Jens Stoye

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

PEVZ-ID
65864

238 Publications

Mark all

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

Search

Filter Publications

Display / Sort

Export / Embed