, vol. 21, 2020, : 273.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [213]
    2020 | Journal Article | Published | PUB-ID: 2953267
    J. Schulte-Schrepping, et al., “Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment”, Cell, vol. 182, 2020, pp. 1419-1440.e23.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [212]
    2020 | Report | PUB-ID: 2944669
    F.O. Glöckner, et al., NFDI4BioDiversity - A Consortium for the National Research Data Infrastructure (NFDI) : Proposal, Zenodo, 2020.
    PUB | DOI
     
  • [211]
    2020 | Journal Article | Published | PUB-ID: 2948972
    J.C. Setubal, J. Stoye, and B.E. Dutilh, “Editorial: Computational Methods for Microbiome Analysis”, Frontiers in Genetics, vol. 11, 2020, : 623897.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [210]
    2020 | Preprint | Published | PUB-ID: 2940602
    E. Haghshenas, et al., “HASLR: Fast Hybrid Assembly of Long Reads”, bioRxiv, 2020.
    PUB | DOI | Download (ext.) | Preprint
     
  • [209]
    2020 | Preprint | Published | PUB-ID: 2945720
    T. Schulz, et al., “Detecting High Scoring Local Alignments in Pangenome Graphs”, bioRxiv, 2020.
    PUB | DOI | Preprint
     
  • [208]
    2020 | Journal Article | Published | PUB-ID: 2939618 OA
    J. Alanko, et al., “Finding all maximal perfect haplotype blocks in linear time”, Algorithms for Molecular Biology, vol. 15, 2020, : 2.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [207]
    2020 | Journal Article | Published | PUB-ID: 2945430
    E. Haghshenas, et al., “HASLR: Fast Hybrid Assembly of Long Reads”, iScience, vol. 23, 2020, : 101389.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [206]
    2020 | Journal Article | Published | PUB-ID: 2939598
    G. Sevillya, et al., “Horizontal Gene Transfer Phylogenetics: A Random Walk Approach”, Molecular Biology and Evolution, vol. 37, 2020, pp. 1470–1479.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [205]
    2020 | Preprint | Published | PUB-ID: 2939861
    L. Bohnenkämper, et al., “Computing the rearrangement distance of natural genomes”, arXiv:2001.02139, 2020.
    PUB | Download (ext.) | arXiv
     
  • [204]
    2020 | Conference Paper | Published | PUB-ID: 2939729
    L. Bohnenkämper, et al., “Computing the rearrangement distance of natural genomes”, Proceedings of RECOMB 2020, LNBI, vol. 12074, 2020, pp.3-18.
    PUB | DOI
     
  • [203]
    2019 | Journal Article | Published | PUB-ID: 2932884
    H. Oey, et al., “Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium”, PLOS Pathogens, vol. 15, 2019, : e1007513.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [202]
    2019 | Report | Published | PUB-ID: 2939260
    T. Gagie, et al., 25 Years of the Burrows-Wheeler Transform. Report from Dagstuhl Seminar 19241, Dagstuhl Reports, vol. 9(6), Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, 2019.
    PUB | DOI
     
  • [201]
    2019 | Conference Paper | Published | PUB-ID: 2937148
    J. Alanko, et al., “Finding All Maximal Perfect Haplotype Blocks in Linear Time”, Proceedings of WABI 2019, Leibniz International Proceedings in Informatics. LIPIcs, vol. 143, Dagstuhl: Schloss Dagstuhl, Leibniz-Zentrum für Informatik , 2019, pp.8:1-8:9.
    PUB | DOI
     
  • [200]
    2019 | Book Chapter | Published | PUB-ID: 2932883
    D. Dörr and J. Stoye, “A Perspective on Comparative and Functional Genomics”, Bioinformatics and Phylogenetics, T. Warnow, ed., Computational Biology, vol. 29, Cham: Springer , 2019, pp.361-372.
    PUB | DOI
     
  • [199]
    2018 | Journal Article | Published | PUB-ID: 2919006 OA
    D. Rubert, et al., “Computing the family-free DCJ similarity”, BMC Bioinformatics, vol. 19, 2018, : 152.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [198]
    2018 | Journal Article | Published | PUB-ID: 2919012
    S. Jaenicke, et al., “Flexible metagenome analysis using the MGX framework”, Microbiome, vol. 6, 2018, : 76.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [197]
    2018 | Journal Article | Published | PUB-ID: 2919005 OA
    T. Schulz, J. Stoye, and D. Dörr, “GraphTeams. A method for discovering spatial gene clusters in Hi-C sequencing data”, BMC Genomics, vol. 19, 2018, : 308.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [196]
    2018 | Journal Article | Published | PUB-ID: 2930268
    G. Holley, et al., “Dynamic Alignment-Free and Reference-Free Read Compression”, JOURNAL OF COMPUTATIONAL BIOLOGY, vol. 25, 2018, pp. 825-836.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [195]
    2018 | Book Chapter | Published | PUB-ID: 2913921
    T. Zekic, G. Holley, and J. Stoye, “Pan-genome Storage and Analysis Techniques”, Comparative Genomics. Methods and Protocols, J.C. Setubal, P. Stadler, and J. Stoye, eds., Methods in Molecular Biology, vol. 1704, New York: Springer Verlag, 2018, pp.29-53.
    PUB | DOI
     
  • [194]
    2018 | Book Chapter | Published | PUB-ID: 2913922
    D. Dörr, P. Feijão, and J. Stoye, “Family-Free Genome Comparison”, Comparative Genomics: Methods and Protocols, J.C. Setubal, P. Stadler, and J. Stoye, eds., Methods in Molecular Biology, vol. 1704, New York: Springer Verlag, 2018, pp.331-342.
    PUB | DOI
     
  • [193]
    2018 | Book (Editor) | Published | PUB-ID: 2913920
    J.C. Setubal, P. Stadler, and J. Stoye, eds., Comparative Genomics: Methods and Protocols, Methods in Molecular Biology, vol. 1704, New York: Springer Verlag, 2018.
    PUB | DOI
     
  • [192]
    2018 | Journal Article | Published | PUB-ID: 2918481
    N. Luhmann, et al., “Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 15, 2018, pp. 2094-2100.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [191]
    2018 | Conference Paper | Published | PUB-ID: 2930445
    L. Cunha, et al., “Identifying Maximal Perfect Haplotype Blocks”, Proceedings of BSB 2018, LNBI, vol. 11228, Springer Verlag, 2018, pp.26-37.
    PUB | DOI
     
  • [190]
    2017 | Conference Paper | Published | PUB-ID: 2913015
    D. Rubert, et al., “Algorithms for Computing the Family-Free Genomic Similarity under DCJ”, Comparative Genomics. RECOMB-CG 2017, J. Meidanis and L. Nakhleh, eds., Lecture Notes in Bioinformatics, vol. 10562, Cham: Springer Verlag, 2017, pp.76-100.
    PUB | DOI
     
  • [189]
    2017 | Journal Article | Published | PUB-ID: 2909057 OA
    D. Rubert, et al., “Approximating the DCJ distance of balanced genomes in linear time”, Algorithms for Molecular Biology, vol. 12, 2017, : 3.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [188]
    2017 | Preprint | Published | PUB-ID: 2908521
    L. Cunha, et al., “Faster Jumbled Indexing for Binary Run-Length Encoded Strings”, arXiv: 1702.01280, 2017.
    PUB | Download (ext.) | arXiv
     
  • [187]
    2017 | Conference Paper | Published | PUB-ID: 2909409
    L. Cunha, et al., “Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings”, Proceedings of CPM 2017, LIPIcs, vol. 78, 2017, pp.19:1-19:9.
    PUB | DOI
     
  • [186]
    2017 | Journal Article | Published | PUB-ID: 2913556
    S. Jünemann, et al., “Bioinformatics for NGS-based metagenomics and the application to biogas research”, Journal of Biotechnology, vol. 261, 2017, pp. 10-23.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [185]
    2017 | Conference Paper | Published | PUB-ID: 2907587
    G. Holley, et al., “Dynamic Alignment-Free and Reference-Free Read Compression”, Proceedings of RECOMB 2017, Lecture Notes in Bioinformatics, vol. 10229, 2017, pp.50-65.
    PUB | DOI
     
  • [184]
    2017 | Conference Paper | Published | PUB-ID: 2913016
    T. Schulz, J. Stoye, and D. Dörr, “Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery”, Proceedings of RECOMB-CG 2017, Lecture Notes in Bioinformatics, vol. 1704, Berlin: Springer Verlag, 2017, pp.197-212.
    PUB | DOI
     
  • [183]
    2017 | Journal Article | Published | PUB-ID: 2909967
    D. Dörr, et al., “New Genome Similarity Measures based on Conserved Gene Adjacencies”, Journal of Computational Biology, vol. 24, 2017, pp. 616-634.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [182]
    2016 | Conference Paper | Published | PUB-ID: 2903708
    D. Rubert, et al., “A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates”, Algorithms in Bioinformatics. WABI 2016, M. Frith and C.N. Storm Pedersen, eds., Lecture Notes in Bioinformatics, vol. 9838, Cham: Springer, 2016, pp.293-306.
    PUB | DOI
     
  • [181]
    2016 | Journal Article | Published | PUB-ID: 2905930
    S. Winter, et al., “Finding approximate gene clusters with GECKO 3”, Nucleic Acids Research, vol. 44, 2016, pp. 9600-9610.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [180]
    2016 | Journal Article | Published | PUB-ID: 2900421
    L. Krause, et al., “Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma”, Carcinogenesis, vol. 37, 2016, pp. 356-365.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [179]
    2016 | Journal Article | Published | PUB-ID: 2900129 OA
    G. Holley, R. Wittler, and J. Stoye, “Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage”, Algorithms for Molecular Biology, vol. 11, 2016, : 3.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [178]
    2016 | Conference Paper | Published | PUB-ID: 2900111
    L.A.B. Kowada, et al., “New Genome Similarity Measures based on Conserved Gene Adjacencies”, Research in Computational Molecular Biology. RECOMB 2016, M. Singh, ed., Lecture Notes in Bioinformatics (LNBI), vol. 9649, Springer, 2016, pp.204-224.
    PUB | DOI
     
  • [177]
    2015 | Conference Paper | Published | PUB-ID: 2757497
    G. Holley, R. Wittler, and J. Stoye, “Bloom Filter Trie - a data structure for pan-genome storage”, Algorithms in Bioinformatics. WABI 2015. Proceedings, M. Pop and H. Touzet, eds., Lecture Notes in Computer Science , vol. 9289, Berlin, Heidelberg: Springer, 2015, pp.217-230.
    PUB | DOI
     
  • [176]
    2015 | Journal Article | Published | PUB-ID: 2726366 OA
    F.H. Viduani Martinez, et al., “On the family-free DCJ distance and similarity”, Algorithms for Molecular Biology, vol. 10, 2015, : 13.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [175]
    2015 | Journal Article | Published | PUB-ID: 2677844
    M. Dias Vieira Braga and J. Stoye, “Sorting linear genomes with rearrangements and indels”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 12, 2015, pp. 500-506.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [174]
    2015 | Conference (Editor) | Published | PUB-ID: 2780229
    J. Meidanis and J. Stoye, eds., “Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Bioinformatics”, BMC Bioinformatics, vol. 16, 2015.
    PUB | Download (ext.)
     
  • [173]
    2015 | Conference (Editor) | Published | PUB-ID: 2780232
    J. Meidanis and J. Stoye, eds., “Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Genomics”, BMC Genomics, vol. 16, 2015.
    PUB | Download (ext.)
     
  • [172]
    2014 | Journal Article | Published | PUB-ID: 2689773
    S. Jünemann, et al., “GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers”, PLOS ONE, vol. 9, 2014, : e107014.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [171]
    2014 | Journal Article | Published | PUB-ID: 2685362 OA
    M. Lechner, et al., “Orthology Detection Combining Clustering and Synteny for Very Large Datasets”, PLoS ONE, vol. 9, 2014, : e105015.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [170]
    2014 | Conference Paper | Published | PUB-ID: 2684241
    F.H. Viduani Martinez, et al., “On the family-free DCJ distance”, Algorithms in Bioinformatics. WABI 2014, D. Brown and B. Morgenstern, eds., Lecture Notes in Bioinformatics, vol. 8701, Berlin ; Heidelberg: Springer Verlag, 2014, pp.174-186.
    PUB | DOI
     
  • [169]
    2014 | Journal Article | Published | PUB-ID: 2687033 OA
    D. Dörr, et al., “Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings”, BMC Genomics, vol. 15, 2014, : S2.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [168]
    2014 | Journal Article | Published | PUB-ID: 2674387
    R. Hilker, et al., “ReadXplorer - Visualization and Analysis of Mapped Sequences”, Bioinformatics, vol. 30, 2014, pp. 2247-2254.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [167]
    2014 | Journal Article | Published | PUB-ID: 2665038
    P. Schwientek, et al., “Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts”, Journal of Biotechnology, vol. 190, 2014, pp. 85-95.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [166]
    2014 | Journal Article | Published | PUB-ID: 2685988
    T. Jakobi, et al., “Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing”, Journal of Biotechnology, vol. 190, 2014, pp. 64-75.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [165]
    2014 | Conference Paper | Published | PUB-ID: 2690122
    N. Luhmann, et al., “Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework”, Proc. of BSB 2014, C. Sérgio, ed., LNBI, vol. 8826, Springer Verlag, 2014, pp.135-143.
    PUB | DOI
     
  • [164]
    2014 | Encyclopedia Article | Published | PUB-ID: 2693552
    J. Stoye, “Suffix Tree Construction”, Encyclopedia of Algorithms, M.-Y. Kao, ed., Springer Verlag, 2014.
    PUB | DOI
     
  • [163]
    2014 | Journal Article | Published | PUB-ID: 2693409
    E. Fredrich, et al., “Metatranskriptomik der Mikrobiota aus der menschlichen Achselhöhle”, BIOspektrum, vol. 20, 2014, pp. 294-296.
    PUB | DOI
     
  • [162]
    2014 | Journal Article | Published | PUB-ID: 2643941
    N. Hoffmann, et al., “BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry”, Bioinformatics, vol. 30, 2014, pp. 988-995.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [161]
    2014 | Journal Article | Published | PUB-ID: 2665333
    B. Henrich, et al., “Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma”, PLoS ONE, vol. 9, 2014, : e92297.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [160]
    2013 | Journal Article | Published | PUB-ID: 2575011
    C. Ander, et al., “metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences”, BMC Bioinformatics, vol. 14, 2013, : S2.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [159]
    2013 | Encyclopedia Article | Published | PUB-ID: 2577323
    W. Gerlach and J. Stoye, “Taxonomic classification of metagenomic shotgun sequences with CARMA3”, Encyclopedia of Metagenomics, K.E. Nelson, ed., Springer Verlag, 2013.
    PUB | DOI
     
  • [158]
    2013 | Journal Article | Published | PUB-ID: 2611630 OA
    E. Willing, et al., “On the Inversion-Indel Distance”, BMC Bioinformatics, vol. 14, 2013, : S3.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [157]
    2013 | Conference Paper | Published | PUB-ID: 2611641
    M. Dias Vieira Braga and J. Stoye, “Restricted DCJ-Indel Model Revisited”, Advances in Bioinformatics and Computational Biology. BSB 2013, J.C. Setubal and N.F. Almeida, eds., Lecture Notes in Bioinformatics, vol. 8213, Cham: Springer Verlag, 2013, pp.36-46.
    PUB | DOI
     
  • [156]
    2013 | Book Chapter | Published | PUB-ID: 2611648
    M. Dias Vieira Braga, et al., “The Potential of Family-Free Genome Comparison”, Models and Algorithms for Genome Evolution, C. Chauve, N. El-Mabrouk, and E. Tannier, eds., Computational Biology Series, vol. 19, London: Springer Verlag, 2013, pp.287-307.
    PUB | DOI
     
  • [155]
    2013 | Journal Article | Published | PUB-ID: 2641228
    S. Jünemann, et al., “Corrigendum: Updating benchtop sequencing performance comparison”, Nature biotechnology, vol. 31, 2013, pp. 1148.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [154]
    2013 | Book Chapter | Published | PUB-ID: 2611643
    A. Bergeron and J. Stoye, “The Genesis of the DCJ Formula”, Models and Algorithms for Genome Evolution, C. Chauve, N. El-Mabrouk, and E. Tannier, eds., Computational Biology Series, vol. 19, London: Springer Verlag, 2013, pp.63-81.
    PUB | DOI
     
  • [153]
    2013 | Journal Article | Published | PUB-ID: 2575361
    P. Krell, et al., “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, vol. 98, 2013, pp. 1388-1396.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [152]
    2013 | Journal Article | Published | PUB-ID: 2566922
    S. Jünemann, et al., “Updating benchtop sequencing performance comparison”, Nature Biotechnology, vol. 31, 2013, pp. 294-296.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [151]
    2013 | Conference (Editor) | Published | PUB-ID: 2616537
    A. Darling and J. Stoye, eds., “Algorithms in Bioinformatics”, Lecture Notes in Bioinformatics, vol. 8126, 2013.
    PUB | DOI
     
  • [150]
    2013 | Journal Article | Published | PUB-ID: 2611633 OA
    K. Jahn, et al., “Statistics for approximate gene clusters”, BMC Bioinformatics, vol. 14, 2013, : S14.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [149]
    2013 | Journal Article | Published | PUB-ID: 2548236
    P. Schwientek, et al., “Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media”, Journal of Biotechnology, vol. 167, 2013, pp. 166-177.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [148]
    2013 | Journal Article | Published | PUB-ID: 2529202
    M. Zakrzewski, et al., “MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets”, Journal of Biotechnology, vol. 167, 2013, pp. 156-165.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [147]
    2012 | Journal Article | Published | PUB-ID: 2517230
    S. Jünemann, et al., “Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing”, PLoS ONE, vol. 7, 2012, : e41606.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [146]
    2012 | Journal Article | Published | PUB-ID: 2512642 OA
    D. Dörr, A. Thévenin, and J. Stoye, “Gene family assignment-free comparative genomics”, BMC Bioinformatics, vol. 13, 2012, : S3.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [145]
    2012 | Journal Article | Published | PUB-ID: 2517239 OA
    N. Hoffmann, et al., “Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets”, BMC Bioinformatics, vol. 13, 2012, : 21.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [144]
    2012 | Journal Article | Published | PUB-ID: 2512644 OA
    K. Jahn, H. Sudek, and J. Stoye, “Multiple genome comparison based on overlap regions of pairwise local alignments”, BMC Bioinformatics, vol. 13, 2012, : S7.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [143]
    2012 | Journal Article | Published | PUB-ID: 2486060 OA
    P. Schwientek, et al., “The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110”, BMC Genomics, vol. 13, 2012, : 112.
    PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [142]
    2012 | Conference (Editor) | Published | PUB-ID: 2510416
    J. Kärkkäinen and J. Stoye, eds., “Combinatorial Pattern Matching”, Lecture Notes in Computer Science, vol. 7354, 2012.
    PUB | DOI
     
  • [141]
    2012 | Book Chapter | Published | PUB-ID: 2468382 OA
    N. Hoffmann and J. Stoye, “Generic Software Frameworks for GC-MS Based Metabolomics”, Metabolomics, U. Roessner, ed., InTech, 2012, pp.73-98.
    PUB | PDF | DOI | Download (ext.)
     
  • [140]
    2012 | Journal Article | Published | PUB-ID: 2510984
    R. Hilker, et al., “UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ”, Bioinformatics, vol. 28, 2012, pp. 2509-2511.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [139]
    2011 | Journal Article | Published | PUB-ID: 2091779
    F. Hufsky, et al., “Swiftly Computing Center Strings”, BMC Bioinformatics, vol. 12, 2011, : 106.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [138]
    2011 | Journal Article | Published | PUB-ID: 2396509 OA
    M. Dias Vieira Braga, et al., “Genomic distance under gene substitutions”, BMC Bioinformatics, vol. 12, 2011, : S8.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [137]
    2011 | Journal Article | Published | PUB-ID: 2396558 OA
    M. Dias Vieira Braga, et al., “On the weight of indels in genomic distances”, BMC Bioinformatics, vol. 12, 2011, : S13.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [136]
    2011 | Journal Article | Published | PUB-ID: 1897974
    P.L. Erdős, L. Soukup, and J. Stoye, “Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance”, Applied Mathematics Letters, vol. 24, 2011, pp. 82-86.
    PUB | DOI | WoS | arXiv
     
  • [135]
    2011 | Journal Article | Published | PUB-ID: 2091794
    M. Dias Vieira Braga, E. Willing, and J. Stoye, “Double Cut and Join with Insertions and Deletions”, Journal of Computational Biology, vol. 18, 2011, pp. 1167-1184.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [134]
    2011 | Journal Article | Published | PUB-ID: 2091790
    J. Kovac, et al., “Restricted DCJ Model. Rearrangement Problems with Chromosome Reincorporation”, Journal of Computational Biology, vol. 18, 2011, pp. 1231-1241.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [133]
    2011 | Journal Article | Published | PUB-ID: 2354746
    P. Schwientek, et al., “Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology”, Journal of Biotechnology, vol. 155, 2011, pp. 68-77.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [132]
    2011 | Journal Article | Published | PUB-ID: 2289952
    J. Blom, et al., “Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming”, Bioinformatics, vol. 27, 2011, pp. 1351-1358.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [131]
    2011 | Journal Article | Published | PUB-ID: 1918550
    S. Heber, R. Mayr, and J. Stoye, “Common Intervals of Multiple Permutations”, Algorithmica, vol. 60, 2011, pp. 175-206.
    PUB | DOI | WoS
     
  • [130]
    2011 | Journal Article | Published | PUB-ID: 2298170 OA
    W. Gerlach and J. Stoye, “Taxonomic classification of metagenomic shotgun sequences with CARMA3.”, Nucleic Acids Res, vol. 39, 2011, pp. e91.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [129]
    2011 | Journal Article | Published | PUB-ID: 2091787
    R. Wittler, et al., “Consistency of Sequence-Based Gene Clusters”, Journal of Computational Biology, vol. 18, 2011, pp. 1023-1039.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [128]
    2010 | Conference Paper | Published | PUB-ID: 1919211
    F. Hufsky, et al., “Swiftly Computing Center Strings”, Proc. of WABI 2010, LNBI, vol. 6293, 2010, pp.325-336.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [127]
    2010 | Journal Article | Published | PUB-ID: 1966439
    E. Trost, et al., “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, vol. 11, 2010, : 728.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [126]
    2010 | Conference Abstract / Poster | Published | PUB-ID: 2445157
    A. Bergeron, J. Mixtacki, and J. Stoye, “Computing the Genomic Distance in Linear Time”, Dagstuhl Seminar Proceedings: 10231 Abstracts Collection : Structure Discovery in Biology: Motifs, Networks & Phylogenies, A. Apostolico, A. Dress, and L. Parida, eds., vol. 10231, Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp.18.
    PUB | Download (ext.)
     
  • [125]
    2010 | Conference Abstract / Poster | Published | PUB-ID: 2907492
    A. Bergeron, J. Mixtacki, and J. Stoye, “A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance”, Structure Discovery in Biology: Motifs, Networks & Phylogenies, A. Apostolico, et al., eds., Dagstuhl Seminar Proceedings, vol. 10231, Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, 2010, pp.Online-Ressource.
    PUB | Download (ext.)
     
  • [124]
    2010 | Journal Article | Published | PUB-ID: 1893893 OA
    P. Husemann and J. Stoye, “Phylogenetic Comparative Assembly”, Algorithms for Molecular Biology, vol. 5, 2010, : 3.
    PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [123]
    2010 | Book Chapter | Published | PUB-ID: 1918836
    S. Besenbacher, B. Schwikowski, and J. Stoye, “Indexing and Searching a Mass Spectrometry Database”, Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday, T. Elomaa, H. Mannila, and P. Orponen, eds., LNCS, vol. 6060, Berlin, Heidelberg: Springer Berlin Heidelberg, 2010, pp.62-76.
    PUB | DOI
     
  • [122]
    2010 | Journal Article | Published | PUB-ID: 1795670
    T. Wittkop, et al., “Partitioning Biological Data with Transitivity Clustering”, Nature Methods, vol. 7, 2010, pp. 419-420.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [121]
    2010 | Journal Article | Published | PUB-ID: 1898012
    G. Blin, D. Faye, and J. Stoye, “Finding Nested Common Intervals Efficiently”, Journal of Computational Biology, vol. 17, 2010, pp. 1183-1194.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [120]
    2010 | Conference Paper | Published | PUB-ID: 1919217
    R. Wittler and J. Stoye, “Consistency of Sequence-based Gene Clusters”, Proc. of Recomb-CG 2010, LNBI, vol. 6398, Springer Verlag, 2010, pp.252-263.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [119]
    2010 | Conference Paper | Published | PUB-ID: 1893890
    P. Husemann and J. Stoye, “Repeat-aware Comparative Genome Assembly”, Proc. of GCB 2010, LNI, vol. P-173, 2010, pp.61-70.
    PUB | Download (ext.)
     
  • [118]
    2010 | Journal Article | Published | PUB-ID: 1588556
    P. Husemann and J. Stoye, “r2cat: Synteny Plots and Comparative Assembly”, Bioinformatics, vol. 26, 2010, pp. 570-571.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [117]
    2010 | Journal Article | Published | PUB-ID: 1897997
    A. Bergeron, P. Medvedev, and J. Stoye, “Rearrangement Models and Single-Cut Operations”, Journal of Computational Biology, vol. 17, 2010, pp. 1213-1225.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [116]
    2010 | Conference Paper | Published | PUB-ID: 1919216
    J. Kovac, M. Dias Vieira Braga, and J. Stoye, “The Problem of Chromosome Reincorporation in DCJ Sorting and Halving”, Proc. of Recomb-CG 2010, LNBI, vol. 6398, 2010, pp.13-24.
    PUB | DOI
     
  • [115]
    2010 | Journal Article | Published | PUB-ID: 1898025
    M. Dias Vieira Braga and J. Stoye, “The Solution Space of Sorting by DCJ”, Journal of Computational Biology, vol. 17, 2010, pp. 1145-1165.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [114]
    2010 | Conference Paper | Published | PUB-ID: 1919215
    M. Dias Vieira Braga, E. Willing, and J. Stoye, “Genomic Distance with DCJ and Indels”, Proc. of WABI 2010, LNBI, vol. 6293, 2010, pp.90-101.
    PUB | DOI
     
  • [113]
    2009 | Conference Paper | Published | PUB-ID: 1893884
    P. Husemann and J. Stoye, “Phylogenetic Comparative Assembly”, Proc. of WABI 2009, LNBI, vol. 5724, 2009, pp.145-156.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [112]
    2009 | Journal Article | Published | PUB-ID: 1589663
    A. Bergeron, J. Mixtacki, and J. Stoye, “A New Linear Time Algorithm to Compute the Genomic Distance via the Double Cut and Join Distance”, Theoretical Computer Science, vol. 410, 2009, pp. 5300-5316.
    PUB | DOI | WoS
     
  • [111]
    2009 | Conference Paper | Published | PUB-ID: 1919206
    M. Dias Vieira Braga and J. Stoye, “Counting All DCJ Sorting Scenarios”, Proc. of Recomb-CG 2009, LNBI, vol. 5817, 2009, pp.36-47.
    PUB | DOI
     
  • [110]
    2009 | Conference Paper | Published | PUB-ID: 1919207
    G. Blin and J. Stoye, “Finding Nested Common Intervals Efficiently”, Proc. of Recomb-CG 2009, LNBI, vol. 5817, 2009, pp.59-69.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [109]
    2009 | Journal Article | Published | PUB-ID: 1898137
    K. Jahn and J. Stoye, “Approximative Gencluster und ihre Anwendung in der komparativen Genomik”, Informatik-Spektrum, vol. 32, 2009, pp. 288-300.
    PUB | DOI
     
  • [108]
    2009 | Journal Article | Published | PUB-ID: 1591507
    J. Stoye and R. Wittler, “A Unified Approach for Reconstructing Ancient Gene Clusters”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, 2009, pp. 387-400.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [107]
    2009 | Journal Article | Published | PUB-ID: 1590204
    M. Brudno, et al., “A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)”, BIOINFORMATICS, vol. 25, 2009, pp. 2863-2864.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [106]
    2009 | Journal Article | Published | PUB-ID: 1589098 OA
    W. Gerlach, et al., “WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads”, BMC Bioinformatics, vol. 10, 2009, pp. 430.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [105]
    2009 | Journal Article | Published | PUB-ID: 1898105
    S. Böcker, et al., “Computation of Median Gene Clusters”, Journal of Computational Biology, vol. 16, 2009, pp. 1085-1099.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [104]
    2009 | Journal Article | Published | PUB-ID: 1591319
    N. Hoffmann and J. Stoye, “ChromA: signal-based retention time alignment for chromatography-mass spectrometry data”, Bioinformatics, vol. 25, 2009, pp. 2080-2081.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [103]
    2009 | Conference Paper | Published | PUB-ID: 1919209
    P. Medvedev and J. Stoye, “Rearrangement Models and Single-Cut Operations”, Comparative Genomics : International Workshop, RECOMB-CG 2009, Budapest, Hungary, September 27-29, 2009. Proceedings, Lecture Notes in Computer Science, vol. 5817, Berlin, Heidelberg: Springer, 2009, pp.84-97.
    PUB | DOI
     
  • [102]
    2009 | Conference Abstract / Poster | Published | PUB-ID: 1918945
    J. Stoye, “Computational Short Read Metagenomics”, Presented at the JOBIM 2009, Nantes, France, 2009.
    PUB
     
  • [101]
    2009 | Journal Article | Published | PUB-ID: 1634447
    T. Bekel, et al., “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, vol. 140, 2009, pp. 3-12.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [100]
    2008 | Conference Paper | Published | PUB-ID: 1919198
    J.A.A. Quitzau and J. Stoye, “Detecting Repeat Families in Incompletely Sequenced Genomes”, Proc. of WABI 2008, LNBI, vol. 5251, 2008, pp.342-353.
    PUB | DOI
     
  • [99]
    2008 | Report | PUB-ID: 1970459 OA
    J.A.A. Quitzau and J. Stoye, A space efficient representation for sparse de Bruijn subgraphs, Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld, Bielefeld: Technische Fakultät der Universität Bielefeld, 2008.
    PUB | PDF
     
  • [98]
    2008 | Report | PUB-ID: 1970461 OA
    T. Ejaz, S. Rahmann, and J. Stoye, Online Abelian Pattern Matching, Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld, Bielefeld: Technische Fakultät der Universität Bielefeld, 2008.
    PUB | PDF
     
  • [97]
    2008 | Journal Article | Published | PUB-ID: 1636699
    H. Neuweger, et al., “MeltDB: a software platform for the analysis and integration of metabolomics experiment data”, Bioinformatics, vol. 24, 2008, pp. 2726-2732.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [96]
    2008 | Encyclopedia Article | Published | PUB-ID: 1918834
    J. Stoye, “Suffix Tree Construction in RAM (1997; Farach-Colton)”, Encyclopedia of Algorithms, M.-Y. Kao, ed., Springer Verlag, 2008, pp.925-928.
    PUB | DOI
     
  • [95]
    2008 | Conference Paper | Published | PUB-ID: 1919192
    S. Böcker, et al., “Computation of Median Gene Clusters”, Proc. of RECOMB 2008, LNBI, vol. 4955, 2008, pp.331-345.
    PUB | DOI
     
  • [94]
    2008 | Conference Paper | Published | PUB-ID: 1919200
    A. Bergeron, J. Mixtacki, and J. Stoye, “On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios”, Proc. of Recomb-CG 2008, LNBI, vol. 5267, 2008, pp.226-240.
    PUB | DOI
     
  • [93]
    2008 | Journal Article | Published | PUB-ID: 1587078
    K.-B. Schürmann and J. Stoye, “Counting suffix arrays and strings”, THEORETICAL COMPUTER SCIENCE, vol. 395, 2008, pp. 220-234.
    PUB | DOI | WoS
     
  • [92]
    2008 | Journal Article | Published | PUB-ID: 1586009
    L. Krause, et al., “Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor”, JOURNAL OF BIOTECHNOLOGY, vol. 136, 2008, pp. 91-101.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [91]
    2008 | Journal Article | Published | PUB-ID: 1586785 OA
    S. Oehm, et al., “Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms”, NUCLEIC ACIDS RESEARCH, vol. 36, 2008, pp. W433-W437.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [90]
    2008 | Journal Article | Published | PUB-ID: 1783364 OA
    L. Krause, et al., “Phylogenetic classification of short environmental DNA fragments”, Nucleic Acids Research, vol. 36, 2008, pp. 2230-2239.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [89]
    2008 | Conference Paper | Published | PUB-ID: 1919195
    A. Bergeron, J. Mixtacki, and J. Stoye, “HP Distance via Double Cut and Join Distance”, Combinatorial Pattern Matching. 19th Annual Symposium, CPM 2008, Pisa, Italy, June 18-20, 2008 Proceedings, Lecture Notes in Computer Science, 5029, 2008, pp.56-68.
    PUB | DOI
     
  • [88]
    2007 | Journal Article | Published | PUB-ID: 1630781
    A. Mellmann, et al., “Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms”, BMC MICROBIOLOGY, vol. 7, 2007, pp. 98.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [87]
    2007 | Book Chapter | Published | PUB-ID: 1918828
    T. Schmidt and J. Stoye, “Chapter 12: Gecko and GhostFam - Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes”, Comparative Genomics, Volume 2, N.H. Bergman, ed., Methods in Molecular Biology, vol. 396, Totowa, NJ: Humana Press Inc., 2007, pp.165-182.
    PUB | DOI | PubMed | Europe PMC
     
  • [86]
    2007 | Journal Article | Published | PUB-ID: 1918432
    G. Didier, et al., “Character Sets of Strings”, Journal of Discrete Algorithms, vol. 5, 2007, pp. 330-340.
    PUB | DOI
     
  • [85]
    2007 | Journal Article | Published | PUB-ID: 1595253
    K.-B. Schürmann and J. Stoye, “An incomplex algorithm for fast suffix array construction”, SOFTWARE-PRACTICE & EXPERIENCE, vol. 37, 2007, pp. 309-329.
    PUB | DOI | WoS
     
  • [84]
    2007 | Journal Article | Published | PUB-ID: 1783345 OA
    L. Krause, et al., “GISMO - gene identification using a support vector machine for ORF classification”, Nucleic Acids Research, vol. 35, 2007, pp. 540-549.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [83]
    2006 | Journal Article | Published | PUB-ID: 1599943
    M. Sammeth, et al., “Panta rhei (QAlign2): an open graphical environment for sequence analysis”, BIOINFORMATICS, vol. 22, 2006, pp. 889-890.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [82]
    2006 | Journal Article | Published | PUB-ID: 1599570
    K.R. Rasmussen, J. Stoye, and E.W. Myers, “Efficient q-gram filters for finding all epsilon-matches over a given length”, JOURNAL OF COMPUTATIONAL BIOLOGY, vol. 13, 2006, pp. 296-308.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [81]
    2006 | Journal Article | Published | PUB-ID: 1599574
    A. Bergeron, J. Mixtacki, and J. Stoye, “On sorting by translocations”, JOURNAL OF COMPUTATIONAL BIOLOGY, vol. 13, 2006, pp. 567-578.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [80]
    2006 | Conference Paper | Published | PUB-ID: 1596811
    A. Bergeron, J. Mixtacki, and J. Stoye, “A Unifying View of Genome Rearrangements”, Proc. of WABI 2006, LNBI, vol. 4175, SPRINGER-VERLAG BERLIN, 2006, pp.163-173.
    PUB | DOI | WoS
     
  • [79]
    2006 | Journal Article | Published | PUB-ID: 1597213
    M. Sammeth and J. Stoye, “Comparing tandem repeats with duplications and excisions of variable degree”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, 2006, pp. 395-407.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [78]
    2006 | Journal Article | Published | PUB-ID: 1597313
    A. Bergeron and J. Stoye, “On the similarity of sets of permutations and its applications to genome comparison”, JOURNAL OF COMPUTATIONAL BIOLOGY, vol. 13, 2006, pp. 1340-1354.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [77]
    2006 | Conference Abstract / Poster | Published | PUB-ID: 1918946
    J. Stoye, “Index Structures in Biological Sequence Analysis: From Simplicity to Complexity and Back”, Presented at the JOBIM 2006, Bordeaux, France, 2006.
    PUB
     
  • [76]
    2006 | Report | PUB-ID: 1970464 OA
    C. Chauve, et al., On Common Intervals with Errors, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld, 2006.
    PUB | PDF
     
  • [75]
    2006 | Journal Article | Published | PUB-ID: 1631957
    L. Krause, et al., “Finding novel genes in bacterial communities isolated from the environment”, BIOINFORMATICS, vol. 22, 2006, pp. e281-e289.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [74]
    2005 | Report | PUB-ID: 1970470 OA
    M. Sammeth and J. Stoye, Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI), Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld, 2005.
    PUB | PDF | DOI
     
  • [73]
    2005 | Conference Paper | Published | PUB-ID: 1919012
    K.-B. Schürmann and J. Stoye, “An Incomplex Algorithm for Fast Suffix Array Construction”, Proc. of ALENEX/ANALCO 2005, 2005, pp.77-85.
    PUB
     
  • [72]
    2005 | Book Chapter | Published | PUB-ID: 1918824
    A. Bergeron, J. Mixtacki, and J. Stoye, “Chapter 10: The Inversion Distance Problem”, Mathematics of Evolution and Phylogeny, O. Gascuel, ed., Oxford University Press, 2005, pp.262-290.
    PUB
     
  • [71]
    2005 | Conference Paper | Published | PUB-ID: 1603220
    A. Bergeron, J. Mixtacki, and J. Stoye, “On Sorting by Translocations”, Proc. of RECOMB 2005, LNBI, vol. 3500, SPRINGER-VERLAG BERLIN, 2005, pp.615-629.
    PUB | DOI | WoS
     
  • [70]
    2005 | Journal Article | Published | PUB-ID: 1775168 OA
    A. Krause, J. Stoye, and M. Vingron, “Large scale hierarchical clustering of protein sequences”, BMC Bioinformatics, vol. 6, 2005, : 15.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [69]
    2005 | Journal Article | Published | PUB-ID: 1773302 OA
    D. Bartels, et al., “BACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison”, Bioinformatics, vol. 21, 2005, pp. 853-859.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [68]
    2005 | Journal Article | Published | PUB-ID: 1918947
    S. Böcker and J. Stoye, “Informatische Methoden zur Protein-Identifikation”, LaborPraxis, vol. 29, 2005, pp. 24-26.
    PUB
     
  • [67]
    2005 | Conference Paper | Published | PUB-ID: 1601348
    C. Bannert and J. Stoye, “Protein Annotation by Secondary Structure Based Alignments (PASSTA)”, Proc. of CompLife 2005, LNBI, vol. 3695, Springer-Verlag, 2005, pp.79-90.
    PUB | DOI | WoS
     
  • [66]
    2005 | Conference Paper | Published | PUB-ID: 1601361
    M. Sammeth, et al., “Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)”, Proc. of WABI 2005, LNBI, vol. 3692, SPRINGER-VERLAG BERLIN, 2005, pp.276-290.
    PUB | DOI | WoS
     
  • [65]
    2005 | Conference Paper | Published | PUB-ID: 1603216
    K.R. Rasmussen, J. Stoye, and E.W. Myers, “Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length”, Proc. of RECOMB 2005, LNBI, vol. 3500, SPRINGER-VERLAG BERLIN, 2005, pp.189-203.
    PUB | DOI | WoS
     
  • [64]
    2005 | Conference Paper | Published | PUB-ID: 1919026
    K.-B. Schürmann and J. Stoye, “Counting Suffix Arrays and Strings”, Proc. of SPIRE 2005, LNCS, vol. 3772, 2005, pp.55-66.
    PUB | DOI
     
  • [63]
    2005 | Report | PUB-ID: 1970472 OA
    K.-B. Schürmann and J. Stoye, Counting Suffix Arrays and Strings, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld, 2005.
    PUB | PDF
     
  • [62]
    2004 | Conference (Editor) | Published | PUB-ID: 1918823
    R. Giegerich and J. Stoye, eds., “Proceedings of the German Conference on Bioinformatics, GCB 2004”, Lecture Notes in Informatics, vol. P-53, 2004, pp. 234.
    PUB
     
  • [61]
    2004 | Conference Paper | Published | PUB-ID: 1607260
    T. Schmidt and J. Stoye, “Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences”, Proc. of CPM 2004, LNCS, vol. 3109, 2004, pp.347-358.
    PUB | DOI | WoS
     
  • [60]
    2004 | Conference Paper | Published | PUB-ID: 1606286
    M. Michael, C. Dieterich, and J. Stoye, “Suboptimal Local Alignments across Multiple Scoring Schemes”, Proc. of WABI 2004, LNBI, vol. 3240, SPRINGER-VERLAG BERLIN, 2004, pp.99-110.
    PUB | DOI | WoS
     
  • [59]
    2004 | Journal Article | Published | PUB-ID: 1773554 OA
    D.A. Pollard, et al., “Correction: Benchmarking tools for the alignment of functional noncoding DNA”, BMC Bioinformatics, vol. 5, 2004, : 73.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [58]
    2004 | Journal Article | Published | PUB-ID: 1773560 OA
    M. Cieliebak, et al., “Algorithmic complexity of protein identification: combinatorics of weighted strings”, Discrete Applied Mathematics, vol. 137, 2004, pp. 27-46.
    PUB | PDF | DOI | WoS
     
  • [57]
    2004 | Journal Article | Published | PUB-ID: 1773312 OA
    D.A. Pollard, et al., “Benchmarking tools for the alignment of functional noncoding DNA”, BMC Bioinformatics, vol. 5, 2004, : 6.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [56]
    2004 | Journal Article | Published | PUB-ID: 1773569 OA
    D. Gusfield and J. Stoye, “Linear time algorithms for finding and representing all the tandem repeats in a string”, Journal of computer and system sciences, vol. 69, 2004, pp. 525-546.
    PUB | PDF | DOI | WoS
     
  • [55]
    2004 | Conference Paper | Published | PUB-ID: 1607263
    A. Bergeron, J. Mixtacki, and J. Stoye, “Reversal Distance without Hurdles and Fortresses”, Proc. of CPM 2004, LNCS, vol. 3109, SPRINGER-VERLAG BERLIN, 2004, pp.388-399.
    PUB | DOI | WoS
     
  • [54]
    2003 | Report | PUB-ID: 1970475 OA
    K.-B. Schürmann and J. Stoye, Suffix Tree Construction and Storage with Limited Main Memory, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld, 2003.
    PUB | PDF
     
  • [53]
    2003 | Journal Article | Published | PUB-ID: 1612664
    S. Heber and J. Stoye, “The European Conference on Computational Biology”, Drug Discovery Today, vol. 8, 2003, pp. 113-114.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [52]
    2003 | Journal Article | Published | PUB-ID: 1918949
    R. Giegerich and J. Stoye, “Finden, fast ohne zu suchen: Indexstrukturen in der Bioinformatik”, Forschung an der Universität Bielefeld, vol. 26, 2003, pp. 63-68.
    PUB
     
  • [51]
    2003 | Conference Paper | Published | PUB-ID: 1919005
    C. Bannert and J. Stoye, “Evaluation of the Jumping Alignment Algorithm with Artificial and Biological Data”, Proc. of GCB 2003, 2003, pp.21-25.
    PUB
     
  • [50]
    2003 | Journal Article | Published | PUB-ID: 1610397 OA
    R. Giegerich, S. Kurtz, and J. Stoye, “Efficient implementation of lazy suffix trees”, SOFTWARE-PRACTICE & EXPERIENCE, vol. 33, 2003, pp. 1035-1049.
    PUB | PDF | DOI | WoS
     
  • [49]
    2003 | Journal Article | Published | PUB-ID: 1609403 OA
    M. Sammeth, B. Morgenstern, and J. Stoye, “Divide-and-conquer multiple alignment with segment-based constraints”, BIOINFORMATICS, vol. 19, 2003, pp. ii189-ii195.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [48]
    2003 | Conference Paper | Published | PUB-ID: 1610433
    A. Bergeron and J. Stoye, “On the similarity of sets of permutations and its applications to genome comparison”, Proc. of COCOON 2003, LNCS, vol. 2697, 2003, pp.68-79.
    PUB | DOI | WoS
     
  • [47]
    2003 | Journal Article | Published | PUB-ID: 1610503 OA
    M. Sammeth, et al., “QAlign: quality-based multiple alignments with dynamic phylogenetic analysis”, BIOINFORMATICS, vol. 19, 2003, pp. 1592-1593.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [46]
    2003 | Report | PUB-ID: 1970477 OA
    A. Bergeron and J. Stoye, On the Similarity of Sets of Permutations and its Applications to Genome Comparison, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld, 2003.
    PUB | PDF
     
  • [45]
    2002 | Conference Abstract / Poster | Published | PUB-ID: 1918951
    J. Stoye, “Index Structures for Large Sequence Data: Suffix Trees and Affix Trees”, Lecture Notes in Informatics, S. Schubert, B. Reusch, and N. Jesse, eds., vol. P-20, 2002, pp.67-67.
    PUB
     
  • [44]
    2002 | Conference Paper | Published | PUB-ID: 1919000
    M. Cieliebak, et al., “Algorithmic Complexity of Protein Identification: Searching in Weighted Strings”, Proc. of IFIP TCS 2002, 2002, pp.143-156.
    PUB
     
  • [43]
    2002 | Journal Article | Published | PUB-ID: 1773578 OA
    R. Spang, M. Rehmsmeier, and J. Stoye, “A novel approach to remote homology detection: jumping alignments”, Journal of Computational Biology, vol. 9, 2002, pp. 747-760.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [42]
    2002 | Journal Article | Published | PUB-ID: 1773332 OA
    J. Stoye and D. Gusfield, “Simple and flexible detection of contiguous repeats using a suffix tree”, Theoretical Computer Science, vol. 270, 2002, pp. 843-856.
    PUB | PDF | DOI | WoS
     
  • [41]
    2002 | Journal Article | Published | PUB-ID: 1773329 OA
    A. Bergeron, S. Heber, and J. Stoye, “Common intervals and sorting by reversals: a marriage of necessity”, Bioinformatics, vol. 18, 2002, pp. S54-S63.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [40]
    2002 | Conference Paper | Published | PUB-ID: 1918995
    S. Heber, et al., “Resampling Methods in Physical Mapping”, Proc. of GfKl 2000, 2002, pp.437-444.
    PUB
     
  • [39]
    2001 | Journal Article | Published | PUB-ID: 1773335 OA
    S. Kurtz, et al., “REPuter: the manifold applications of repeat analysis on a genomic scale”, Nucleic Acids Research, vol. 29, 2001, pp. 4633-4642.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [38]
    2001 | Conference Paper | Published | PUB-ID: 1918992
    S. Heber and J. Stoye, “Finding all Common Intervals of k Permutations”, Proc. of CPM 2001, LNCS, vol. 2089, 2001, pp.207-218.
    PUB | DOI
     
  • [37]
    2001 | Conference Paper | Published | PUB-ID: 1880197
    S. Heber and J. Stoye, “Algorithms for Finding Gene Clusters”, Proc. of WABI 2001, LNCS, vol. 2149, Berlin: Sppringer, 2001, pp.252-263.
    PUB | DOI
     
  • [36]
    2001 | Report | PUB-ID: 1970479
    M. Cieliebak, et al., Algorithmic Complexity of Protein Identification: Combinatorics of Weighted Strings, Technical Report, ETH Zürich, Dept. of Computer Science: 2001.
    PUB
     
  • [35]
    2000 | Conference Paper | Published | PUB-ID: 1918981
    S. Heber, et al., “Contig Selection in Physical Mapping”, Proc. of RECOMB 2000, 2000, pp.155-164.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [34]
    2000 | Book Chapter | Published | PUB-ID: 1918817
    G.S. Brodal, et al., “Finding Maximal Pairs with Bounded Gap”, Matching Patterns (Journal of Discrete Algorithms), M. Crochemore and L. Gąsieniec, eds., 2000, pp.77-104.
    PUB
     
  • [33]
    2000 | Journal Article | Published | PUB-ID: 1773345 OA
    A. Krause, J. Stoye, and M. Vingron, “The SYSTERS protein sequence cluster set”, Nucleic Acids Research, vol. 28, 2000, pp. 270-272.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [32]
    2000 | Journal Article | Published | PUB-ID: 1773572 OA
    S. Heber, et al., “Contig selection in physical mapping”, Journal of Computational Biology, vol. 7, 2000, pp. 395-408.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [31]
    2000 | Conference Paper | Published | PUB-ID: 1918985
    R. Spang, M. Rehmsmeier, and J. Stoye, “Sequence Database Search Using Jumping Alignments”, Proc. of ISMB 2000, 2000, pp.367-375.
    PUB | PubMed | Europe PMC
     
  • [30]
    2000 | Report | PUB-ID: 1970490 OA
    J. Stoye, Affix Trees, Forschungsberichte, Technische Fakultät der Universität Bielefeld: 2000.
    PUB | PDF
     
  • [29]
    2000 | Journal Article | Published | PUB-ID: 1773341 OA
    K. Reinert, J. Stoye, and T. Will, “An iterative method for faster sum-of-pairs multiple sequence alignment”, Bioinformatics, vol. 16, 2000, pp. 808-814.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [28]
    2000 | Conference Paper | Published | PUB-ID: 1918988
    S. Kurtz, et al., “Computation and Visualization of Degenerate Repeats in Complete Genomes”, Proc. of ISMB 2000, 2000, pp.228-238.
    PUB | PubMed | Europe PMC
     
  • [27]
    2000 | Conference (Editor) | Published | PUB-ID: 1918813
    E. Bornberg-Bauer, et al., eds., Proceedings of the German Conference on Bioinformatics, GCB 2000, Berlin: Logos Verlag, 2000.
    PUB
     
  • [26]
    1999 | Conference Paper | Published | PUB-ID: 1620435
    R. Giegerich, S. Kurtz, and J. Stoye, “Efficient implementation of lazy suffix trees”, Algorithm Engineering. 3rd International Workshop, WAE’99 London, UK, July 19–21, 1999 Proceedings, LNCS, vol. 1668, 1999, pp.30-42.
    PUB | DOI | WoS
     
  • [25]
    1999 | Conference Paper | Published | PUB-ID: 1918978
    K. Reinert, T. Will, and J. Stoye, “Combining Divide-and-Conquer, the A*-Algorithm, and Successive Realignment Approaches to Speed up Multiple Sequence Alignment”, Proc. of GCB 1999, 1999, pp.17-24.
    PUB | Download (ext.)
     
  • [24]
    1999 | Report | PUB-ID: 1970495
    B. Morgenstern, J. Stoye, and A. Dress, Consistent Equivalence Relations: A Set-Theoretical Framework for Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1999.
    PUB
     
  • [23]
    1999 | Report | PUB-ID: 1970509
    G.S. Brodal, et al., Finding Maximal Pairs with Bounded Gap, Report, BRICS, Department of Computer Science, University of Aarhus: 1999.
    PUB
     
  • [22]
    1999 | Conference Paper | Published | PUB-ID: 1918971
    G.S. Brodal, et al., “Finding Maximal Pairs with Bounded Gap”, Proc. of CPM 1999, LNCS, vol. 1645, 1999, pp.134-149.
    PUB | DOI
     
  • [21]
    1998 | Journal Article | Published | PUB-ID: 2488102
    A. Dress, B. Morgenstern, and J. Stoye, “The Number of Standard and of Effective Multiple Alignments”, Appl. Math. Lett., vol. 11, 1998, pp. 43-49.
    PUB
     
  • [20]
    1998 | Journal Article | Published | PUB-ID: 1918538
    M. Hildebrand and J. Stoye, “Die Bedeutung der Zusammenarbeit der Disziplinen in der Anwendung - erläutert anhand von Beispielen”, Der Mathematikunterricht, vol. 44, 1998, pp. 34-53.
    PUB
     
  • [19]
    1998 | Journal Article | Published | PUB-ID: 1667771 OA
    J. Stoye, “Multiple sequence alignment with the Divide-and-Conquer method.”, Gene, vol. 211, 1998, pp. GC45-GC56.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [18]
    1998 | Journal Article | Published | PUB-ID: 1625402 OA
    J. Stoye, D. Evers, and F. Meyer, “Rose: generating sequence families”, BIOINFORMATICS, vol. 14, 1998, pp. 157-163.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [17]
    1998 | Report | PUB-ID: 1970515
    J. Stoye and D. Gusfield, Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree, Report, Department of Computer Science, University of California, Davis: 1998.
    PUB
     
  • [16]
    1998 | Conference Paper | Published | PUB-ID: 1918964
    J. Stoye and D. Gusfield, “Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version)”, Proc. of CPM 1998, LNCS, vol. 1448, 1998, pp.140-152.
    PUB | DOI
     
  • [15]
    1998 | Report | PUB-ID: 1970513
    D. Gusfield and J. Stoye, Linear Time Algorithms for Finding and Representing all the Tandem Repeats in a String, Report, Department of Computer Science, University of California, Davis: 1998.
    PUB
     
  • [14]
    1997 | Journal Article | Published | PUB-ID: 1773358
    G. Brinkmann, et al., “Two applications of the Divide & Conquer principle in the molecular sciences”, Mathematical programming, vol. 79, 1997, pp. 71-97.
    PUB | DOI | WoS
     
  • [13]
    1997 | Journal Article | Published | PUB-ID: 2488107
    J. Stoye, V. Moulton, and A. Dress, “DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment”, CABIOS, vol. 13, 1997, pp. 625-626.
    PUB
     
  • [12]
    1997 | Report | PUB-ID: 1970526
    S.W. Perrey, et al., On Simultaneous versus Iterative Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1997.
    PUB
     
  • [11]
    1997 | Report | PUB-ID: 1970517
    J. Stoye, D. Evers, and F. Meyer, Rose: Generating Sequence Families, Forschungsberichte, Technische Fakultät der Universität Bielefeld: 1997.
    PUB
     
  • [10]
    1997 | Report | PUB-ID: 1970529
    G. Brinkmann, et al., Two Applications of the Divide & Conquer Principle in the Molecular Sciences, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1997.
    PUB
     
  • [9]
    1997 | Conference Paper | Published | PUB-ID: 1667885
    J. Stoye, D. Evers, and F. Meyer, “Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions”, Proc. of ISMB 1997, 1997, pp.303-306.
    PUB | PubMed | Europe PMC
     
  • [8]
    1997 | Journal Article | Published | PUB-ID: 1773355 OA
    J. Stoye, S.W. Perrey, and A. Dress, “Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment”, Applied mathematics letters, vol. 10, 1997, pp. 67-73.
    PUB | PDF | DOI | WoS
     
  • [7]
    1997 | Report | PUB-ID: 1970523
    A. Dress, B. Morgenstern, and J. Stoye, On the Number of Standard and Effective Multiple Alignments, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1997.
    PUB
     
  • [6]
    1997 | Report | PUB-ID: 1970520
    S.W. Perrey, J. Stoye, and V. Moulton, FDCA: Fast and Accurate Approximation to Sum-of-Pairs Score Optimal Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1997.
    PUB
     
  • [5]
    1997 | Report | PUB-ID: 1970532
    J. Stoye, Divide-and-Conquer Multiple Sequence Alignment, Forschungsberichte, Technische Fakultät der Universität Bielefeld: 1997.
    PUB
     
  • [4]
    1996 | Report | PUB-ID: 1970533
    S.W. Perrey and J. Stoye, 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: 1996.
    PUB
     
  • [3]
    1996 | Journal Article | Published | PUB-ID: 1773351
    U. Tönges, et al., “A general method for fast multiple sequence alignment”, Gene, vol. 172, 1996, pp. GC33-GC41.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [2]
    1996 | Report | PUB-ID: 1970535
    J. Stoye, A. Dress, and S.W. Perrey, Improving the Divide-and-Conquer Approach to Sum-of-Pairs Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1996.
    PUB
     
  • [1]
    1996 | Report | PUB-ID: 1970537
    U. Tönges, et al., A General Method for Fast Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1996.
    PUB
     
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