Jens Stoye

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

PEVZ-ID
65864

238 Publications

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  • [238]
    2024 | Journal Article | Published | PUB-ID: 2999592
    Parmigiani L, Garrison E, Stoye J, Marschall T, Doerr D (2024)
    Panacus: fast and exact pangenome growth and core size estimation.
    Bioinformatics.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [237]
    2024 | Conference Paper | Published | PUB-ID: 2992085
    Bohnenkämper L, Stoye J, Dörr D (2024)
    Reconstructing Rearrangement Phylogenies of Natural Genomes.
    LIPIcs 312: 12.
    PUB | DOI
     
  • [236]
    2024 | Journal Article | Published | PUB-ID: 2988749
    Parmigiani L, Wittler R, Stoye J (2024)
    Revisiting pangenome openness with k-mers.
    Peer Community Journal 4: e47.
    PUB | DOI | WoS
     
  • [235]
    2024 | Journal Article | Published | PUB-ID: 2990552
    Frolova D, Lima L, Roberts L, Bohnenkämper L, Wittler R, Stoye J, Iqbal Z (2024)
    Applying rearrangement distances to enable plasmid epidemiology with pling.
    Microbial Genomics 10(10): 001300.
    PUB | DOI | PubMed | Europe PMC | Preprint
     
  • [234]
    2024 | Book (Editor) | Published | PUB-ID: 2990269
    Setubal JC, Stadler PF, Stoye J (Eds) (2024)
    Comparative Genomics. Methods and Protocols. Methods in Molecular Biology; 2802, 2nd ed.
    New York, NY: Humana.
    PUB | DOI
     
  • [233]
    2024 | Book Chapter | Published | PUB-ID: 2990270
    Dias Vieira Braga M, Doerr D, Rubert DP, Stoye J (2024)
    Family-Free Genome Comparison.
    In: Comparative Genomics. Methods and Protocols. Setubal JC, Stadler PF, Stoye J (Eds); Methods in Molecular Biology, 2802. 2nd ed. New York, NY: Humana: 57-72.
    PUB | DOI
     
  • [232]
    2024 | Book Chapter | Published | PUB-ID: 2990271
    Schulz T, Parmigiani L, Rempel A, Stoye J (2024)
    Methods for Pangenomic Core Detection.
    In: Comparative Genomics. Methods and Protocols. Setubal JC, Stadler PF, Stoye J (Eds); Methods in Molecular Biology, 2802. New York, NY: Humana: 73-106.
    PUB | DOI
     
  • [231]
    2024 | Journal Article | Published | PUB-ID: 2985702 OA
    Dias Vieira Braga M, Brockmann LR, Klerx K, Stoye J (2024)
    Investigating the complexity of the double distance problems.
    Algorithms for Molecular Biology 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 (2023)
    On the Class of Double Distance Problems.
    In: Comparative Genomics. 20th International Conference, RECOMB-CG 2023, Istanbul, Turkey, April 14–15, 2023, Proceedings. Jahn K, Vinař T (Eds); Lecture Notes in Computer Science, 13883. Cham: Springer Nature : 35-50.
    PUB | DOI | WoS
     
  • [229]
    2023 | Journal Article | Published | PUB-ID: 2984551
    Förstner KU, Becker A, Blom J, Bork P, Clavel T, Dieckmann M, Goesmann A, Götz B, Gübitz T, Hufsky F, Jünemann S, Körner M-L, Marz M, Da Rocha UN, Overmann J, Pühler A, Rebholz-Schuhmann D, Sczyrba A, Stoye J, Vandendorpe J, Van Rossum T, McHardy A (2023)
    NFDI4Microbiota – national research data infrastructure for microbiota research.
    Research Ideas and Outcomes 9.
    PUB | DOI
     
  • [228]
    2023 | Journal Article | Published | PUB-ID: 2969065
    Kirsch-Gerweck B, Bohnenkämper L, Henrichs MT, Alanko JN, Bannai H, Cazaux B, Peterlongo P, Burger J, Stoye J, Diekmann Y (2023)
    HaploBlocks: efficient detection of positive selection in large population genomic datasets.
    Molecular Biology and Evolution 40(3): msad027.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [227]
    2022 | Preprint | Published | PUB-ID: 2967089
    Parmigiani L, Wittler R, Stoye J (2022)
    Revisiting pangenome openness with k-mers.
    bioRxiv.
    PUB | DOI
     
  • [226]
    2022 | Conference Paper | Published | PUB-ID: 2965398
    Dias Vieira Braga M, Brockmann LR, Klerx K, Stoye J (2022)
    A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance.
    In: 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Boucher C, Rahmann S (Eds); Leibniz International Proceedings in Informatics. LIPIcs, 242. Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik: 13:1-13:16.
    PUB | DOI
     
  • [225]
    2022 | Journal Article | Published | PUB-ID: 2963777
    Bonizzoni P, Costantini M, De Felice C, Petescia A, Pirola Y, Previtali M, Rizzi R, Stoye J, Zaccagnino R, Zizza R (2022)
    Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches.
    Information Sciences 607: 458-476.
    PUB | DOI | WoS
     
  • [224]
    2022 | Journal Article | Published | PUB-ID: 2963659 OA
    Schulz T, Wittler R, Stoye J (2022)
    Sequence-based pangenomic core detection.
    iScience 25(6): 104413.
    PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [223]
    2021 | Book (Editor) | Published | PUB-ID: 2959449 OA
    Stoye J, Wittler R (Eds) (2021)
    The Bielefeld Institute for Bioinformatics Infrastructure.
    Bielefeld: Universität Bielefeld, Techn. Fakultät.
    PUB | PDF | DOI
     
  • [222]
    2021 | Journal Article | Published | PUB-ID: 2942686
    Willing E, Stoye J, Dias Vieira Braga M (2021)
    Computing the Inversion-Indel Distance.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 18(6): 2314-2326.
    PUB | DOI | WoS | PubMed | Europe PMC | arXiv
     
  • [221]
    2021 | Journal Article | Published | PUB-ID: 2950825 OA
    Schulz T, Wittler R, Rahmann S, Hach F, Stoye J (2021)
    Detecting High Scoring Local Alignments in Pangenome Graphs.
    Bioinformatics 37(16): 2266-2274.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [220]
    2021 | Conference Paper | Published | PUB-ID: 2952705
    Bonizzoni P, De Felice C, Petescia A, Pirola Y, Rizzi R, Stoye J, Zaccagnino R, Zizza R (2021)
    Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning.
    In: Proceedings of AlCoB 2021. LNBI, 12715. 16-28.
    PUB
     
  • [219]
    2021 | Journal Article | Published | PUB-ID: 2946303
    Bohnenkämper L, Dias Vieira Braga M, Dörr D, Stoye J (2021)
    Computing the rearrangement distance of natural genomes.
    Journal of Computational Biology 28(4): 410-431.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [218]
    2021 | Journal Article | Published | PUB-ID: 2945991
    Sundermann LK, Wintersinger J, Rätsch G, Stoye J, Morris Q (2021)
    Reconstructing Tumor Evolutionary Histories and Clone Trees in Polynomial-time with SubMARine.
    PLOS Computational Biology 17(1): e1008400.
    PUB | DOI | WoS | PubMed | Europe PMC | Preprint
     
  • [217]
    2021 | Special Issue | Published | PUB-ID: 2949108
    Setubal JC, Stoye J, Dutilh BE (Eds) (2021)
    Computational Methods for Microbiome Analysis.
    Frontiers in Genetics Research Topic.
    PUB | DOI | Download (ext.)
     
  • [216]
    2020 | Preprint | Published | PUB-ID: 2943670
    Rubert D, Araujo E, Stefanes MA, Stoye J, Martinez FV (2020)
    On motifs in colored graphs.
    arXiv:2005.13634.
    PUB | Download (ext.) | arXiv
     
  • [215]
    2020 | Journal Article | Published | PUB-ID: 2942995
    Rubert D, Araujo E, Stefanes MA, Stoye J, Martinez F (2020)
    Searching and Inferring Colorful Topological Motifs in Vertex-Colored Graphs.
    Journal of Combinatorial Optimization 40: 379–411.
    PUB | DOI | WoS
     
  • [214]
    2020 | Journal Article | Published | PUB-ID: 2937712 OA
    Rubert D, Martinez FHV, Stoye J, Dörr D (2020)
    Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants.
    BMC Genomics 21(Suppl. 2): 273.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [213]
    2020 | Journal Article | Published | PUB-ID: 2953267
    Schulte-Schrepping J, Reusch N, Paclik D, Baßler K, Schlickeiser S, Zhang B, Krämer B, Krammer T, Brumhard S, Bonaguro L, De Domenico E, Wendisch D, Grasshoff M, Kapellos TS, Beckstette M, Pecht T, Saglam A, Dietrich O, Mei HE, Schulz AR, Conrad C, Kunkel D, Vafadarnejad E, Xu C-J, Horne A, Herbert M, Drews A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, Müller-Redetzky H, Heim K-M, Machleidt F, Uhrig A, Bosquillon de Jarcy L, Jürgens L, Stegemann M, Glösenkamp CR, Volk H-D, Goffinet C, Landthaler M, Wyler E, Georg P, Schneider M, Dang-Heine C, Neuwinger N, Kappert K, Tauber R, Corman V, Raabe J, Kaiser KM, Vinh MT, Rieke G, Meisel C, Ulas T, Becker M, Geffers R, Witzenrath M, Drosten C, Suttorp N, von Kalle C, Kurth F, Händler K, Schultze JL, Aschenbrenner AC, Li Y, Nattermann J, Sawitzki B, Saliba A-E, Sander LE, Angelov A, Bals R, Bartholomäus A, Becker A, Bezdan D, Bonifacio E, Bork P, Clavel T, Colome-Tatche M, Diefenbach A, Dilthey A, Fischer N, Förstner K, Frick J-S, Gagneur J, Goesmann A, Hain T, Hummel M, Janssen S, Kalinowski J, Kallies R, Kehr B, Keller A, Kim-Hellmuth S, Klein C, Kohlbacher O, Korbel JO, Kurth I, Landthaler M, Li Y, Ludwig K, Makarewicz O, Marz M, McHardy A, Mertes C, Nöthen M, Nürnberg P, Ohler U, Ossowski S, Overmann J, Peter S, Pfeffer K, Poetsch AR, Pühler A, Rajewsky N, Ralser M, Rieß O, Ripke S, Nunes da Rocha U, Rosenstiel P, Saliba A-E, Sander LE, Sawitzki B, Schiffer P, Schulte E-C, Schultze JL, Sczyrba A, Stegle O, Stoye J, Theis F, Vehreschild J, Vogel J, von Kleist M, Walker A, Walter J, Wieczorek D, Ziebuhr J (2020)
    Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment.
    Cell 182(6): 1419-1440.e23.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [212]
    2020 | Report | PUB-ID: 2944669
    Glöckner FO, Diepenbroek M, Felden J, Güntsch A, Stoye J, Overmann J, Wimmers K, Kostadinov I, Yahyapour R, Müller W, Scholz U, Triebel D, Frenzel M, Gemeinholzer B, Goesmann A, König-Ries B, Bonn A, Seeger B (2020)
    NFDI4BioDiversity - A Consortium for the National Research Data Infrastructure (NFDI) : Proposal.
    Zenodo.
    PUB | DOI
     
  • [211]
    2020 | Journal Article | Published | PUB-ID: 2948972
    Setubal JC, Stoye J, Dutilh BE (2020)
    Editorial: Computational Methods for Microbiome Analysis.
    Frontiers in Genetics 11: 623897.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [210]
    2020 | Preprint | Published | PUB-ID: 2940602
    Haghshenas E, Asghari H, Stoye J, Chauve C, Hach F (2020)
    HASLR: Fast Hybrid Assembly of Long Reads.
    bioRxiv.
    PUB | DOI | Download (ext.) | Preprint
     
  • [209]
    2020 | Preprint | Published | PUB-ID: 2945720
    Schulz T, Wittler R, Rahmann S, Hach F, Stoye J (2020)
    Detecting High Scoring Local Alignments in Pangenome Graphs.
    bioRxiv.
    PUB | DOI | Preprint
     
  • [208]
    2020 | Journal Article | Published | PUB-ID: 2939618 OA
    Alanko J, Bannai H, Cazaux B, Peterlongo P, Stoye J (2020)
    Finding all maximal perfect haplotype blocks in linear time.
    Algorithms for Molecular Biology 15: 2.
    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 (2020)
    HASLR: Fast Hybrid Assembly of Long Reads.
    iScience 23(8): 101389.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [206]
    2020 | Journal Article | Published | PUB-ID: 2939598
    Sevillya G, Dörr D, Lerner Y, Stoye J, Steel M, Snir S (2020)
    Horizontal Gene Transfer Phylogenetics: A Random Walk Approach.
    Molecular Biology and Evolution 37(5): 1470–1479.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [205]
    2020 | Preprint | Published | PUB-ID: 2939861
    Bohnenkämper L, Dias Vieira Braga M, Dörr D, Stoye J (2020)
    Computing the rearrangement distance of natural genomes.
    arXiv:2001.02139.
    PUB | Download (ext.) | arXiv
     
  • [204]
    2020 | Conference Paper | Published | PUB-ID: 2939729
    Bohnenkämper L, Dias Vieira Braga M, Dörr D, Stoye J (2020)
    Computing the rearrangement distance of natural genomes.
    In: Proceedings of RECOMB 2020. LNBI, 12074. 3-18.
    PUB | DOI
     
  • [203]
    2019 | Journal Article | Published | PUB-ID: 2932884
    Oey H, Zakrzewski M, Gravermann K, Young ND, Korhonen PK, Gobert GN, Nawaratna S, Hasan S, Martínez DM, You H, Lavin M, Jones M, Ragan MA, Stoye J, Oleaga A, Emery AM, Webster B, Rollinson D, Gasser RB, McManus DP, Krause L (2019)
    Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium.
    PLOS Pathogens 15(1): e1007513.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [202]
    2019 | Report | Published | PUB-ID: 2939260
    Gagie T, Manzini G, Navarro G, Stoye J (2019)
    25 Years of the Burrows-Wheeler Transform. Report from Dagstuhl Seminar 19241. Dagstuhl Reports; 9(6).
    Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik.
    PUB | DOI
     
  • [201]
    2019 | Conference Paper | Published | PUB-ID: 2937148
    Alanko J, Bannai H, Cazaux B, Peterlongo P, Stoye J (2019)
    Finding All Maximal Perfect Haplotype Blocks in Linear Time.
    In: Proceedings of WABI 2019. Leibniz International Proceedings in Informatics. LIPIcs, 143. Dagstuhl: Schloss Dagstuhl, Leibniz-Zentrum für Informatik : 8:1-8:9.
    PUB | DOI
     
  • [200]
    2019 | Book Chapter | Published | PUB-ID: 2932883
    Dörr D, Stoye J (2019)
    A Perspective on Comparative and Functional Genomics.
    In: Bioinformatics and Phylogenetics. Warnow T (Ed); Computational Biology, 29. Cham: Springer : 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 (2018)
    Computing the family-free DCJ similarity.
    BMC Bioinformatics 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 (2018)
    Flexible metagenome analysis using the MGX framework.
    Microbiome 6(1): 76.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [197]
    2018 | Journal Article | Published | PUB-ID: 2919005 OA
    Schulz T, Stoye J, Dörr D (2018)
    GraphTeams. A method for discovering spatial gene clusters in Hi-C sequencing data.
    BMC Genomics 19(Suppl. 5): 308.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [196]
    2018 | Journal Article | Published | PUB-ID: 2930268
    Holley G, Wittler R, Stoye J, Hach F (2018)
    Dynamic Alignment-Free and Reference-Free Read Compression.
    JOURNAL OF COMPUTATIONAL BIOLOGY 25(7): 825-836.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [195]
    2018 | Book Chapter | Published | PUB-ID: 2913921
    Zekic T, Holley G, Stoye J (2018)
    Pan-genome Storage and Analysis Techniques.
    In: Comparative Genomics. Methods and Protocols. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, 1704. New York: Springer Verlag: 29-53.
    PUB | DOI
     
  • [194]
    2018 | Book Chapter | Published | PUB-ID: 2913922
    Dörr D, Feijão P, Stoye J (2018)
    Family-Free Genome Comparison.
    In: Comparative Genomics: Methods and Protocols. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, 1704. New York: Springer Verlag: 331-342.
    PUB | DOI
     
  • [193]
    2018 | Book (Editor) | Published | PUB-ID: 2913920
    Setubal JC, Stadler P, Stoye J (Eds) (2018)
    Comparative Genomics: Methods and Protocols. Methods in Molecular Biology; 1704.
    New York: Springer Verlag.
    PUB | DOI
     
  • [192]
    2018 | Journal Article | Published | PUB-ID: 2918481
    Luhmann N, Chauve C, Stoye J, Wittler R (2018)
    Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 15(6): 2094-2100.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [191]
    2018 | Conference Paper | Published | PUB-ID: 2930445
    Cunha L, Diekmann Y, Kowada L, Stoye J (2018)
    Identifying Maximal Perfect Haplotype Blocks.
    In: Proceedings of BSB 2018. LNBI, 11228. Springer Verlag: 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 (2017)
    Algorithms for Computing the Family-Free Genomic Similarity under DCJ.
    In: Comparative Genomics. RECOMB-CG 2017. Meidanis J, Nakhleh L (Eds); Lecture Notes in Bioinformatics, 10562. Cham: Springer Verlag: 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 (2017)
    Approximating the DCJ distance of balanced genomes in linear time.
    Algorithms for Molecular Biology 12(1): 3.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [188]
    2017 | Conference Paper | Published | PUB-ID: 2909409
    Cunha L, Dantas S, Gagie T, Wittler R, Kowada L, Stoye J (2017)
    Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings.
    In: Proceedings of CPM 2017. LIPIcs, 78. 19:1-19:9.
    PUB | DOI
     
  • [187]
    2017 | Preprint | Published | PUB-ID: 2908521
    Cunha L, Dantas S, Gagie T, Wittler R, Kowada L, Stoye J (2017)
    Faster Jumbled Indexing for Binary Run-Length Encoded Strings.
    arXiv: 1702.01280.
    PUB | Download (ext.) | arXiv
     
  • [186]
    2017 | Journal Article | Published | PUB-ID: 2913556
    Jünemann S, Kleinbölting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum S, Schlüter A, Goesmann A, Sczyrba A, Stoye J (2017)
    Bioinformatics for NGS-based metagenomics and the application to biogas research.
    Journal of Biotechnology 261(SI): 10-23.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [185]
    2017 | Conference Paper | Published | PUB-ID: 2907587
    Holley G, Wittler R, Stoye J, Hach F (2017)
    Dynamic Alignment-Free and Reference-Free Read Compression.
    In: Proceedings of RECOMB 2017. Lecture Notes in Bioinformatics, 10229. 50-65.
    PUB | DOI
     
  • [184]
    2017 | Conference Paper | Published | PUB-ID: 2913016
    Schulz T, Stoye J, Dörr D (2017)
    Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery.
    In: Proceedings of RECOMB-CG 2017. Lecture Notes in Bioinformatics, 1704. Berlin: Springer Verlag: 197-212.
    PUB | DOI
     
  • [183]
    2017 | Journal Article | Published | PUB-ID: 2909967
    Dörr D, Kowada LAB, Soares de Araujo FE, Deshpande S, Dantas S, Moret BME, Stoye J (2017)
    New Genome Similarity Measures based on Conserved Gene Adjacencies.
    Journal of Computational Biology 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 (2016)
    A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates.
    In: Algorithms in Bioinformatics. WABI 2016. Frith M, Storm Pedersen CN (Eds); Lecture Notes in Bioinformatics, 9838. Cham: Springer: 293-306.
    PUB | DOI
     
  • [181]
    2016 | Journal Article | Published | PUB-ID: 2905930
    Winter S, Jahn K, Wehner S, Kuchenbecker L, Marz M, Stoye J, Böcker S (2016)
    Finding approximate gene clusters with GECKO 3.
    Nucleic Acids Research 44(20): 9600-9610.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [180]
    2016 | Journal Article | Published | PUB-ID: 2900421
    Krause L, Nones K, Loffler KA, Nancarrow D, Oey H, Tang YH, Wayte NJ, Patch AM, Patel K, Brosda S, Manning S, Lampe G, Clouston A, Thomas J, Stoye J, Hussey DJ, Watson DI, Lord RV, Phillips WA, Gotley D, Smithers BM, Whiteman DC, Hayward NK, Grimmond SM, Waddell N, Barbour AP (2016)
    Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma.
    Carcinogenesis 37(4): 356-365.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [179]
    2016 | Journal Article | Published | PUB-ID: 2900129 OA
    Holley G, Wittler R, Stoye J (2016)
    Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage.
    Algorithms for Molecular Biology 11(1): 3.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [178]
    2016 | Conference Paper | Published | PUB-ID: 2900111
    Kowada LAB, Doerr D, Dantas S, Stoye J (2016)
    New Genome Similarity Measures based on Conserved Gene Adjacencies.
    In: Research in Computational Molecular Biology. RECOMB 2016. Singh M (Ed); Lecture Notes in Bioinformatics (LNBI), 9649. Springer: 204-224.
    PUB | DOI
     
  • [177]
    2015 | Conference Paper | Published | PUB-ID: 2757497
    Holley G, Wittler R, Stoye J (2015)
    Bloom Filter Trie - a data structure for pan-genome storage.
    In: Algorithms in Bioinformatics. WABI 2015. Proceedings. Pop M, Touzet H (Eds); Lecture Notes in Computer Science , 9289. Berlin, Heidelberg: Springer: 217-230.
    PUB | DOI
     
  • [176]
    2015 | Journal Article | Published | PUB-ID: 2726366 OA
    Viduani Martinez FH, Feijão P, Dias Vieira Braga M, Stoye J (2015)
    On the family-free DCJ distance and similarity.
    Algorithms for Molecular Biology 10(1): 13.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [175]
    2015 | Journal Article | Published | PUB-ID: 2677844
    Dias Vieira Braga M, Stoye J (2015)
    Sorting linear genomes with rearrangements and indels.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 12(3): 500-506.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [174]
    2015 | Conference (Editor) | Published | PUB-ID: 2780229
    Meidanis J, Stoye J (Eds) (2015)
    Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Bioinformatics.
    BMC Bioinformatics 16(Supplement 14).
    PUB | Download (ext.)
     
  • [173]
    2015 | Conference (Editor) | Published | PUB-ID: 2780232
    Meidanis J, Stoye J (Eds) (2015)
    Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Genomics.
    BMC Genomics 16(Supplement 10).
    PUB | Download (ext.)
     
  • [172]
    2014 | Journal Article | Published | PUB-ID: 2689773
    Jünemann S, Prior K, Albersmeier A, Albaum S, Kalinowski J, Goesmann A, Stoye J, Harmsen D (2014)
    GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers.
    PLOS ONE 9(9): e107014.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [171]
    2014 | Journal Article | Published | PUB-ID: 2685362 OA
    Lechner M, Hernandez-Rosales M, Dörr D, Wieseke N, Thévenin A, Stoye J, Hartmann RK, Prohaska SJ, Stadler PF (2014)
    Orthology Detection Combining Clustering and Synteny for Very Large Datasets.
    PLoS ONE 9(8): e105015.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [170]
    2014 | Conference Paper | Published | PUB-ID: 2684241
    Viduani Martinez FH, Feijão P, Dias Vieira Braga M, Stoye J (2014)
    On the family-free DCJ distance.
    In: Algorithms in Bioinformatics. WABI 2014. Brown D, Morgenstern B (Eds); Lecture Notes in Bioinformatics, 8701. Berlin ; Heidelberg: Springer Verlag: 174-186.
    PUB | DOI
     
  • [169]
    2014 | Journal Article | Published | PUB-ID: 2687033 OA
    Dörr D, Stoye J, Böcker S, Jahn K (2014)
    Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings.
    BMC Genomics 15(Suppl. 6: Proc. of RECOMB-CG 2014): S2.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [168]
    2014 | Journal Article | Published | PUB-ID: 2674387
    Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A (2014)
    ReadXplorer - Visualization and Analysis of Mapped Sequences.
    Bioinformatics 30(16): 2247-2254.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [167]
    2014 | Journal Article | Published | PUB-ID: 2665038
    Schwientek P, Neshat A, Kalinowski J, Klein A, Rückert C, Schneiker-Bekel S, Wendler S, Stoye J, Pühler A (2014)
    Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts.
    Journal of Biotechnology 190: 85-95.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [166]
    2014 | Journal Article | Published | PUB-ID: 2685988
    Jakobi T, Brinkrolf K, Tauch A, Noll T, Stoye J, Pühler A, Goesmann A (2014)
    Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing.
    Journal of Biotechnology 190: 64-75.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [165]
    2014 | Conference Paper | Published | PUB-ID: 2690122
    Luhmann N, Chauve C, Stoye J, Wittler R (2014)
    Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.
    In: Proc. of BSB 2014. Sérgio C (Ed); LNBI, 8826. Springer Verlag: 135-143.
    PUB | DOI
     
  • [164]
    2014 | Encyclopedia Article | Published | PUB-ID: 2693552
    Stoye J (2014)
    Suffix Tree Construction.
    In: Encyclopedia of Algorithms. Kao M-Y (Ed); Springer Verlag.
    PUB | DOI
     
  • [163]
    2014 | Journal Article | Published | PUB-ID: 2643941
    Hoffmann N, Wilhelm M, Doebbe A, Niehaus K, Stoye J (2014)
    BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry.
    Bioinformatics 30(7): 988-995.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [162]
    2014 | Journal Article | Published | PUB-ID: 2693409
    Fredrich E, Ander C, Stoye J, Brune I, Tauch A (2014)
    Metatranskriptomik der Mikrobiota aus der menschlichen Achselhöhle.
    BIOspektrum 20(5): 294-296.
    PUB | DOI
     
  • [161]
    2014 | Journal Article | Published | PUB-ID: 2665333
    Henrich B, Rumming M, Sczyrba A, Velleuer E, Dietrich R, Gerlach W, Gombert M, Rahn S, Stoye J, Borkhardt A, Fischer U (2014)
    Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma.
    PLoS ONE 9(3): e92297.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [160]
    2013 | Journal Article | Published | PUB-ID: 2575011
    Ander C, Schulz-Trieglaff OB, Stoye J, Cox AJ (2013)
    metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences.
    BMC Bioinformatics 14(Suppl 5: Proc. of RECOMB-Seq 2013): S2.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [159]
    2013 | Encyclopedia Article | Published | PUB-ID: 2577323
    Gerlach W, Stoye J (2013)
    Taxonomic classification of metagenomic shotgun sequences with CARMA3.
    In: Encyclopedia of Metagenomics. Nelson KE (Ed); Springer Verlag.
    PUB | DOI
     
  • [158]
    2013 | Journal Article | Published | PUB-ID: 2611630 OA
    Willing E, Zaccaria S, Dias Vieira Braga M, Stoye J (2013)
    On the Inversion-Indel Distance.
    BMC Bioinformatics 14(Suppl 15: Proc. of RECOMB-CG 2013): S3.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [157]
    2013 | Conference Paper | Published | PUB-ID: 2611641
    Dias Vieira Braga M, Stoye J (2013)
    Restricted DCJ-Indel Model Revisited.
    In: Advances in Bioinformatics and Computational Biology. BSB 2013. Setubal JC, Almeida NF (Eds); Lecture Notes in Bioinformatics, 8213. Cham: Springer Verlag: 36-46.
    PUB | DOI
     
  • [156]
    2013 | Book Chapter | Published | PUB-ID: 2611648
    Dias Vieira Braga M, Chauve C, Dörr D, Jahn K, Stoye J, Thévenin A, Wittler R (2013)
    The Potential of Family-Free Genome Comparison.
    In: Models and Algorithms for Genome Evolution. Chauve C, El-Mabrouk N, Tannier E (Eds); Computational Biology Series, 19. London: Springer Verlag: 287-307.
    PUB | DOI
     
  • [155]
    2013 | Journal Article | Published | PUB-ID: 2641228
    Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D (2013)
    Corrigendum: Updating benchtop sequencing performance comparison.
    Nature biotechnology 31(12): 1148.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [154]
    2013 | Book Chapter | Published | PUB-ID: 2611643
    Bergeron A, Stoye J (2013)
    The Genesis of the DCJ Formula.
    In: Models and Algorithms for Genome Evolution. Chauve C, El-Mabrouk N, Tannier E (Eds); Computational Biology Series, 19. London: Springer Verlag: 63-81.
    PUB | DOI
     
  • [153]
    2013 | Journal Article | Published | PUB-ID: 2575361
    Krell P, Reuther S, Fischer U, Keller T, Weber S, Gombert M, Schuster FR, Asang C, Stepensky P, Strahm B, Meisel R, Stoye J, Borkhardt A (2013)
    Next-generation-sequencing-spectratyping reveals public T-cell receptor repertoires in pediatric very severe aplastic anemia and identifies a beta chain CDR3 sequence associated with hepatitis-induced pathogenesis.
    Haematologica 98(9): 1388-1396.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [152]
    2013 | Journal Article | Published | PUB-ID: 2566922
    Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D (2013)
    Updating benchtop sequencing performance comparison.
    Nature Biotechnology 31(4): 294-296.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [151]
    2013 | Conference (Editor) | Published | PUB-ID: 2616537
    Darling A, Stoye J (Eds) (2013)
    Algorithms in Bioinformatics.
    Lecture Notes in Bioinformatics 8126.
    PUB | DOI
     
  • [150]
    2013 | Journal Article | Published | PUB-ID: 2611633 OA
    Jahn K, Winter S, Stoye J, Böcker S (2013)
    Statistics for approximate gene clusters.
    BMC Bioinformatics 14(Suppl 15: Proc. of RECOMB-CG 2013): S14.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [149]
    2013 | Journal Article | Published | PUB-ID: 2548236
    Schwientek P, Wendler S, Neshat A, Eirich C, Rückert C, Klein A, Wehmeier UF, Kalinowski J, Stoye J, Pühler A (2013)
    Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media.
    Journal of Biotechnology 167(2): 166-177.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [148]
    2013 | Journal Article | Published | PUB-ID: 2529202
    Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A (2013)
    MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets.
    Journal of Biotechnology 167(2): 156-165.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [147]
    2012 | Journal Article | Published | PUB-ID: 2517230
    Jünemann S, Prior K, Szczepanowski R, Harks I, Ehmke B, Goesmann A, Stoye J, Harmsen D (2012)
    Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing.
    PLoS ONE 7(8): e41606.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [146]
    2012 | Journal Article | Published | PUB-ID: 2512642 OA
    Dörr D, Thévenin A, Stoye J (2012)
    Gene family assignment-free comparative genomics.
    BMC Bioinformatics 13(Suppl 19: Proc. of RECOMB-CG 2012): S3.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [145]
    2012 | Journal Article | Published | PUB-ID: 2517239 OA
    Hoffmann N, Keck M, Neuweger H, Wilhelm M, Högy P, Niehaus K, Stoye J (2012)
    Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets.
    BMC Bioinformatics 13(1): 21.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [144]
    2012 | Journal Article | Published | PUB-ID: 2512644 OA
    Jahn K, Sudek H, Stoye J (2012)
    Multiple genome comparison based on overlap regions of pairwise local alignments.
    BMC Bioinformatics 13(Suppl. 19: Proc. of RECOMB-CG 2012): S7.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [143]
    2012 | Journal Article | Published | PUB-ID: 2486060 OA
    Schwientek P, Szczepanowski R, Rückert C, Kalinowski J, Klein A, Selber K, Wehmeier UF, Stoye J, Pühler A (2012)
    The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110.
    BMC Genomics 13(1): 112.
    PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [142]
    2012 | Conference (Editor) | Published | PUB-ID: 2510416
    Kärkkäinen J, Stoye J (Eds) (2012)
    Combinatorial Pattern Matching.
    Lecture Notes in Computer Science 7354.
    PUB | DOI
     
  • [141]
    2012 | Book Chapter | Published | PUB-ID: 2468382 OA
    Hoffmann N, Stoye J (2012)
    Generic Software Frameworks for GC-MS Based Metabolomics.
    In: Metabolomics. Roessner U (Ed); InTech: 73-98.
    PUB | PDF | DOI | Download (ext.)
     
  • [140]
    2012 | Journal Article | Published | PUB-ID: 2510984
    Hilker R, Sickinger C, Pedersen CNS, Stoye J (2012)
    UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ.
    Bioinformatics 28(19): 2509-2511.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [139]
    2011 | Journal Article | Published | PUB-ID: 2091779
    Hufsky F, Kuchenbecker L, Jahn K, Stoye J, Böcker S (2011)
    Swiftly Computing Center Strings.
    BMC Bioinformatics 12(1): 106.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [138]
    2011 | Journal Article | Published | PUB-ID: 2396509 OA
    Dias Vieira Braga M, Machado R, Ribeiro LC, Stoye J (2011)
    Genomic distance under gene substitutions.
    BMC Bioinformatics 12(Suppl 9: Proc. of RECOMB-CG 2011): S8.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [137]
    2011 | Journal Article | Published | PUB-ID: 2396558 OA
    Dias Vieira Braga M, Machado R, Ribeiro LC, Stoye J (2011)
    On the weight of indels in genomic distances.
    BMC Bioinformatics 12(Suppl 9: RECOMB-CG 2011): S13.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [136]
    2011 | Journal Article | Published | PUB-ID: 1897974
    Erdős PL, Soukup L, Stoye J (2011)
    Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance.
    Applied Mathematics Letters 24(1): 82-86.
    PUB | DOI | WoS | arXiv
     
  • [135]
    2011 | Journal Article | Published | PUB-ID: 2091794
    Dias Vieira Braga M, Willing E, Stoye J (2011)
    Double Cut and Join with Insertions and Deletions.
    Journal of Computational Biology 18(9): 1167-1184.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [134]
    2011 | Journal Article | Published | PUB-ID: 2091790
    Kovac J, Warren R, Dias Vieira Braga M, Stoye J (2011)
    Restricted DCJ Model. Rearrangement Problems with Chromosome Reincorporation.
    Journal of Computational Biology 18(9): 1231-1241.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [133]
    2011 | Journal Article | Published | PUB-ID: 2354746
    Schwientek P, Szczepanowski R, Rückert C, Stoye J, Pühler A (2011)
    Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology.
    Journal of Biotechnology 155(1): 68-77.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [132]
    2011 | Journal Article | Published | PUB-ID: 2289952
    Blom J, Jakobi T, Doppmeier D, Jaenicke S, Kalinowski J, Stoye J, Goesmann A (2011)
    Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming.
    Bioinformatics 27(10): 1351-1358.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [131]
    2011 | Journal Article | Published | PUB-ID: 1918550
    Heber S, Mayr R, Stoye J (2011)
    Common Intervals of Multiple Permutations.
    Algorithmica 60(2): 175-206.
    PUB | DOI | WoS
     
  • [130]
    2011 | Journal Article | Published | PUB-ID: 2298170 OA
    Gerlach W, Stoye J (2011)
    Taxonomic classification of metagenomic shotgun sequences with CARMA3.
    Nucleic Acids Res 39(14): e91.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [129]
    2011 | Journal Article | Published | PUB-ID: 2091787
    Wittler R, Maňuch J, Patterson M, Stoye J (2011)
    Consistency of Sequence-Based Gene Clusters.
    Journal of Computational Biology 18(9): 1023-1039.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [128]
    2010 | Conference Paper | Published | PUB-ID: 1919211
    Hufsky F, Kuchenbecker L, Jahn K, Stoye J, Böcker S (2010)
    Swiftly Computing Center Strings.
    In: Proc. of WABI 2010. LNBI, 6293. 325-336.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [127]
    2010 | Journal Article | Published | PUB-ID: 1966439
    Trost E, Ott L, Schneider J, Schröder J, Jaenicke S, Goesmann A, Husemann P, Stoye J, Alves Dorella F, Souza Rocha F, de Castro Soares S, D'Afonseca V, Miyoshi A, Ruiz J, Silva A, Azevedo V, Burkovski A, Guiso N, Join-Lambert OF, Kayal S, Tauch A (2010)
    The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence.
    BMC Genomics 11(1): 728.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [126]
    2010 | Conference Abstract / Poster | Published | PUB-ID: 2445157
    Bergeron A, Mixtacki J, Stoye J (2010)
    Computing the Genomic Distance in Linear Time.
    In: Dagstuhl Seminar Proceedings: 10231 Abstracts Collection : Structure Discovery in Biology: Motifs, Networks & Phylogenies. Apostolico A, Dress A, Parida L (Eds);10231. Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik: 18.
    PUB | Download (ext.)
     
  • [125]
    2010 | Conference Abstract / Poster | Published | PUB-ID: 2907492
    Bergeron A, Mixtacki J, Stoye J (2010)
    A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance.
    In: Structure Discovery in Biology: Motifs, Networks & Phylogenies. Apostolico A, Dress A, Parida L, Schloss Dagstuhl, Leibniz-Zentrum für Informatik (Eds); Dagstuhl Seminar Proceedings, 10231. Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany: Online-Ressource.
    PUB | Download (ext.)
     
  • [124]
    2010 | Journal Article | Published | PUB-ID: 1893893 OA
    Husemann P, Stoye J (2010)
    Phylogenetic Comparative Assembly.
    Algorithms for Molecular Biology 5(1): 3.
    PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [123]
    2010 | Book Chapter | Published | PUB-ID: 1918836
    Besenbacher S, Schwikowski B, Stoye J (2010)
    Indexing and Searching a Mass Spectrometry Database.
    In: Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday. Elomaa T, Mannila H, Orponen P (Eds); LNCS, 6060. Berlin, Heidelberg: Springer Berlin Heidelberg: 62-76.
    PUB | DOI
     
  • [122]
    2010 | Journal Article | Published | PUB-ID: 1795670
    Wittkop T, Emig D, Lange SJ, Rahmann S, Albrecht M, Morris JH, Böcker S, Stoye J, Baumbach J (2010)
    Partitioning Biological Data with Transitivity Clustering.
    Nature Methods 7(6): 419-420.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [121]
    2010 | Journal Article | Published | PUB-ID: 1898012
    Blin G, Faye D, Stoye J (2010)
    Finding Nested Common Intervals Efficiently.
    Journal of Computational Biology 17(9): 1183-1194.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [120]
    2010 | Conference Paper | Published | PUB-ID: 1919217
    Wittler R, Stoye J (2010)
    Consistency of Sequence-based Gene Clusters.
    In: Proc. of Recomb-CG 2010. LNBI, 6398. Springer Verlag: 252-263.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [119]
    2010 | Conference Paper | Published | PUB-ID: 1893890
    Husemann P, Stoye J (2010)
    Repeat-aware Comparative Genome Assembly.
    In: Proc. of GCB 2010. LNI, P-173. 61-70.
    PUB | Download (ext.)
     
  • [118]
    2010 | Journal Article | Published | PUB-ID: 1588556
    Husemann P, Stoye J (2010)
    r2cat: Synteny Plots and Comparative Assembly.
    Bioinformatics 26(4): 570-571.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [117]
    2010 | Journal Article | Published | PUB-ID: 1897997
    Bergeron A, Medvedev P, Stoye J (2010)
    Rearrangement Models and Single-Cut Operations.
    Journal of Computational Biology 17(9): 1213-1225.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [116]
    2010 | Conference Paper | Published | PUB-ID: 1919216
    Kovac J, Dias Vieira Braga M, Stoye J (2010)
    The Problem of Chromosome Reincorporation in DCJ Sorting and Halving.
    In: Proc. of Recomb-CG 2010. LNBI, 6398. 13-24.
    PUB | DOI
     
  • [115]
    2010 | Journal Article | Published | PUB-ID: 1898025
    Dias Vieira Braga M, Stoye J (2010)
    The Solution Space of Sorting by DCJ.
    Journal of Computational Biology 17(9): 1145-1165.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [114]
    2010 | Conference Paper | Published | PUB-ID: 1919215
    Dias Vieira Braga M, Willing E, Stoye J (2010)
    Genomic Distance with DCJ and Indels.
    In: Proc. of WABI 2010. LNBI, 6293. 90-101.
    PUB | DOI
     
  • [113]
    2009 | Conference Paper | Published | PUB-ID: 1893884
    Husemann P, Stoye J (2009)
    Phylogenetic Comparative Assembly.
    In: Proc. of WABI 2009. LNBI, 5724. 145-156.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [112]
    2009 | Journal Article | Published | PUB-ID: 1589663
    Bergeron A, Mixtacki J, Stoye J (2009)
    A New Linear Time Algorithm to Compute the Genomic Distance via the Double Cut and Join Distance.
    Theoretical Computer Science 410(51): 5300-5316.
    PUB | DOI | WoS
     
  • [111]
    2009 | Conference Paper | Published | PUB-ID: 1919206
    Dias Vieira Braga M, Stoye J (2009)
    Counting All DCJ Sorting Scenarios.
    In: Proc. of Recomb-CG 2009. LNBI, 5817. 36-47.
    PUB | DOI
     
  • [110]
    2009 | Conference Paper | Published | PUB-ID: 1919207
    Blin G, Stoye J (2009)
    Finding Nested Common Intervals Efficiently.
    In: Proc. of Recomb-CG 2009. LNBI, 5817. 59-69.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [109]
    2009 | Journal Article | Published | PUB-ID: 1898137
    Jahn K, Stoye J (2009)
    Approximative Gencluster und ihre Anwendung in der komparativen Genomik.
    Informatik-Spektrum 32(4): 288-300.
    PUB | DOI
     
  • [108]
    2009 | Journal Article | Published | PUB-ID: 1591507
    Stoye J, Wittler R (2009)
    A Unified Approach for Reconstructing Ancient Gene Clusters.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 6(3): 387-400.
    PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
     
  • [107]
    2009 | Journal Article | Published | PUB-ID: 1590204
    Brudno M, Medvedev P, Stoye J, De La Vega FM (2009)
    A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG).
    BIOINFORMATICS 25(21): 2863-2864.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [106]
    2009 | Journal Article | Published | PUB-ID: 1589098 OA
    Gerlach W, Jünemann S, Tille F, Goesmann A, Stoye J (2009)
    WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads.
    BMC Bioinformatics 10(1): 430.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [105]
    2009 | Journal Article | Published | PUB-ID: 1898105
    Böcker S, Jahn K, Mixtacki J, Stoye J (2009)
    Computation of Median Gene Clusters.
    Journal of Computational Biology 16(8): 1085-1099.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [104]
    2009 | Journal Article | Published | PUB-ID: 1591319
    Hoffmann N, Stoye J (2009)
    ChromA: signal-based retention time alignment for chromatography-mass spectrometry data.
    Bioinformatics 25(16): 2080-2081.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [103]
    2009 | Conference Paper | Published | PUB-ID: 1919209
    Medvedev P, Stoye J (2009)
    Rearrangement Models and Single-Cut Operations.
    In: Comparative Genomics : International Workshop, RECOMB-CG 2009, Budapest, Hungary, September 27-29, 2009. Proceedings. Lecture Notes in Computer Science, 5817. Berlin, Heidelberg: Springer: 84-97.
    PUB | DOI
     
  • [102]
    2009 | Conference Abstract / Poster | Published | PUB-ID: 1918945
    Stoye J (2009)
    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, Meyer F, Mittard-Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, Goesmann A (2009)
    The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies.
    Journal of Biotechnology 140(1-2): 3-12.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [100]
    2008 | Conference Paper | Published | PUB-ID: 1919198
    Quitzau JAA, Stoye J (2008)
    Detecting Repeat Families in Incompletely Sequenced Genomes.
    In: Proc. of WABI 2008. LNBI, 5251. 342-353.
    PUB | DOI
     
  • [99]
    2008 | Report | PUB-ID: 1970459 OA
    Quitzau JAA, Stoye J (2008)
    A space efficient representation for sparse de Bruijn subgraphs. Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld.
    Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [98]
    2008 | Report | PUB-ID: 1970461 OA
    Ejaz T, Rahmann S, Stoye J (2008)
    Online Abelian Pattern Matching. Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld.
    Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [97]
    2008 | Journal Article | Published | PUB-ID: 1636699
    Neuweger H, Albaum S, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A (2008)
    MeltDB: a software platform for the analysis and integration of metabolomics experiment data.
    Bioinformatics 24(23): 2726-2732.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [96]
    2008 | Encyclopedia Article | Published | PUB-ID: 1918834
    Stoye J (2008)
    Suffix Tree Construction in RAM (1997; Farach-Colton).
    In: Encyclopedia of Algorithms. Kao M-Y (Ed); Springer Verlag: 925-928.
    PUB | DOI
     
  • [95]
    2008 | Conference Paper | Published | PUB-ID: 1919192
    Böcker S, Jahn K, Mixtacki J, Stoye J (2008)
    Computation of Median Gene Clusters.
    In: Proc. of RECOMB 2008. LNBI, 4955. 331-345.
    PUB | DOI
     
  • [94]
    2008 | Conference Paper | Published | PUB-ID: 1919200
    Bergeron A, Mixtacki J, Stoye J (2008)
    On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios.
    In: Proc. of Recomb-CG 2008. LNBI, 5267. 226-240.
    PUB | DOI
     
  • [93]
    2008 | Journal Article | Published | PUB-ID: 1587078
    Schürmann K-B, Stoye J (2008)
    Counting suffix arrays and strings.
    THEORETICAL COMPUTER SCIENCE 395(2-3): 220-234.
    PUB | DOI | WoS
     
  • [92]
    2008 | Journal Article | Published | PUB-ID: 1586009
    Krause L, Diaz NN, Edwards RA, Gartemann K-H, Krömeke H, Neuweger H, Pühler A, Runte KJ, Schlüter A, Stoye J, Szczepanowski R, Tauch A, Goesmann A (2008)
    Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor.
    JOURNAL OF BIOTECHNOLOGY 136(1-2): 91-101.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [91]
    2008 | Journal Article | Published | PUB-ID: 1586785 OA
    Oehm S, Gilbert D, Tauch A, Stoye J, Goesmann A (2008)
    Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms.
    NUCLEIC ACIDS RESEARCH 36(Web Server): W433-W437.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [90]
    2008 | Journal Article | Published | PUB-ID: 1783364 OA
    Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J (2008)
    Phylogenetic classification of short environmental DNA fragments.
    Nucleic Acids Research 36(7): 2230-2239.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [89]
    2008 | Conference Paper | Published | PUB-ID: 1919195
    Bergeron A, Mixtacki J, Stoye J (2008)
    HP Distance via Double Cut and Join Distance.
    In: Combinatorial Pattern Matching. 19th Annual Symposium, CPM 2008, Pisa, Italy, June 18-20, 2008 Proceedings. Lecture Notes in Computer Science, 5029, 56-68.
    PUB | DOI
     
  • [88]
    2007 | Journal Article | Published | PUB-ID: 1630781
    Mellmann A, Weniger T, Berssenbrügge C, Rothgänger J, Sammeth M, Stoye J, Harmsen D (2007)
    Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms.
    BMC MICROBIOLOGY 7(1): 98.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [87]
    2007 | Book Chapter | Published | PUB-ID: 1918828
    Schmidt T, Stoye J (2007)
    Chapter 12: Gecko and GhostFam - Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes.
    In: Comparative Genomics, Volume 2. Bergman NH (Ed); Methods in Molecular Biology, 396. Totowa, NJ: Humana Press Inc.: 165-182.
    PUB | DOI | PubMed | Europe PMC
     
  • [86]
    2007 | Journal Article | Published | PUB-ID: 1918432
    Didier G, Schmidt T, Stoye J, Tsur D (2007)
    Character Sets of Strings.
    Journal of Discrete Algorithms 5(2): 330-340.
    PUB | DOI
     
  • [85]
    2007 | Journal Article | Published | PUB-ID: 1595253
    Schürmann K-B, Stoye J (2007)
    An incomplex algorithm for fast suffix array construction.
    SOFTWARE-PRACTICE & EXPERIENCE 37(3): 309-329.
    PUB | DOI | WoS
     
  • [84]
    2007 | Journal Article | Published | PUB-ID: 1783345 OA
    Krause L, McHardy AC, Nattkemper TW, Pühler A, Stoye J, Meyer F (2007)
    GISMO - gene identification using a support vector machine for ORF classification.
    Nucleic Acids Research 35(2): 540-549.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [83]
    2006 | Journal Article | Published | PUB-ID: 1599943
    Sammeth M, Griebel T, Tille F, Stoye J (2006)
    Panta rhei (QAlign2): an open graphical environment for sequence analysis.
    BIOINFORMATICS 22(7): 889-890.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [82]
    2006 | Journal Article | Published | PUB-ID: 1599570
    Rasmussen KR, Stoye J, Myers EW (2006)
    Efficient q-gram filters for finding all epsilon-matches over a given length.
    JOURNAL OF COMPUTATIONAL BIOLOGY 13(2): 296-308.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [81]
    2006 | Journal Article | Published | PUB-ID: 1599574
    Bergeron A, Mixtacki J, Stoye J (2006)
    On sorting by translocations.
    JOURNAL OF COMPUTATIONAL BIOLOGY 13(2): 567-578.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [80]
    2006 | Conference Paper | Published | PUB-ID: 1596811
    Bergeron A, Mixtacki J, Stoye J (2006)
    A Unifying View of Genome Rearrangements.
    In: Proc. of WABI 2006. LNBI, 4175. SPRINGER-VERLAG BERLIN: 163-173.
    PUB | DOI | WoS
     
  • [79]
    2006 | Journal Article | Published | PUB-ID: 1597213
    Sammeth M, Stoye J (2006)
    Comparing tandem repeats with duplications and excisions of variable degree.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 3(4): 395-407.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [78]
    2006 | Journal Article | Published | PUB-ID: 1597313
    Bergeron A, Stoye J (2006)
    On the similarity of sets of permutations and its applications to genome comparison.
    JOURNAL OF COMPUTATIONAL BIOLOGY 13(7): 1340-1354.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [77]
    2006 | Conference Abstract / Poster | Published | PUB-ID: 1918946
    Stoye J (2006)
    Index Structures in Biological Sequence Analysis: From Simplicity to Complexity and Back.
    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 (2006)
    On Common Intervals with Errors. Forschungsberichte.
    Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [75]
    2006 | Journal Article | Published | PUB-ID: 1631957
    Krause L, Diaz NN, Bartels D, Edwards RA, Pühler A, Rohwer F, Meyer F, Stoye J (2006)
    Finding novel genes in bacterial communities isolated from the environment.
    BIOINFORMATICS 22(14): e281-e289.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [74]
    2005 | Report | PUB-ID: 1970470 OA
    Sammeth M, Stoye J (2005)
    Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). Forschungsberichte.
    Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF | DOI
     
  • [73]
    2005 | Conference Paper | Published | PUB-ID: 1919012
    Schürmann K-B, Stoye J (2005)
    An Incomplex Algorithm for Fast Suffix Array Construction.
    In: Proc. of ALENEX/ANALCO 2005. 77-85.
    PUB
     
  • [72]
    2005 | Book Chapter | Published | PUB-ID: 1918824
    Bergeron A, Mixtacki J, Stoye J (2005)
    Chapter 10: The Inversion Distance Problem.
    In: Mathematics of Evolution and Phylogeny. Gascuel O (Ed); Oxford University Press: 262-290.
    PUB
     
  • [71]
    2005 | Conference Paper | Published | PUB-ID: 1603220
    Bergeron A, Mixtacki J, Stoye J (2005)
    On Sorting by Translocations.
    In: Proc. of RECOMB 2005. LNBI, 3500. SPRINGER-VERLAG BERLIN: 615-629.
    PUB | DOI | WoS
     
  • [70]
    2005 | Journal Article | Published | PUB-ID: 1775168 OA
    Krause A, Stoye J, Vingron M (2005)
    Large scale hierarchical clustering of protein sequences.
    BMC Bioinformatics 6(1): 15.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [69]
    2005 | Journal Article | Published | PUB-ID: 1773302 OA
    Bartels D, Kespohl S, Albaum S, Drüke T, Goesmann A, Herold J, Kaiser O, Pühler A, Pfeiffer F, Raddatz G, Stoye J, Meyer F, Schuster SC (2005)
    BACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.
    Bioinformatics 21(7): 853-859.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [68]
    2005 | Journal Article | Published | PUB-ID: 1918947
    Böcker S, Stoye J (2005)
    Informatische Methoden zur Protein-Identifikation.
    LaborPraxis 29(10): 24-26.
    PUB
     
  • [67]
    2005 | Conference Paper | Published | PUB-ID: 1601348
    Bannert C, Stoye J (2005)
    Protein Annotation by Secondary Structure Based Alignments (PASSTA).
    In: Proc. of CompLife 2005. LNBI, 3695. Springer-Verlag: 79-90.
    PUB | DOI | WoS
     
  • [66]
    2005 | Conference Paper | Published | PUB-ID: 1601361
    Sammeth M, Weniger T, Harmsen D, Stoye J (2005)
    Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI).
    In: Proc. of WABI 2005. LNBI, 3692. SPRINGER-VERLAG BERLIN: 276-290.
    PUB | DOI | WoS
     
  • [65]
    2005 | Conference Paper | Published | PUB-ID: 1603216
    Rasmussen KR, Stoye J, Myers EW (2005)
    Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length.
    In: Proc. of RECOMB 2005. LNBI, 3500. SPRINGER-VERLAG BERLIN: 189-203.
    PUB | DOI | WoS
     
  • [64]
    2005 | Conference Paper | Published | PUB-ID: 1919026
    Schürmann K-B, Stoye J (2005)
    Counting Suffix Arrays and Strings.
    In: Proc. of SPIRE 2005. LNCS, 3772. 55-66.
    PUB | DOI
     
  • [63]
    2005 | Report | PUB-ID: 1970472 OA
    Schürmann K-B, Stoye J (2005)
    Counting Suffix Arrays and Strings. Forschungsberichte.
    Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [62]
    2004 | Conference (Editor) | Published | PUB-ID: 1918823
    Giegerich R, Stoye J (Eds) (2004)
    Proceedings of the German Conference on Bioinformatics, GCB 2004.
    Lecture Notes in Informatics P-53: 234.
    PUB
     
  • [61]
    2004 | Conference Paper | Published | PUB-ID: 1606286
    Michael M, Dieterich C, Stoye J (2004)
    Suboptimal Local Alignments across Multiple Scoring Schemes.
    In: Proc. of WABI 2004. LNBI, 3240. SPRINGER-VERLAG BERLIN: 99-110.
    PUB | DOI | WoS
     
  • [60]
    2004 | Conference Paper | Published | PUB-ID: 1607260
    Schmidt T, Stoye J (2004)
    Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences.
    In: Proc. of CPM 2004. LNCS, 3109. 347-358.
    PUB | DOI | WoS
     
  • [59]
    2004 | Journal Article | Published | PUB-ID: 1773554 OA
    Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB (2004)
    Correction: Benchmarking tools for the alignment of functional noncoding DNA.
    BMC Bioinformatics 5(1): 73.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [58]
    2004 | Journal Article | Published | PUB-ID: 1773560 OA
    Cieliebak M, Erlebach T, Lipták Z, Stoye J, Welzl E (2004)
    Algorithmic complexity of protein identification: combinatorics of weighted strings.
    Discrete Applied Mathematics 137(1): 27-46.
    PUB | PDF | DOI | WoS
     
  • [57]
    2004 | Journal Article | Published | PUB-ID: 1773312 OA
    Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB (2004)
    Benchmarking tools for the alignment of functional noncoding DNA.
    BMC Bioinformatics 5(1): 6.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [56]
    2004 | Journal Article | Published | PUB-ID: 1773569 OA
    Gusfield D, Stoye J (2004)
    Linear time algorithms for finding and representing all the tandem repeats in a string.
    Journal of computer and system sciences 69(4): 525-546.
    PUB | PDF | DOI | WoS
     
  • [55]
    2004 | Conference Paper | Published | PUB-ID: 1607263
    Bergeron A, Mixtacki J, Stoye J (2004)
    Reversal Distance without Hurdles and Fortresses.
    In: Proc. of CPM 2004. LNCS, 3109. SPRINGER-VERLAG BERLIN: 388-399.
    PUB | DOI | WoS
     
  • [54]
    2003 | Report | PUB-ID: 1970475 OA
    Schürmann K-B, Stoye J (2003)
    Suffix Tree Construction and Storage with Limited Main Memory. Forschungsberichte.
    Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [53]
    2003 | Journal Article | Published | PUB-ID: 1612664
    Heber S, Stoye J (2003)
    The European Conference on Computational Biology.
    Drug Discovery Today 8(3): 113-114.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [52]
    2003 | Journal Article | Published | PUB-ID: 1918949
    Giegerich R, Stoye J (2003)
    Finden, fast ohne zu suchen: Indexstrukturen in der Bioinformatik.
    Forschung an der Universität Bielefeld 26: 63-68.
    PUB
     
  • [51]
    2003 | Conference Paper | Published | PUB-ID: 1919005
    Bannert C, Stoye J (2003)
    Evaluation of the Jumping Alignment Algorithm with Artificial and Biological Data.
    In: Proc. of GCB 2003. 21-25.
    PUB
     
  • [50]
    2003 | Journal Article | Published | PUB-ID: 1610397 OA
    Giegerich R, Kurtz S, Stoye J (2003)
    Efficient implementation of lazy suffix trees.
    SOFTWARE-PRACTICE & EXPERIENCE 33(11): 1035-1049.
    PUB | PDF | DOI | WoS
     
  • [49]
    2003 | Journal Article | Published | PUB-ID: 1609403 OA
    Sammeth M, Morgenstern B, Stoye J (2003)
    Divide-and-conquer multiple alignment with segment-based constraints.
    BIOINFORMATICS 19(Suppl 2): ii189-ii195.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [48]
    2003 | Conference Paper | Published | PUB-ID: 1610433
    Bergeron A, Stoye J (2003)
    On the similarity of sets of permutations and its applications to genome comparison.
    In: Proc. of COCOON 2003. LNCS, 2697. 68-79.
    PUB | DOI | WoS
     
  • [47]
    2003 | Journal Article | Published | PUB-ID: 1610503 OA
    Sammeth M, Rothgänger J, Esser W, Albert J, Stoye J, Harmsen D (2003)
    QAlign: quality-based multiple alignments with dynamic phylogenetic analysis.
    BIOINFORMATICS 19(12): 1592-1593.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [46]
    2003 | Report | PUB-ID: 1970477 OA
    Bergeron A, Stoye J (2003)
    On the Similarity of Sets of Permutations and its Applications to Genome Comparison. Forschungsberichte.
    Bielefeld: Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [45]
    2002 | Conference Abstract / Poster | Published | PUB-ID: 1918951
    Stoye J (2002)
    Index Structures for Large Sequence Data: Suffix Trees and Affix Trees.
    In: Lecture Notes in Informatics. Schubert S, Reusch B, Jesse N (Eds);P-20. 67-67.
    PUB
     
  • [44]
    2002 | Conference Paper | Published | PUB-ID: 1919000
    Cieliebak M, Lipták Z, Welzl E, Erlebach T, Stoye J (2002)
    Algorithmic Complexity of Protein Identification: Searching in Weighted Strings.
    In: Proc. of IFIP TCS 2002. 143-156.
    PUB
     
  • [43]
    2002 | Journal Article | Published | PUB-ID: 1773578 OA
    Spang R, Rehmsmeier M, Stoye J (2002)
    A novel approach to remote homology detection: jumping alignments.
    Journal of Computational Biology 9(5): 747-760.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [42]
    2002 | Journal Article | Published | PUB-ID: 1773332 OA
    Stoye J, Gusfield D (2002)
    Simple and flexible detection of contiguous repeats using a suffix tree.
    Theoretical Computer Science 270(1-2): 843-856.
    PUB | PDF | DOI | WoS
     
  • [41]
    2002 | Journal Article | Published | PUB-ID: 1773329 OA
    Bergeron A, Heber S, Stoye J (2002)
    Common intervals and sorting by reversals: a marriage of necessity.
    Bioinformatics 18(Suppl 2): S54-S63.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [40]
    2002 | Conference Paper | Published | PUB-ID: 1918995
    Heber S, Stoye J, Frohme M, Hoheisel J, Vingron M (2002)
    Resampling Methods in Physical Mapping.
    In: Proc. of GfKl 2000. 437-444.
    PUB
     
  • [39]
    2001 | Journal Article | Published | PUB-ID: 1773335 OA
    Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001)
    REPuter: the manifold applications of repeat analysis on a genomic scale.
    Nucleic Acids Research 29(22): 4633-4642.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [38]
    2001 | Conference Paper | Published | PUB-ID: 1918992
    Heber S, Stoye J (2001)
    Finding all Common Intervals of k Permutations.
    In: Proc. of CPM 2001. LNCS, 2089. 207-218.
    PUB | DOI
     
  • [37]
    2001 | Conference Paper | Published | PUB-ID: 1880197
    Heber S, Stoye J (2001)
    Algorithms for Finding Gene Clusters.
    In: Proc. of WABI 2001. LNCS, 2149. Berlin: Sppringer: 252-263.
    PUB | DOI
     
  • [36]
    2001 | Report | PUB-ID: 1970479
    Cieliebak M, Erlebach T, Lipták Z, Stoye J, Welzl E (2001)
    Algorithmic Complexity of Protein Identification: Combinatorics of Weighted Strings. Technical Report.
    ETH Zürich, Dept. of Computer Science.
    PUB
     
  • [35]
    2000 | Conference Paper | Published | PUB-ID: 1918981
    Heber S, Stoye J, Hoheisel J, Vingron M (2000)
    Contig Selection in Physical Mapping.
    In: Proc. of RECOMB 2000. 155-164.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [34]
    2000 | Book Chapter | Published | PUB-ID: 1918817
    Brodal GS, Lyngsø RB, Pedersen CNS, Stoye J (2000)
    Finding Maximal Pairs with Bounded Gap.
    In: Matching Patterns (Journal of Discrete Algorithms). Crochemore M, Gąsieniec L (Eds); 77-104.
    PUB
     
  • [33]
    2000 | Journal Article | Published | PUB-ID: 1773345 OA
    Krause A, Stoye J, Vingron M (2000)
    The SYSTERS protein sequence cluster set.
    Nucleic Acids Research 28(1): 270-272.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [32]
    2000 | Journal Article | Published | PUB-ID: 1773572 OA
    Heber S, Stoye J, Frohme M, Hoheisel J, Vingron M (2000)
    Contig selection in physical mapping.
    Journal of Computational Biology 7(3-4): 395-408.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [31]
    2000 | Conference Paper | Published | PUB-ID: 1918985
    Spang R, Rehmsmeier M, Stoye J (2000)
    Sequence Database Search Using Jumping Alignments.
    In: Proc. of ISMB 2000. 367-375.
    PUB | PubMed | Europe PMC
     
  • [30]
    2000 | Report | PUB-ID: 1970490 OA
    Stoye J (2000)
    Affix Trees. Forschungsberichte.
    Technische Fakultät der Universität Bielefeld.
    PUB | PDF
     
  • [29]
    2000 | Journal Article | Published | PUB-ID: 1773341 OA
    Reinert K, Stoye J, Will T (2000)
    An iterative method for faster sum-of-pairs multiple sequence alignment.
    Bioinformatics 16(9): 808-814.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [28]
    2000 | Conference Paper | Published | PUB-ID: 1918988
    Kurtz S, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2000)
    Computation and Visualization of Degenerate Repeats in Complete Genomes.
    In: Proc. of ISMB 2000. 228-238.
    PUB | PubMed | Europe PMC
     
  • [27]
    2000 | Conference (Editor) | Published | PUB-ID: 1918813
    Bornberg-Bauer E, Rost U, Stoye J, Vingron M (Eds) (2000)
    Proceedings of the German Conference on Bioinformatics, GCB 2000.
    Berlin: Logos Verlag.
    PUB
     
  • [26]
    1999 | Conference Paper | Published | PUB-ID: 1620435
    Giegerich R, Kurtz S, Stoye J (1999)
    Efficient implementation of lazy suffix trees.
    In: Algorithm Engineering. 3rd International Workshop, WAE’99 London, UK, July 19–21, 1999 Proceedings. LNCS, 1668. 30-42.
    PUB | DOI | WoS
     
  • [25]
    1999 | Conference Paper | Published | PUB-ID: 1918978
    Reinert K, Will T, Stoye J (1999)
    Combining Divide-and-Conquer, the A*-Algorithm, and Successive Realignment Approaches to Speed up Multiple Sequence Alignment.
    In: Proc. of GCB 1999. 17-24.
    PUB | Download (ext.)
     
  • [24]
    1999 | Report | PUB-ID: 1970495
    Morgenstern B, Stoye J, Dress A (1999)
    Consistent Equivalence Relations: A Set-Theoretical Framework for Multiple Sequence Alignment. Materialien/Preprints.
    Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
  • [23]
    1999 | Report | PUB-ID: 1970509
    Brodal GS, Lyngsø RB, Pedersen CNS, Stoye J (1999)
    Finding Maximal Pairs with Bounded Gap. Report.
    BRICS, Department of Computer Science, University of Aarhus.
    PUB
     
  • [22]
    1999 | Conference Paper | Published | PUB-ID: 1918971
    Brodal GS, Lyngsø RB, Pedersen CNS, Stoye J (1999)
    Finding Maximal Pairs with Bounded Gap.
    In: Proc. of CPM 1999. LNCS, 1645. 134-149.
    PUB | DOI
     
  • [21]
    1998 | Journal Article | Published | PUB-ID: 2488102
    Dress A, Morgenstern B, Stoye J (1998)
    The Number of Standard and of Effective Multiple Alignments.
    Appl. Math. Lett. 11(4): 43-49.
    PUB
     
  • [20]
    1998 | Journal Article | Published | PUB-ID: 1918538
    Hildebrand M, Stoye J (1998)
    Die Bedeutung der Zusammenarbeit der Disziplinen in der Anwendung - erläutert anhand von Beispielen.
    Der Mathematikunterricht 44(6): 34-53.
    PUB
     
  • [19]
    1998 | Journal Article | Published | PUB-ID: 1667771 OA
    Stoye J (1998)
    Multiple sequence alignment with the Divide-and-Conquer method.
    Gene 211(2): GC45-GC56.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [18]
    1998 | Journal Article | Published | PUB-ID: 1625402 OA
    Stoye J, Evers D, Meyer F (1998)
    Rose: generating sequence families.
    BIOINFORMATICS 14(2): 157-163.
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [17]
    1998 | Report | PUB-ID: 1970515
    Stoye J, Gusfield D (1998)
    Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree. Report.
    Department of Computer Science, University of California, Davis.
    PUB
     
  • [16]
    1998 | Conference Paper | Published | PUB-ID: 1918964
    Stoye J, Gusfield D (1998)
    Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version).
    In: Proc. of CPM 1998. LNCS, 1448. 140-152.
    PUB | DOI
     
  • [15]
    1998 | Report | PUB-ID: 1970513
    Gusfield D, Stoye J (1998)
    Linear Time Algorithms for Finding and Representing all the Tandem Repeats in a String. Report.
    Department of Computer Science, University of California, Davis.
    PUB
     
  • [14]
    1997 | Journal Article | Published | PUB-ID: 1773358
    Brinkmann G, Dress A, Perrey SW, Stoye J (1997)
    Two applications of the Divide & Conquer principle in the molecular sciences.
    Mathematical programming 79(1-3): 71-97.
    PUB | DOI | WoS
     
  • [13]
    1997 | Journal Article | Published | PUB-ID: 2488107
    Stoye J, Moulton V, Dress A (1997)
    DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment.
    CABIOS 13(6): 625-626.
    PUB
     
  • [12]
    1997 | Report | PUB-ID: 1970526
    Perrey SW, Stoye J, Moulton V, Dress A (1997)
    On Simultaneous versus Iterative Multiple Sequence Alignment. Materialien/Preprints.
    Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
  • [11]
    1997 | Report | PUB-ID: 1970517
    Stoye J, Evers D, Meyer F (1997)
    Rose: Generating Sequence Families. Forschungsberichte.
    Technische Fakultät der Universität Bielefeld.
    PUB
     
  • [10]
    1997 | Report | PUB-ID: 1970529
    Brinkmann G, Dress A, Perrey SW, Stoye J (1997)
    Two Applications of the Divide & Conquer Principle in the Molecular Sciences. Materialien/Preprints.
    Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
  • [9]
    1997 | Conference Paper | Published | PUB-ID: 1667885
    Stoye J, Evers D, Meyer F (1997)
    Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions.
    In: Proc. of ISMB 1997. 303-306.
    PUB | PubMed | Europe PMC
     
  • [8]
    1997 | Journal Article | Published | PUB-ID: 1773355 OA
    Stoye J, Perrey SW, Dress A (1997)
    Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment.
    Applied mathematics letters 10(2): 67-73.
    PUB | PDF | DOI | WoS
     
  • [7]
    1997 | Report | PUB-ID: 1970523
    Dress A, Morgenstern B, Stoye J (1997)
    On the Number of Standard and Effective Multiple Alignments. Materialien/Preprints.
    Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
  • [6]
    1997 | Report | PUB-ID: 1970520
    Perrey SW, Stoye J, Moulton V (1997)
    FDCA: Fast and Accurate Approximation to Sum-of-Pairs Score Optimal Multiple Sequence Alignment. Materialien/Preprints.
    Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
  • [5]
    1997 | Report | PUB-ID: 1970532
    Stoye J (1997)
    Divide-and-Conquer Multiple Sequence Alignment. Forschungsberichte.
    Technische Fakultät der Universität Bielefeld.
    PUB
     
  • [4]
    1996 | Report | PUB-ID: 1970533
    Perrey SW, Stoye J (1996)
    Fast Approximation to the NP-hard Problem of Multiple Sequence Alignment. Information and Mathematical Sciences Reports, Series B.
    Dept. of Mathematics, Massey University, Palmerston North, New Zealand.
    PUB
     
  • [3]
    1996 | Journal Article | Published | PUB-ID: 1773351
    Tönges U, Perrey SW, Stoye J, Dress A (1996)
    A general method for fast multiple sequence alignment.
    Gene 172(1): GC33-GC41.
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [2]
    1996 | Report | PUB-ID: 1970535
    Stoye J, Dress A, Perrey SW (1996)
    Improving the Divide-and-Conquer Approach to Sum-of-Pairs Multiple Sequence Alignment. Materialien/Preprints.
    Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
  • [1]
    1996 | Report | PUB-ID: 1970537
    Tönges U, Perrey SW, Stoye J, Dress A (1996)
    A General Method for Fast Multiple Sequence Alignment. Materialien/Preprints.
    Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
    PUB
     
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