PUB - Publications at Bielefeld University

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• [238]
  

  2024 | Journal Article | Published | PUB-ID: 2999592

  L. Parmigiani, E. Garrison, J. Stoye, T. Marschall, and D. Doerr, “Panacus: fast and exact pangenome growth and core size estimation”, Bioinformatics, 2024.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [237]
  

  2024 | Conference Paper | Published | PUB-ID: 2992085

  L. Bohnenkämper, J. Stoye, and D. Dörr, “Reconstructing Rearrangement Phylogenies of Natural Genomes”, LIPIcs, 2024, 312, : 12.

  PUB | DOI
   
• [236]
  

  2024 | Journal Article | Published | PUB-ID: 2988749

  L. Parmigiani, R. Wittler, and J. Stoye, “Revisiting pangenome openness with k-mers”, Peer Community Journal, 2024, 4, : e47.

  PUB | DOI | WoS
   
• [235]
  

  2024 | Journal Article | Published | PUB-ID: 2990552

  D. Frolova, L. Lima, L. Roberts, L. Bohnenkämper, R. Wittler, J. Stoye, and Z. Iqbal, “Applying rearrangement distances to enable plasmid epidemiology with pling”, Microbial Genomics , 2024, 10, : 001300.

  PUB | DOI | PubMed | Europe PMC | Preprint
   
• [234]
  

  2024 | Book (Editor) | Published | PUB-ID: 2990269

  Comparative Genomics. Methods and Protocols, Humana, New York, NY, 2024.

  PUB | DOI
   
• [233]
  

  2024 | Book Chapter | Published | PUB-ID: 2990270

  M. Dias Vieira Braga, D. Doerr, D. P. Rubert, and J. Stoye, in Comparative Genomics. Methods and Protocols (Eds.: J.C. Setubal, P.F. Stadler, J. Stoye), Humana, New York, NY, 2024, p. 57-72.

  PUB | DOI
   
• [232]
  

  2024 | Book Chapter | Published | PUB-ID: 2990271

  T. Schulz, L. Parmigiani, A. Rempel, and J. Stoye, in Comparative Genomics. Methods and Protocols (Eds.: J.C. Setubal, P.F. Stadler, J. Stoye), Humana, New York, NY, 2024, p. 73-106.

  PUB | DOI
   
• [231]
  

  2024 | Journal Article | Published | PUB-ID: 2985702

  M. Dias Vieira Braga, L. R. Brockmann, K. Klerx, and J. Stoye, “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

  M. Dias Vieira Braga, L. R. Brockmann, K. Klerx, and J. Stoye, in Comparative Genomics. 20th International Conference, RECOMB-CG 2023, Istanbul, Turkey, April 14–15, 2023, Proceedings (Eds.: K. Jahn, T. Vinař), Springer Nature , Cham, 2023, p. 35-50.

  PUB | DOI | WoS
   
• [229]
  

  2023 | Journal Article | Published | PUB-ID: 2984551

  K. U. Förstner, A. Becker, J. Blom, P. Bork, T. Clavel, M. Dieckmann, A. Goesmann, B. Götz, T. Gübitz, F. Hufsky, 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

  B. Kirsch-Gerweck, L. Bohnenkämper, M. T. Henrichs, J. N. Alanko, H. Bannai, B. Cazaux, P. Peterlongo, J. Burger, J. Stoye, and Y. Diekmann, “HaploBlocks: efficient detection of positive selection in large population genomic datasets”, Molecular Biology and Evolution, 2023, 40, : msad027.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [227]
  

  2022 | Preprint | Published | PUB-ID: 2967089

  L. Parmigiani, R. Wittler, and J. Stoye, “Revisiting pangenome openness with k-mers”, bioRxiv, 2022.

  PUB | DOI
   
• [226]
  

  2022 | Conference Paper | Published | PUB-ID: 2965398

  M. Dias Vieira Braga, L. R. Brockmann, K. Klerx, and J. Stoye, in 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022) (Eds.: C. Boucher, S. Rahmann), Schloss Dagstuhl - Leibniz-Zentrum Für Informatik, Dagstuhl, 2022, p. 13:1-13:16.

  PUB | DOI
   
• [225]
  

  2022 | Journal Article | Published | PUB-ID: 2963777

  P. Bonizzoni, M. Costantini, C. De Felice, A. Petescia, Y. Pirola, M. Previtali, R. Rizzi, J. Stoye, R. Zaccagnino, and R. Zizza, “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

  T. Schulz, R. Wittler, and J. Stoye, “Sequence-based pangenomic core detection”, iScience, 2022, 25, : 104413.

  PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [223]
  

  2021 | Book (Editor) | Published | PUB-ID: 2959449

  The Bielefeld Institute for Bioinformatics Infrastructure, Universität Bielefeld, Techn. Fakultät, Bielefeld, 2021.

  PUB | PDF | DOI
   
• [222]
  

  2021 | Journal Article | Published | PUB-ID: 2942686

  E. Willing, J. Stoye, and M. Dias Vieira Braga, “Computing the Inversion-Indel Distance”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2021, 18, 2314-2326.

  PUB | DOI | WoS | PubMed | Europe PMC | arXiv
   
• [221]
  

  2021 | Journal Article | Published | PUB-ID: 2950825

  T. Schulz, R. Wittler, S. Rahmann, F. Hach, and J. Stoye, “Detecting High Scoring Local Alignments in Pangenome Graphs”, Bioinformatics, 2021, 37, 2266-2274.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [220]
  

  2021 | Conference Paper | Published | PUB-ID: 2952705

  P. Bonizzoni, C. De Felice, A. Petescia, Y. Pirola, R. Rizzi, J. Stoye, R. Zaccagnino, and R. Zizza, in Proceedings of AlCoB 2021, 2021, p. 16-28.

  PUB
   
• [219]
  

  2021 | Journal Article | Published | PUB-ID: 2946303

  L. Bohnenkämper, M. Dias Vieira Braga, D. Dörr, and J. Stoye, “Computing the rearrangement distance of natural genomes”, Journal of Computational Biology, 2021, 28, 410-431.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [218]
  

  2021 | Journal Article | Published | PUB-ID: 2945991

  L. K. Sundermann, J. Wintersinger, G. Rätsch, J. Stoye, and Q. Morris, “Reconstructing Tumor Evolutionary Histories and Clone Trees in Polynomial-time with SubMARine”, PLOS Computational Biology, 2021, 17, : e1008400.

  PUB | DOI | WoS | PubMed | Europe PMC | Preprint
   
• [217]
  

  2021 | Special Issue | Published | PUB-ID: 2949108

  “Computational Methods for Microbiome Analysis”, Frontiers in Genetics, 2021, Research Topic.

  PUB | DOI | Download (ext.)
   
• [216]
  

  2020 | Preprint | Published | PUB-ID: 2943670

  D. Rubert, E. Araujo, M. A. Stefanes, J. Stoye, and F. V. Martinez, “On motifs in colored graphs”, arXiv:2005.13634, 2020.

  PUB | Download (ext.) | arXiv
   
• [215]
  

  2020 | Journal Article | Published | PUB-ID: 2942995

  D. Rubert, E. Araujo, M. A. Stefanes, J. Stoye, and F. Martinez, “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

  D. Rubert, F. H. V. Martinez, J. Stoye, and D. Dörr, “Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants”, BMC Genomics, 2020, 21, : 273.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [213]
  

  2020 | Journal Article | Published | PUB-ID: 2953267

  J. Schulte-Schrepping, N. Reusch, D. Paclik, K. Baßler, S. Schlickeiser, B. Zhang, B. Krämer, T. Krammer, S. Brumhard, L. Bonaguro, et al., “Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment”, Cell, 2020, 182, 1419-1440.e23.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [212]
  

  2020 | Report | PUB-ID: 2944669

  F. O. Glöckner, M. Diepenbroek, J. Felden, A. Güntsch, J. Stoye, J. Overmann, K. Wimmers, I. Kostadinov, R. Yahyapour, W. Müller, et al., NFDI4BioDiversity - A Consortium for the National Research Data Infrastructure (NFDI) : Proposal, Zenodo, 2020.

  PUB | DOI
   
• [211]
  

  2020 | Journal Article | Published | PUB-ID: 2948972

  J. C. Setubal, J. Stoye, and B. E. Dutilh, “Editorial: Computational Methods for Microbiome Analysis”, Frontiers in Genetics, 2020, 11, : 623897.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [210]
  

  2020 | Preprint | Published | PUB-ID: 2940602

  E. Haghshenas, H. Asghari, J. Stoye, C. Chauve, and F. Hach, “HASLR: Fast Hybrid Assembly of Long Reads”, bioRxiv, 2020.

  PUB | DOI | Download (ext.) | Preprint
   
• [209]
  

  2020 | Preprint | Published | PUB-ID: 2945720

  T. Schulz, R. Wittler, S. Rahmann, F. Hach, and J. Stoye, “Detecting High Scoring Local Alignments in Pangenome Graphs”, bioRxiv, 2020.

  PUB | DOI | Preprint
   
• [208]
  

  2020 | Journal Article | Published | PUB-ID: 2939618

  J. Alanko, H. Bannai, B. Cazaux, P. Peterlongo, and J. Stoye, “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

  E. Haghshenas, H. Asghari, J. Stoye, C. Chauve, and F. Hach, “HASLR: Fast Hybrid Assembly of Long Reads”, iScience, 2020, 23, : 101389.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [206]
  

  2020 | Journal Article | Published | PUB-ID: 2939598

  G. Sevillya, D. Dörr, Y. Lerner, J. Stoye, M. Steel, and S. Snir, “Horizontal Gene Transfer Phylogenetics: A Random Walk Approach”, Molecular Biology and Evolution, 2020, 37, 1470–1479.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [205]
  

  2020 | Preprint | Published | PUB-ID: 2939861

  L. Bohnenkämper, M. Dias Vieira Braga, D. Dörr, and J. Stoye, “Computing the rearrangement distance of natural genomes”, arXiv:2001.02139, 2020.

  PUB | Download (ext.) | arXiv
   
• [204]
  

  2020 | Conference Paper | Published | PUB-ID: 2939729

  L. Bohnenkämper, M. Dias Vieira Braga, D. Dörr, and J. Stoye, in Proceedings of RECOMB 2020, 2020, p. 3-18.

  PUB | DOI
   
• [203]
  

  2019 | Journal Article | Published | PUB-ID: 2932884

  H. Oey, M. Zakrzewski, K. Gravermann, N. D. Young, P. K. Korhonen, G. N. Gobert, S. Nawaratna, S. Hasan, D. M. Martínez, H. You, et al., “Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium”, PLOS Pathogens, 2019, 15, : e1007513.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [202]
  

  2019 | Report | Published | PUB-ID: 2939260

  T. Gagie, G. Manzini, G. Navarro, and J. Stoye, 25 Years of the Burrows-Wheeler Transform. Report from Dagstuhl Seminar 19241, Schloss Dagstuhl--Leibniz-Zentrum Fuer Informatik, 2019.

  PUB | DOI
   
• [201]
  

  2019 | Conference Paper | Published | PUB-ID: 2937148

  J. Alanko, H. Bannai, B. Cazaux, P. Peterlongo, and J. Stoye, in Proceedings of WABI 2019, Schloss Dagstuhl, Leibniz-Zentrum Für Informatik , Dagstuhl, 2019, p. 8:1-8:9.

  PUB | DOI
   
• [200]
  

  2019 | Book Chapter | Published | PUB-ID: 2932883

  D. Dörr, and J. Stoye, in Bioinformatics and Phylogenetics (Ed.: T. Warnow), Springer , Cham, 2019, p. 361-372.

  PUB | DOI
   
• [199]
  

  2018 | Journal Article | Published | PUB-ID: 2919006

  D. Rubert, E. A. Hoshino, M. Dias Vieira Braga, J. Stoye, and F. H. V. Martinez, “Computing the family-free DCJ similarity”, BMC Bioinformatics, 2018, 19, : 152.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [198]
  

  2018 | Journal Article | Published | PUB-ID: 2919012

  S. Jaenicke, S. Albaum, P. Blumenkamp, B. Linke, J. Stoye, and A. Goesmann, “Flexible metagenome analysis using the MGX framework”, Microbiome, 2018, 6, : 76.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [197]
  

  2018 | Journal Article | Published | PUB-ID: 2919005

  T. Schulz, J. Stoye, and D. Dörr, “GraphTeams. A method for discovering spatial gene clusters in Hi-C sequencing data”, BMC Genomics, 2018, 19, : 308.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [196]
  

  2018 | Journal Article | Published | PUB-ID: 2930268

  G. Holley, R. Wittler, J. Stoye, and F. Hach, “Dynamic Alignment-Free and Reference-Free Read Compression”, JOURNAL OF COMPUTATIONAL BIOLOGY, 2018, 25, 825-836.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [195]
  

  2018 | Book Chapter | Published | PUB-ID: 2913921

  T. Zekic, G. Holley, and J. Stoye, in Comparative Genomics. Methods and Protocols (Eds.: J.C. Setubal, P. Stadler, J. Stoye), Springer Verlag, New York, 2018, p. 29-53.

  PUB | DOI
   
• [194]
  

  2018 | Book Chapter | Published | PUB-ID: 2913922

  D. Dörr, P. Feijão, and J. Stoye, in Comparative Genomics: Methods and Protocols (Eds.: J.C. Setubal, P. Stadler, J. Stoye), Springer Verlag, New York, 2018, p. 331-342.

  PUB | DOI
   
• [193]
  

  2018 | Book (Editor) | Published | PUB-ID: 2913920

  Comparative Genomics: Methods and Protocols, Springer Verlag, New York, 2018.

  PUB | DOI
   
• [192]
  

  2018 | Journal Article | Published | PUB-ID: 2918481

  N. Luhmann, C. Chauve, J. Stoye, and R. Wittler, “Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018, 15, 2094-2100.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [191]
  

  2018 | Conference Paper | Published | PUB-ID: 2930445

  L. Cunha, Y. Diekmann, L. Kowada, and J. Stoye, in Proceedings of BSB 2018, Springer Verlag, 2018, p. 26-37.

  PUB | DOI
   
• [190]
  

  2017 | Conference Paper | Published | PUB-ID: 2913015

  D. Rubert, G. L. Medeiros, E. A. Hoshino, M. Dias Vieira Braga, J. Stoye, and F. H. V. Martinez, in Comparative Genomics. RECOMB-CG 2017 (Eds.: J. Meidanis, L. Nakhleh), Springer Verlag, Cham, 2017, p. 76-100.

  PUB | DOI
   
• [189]
  

  2017 | Journal Article | Published | PUB-ID: 2909057

  D. Rubert, P. Feijão, M. Dias Vieira Braga, J. Stoye, and F. H. V. Martinez, “Approximating the DCJ distance of balanced genomes in linear time”, Algorithms for Molecular Biology, 2017, 12, : 3.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [188]
  

  2017 | Preprint | Published | PUB-ID: 2908521

  L. Cunha, S. Dantas, T. Gagie, R. Wittler, L. Kowada, and J. Stoye, “Faster Jumbled Indexing for Binary Run-Length Encoded Strings”, arXiv: 1702.01280, 2017.

  PUB | Download (ext.) | arXiv
   
• [187]
  

  2017 | Conference Paper | Published | PUB-ID: 2909409

  L. Cunha, S. Dantas, T. Gagie, R. Wittler, L. Kowada, and J. Stoye, in Proceedings of CPM 2017, 2017, p. 19:1-19:9.

  PUB | DOI
   
• [186]
  

  2017 | Journal Article | Published | PUB-ID: 2913556

  S. Jünemann, N. Kleinbölting, S. Jaenicke, C. Henke, J. Hassa, J. Nelkner, Y. Stolze, S. Albaum, A. Schlüter, A. Goesmann, et al., “Bioinformatics for NGS-based metagenomics and the application to biogas research”, Journal of Biotechnology, 2017, 261, 10-23.

  PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [185]
  

  2017 | Conference Paper | Published | PUB-ID: 2907587

  G. Holley, R. Wittler, J. Stoye, and F. Hach, in Proceedings of RECOMB 2017, 2017, p. 50-65.

  PUB | DOI
   
• [184]
  

  2017 | Conference Paper | Published | PUB-ID: 2913016

  T. Schulz, J. Stoye, and D. Dörr, in Proceedings of RECOMB-CG 2017, Springer Verlag, Berlin, 2017, p. 197-212.

  PUB | DOI
   
• [183]
  

  2017 | Journal Article | Published | PUB-ID: 2909967

  D. Dörr, L. A. B. Kowada, F. E. Soares de Araujo, S. Deshpande, S. Dantas, B. M. E. Moret, and J. Stoye, “New Genome Similarity Measures based on Conserved Gene Adjacencies”, Journal of Computational Biology, 2017, 24, 616-634.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [182]
  

  2016 | Conference Paper | Published | PUB-ID: 2903708

  D. Rubert, P. Feijão, M. Dias Vieira Braga, J. Stoye, and F. H. V. Martinez, in Algorithms in Bioinformatics. WABI 2016 (Eds.: M. Frith, C.N. Storm Pedersen), Springer, Cham, 2016, p. 293-306.

  PUB | DOI
   
• [181]
  

  2016 | Journal Article | Published | PUB-ID: 2905930

  S. Winter, K. Jahn, S. Wehner, L. Kuchenbecker, M. Marz, J. Stoye, and S. Böcker, “Finding approximate gene clusters with GECKO 3”, Nucleic Acids Research, 2016, 44, 9600-9610.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [180]
  

  2016 | Journal Article | Published | PUB-ID: 2900421

  L. Krause, K. Nones, K. A. Loffler, D. Nancarrow, H. Oey, Y. H. Tang, N. J. Wayte, A. M. Patch, K. Patel, S. Brosda, 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, 356-365.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [179]
  

  2016 | Journal Article | Published | PUB-ID: 2900129

  G. Holley, R. Wittler, and J. Stoye, “Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage”, Algorithms for Molecular Biology, 2016, 11, : 3.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [178]
  

  2016 | Conference Paper | Published | PUB-ID: 2900111

  L. A. B. Kowada, D. Doerr, S. Dantas, and J. Stoye, in Research in Computational Molecular Biology. RECOMB 2016 (Ed.: M. Singh), Springer, 2016, p. 204-224.

  PUB | DOI
   
• [177]
  

  2015 | Conference Paper | Published | PUB-ID: 2757497

  G. Holley, R. Wittler, and J. Stoye, in Algorithms in Bioinformatics. WABI 2015. Proceedings (Eds.: M. Pop, H. Touzet), Springer, Berlin, Heidelberg, 2015, p. 217-230.

  PUB | DOI
   
• [176]
  

  2015 | Journal Article | Published | PUB-ID: 2726366

  F. H. Viduani Martinez, P. Feijão, M. Dias Vieira Braga, and J. Stoye, “On the family-free DCJ distance and similarity”, Algorithms for Molecular Biology, 2015, 10, : 13.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [175]
  

  2015 | Journal Article | Published | PUB-ID: 2677844

  M. Dias Vieira Braga, and J. Stoye, “Sorting linear genomes with rearrangements and indels”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015, 12, 500-506.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [174]
  

  2015 | Conference (Editor) | Published | PUB-ID: 2780229

  “Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Bioinformatics”, BMC Bioinformatics, 2015, 16.

  PUB | Download (ext.)
   
• [173]
  

  2015 | Conference (Editor) | Published | PUB-ID: 2780232

  “Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Genomics”, BMC Genomics, 2015, 16.

  PUB | Download (ext.)
   
• [172]
  

  2014 | Journal Article | Published | PUB-ID: 2689773

  S. Jünemann, K. Prior, A. Albersmeier, S. Albaum, J. Kalinowski, A. Goesmann, J. Stoye, and D. Harmsen, “GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers”, PLOS ONE, 2014, 9, : e107014.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [171]
  

  2014 | Journal Article | Published | PUB-ID: 2685362

  M. Lechner, M. Hernandez-Rosales, D. Dörr, N. Wieseke, A. Thévenin, J. Stoye, R. K. Hartmann, S. J. Prohaska, and P. F. Stadler, “Orthology Detection Combining Clustering and Synteny for Very Large Datasets”, PLoS ONE, 2014, 9, : e105015.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [170]
  

  2014 | Conference Paper | Published | PUB-ID: 2684241

  F. H. Viduani Martinez, P. Feijão, M. Dias Vieira Braga, and J. Stoye, in Algorithms in Bioinformatics. WABI 2014 (Eds.: D. Brown, B. Morgenstern), Springer Verlag, Berlin ; Heidelberg, 2014, p. 174-186.

  PUB | DOI
   
• [169]
  

  2014 | Journal Article | Published | PUB-ID: 2687033

  D. Dörr, J. Stoye, S. Böcker, and K. Jahn, “Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings”, BMC Genomics, 2014, 15, : S2.

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• [168]
  

  2014 | Journal Article | Published | PUB-ID: 2674387

  R. Hilker, K. B. Stadermann, D. Doppmeier, J. Kalinowski, J. Stoye, J. Straube, J. Winnebald, and A. Goesmann, “ReadXplorer - Visualization and Analysis of Mapped Sequences”, Bioinformatics, 2014, 30, 2247-2254.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [167]
  

  2014 | Journal Article | Published | PUB-ID: 2665038

  P. Schwientek, A. Neshat, J. Kalinowski, A. Klein, C. Rückert, S. Schneiker-Bekel, S. Wendler, J. Stoye, and A. Pühler, “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.

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• [166]
  

  2014 | Journal Article | Published | PUB-ID: 2685988

  T. Jakobi, K. Brinkrolf, A. Tauch, T. Noll, J. Stoye, A. Pühler, and A. Goesmann, “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

  N. Luhmann, C. Chauve, J. Stoye, and R. Wittler, in Proc. of BSB 2014 (Ed.: C. Sérgio), Springer Verlag, 2014, p. 135-143.

  PUB | DOI
   
• [164]
  

  2014 | Encyclopedia Article | Published | PUB-ID: 2693552

  J. Stoye, in Encyclopedia of Algorithms (Ed.: M.-Y. Kao), Springer Verlag, 2014.

  PUB | DOI
   
• [163]
  

  2014 | Journal Article | Published | PUB-ID: 2693409

  E. Fredrich, C. Ander, J. Stoye, I. Brune, and A. Tauch, “Metatranskriptomik der Mikrobiota aus der menschlichen Achselhöhle”, BIOspektrum, 2014, 20, 294-296.

  PUB | DOI
   
• [162]
  

  2014 | Journal Article | Published | PUB-ID: 2643941

  N. Hoffmann, M. Wilhelm, A. Doebbe, K. Niehaus, and J. Stoye, “BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry”, Bioinformatics, 2014, 30, 988-995.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [161]
  

  2014 | Journal Article | Published | PUB-ID: 2665333

  B. Henrich, M. Rumming, A. Sczyrba, E. Velleuer, R. Dietrich, W. Gerlach, M. Gombert, S. Rahn, J. Stoye, A. Borkhardt, et al., “Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma”, PLoS ONE, 2014, 9, : e92297.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [160]
  

  2013 | Journal Article | Published | PUB-ID: 2575011

  C. Ander, O. B. Schulz-Trieglaff, J. Stoye, and A. J. Cox, “metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences”, BMC Bioinformatics, 2013, 14, : S2.

  PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [159]
  

  2013 | Encyclopedia Article | Published | PUB-ID: 2577323

  W. Gerlach, and J. Stoye, in Encyclopedia of Metagenomics (Ed.: K.E. Nelson), Springer Verlag, 2013.

  PUB | DOI
   
• [158]
  

  2013 | Journal Article | Published | PUB-ID: 2611630

  E. Willing, S. Zaccaria, M. Dias Vieira Braga, and J. Stoye, “On the Inversion-Indel Distance”, BMC Bioinformatics, 2013, 14, : S3.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [157]
  

  2013 | Conference Paper | Published | PUB-ID: 2611641

  M. Dias Vieira Braga, and J. Stoye, in Advances in Bioinformatics and Computational Biology. BSB 2013 (Eds.: J.C. Setubal, N.F. Almeida), Springer Verlag, Cham, 2013, p. 36-46.

  PUB | DOI
   
• [156]
  

  2013 | Book Chapter | Published | PUB-ID: 2611648

  M. Dias Vieira Braga, C. Chauve, D. Dörr, K. Jahn, J. Stoye, A. Thévenin, and R. Wittler, in Models and Algorithms for Genome Evolution (Eds.: C. Chauve, N. El-Mabrouk, E. Tannier), Springer Verlag, London, 2013, p. 287-307.

  PUB | DOI
   
• [155]
  

  2013 | Journal Article | Published | PUB-ID: 2641228

  S. Jünemann, F. J. Sedlazeck, K. Prior, A. Albersmeier, U. John, J. Kalinowski, A. Mellmann, A. Goesmann, A. von Haeseler, J. Stoye, et al., “Corrigendum: Updating benchtop sequencing performance comparison”, Nature biotechnology, 2013, 31, 1148.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [154]
  

  2013 | Book Chapter | Published | PUB-ID: 2611643

  A. Bergeron, and J. Stoye, in Models and Algorithms for Genome Evolution (Eds.: C. Chauve, N. El-Mabrouk, E. Tannier), Springer Verlag, London, 2013, p. 63-81.

  PUB | DOI
   
• [153]
  

  2013 | Journal Article | Published | PUB-ID: 2575361

  P. Krell, S. Reuther, U. Fischer, T. Keller, S. Weber, M. Gombert, F. R. Schuster, C. Asang, P. Stepensky, B. Strahm, 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, 1388-1396.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [152]
  

  2013 | Journal Article | Published | PUB-ID: 2566922

  S. Jünemann, F. J. Sedlazeck, K. Prior, A. Albersmeier, U. John, J. Kalinowski, A. Mellmann, A. Goesmann, A. von Haeseler, J. Stoye, et al., “Updating benchtop sequencing performance comparison”, Nature Biotechnology, 2013, 31, 294-296.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [151]
  

  2013 | Conference (Editor) | Published | PUB-ID: 2616537

  “Algorithms in Bioinformatics”, Lecture Notes in Bioinformatics, 2013, 8126.

  PUB | DOI
   
• [150]
  

  2013 | Journal Article | Published | PUB-ID: 2611633

  K. Jahn, S. Winter, J. Stoye, and S. Böcker, “Statistics for approximate gene clusters”, BMC Bioinformatics, 2013, 14, : S14.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [149]
  

  2013 | Journal Article | Published | PUB-ID: 2548236

  P. Schwientek, S. Wendler, A. Neshat, C. Eirich, C. Rückert, A. Klein, U. F. Wehmeier, J. Kalinowski, J. Stoye, and A. Pühler, “Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media”, Journal of Biotechnology, 2013, 167, 166-177.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [148]
  

  2013 | Journal Article | Published | PUB-ID: 2529202

  M. Zakrzewski, T. Bekel, C. Ander, A. Pühler, O. Rupp, J. Stoye, A. Schlüter, and A. Goesmann, “MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets”, Journal of Biotechnology, 2013, 167, 156-165.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [147]
  

  2012 | Journal Article | Published | PUB-ID: 2517230

  S. Jünemann, K. Prior, R. Szczepanowski, I. Harks, B. Ehmke, A. Goesmann, J. Stoye, and D. Harmsen, “Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing”, PLoS ONE, 2012, 7, : e41606.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [146]
  

  2012 | Journal Article | Published | PUB-ID: 2512642

  D. Dörr, A. Thévenin, and J. Stoye, “Gene family assignment-free comparative genomics”, BMC Bioinformatics, 2012, 13, : S3.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [145]
  

  2012 | Journal Article | Published | PUB-ID: 2517239

  N. Hoffmann, M. Keck, H. Neuweger, M. Wilhelm, P. Högy, K. Niehaus, and J. Stoye, “Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets”, BMC Bioinformatics, 2012, 13, : 21.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [144]
  

  2012 | Journal Article | Published | PUB-ID: 2512644

  K. Jahn, H. Sudek, and J. Stoye, “Multiple genome comparison based on overlap regions of pairwise local alignments”, BMC Bioinformatics, 2012, 13, : S7.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [143]
  

  2012 | Journal Article | Published | PUB-ID: 2486060

  P. Schwientek, R. Szczepanowski, C. Rückert, J. Kalinowski, A. Klein, K. Selber, U. F. Wehmeier, J. Stoye, and A. Pühler, “The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110”, BMC Genomics, 2012, 13, : 112.

  PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [142]
  

  2012 | Conference (Editor) | Published | PUB-ID: 2510416

  “Combinatorial Pattern Matching”, Lecture Notes in Computer Science, 2012, 7354.

  PUB | DOI
   
• [141]
  

  2012 | Book Chapter | Published | PUB-ID: 2468382

  N. Hoffmann, and J. Stoye, in Metabolomics (Ed.: U. Roessner), Intech, 2012, p. 73-98.

  PUB | PDF | DOI | Download (ext.)
   
• [140]
  

  2012 | Journal Article | Published | PUB-ID: 2510984

  R. Hilker, C. Sickinger, C. N. S. Pedersen, and J. Stoye, “UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ”, Bioinformatics, 2012, 28, 2509-2511.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [139]
  

  2011 | Journal Article | Published | PUB-ID: 2091779

  F. Hufsky, L. Kuchenbecker, K. Jahn, J. Stoye, and S. Böcker, “Swiftly Computing Center Strings”, BMC Bioinformatics, 2011, 12, : 106.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [138]
  

  2011 | Journal Article | Published | PUB-ID: 2396509

  M. Dias Vieira Braga, R. Machado, L. C. Ribeiro, and J. Stoye, “Genomic distance under gene substitutions”, BMC Bioinformatics, 2011, 12, : S8.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [137]
  

  2011 | Journal Article | Published | PUB-ID: 2396558

  M. Dias Vieira Braga, R. Machado, L. C. Ribeiro, and J. Stoye, “On the weight of indels in genomic distances”, BMC Bioinformatics, 2011, 12, : S13.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [136]
  

  2011 | Journal Article | Published | PUB-ID: 1897974

  P. L. Erdős, L. Soukup, and J. Stoye, “Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance”, Applied Mathematics Letters, 2011, 24, 82-86.

  PUB | DOI | WoS | arXiv
   
• [135]
  

  2011 | Journal Article | Published | PUB-ID: 2091794

  M. Dias Vieira Braga, E. Willing, and J. Stoye, “Double Cut and Join with Insertions and Deletions”, Journal of Computational Biology, 2011, 18, 1167-1184.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [134]
  

  2011 | Journal Article | Published | PUB-ID: 2091790

  J. Kovac, R. Warren, M. Dias Vieira Braga, and J. Stoye, “Restricted DCJ Model. Rearrangement Problems with Chromosome Reincorporation”, Journal of Computational Biology, 2011, 18, 1231-1241.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [133]
  

  2011 | Journal Article | Published | PUB-ID: 2354746

  P. Schwientek, R. Szczepanowski, C. Rückert, J. Stoye, and A. Pühler, “Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology”, Journal of Biotechnology, 2011, 155, 68-77.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [132]
  

  2011 | Journal Article | Published | PUB-ID: 2289952

  J. Blom, T. Jakobi, D. Doppmeier, S. Jaenicke, J. Kalinowski, J. Stoye, and A. Goesmann, “Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming”, Bioinformatics, 2011, 27, 1351-1358.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [131]
  

  2011 | Journal Article | Published | PUB-ID: 1918550

  S. Heber, R. Mayr, and J. Stoye, “Common Intervals of Multiple Permutations”, Algorithmica, 2011, 60, 175-206.

  PUB | DOI | WoS
   
• [130]
  

  2011 | Journal Article | Published | PUB-ID: 2298170

  W. Gerlach, and J. Stoye, “Taxonomic classification of metagenomic shotgun sequences with CARMA3.”, Nucleic Acids Res, 2011, 39, e91.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [129]
  

  2011 | Journal Article | Published | PUB-ID: 2091787

  R. Wittler, J. Maňuch, M. Patterson, and J. Stoye, “Consistency of Sequence-Based Gene Clusters”, Journal of Computational Biology, 2011, 18, 1023-1039.

  PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [128]
  

  2010 | Conference Paper | Published | PUB-ID: 1919211

  F. Hufsky, L. Kuchenbecker, K. Jahn, J. Stoye, and S. Böcker, in Proc. of WABI 2010, 2010, p. 325-336.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [127]
  

  2010 | Journal Article | Published | PUB-ID: 1966439

  E. Trost, L. Ott, J. Schneider, J. Schröder, S. Jaenicke, A. Goesmann, P. Husemann, J. Stoye, F. Alves Dorella, F. Souza Rocha, 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, : 728.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [126]
  

  2010 | Conference Abstract / Poster | Published | PUB-ID: 2445157

  A. Bergeron, J. Mixtacki, and J. Stoye, in Dagstuhl Seminar Proceedings: 10231 Abstracts Collection : Structure Discovery in Biology: Motifs, Networks & Phylogenies (Eds.: A. Apostolico, A. Dress, L. Parida), Schloss Dagstuhl - Leibniz-Zentrum Für Informatik, Dagstuhl, 2010, p. 18.

  PUB | Download (ext.)
   
• [125]
  

  2010 | Conference Abstract / Poster | Published | PUB-ID: 2907492

  A. Bergeron, J. Mixtacki, and J. Stoye, in Structure Discovery in Biology: Motifs, Networks & Phylogenies (Eds.: A. Apostolico, A. Dress, L. Parida, Schloss Dagstuhl, Leibniz-Zentrum für Informatik), Schloss Dagstuhl - Leibniz-Zentrum Fuer Informatik, Germany, Dagstuhl, Germany, 2010, p. Online-Ressource.

  PUB | Download (ext.)
   
• [124]
  

  2010 | Journal Article | Published | PUB-ID: 1893893

  P. Husemann, and J. Stoye, “Phylogenetic Comparative Assembly”, Algorithms for Molecular Biology, 2010, 5, : 3.

  PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [123]
  

  2010 | Book Chapter | Published | PUB-ID: 1918836

  S. Besenbacher, B. Schwikowski, and J. Stoye, in Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday (Eds.: T. Elomaa, H. Mannila, P. Orponen), Springer Berlin Heidelberg, Berlin, Heidelberg, 2010, p. 62-76.

  PUB | DOI
   
• [122]
  

  2010 | Journal Article | Published | PUB-ID: 1795670

  T. Wittkop, D. Emig, S. J. Lange, S. Rahmann, M. Albrecht, J. H. Morris, S. Böcker, J. Stoye, and J. Baumbach, “Partitioning Biological Data with Transitivity Clustering”, Nature Methods, 2010, 7, 419-420.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [121]
  

  2010 | Journal Article | Published | PUB-ID: 1898012

  G. Blin, D. Faye, and J. Stoye, “Finding Nested Common Intervals Efficiently”, Journal of Computational Biology, 2010, 17, 1183-1194.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [120]
  

  2010 | Conference Paper | Published | PUB-ID: 1919217

  R. Wittler, and J. Stoye, in Proc. of Recomb-CG 2010, Springer Verlag, 2010, p. 252-263.

  PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [119]
  

  2010 | Conference Paper | Published | PUB-ID: 1893890

  P. Husemann, and J. Stoye, in Proc. of GCB 2010, 2010, p. 61-70.

  PUB | Download (ext.)
   
• [118]
  

  2010 | Journal Article | Published | PUB-ID: 1588556

  P. Husemann, and J. Stoye, “r2cat: Synteny Plots and Comparative Assembly”, Bioinformatics, 2010, 26, 570-571.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [117]
  

  2010 | Journal Article | Published | PUB-ID: 1897997

  A. Bergeron, P. Medvedev, and J. Stoye, “Rearrangement Models and Single-Cut Operations”, Journal of Computational Biology, 2010, 17, 1213-1225.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [116]
  

  2010 | Conference Paper | Published | PUB-ID: 1919216

  J. Kovac, M. Dias Vieira Braga, and J. Stoye, in Proc. of Recomb-CG 2010, 2010, p. 13-24.

  PUB | DOI
   
• [115]
  

  2010 | Journal Article | Published | PUB-ID: 1898025

  M. Dias Vieira Braga, and J. Stoye, “The Solution Space of Sorting by DCJ”, Journal of Computational Biology, 2010, 17, 1145-1165.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [114]
  

  2010 | Conference Paper | Published | PUB-ID: 1919215

  M. Dias Vieira Braga, E. Willing, and J. Stoye, in Proc. of WABI 2010, 2010, p. 90-101.

  PUB | DOI
   
• [113]
  

  2009 | Conference Paper | Published | PUB-ID: 1893884

  P. Husemann, and J. Stoye, in Proc. of WABI 2009, 2009, p. 145-156.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [112]
  

  2009 | Journal Article | Published | PUB-ID: 1589663

  A. Bergeron, J. Mixtacki, and J. Stoye, “A New Linear Time Algorithm to Compute the Genomic Distance via the Double Cut and Join Distance”, Theoretical Computer Science, 2009, 410, 5300-5316.

  PUB | DOI | WoS
   
• [111]
  

  2009 | Conference Paper | Published | PUB-ID: 1919206

  M. Dias Vieira Braga, and J. Stoye, in Proc. of Recomb-CG 2009, 2009, p. 36-47.

  PUB | DOI
   
• [110]
  

  2009 | Conference Paper | Published | PUB-ID: 1919207

  G. Blin, and J. Stoye, in Proc. of Recomb-CG 2009, 2009, p. 59-69.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [109]
  

  2009 | Journal Article | Published | PUB-ID: 1898137

  K. Jahn, and J. Stoye, “Approximative Gencluster und ihre Anwendung in der komparativen Genomik”, Informatik-Spektrum, 2009, 32, 288-300.

  PUB | DOI
   
• [108]
  

  2009 | Journal Article | Published | PUB-ID: 1591507

  J. Stoye, and R. Wittler, “A Unified Approach for Reconstructing Ancient Gene Clusters”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009, 6, 387-400.

  PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [107]
  

  2009 | Journal Article | Published | PUB-ID: 1590204

  M. Brudno, P. Medvedev, J. Stoye, and F. M. De La Vega, “A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)”, BIOINFORMATICS, 2009, 25, 2863-2864.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [106]
  

  2009 | Journal Article | Published | PUB-ID: 1589098

  W. Gerlach, S. Jünemann, F. Tille, A. Goesmann, and J. Stoye, “WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads”, BMC Bioinformatics, 2009, 10, 430.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [105]
  

  2009 | Journal Article | Published | PUB-ID: 1898105

  S. Böcker, K. Jahn, J. Mixtacki, and J. Stoye, “Computation of Median Gene Clusters”, Journal of Computational Biology, 2009, 16, 1085-1099.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [104]
  

  2009 | Journal Article | Published | PUB-ID: 1591319

  N. Hoffmann, and J. Stoye, “ChromA: signal-based retention time alignment for chromatography-mass spectrometry data”, Bioinformatics, 2009, 25, 2080-2081.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [103]
  

  2009 | Conference Paper | Published | PUB-ID: 1919209

  P. Medvedev, and J. Stoye, in Comparative Genomics : International Workshop, RECOMB-CG 2009, Budapest, Hungary, September 27-29, 2009. Proceedings, Springer, Berlin, Heidelberg, 2009, p. 84-97.

  PUB | DOI
   
• [102]
  

  2009 | Conference Abstract / Poster | Published | PUB-ID: 1918945

  J. Stoye, 2009, p. 3-4.

  PUB
   
• [101]
  

  2009 | Journal Article | Published | PUB-ID: 1634447

  T. Bekel, K. Henckel, H. Küster, F. Meyer, V. Mittard-Runte, H. Neuweger, D. Paarmann, O. Rupp, M. Zakrzewski, A. Pühler, 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, 3-12.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [100]
  

  2008 | Conference Paper | Published | PUB-ID: 1919198

  J. A. A. Quitzau, and J. Stoye, in Proc. of WABI 2008, 2008, p. 342-353.

  PUB | DOI
   
• [99]
  

  2008 | Report | PUB-ID: 1970459

  J. A. A. Quitzau, and J. Stoye, A space efficient representation for sparse de Bruijn subgraphs, Technische Fakultät Der Universität Bielefeld, Bielefeld, 2008.

  PUB | PDF
   
• [98]
  

  2008 | Report | PUB-ID: 1970461

  T. Ejaz, S. Rahmann, and J. Stoye, Online Abelian Pattern Matching, Technische Fakultät Der Universität Bielefeld, Bielefeld, 2008.

  PUB | PDF
   
• [97]
  

  2008 | Journal Article | Published | PUB-ID: 1636699

  H. Neuweger, S. Albaum, M. Dondrup, M. Persicke, T. Watt, K. Niehaus, J. Stoye, and A. Goesmann, “MeltDB: a software platform for the analysis and integration of metabolomics experiment data”, Bioinformatics, 2008, 24, 2726-2732.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [96]
  

  2008 | Encyclopedia Article | Published | PUB-ID: 1918834

  J. Stoye, in Encyclopedia of Algorithms (Ed.: M.-Y. Kao), Springer Verlag, 2008, p. 925-928.

  PUB | DOI
   
• [95]
  

  2008 | Conference Paper | Published | PUB-ID: 1919192

  S. Böcker, K. Jahn, J. Mixtacki, and J. Stoye, in Proc. of RECOMB 2008, 2008, p. 331-345.

  PUB | DOI
   
• [94]
  

  2008 | Conference Paper | Published | PUB-ID: 1919200

  A. Bergeron, J. Mixtacki, and J. Stoye, in Proc. of Recomb-CG 2008, 2008, p. 226-240.

  PUB | DOI
   
• [93]
  

  2008 | Journal Article | Published | PUB-ID: 1587078

  K. - B. Schürmann, and J. Stoye, “Counting suffix arrays and strings”, THEORETICAL COMPUTER SCIENCE, 2008, 395, 220-234.

  PUB | DOI | WoS
   
• [92]
  

  2008 | Journal Article | Published | PUB-ID: 1586009

  L. Krause, N. N. Diaz, R. A. Edwards, K. - H. Gartemann, H. Krömeke, H. Neuweger, A. Pühler, K. J. Runte, A. Schlüter, J. Stoye, et al., “Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor”, JOURNAL OF BIOTECHNOLOGY, 2008, 136, 91-101.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [91]
  

  2008 | Journal Article | Published | PUB-ID: 1586785

  S. Oehm, D. Gilbert, A. Tauch, J. Stoye, and A. Goesmann, “Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms”, NUCLEIC ACIDS RESEARCH, 2008, 36, W433-W437.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [90]
  

  2008 | Journal Article | Published | PUB-ID: 1783364

  L. Krause, N. N. Diaz, A. Goesmann, S. Kelley, T. W. Nattkemper, F. Rohwer, R. A. Edwards, and J. Stoye, “Phylogenetic classification of short environmental DNA fragments”, Nucleic Acids Research, 2008, 36, 2230-2239.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [89]
  

  2008 | Conference Paper | Published | PUB-ID: 1919195

  A. Bergeron, J. Mixtacki, and J. Stoye, in Combinatorial Pattern Matching. 19th Annual Symposium, CPM 2008, Pisa, Italy, June 18-20, 2008 Proceedings, 2008, p. 56-68.

  PUB | DOI
   
• [88]
  

  2007 | Journal Article | Published | PUB-ID: 1630781

  A. Mellmann, T. Weniger, C. Berssenbrügge, J. Rothgänger, M. Sammeth, J. Stoye, and D. Harmsen, “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, 98.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [87]
  

  2007 | Book Chapter | Published | PUB-ID: 1918828

  T. Schmidt, and J. Stoye, in Comparative Genomics, Volume 2 (Ed.: N.H. Bergman), Humana Press Inc., Totowa, NJ, 2007, p. 165-182.

  PUB | DOI | PubMed | Europe PMC
   
• [86]
  

  2007 | Journal Article | Published | PUB-ID: 1918432

  G. Didier, T. Schmidt, J. Stoye, and D. Tsur, “Character Sets of Strings”, Journal of Discrete Algorithms, 2007, 5, 330-340.

  PUB | DOI
   
• [85]
  

  2007 | Journal Article | Published | PUB-ID: 1595253

  K. - B. Schürmann, and J. Stoye, “An incomplex algorithm for fast suffix array construction”, SOFTWARE-PRACTICE & EXPERIENCE, 2007, 37, 309-329.

  PUB | DOI | WoS
   
• [84]
  

  2007 | Journal Article | Published | PUB-ID: 1783345

  L. Krause, A. C. McHardy, T. W. Nattkemper, A. Pühler, J. Stoye, and F. Meyer, “GISMO - gene identification using a support vector machine for ORF classification”, Nucleic Acids Research, 2007, 35, 540-549.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [83]
  

  2006 | Journal Article | Published | PUB-ID: 1599943

  M. Sammeth, T. Griebel, F. Tille, and J. Stoye, “Panta rhei (QAlign2): an open graphical environment for sequence analysis”, BIOINFORMATICS, 2006, 22, 889-890.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [82]
  

  2006 | Journal Article | Published | PUB-ID: 1599570

  K. R. Rasmussen, J. Stoye, and E. W. Myers, “Efficient q-gram filters for finding all epsilon-matches over a given length”, JOURNAL OF COMPUTATIONAL BIOLOGY, 2006, 13, 296-308.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [81]
  

  2006 | Journal Article | Published | PUB-ID: 1599574

  A. Bergeron, J. Mixtacki, and J. Stoye, “On sorting by translocations”, JOURNAL OF COMPUTATIONAL BIOLOGY, 2006, 13, 567-578.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [80]
  

  2006 | Conference Paper | Published | PUB-ID: 1596811

  A. Bergeron, J. Mixtacki, and J. Stoye, in Proc. of WABI 2006, Springer-Verlag Berlin, 2006, p. 163-173.

  PUB | DOI | WoS
   
• [79]
  

  2006 | Journal Article | Published | PUB-ID: 1597213

  M. Sammeth, and J. Stoye, “Comparing tandem repeats with duplications and excisions of variable degree”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2006, 3, 395-407.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [78]
  

  2006 | Journal Article | Published | PUB-ID: 1597313

  A. Bergeron, and J. Stoye, “On the similarity of sets of permutations and its applications to genome comparison”, JOURNAL OF COMPUTATIONAL BIOLOGY, 2006, 13, 1340-1354.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [77]
  

  2006 | Conference Abstract / Poster | Published | PUB-ID: 1918946

  J. Stoye, 2006, p. 3-3.

  PUB
   
• [76]
  

  2006 | Report | PUB-ID: 1970464

  C. Chauve, Y. Diekmann, S. Heber, J. Mixtacki, S. Rahmann, and J. Stoye, On Common Intervals with Errors, Technische Fakultät Der Universität Bielefeld, Bielefeld, 2006.

  PUB | PDF
   
• [75]
  

  2006 | Journal Article | Published | PUB-ID: 1631957

  L. Krause, N. N. Diaz, D. Bartels, R. A. Edwards, A. Pühler, F. Rohwer, F. Meyer, and J. Stoye, “Finding novel genes in bacterial communities isolated from the environment”, BIOINFORMATICS, 2006, 22, e281-e289.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [74]
  

  2005 | Report | PUB-ID: 1970470

  M. Sammeth, and J. Stoye, Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI), Technische Fakultät Der Universität Bielefeld, Bielefeld, 2005.

  PUB | PDF | DOI
   
• [73]
  

  2005 | Conference Paper | Published | PUB-ID: 1919012

  K. - B. Schürmann, and J. Stoye, in Proc. of ALENEX/ANALCO 2005, 2005, p. 77-85.

  PUB
   
• [72]
  

  2005 | Book Chapter | Published | PUB-ID: 1918824

  A. Bergeron, J. Mixtacki, and J. Stoye, in Mathematics of Evolution and Phylogeny (Ed.: O. Gascuel), Oxford University Press, 2005, p. 262-290.

  PUB
   
• [71]
  

  2005 | Conference Paper | Published | PUB-ID: 1603220

  A. Bergeron, J. Mixtacki, and J. Stoye, in Proc. of RECOMB 2005, Springer-Verlag Berlin, 2005, p. 615-629.

  PUB | DOI | WoS
   
• [70]
  

  2005 | Journal Article | Published | PUB-ID: 1775168

  A. Krause, J. Stoye, and M. Vingron, “Large scale hierarchical clustering of protein sequences”, BMC Bioinformatics, 2005, 6, : 15.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [69]
  

  2005 | Journal Article | Published | PUB-ID: 1773302

  D. Bartels, S. Kespohl, S. Albaum, T. Drüke, A. Goesmann, J. Herold, O. Kaiser, A. Pühler, F. Pfeiffer, G. Raddatz, et al., “BACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison”, Bioinformatics, 2005, 21, 853-859.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [68]
  

  2005 | Journal Article | Published | PUB-ID: 1918947

  S. Böcker, and J. Stoye, “Informatische Methoden zur Protein-Identifikation”, LaborPraxis, 2005, 29, 24-26.

  PUB
   
• [67]
  

  2005 | Conference Paper | Published | PUB-ID: 1601348

  C. Bannert, and J. Stoye, in Proc. of CompLife 2005, Springer-Verlag, 2005, p. 79-90.

  PUB | DOI | WoS
   
• [66]
  

  2005 | Conference Paper | Published | PUB-ID: 1601361

  M. Sammeth, T. Weniger, D. Harmsen, and J. Stoye, in Proc. of WABI 2005, Springer-Verlag Berlin, 2005, p. 276-290.

  PUB | DOI | WoS
   
• [65]
  

  2005 | Conference Paper | Published | PUB-ID: 1603216

  K. R. Rasmussen, J. Stoye, and E. W. Myers, in Proc. of RECOMB 2005, Springer-Verlag Berlin, 2005, p. 189-203.

  PUB | DOI | WoS
   
• [64]
  

  2005 | Conference Paper | Published | PUB-ID: 1919026

  K. - B. Schürmann, and J. Stoye, in Proc. of SPIRE 2005, 2005, p. 55-66.

  PUB | DOI
   
• [63]
  

  2005 | Report | PUB-ID: 1970472

  K. - B. Schürmann, and J. Stoye, Counting Suffix Arrays and Strings, Technische Fakultät Der Universität Bielefeld, Bielefeld, 2005.

  PUB | PDF
   
• [62]
  

  2004 | Conference (Editor) | Published | PUB-ID: 1918823

  “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

  T. Schmidt, and J. Stoye, in Proc. of CPM 2004, 2004, p. 347-358.

  PUB | DOI | WoS
   
• [60]
  

  2004 | Conference Paper | Published | PUB-ID: 1606286

  M. Michael, C. Dieterich, and J. Stoye, in Proc. of WABI 2004, Springer-Verlag Berlin, 2004, p. 99-110.

  PUB | DOI | WoS
   
• [59]
  

  2004 | Journal Article | Published | PUB-ID: 1773554

  D. A. Pollard, C. M. Bergman, J. Stoye, S. E. Celniker, and M. B. Eisen, “Correction: Benchmarking tools for the alignment of functional noncoding DNA”, BMC Bioinformatics, 2004, 5, : 73.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [58]
  

  2004 | Journal Article | Published | PUB-ID: 1773560

  M. Cieliebak, T. Erlebach, Z. Lipták, J. Stoye, and E. Welzl, “Algorithmic complexity of protein identification: combinatorics of weighted strings”, Discrete Applied Mathematics, 2004, 137, 27-46.

  PUB | PDF | DOI | WoS
   
• [57]
  

  2004 | Journal Article | Published | PUB-ID: 1773312

  D. A. Pollard, C. M. Bergman, J. Stoye, S. E. Celniker, and M. B. Eisen, “Benchmarking tools for the alignment of functional noncoding DNA”, BMC Bioinformatics, 2004, 5, : 6.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [56]
  

  2004 | Journal Article | Published | PUB-ID: 1773569

  D. Gusfield, and J. Stoye, “Linear time algorithms for finding and representing all the tandem repeats in a string”, Journal of computer and system sciences, 2004, 69, 525-546.

  PUB | PDF | DOI | WoS
   
• [55]
  

  2004 | Conference Paper | Published | PUB-ID: 1607263

  A. Bergeron, J. Mixtacki, and J. Stoye, in Proc. of CPM 2004, Springer-Verlag Berlin, 2004, p. 388-399.

  PUB | DOI | WoS
   
• [54]
  

  2003 | Report | PUB-ID: 1970475

  K. - B. Schürmann, and J. Stoye, Suffix Tree Construction and Storage with Limited Main Memory, Technische Fakultät Der Universität Bielefeld, Bielefeld, 2003.

  PUB | PDF
   
• [53]
  

  2003 | Journal Article | Published | PUB-ID: 1612664

  S. Heber, and J. Stoye, “The European Conference on Computational Biology”, Drug Discovery Today, 2003, 8, 113-114.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [52]
  

  2003 | Journal Article | Published | PUB-ID: 1918949

  R. Giegerich, and J. Stoye, “Finden, fast ohne zu suchen: Indexstrukturen in der Bioinformatik”, Forschung an der Universität Bielefeld, 2003, 26, 63-68.

  PUB
   
• [51]
  

  2003 | Conference Paper | Published | PUB-ID: 1919005

  C. Bannert, and J. Stoye, in Proc. of GCB 2003, 2003, p. 21-25.

  PUB
   
• [50]
  

  2003 | Journal Article | Published | PUB-ID: 1610397

  R. Giegerich, S. Kurtz, and J. Stoye, “Efficient implementation of lazy suffix trees”, SOFTWARE-PRACTICE & EXPERIENCE, 2003, 33, 1035-1049.

  PUB | PDF | DOI | WoS
   
• [49]
  

  2003 | Journal Article | Published | PUB-ID: 1609403

  M. Sammeth, B. Morgenstern, and J. Stoye, “Divide-and-conquer multiple alignment with segment-based constraints”, BIOINFORMATICS, 2003, 19, ii189-ii195.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [48]
  

  2003 | Conference Paper | Published | PUB-ID: 1610433

  A. Bergeron, and J. Stoye, in Proc. of COCOON 2003, 2003, p. 68-79.

  PUB | DOI | WoS
   
• [47]
  

  2003 | Journal Article | Published | PUB-ID: 1610503

  M. Sammeth, J. Rothgänger, W. Esser, J. Albert, J. Stoye, and D. Harmsen, “QAlign: quality-based multiple alignments with dynamic phylogenetic analysis”, BIOINFORMATICS, 2003, 19, 1592-1593.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [46]
  

  2003 | Report | PUB-ID: 1970477

  A. Bergeron, and J. Stoye, On the Similarity of Sets of Permutations and its Applications to Genome Comparison, Technische Fakultät Der Universität Bielefeld, Bielefeld, 2003.

  PUB | PDF
   
• [45]
  

  2002 | Conference Abstract / Poster | Published | PUB-ID: 1918951

  J. Stoye, in Lecture Notes in Informatics (Eds.: S. Schubert, B. Reusch, N. Jesse), 2002, p. 67-67.

  PUB
   
• [44]
  

  2002 | Conference Paper | Published | PUB-ID: 1919000

  M. Cieliebak, Z. Lipták, E. Welzl, T. Erlebach, and J. Stoye, in Proc. of IFIP TCS 2002, 2002, p. 143-156.

  PUB
   
• [43]
  

  2002 | Journal Article | Published | PUB-ID: 1773578

  R. Spang, M. Rehmsmeier, and J. Stoye, “A novel approach to remote homology detection: jumping alignments”, Journal of Computational Biology, 2002, 9, 747-760.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [42]
  

  2002 | Journal Article | Published | PUB-ID: 1773332

  J. Stoye, and D. Gusfield, “Simple and flexible detection of contiguous repeats using a suffix tree”, Theoretical Computer Science, 2002, 270, 843-856.

  PUB | PDF | DOI | WoS
   
• [41]
  

  2002 | Journal Article | Published | PUB-ID: 1773329

  A. Bergeron, S. Heber, and J. Stoye, “Common intervals and sorting by reversals: a marriage of necessity”, Bioinformatics, 2002, 18, S54-S63.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [40]
  

  2002 | Conference Paper | Published | PUB-ID: 1918995

  S. Heber, J. Stoye, M. Frohme, J. Hoheisel, and M. Vingron, in Proc. of GfKl 2000, 2002, p. 437-444.

  PUB
   
• [39]
  

  2001 | Journal Article | Published | PUB-ID: 1773335

  S. Kurtz, J. V. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye, and R. Giegerich, “REPuter: the manifold applications of repeat analysis on a genomic scale”, Nucleic Acids Research, 2001, 29, 4633-4642.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [38]
  

  2001 | Conference Paper | Published | PUB-ID: 1918992

  S. Heber, and J. Stoye, in Proc. of CPM 2001, 2001, p. 207-218.

  PUB | DOI
   
• [37]
  

  2001 | Conference Paper | Published | PUB-ID: 1880197

  S. Heber, and J. Stoye, in Proc. of WABI 2001, Sppringer, Berlin, 2001, p. 252-263.

  PUB | DOI
   
• [36]
  

  2001 | Report | PUB-ID: 1970479

  M. Cieliebak, T. Erlebach, Z. Lipták, J. Stoye, and E. Welzl, Algorithmic Complexity of Protein Identification: Combinatorics of Weighted Strings, ETH Zürich, Dept. of Computer Science, 2001.

  PUB
   
• [35]
  

  2000 | Conference Paper | Published | PUB-ID: 1918981

  S. Heber, J. Stoye, J. Hoheisel, and M. Vingron, in Proc. of RECOMB 2000, 2000, p. 155-164.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [34]
  

  2000 | Book Chapter | Published | PUB-ID: 1918817

  G. S. Brodal, R. B. Lyngsø, C. N. S. Pedersen, and J. Stoye, in Matching Patterns (Journal of Discrete Algorithms) (Eds.: M. Crochemore, L. Gąsieniec), 2000, p. 77-104.

  PUB
   
• [33]
  

  2000 | Journal Article | Published | PUB-ID: 1773345

  A. Krause, J. Stoye, and M. Vingron, “The SYSTERS protein sequence cluster set”, Nucleic Acids Research, 2000, 28, 270-272.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [32]
  

  2000 | Journal Article | Published | PUB-ID: 1773572

  S. Heber, J. Stoye, M. Frohme, J. Hoheisel, and M. Vingron, “Contig selection in physical mapping”, Journal of Computational Biology, 2000, 7, 395-408.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [31]
  

  2000 | Conference Paper | Published | PUB-ID: 1918985

  R. Spang, M. Rehmsmeier, and J. Stoye, in Proc. of ISMB 2000, 2000, p. 367-375.

  PUB | PubMed | Europe PMC
   
• [30]
  

  2000 | Report | PUB-ID: 1970490

  J. Stoye, Affix Trees, Technische Fakultät der Universität Bielefeld, 2000.

  PUB | PDF
   
• [29]
  

  2000 | Journal Article | Published | PUB-ID: 1773341

  K. Reinert, J. Stoye, and T. Will, “An iterative method for faster sum-of-pairs multiple sequence alignment”, Bioinformatics, 2000, 16, 808-814.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [28]
  

  2000 | Conference Paper | Published | PUB-ID: 1918988

  S. Kurtz, E. Ohlebusch, C. Schleiermacher, J. Stoye, and R. Giegerich, in Proc. of ISMB 2000, 2000, p. 228-238.

  PUB | PubMed | Europe PMC
   
• [27]
  

  2000 | Conference (Editor) | Published | PUB-ID: 1918813

  Proceedings of the German Conference on Bioinformatics, GCB 2000, Logos Verlag, Berlin, 2000.

  PUB
   
• [26]
  

  1999 | Conference Paper | Published | PUB-ID: 1620435

  R. Giegerich, S. Kurtz, and J. Stoye, in Algorithm Engineering. 3rd International Workshop, WAE’99 London, UK, July 19–21, 1999 Proceedings, 1999, p. 30-42.

  PUB | DOI | WoS
   
• [25]
  

  1999 | Conference Paper | Published | PUB-ID: 1918978

  K. Reinert, T. Will, and J. Stoye, in Proc. of GCB 1999, 1999, p. 17-24.

  PUB | Download (ext.)
   
• [24]
  

  1999 | Report | PUB-ID: 1970495

  B. Morgenstern, J. Stoye, and A. Dress, Consistent Equivalence Relations: A Set-Theoretical Framework for Multiple Sequence Alignment, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1999.

  PUB
   
• [23]
  

  1999 | Report | PUB-ID: 1970509

  G. S. Brodal, R. B. Lyngsø, C. N. S. Pedersen, and J. Stoye, Finding Maximal Pairs with Bounded Gap, BRICS, Department of Computer Science, University of Aarhus, 1999.

  PUB
   
• [22]
  

  1999 | Conference Paper | Published | PUB-ID: 1918971

  G. S. Brodal, R. B. Lyngsø, C. N. S. Pedersen, and J. Stoye, in Proc. of CPM 1999, 1999, p. 134-149.

  PUB | DOI
   
• [21]
  

  1998 | Journal Article | Published | PUB-ID: 2488102

  A. Dress, B. Morgenstern, and J. Stoye, “The Number of Standard and of Effective Multiple Alignments”, Appl. Math. Lett., 1998, 11, 43-49.

  PUB
   
• [20]
  

  1998 | Journal Article | Published | PUB-ID: 1918538

  M. Hildebrand, and J. Stoye, “Die Bedeutung der Zusammenarbeit der Disziplinen in der Anwendung - erläutert anhand von Beispielen”, Der Mathematikunterricht, 1998, 44, 34-53.

  PUB
   
• [19]
  

  1998 | Journal Article | Published | PUB-ID: 1667771

  J. Stoye, “Multiple sequence alignment with the Divide-and-Conquer method.”, Gene, 1998, 211, GC45-GC56.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [18]
  

  1998 | Journal Article | Published | PUB-ID: 1625402

  J. Stoye, D. Evers, and F. Meyer, “Rose: generating sequence families”, BIOINFORMATICS, 1998, 14, 157-163.

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [17]
  

  1998 | Report | PUB-ID: 1970515

  J. Stoye, and D. Gusfield, Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree, Department of Computer Science, University of California, Davis, 1998.

  PUB
   
• [16]
  

  1998 | Conference Paper | Published | PUB-ID: 1918964

  J. Stoye, and D. Gusfield, in Proc. of CPM 1998, 1998, p. 140-152.

  PUB | DOI
   
• [15]
  

  1998 | Report | PUB-ID: 1970513

  D. Gusfield, and J. Stoye, Linear Time Algorithms for Finding and Representing all the Tandem Repeats in a String, Department of Computer Science, University of California, Davis, 1998.

  PUB
   
• [14]
  

  1997 | Journal Article | Published | PUB-ID: 1773358

  G. Brinkmann, A. Dress, S. W. Perrey, and J. Stoye, “Two applications of the Divide & Conquer principle in the molecular sciences”, Mathematical programming, 1997, 79, 71-97.

  PUB | DOI | WoS
   
• [13]
  

  1997 | Journal Article | Published | PUB-ID: 2488107

  J. Stoye, V. Moulton, and A. Dress, “DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment”, CABIOS, 1997, 13, 625-626.

  PUB
   
• [12]
  

  1997 | Report | PUB-ID: 1970526

  S. W. Perrey, J. Stoye, V. Moulton, and A. Dress, On Simultaneous versus Iterative Multiple Sequence Alignment, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1997.

  PUB
   
• [11]
  

  1997 | Report | PUB-ID: 1970517

  J. Stoye, D. Evers, and F. Meyer, Rose: Generating Sequence Families, Technische Fakultät der Universität Bielefeld, 1997.

  PUB
   
• [10]
  

  1997 | Report | PUB-ID: 1970529

  G. Brinkmann, A. Dress, S. W. Perrey, and J. Stoye, Two Applications of the Divide & Conquer Principle in the Molecular Sciences, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1997.

  PUB
   
• [9]
  

  1997 | Conference Paper | Published | PUB-ID: 1667885

  J. Stoye, D. Evers, and F. Meyer, in Proc. of ISMB 1997, 1997, p. 303-306.

  PUB | PubMed | Europe PMC
   
• [8]
  

  1997 | Journal Article | Published | PUB-ID: 1773355

  J. Stoye, S. W. Perrey, and A. Dress, “Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment”, Applied mathematics letters, 1997, 10, 67-73.

  PUB | PDF | DOI | WoS
   
• [7]
  

  1997 | Report | PUB-ID: 1970523

  A. Dress, B. Morgenstern, and J. Stoye, On the Number of Standard and Effective Multiple Alignments, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1997.

  PUB
   
• [6]
  

  1997 | Report | PUB-ID: 1970520

  S. W. Perrey, J. Stoye, and V. Moulton, FDCA: Fast and Accurate Approximation to Sum-of-Pairs Score Optimal Multiple Sequence Alignment, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1997.

  PUB
   
• [5]
  

  1997 | Report | PUB-ID: 1970532

  J. Stoye, Divide-and-Conquer Multiple Sequence Alignment, Technische Fakultät der Universität Bielefeld, 1997.

  PUB
   
• [4]
  

  1996 | Report | PUB-ID: 1970533

  S. W. Perrey, and J. Stoye, Fast Approximation to the NP-hard Problem of Multiple Sequence Alignment, Dept. of Mathematics, Massey University, Palmerston North, New Zealand, 1996.

  PUB
   
• [3]
  

  1996 | Journal Article | Published | PUB-ID: 1773351

  U. Tönges, S. W. Perrey, J. Stoye, and A. Dress, “A general method for fast multiple sequence alignment”, Gene, 1996, 172, GC33-GC41.

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [2]
  

  1996 | Report | PUB-ID: 1970535

  J. Stoye, A. Dress, and S. W. Perrey, Improving the Divide-and-Conquer Approach to Sum-of-Pairs Multiple Sequence Alignment, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1996.

  PUB
   
• [1]
  

  1996 | Report | PUB-ID: 1970537

  U. Tönges, S. W. Perrey, J. Stoye, and A. Dress, A General Method for Fast Multiple Sequence Alignment, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld, 1996.

  PUB