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485 Publikationen

2019 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2936900 OA
Wittler, R.: Alignment- and reference-free phylogenomics with colored de Bruijn graphs. In: Huber, K. and Gusfield, D. (eds.) Proceedings of WABI 2019. LIPIcs. 143, Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, Dagstuhl, Germany (2019).
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2019 | Preprint | PUB-ID: 2935604 OA
Wittler, R.: Alignment- and reference-free phylogenomics with colored de-Bruijn graphs. arXiv:1905.04165. (2019).
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2019 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2932883
Dörr, D., Stoye, J.: A Perspective on Comparative and Functional Genomics. In: Warnow, T. (ed.) Bioinformatics and Phylogenetics. Computational Biology. 29, p. 361-372. Springer , Cham (2019).
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2932884
Oey, H., Zakrzewski, M., Gravermann, K., Young, N.D., Korhonen, P.K., Gobert, G.N., Nawaratna, S., Hasan, S., Martínez, D.M., You, H., Lavin, M., Jones, M., Ragan, M.A., Stoye, J., Oleaga, A., Emery, A.M., Webster, B., Rollinson, D., Gasser, R.B., McManus, D.P., Krause, L.: Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium. PLOS Pathogens. 15, : e1007513 (2019).
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919005 OA
Schulz, T., Stoye, J., Dörr, D.: GraphTeams. A method for discovering spatial gene clusters in Hi-C sequencing data. BMC Genomics. 19, : 308 (2018).
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919006 OA
Rubert, D., Hoshino, E.A., Dias Vieira Braga, M., Stoye, J., Martinez, F.H.V.: Computing the family-free DCJ similarity. BMC Bioinformatics. 19, : 152 (2018).
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918481
Luhmann, N., Chauve, C., Stoye, J., Wittler, R.: Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 15, 2094-2100 (2018).
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2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913921
Zekic, T., Holley, G., Stoye, J.: Pan-genome Storage and Analysis Techniques. In: Setubal, J.C., Stadler, P., and Stoye, J. (eds.) Comparative Genomics. Methods and Protocols. Methods in Molecular Biology. 1704, p. 29-53. Springer Verlag, New York (2018).
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2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913922
Dörr, D., Feijão, P., Stoye, J.: Family-Free Genome Comparison. In: Setubal, J.C., Stadler, P., and Stoye, J. (eds.) Comparative Genomics: Methods and Protocols. Methods in Molecular Biology. 1704, p. 331-342. Springer Verlag, New York (2018).
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2018 | Herausgeber*in Sammelwerk | Veröffentlicht | PUB-ID: 2913920
Setubal, J.C., Stadler, P., Stoye, J. eds: Comparative Genomics: Methods and Protocols. Methods in Molecular Biology, 1704. Springer Verlag, New York (2018).
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919012
Jaenicke, S., Albaum, S., Blumenkamp, P., Linke, B., Stoye, J., Goesmann, A.: Flexible metagenome analysis using the MGX framework. Microbiome. 6, : 76 (2018).
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909057 OA
Rubert, D., Feijão, P., Dias Vieira Braga, M., Stoye, J., Martinez, F.H.V.: Approximating the DCJ distance of balanced genomes in linear time. Algorithms for Molecular Biology. 12, : 3 (2017).
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2017 | Zeitschriftenaufsatz | E-Veröff. vor dem Druck | PUB-ID: 2908574
Luhmann, N., Lafond, M., Thévenin, A., Ouangraoua, A., Wittler, R., Chauve, C.: The SCJ Small Parsimony Problem for Weighted Gene Adjacencies. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 14, (2017).
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2912492
Luhmann, N., Dörr, D., Chauve, C.: Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes. Microbial Genomics. 3, (2017).
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2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2909409
Cunha, L., Dantas, S., Gagie, T., Wittler, R., Kowada, L., Stoye, J.: Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings. Proceedings of CPM 2017. LIPIcs. 78, p. 19:1-19:9. (2017).
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2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2907587
Holley, G., Wittler, R., Stoye, J., Hach, F.: Dynamic Alignment-Free and Reference-Free Read Compression. Proceedings of RECOMB 2017. Lecture Notes in Bioinformatics. 10229, p. 50-65. (2017).
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2017 | Sammelwerksbeitrag | Im Druck | PUB-ID: 2913924
Anselmetti, Y., Luhmann, N., Bérard, S., Tannier, E., Chauve, C.: Comparative Methods for Reconstructing Ancient Genome Organization. In: Setubal, J.C., Stadler, P., and Stoye, J. (eds.) Comparative Genomics. Methods in Molecular Biology. Springer Verlag (In Press).
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909967
Dörr, D., Kowada, L.A.B., Soares de Araujo, F.E., Deshpande, S., Dantas, S., Moret, B.M.E., Stoye, J.: New Genome Similarity Measures based on Conserved Gene Adjacencies. Journal of Computational Biology. 24, 616-634 (2017).
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901413 OA
Gorzolka, K., Kölling, J., Nattkemper, T.W., Niehaus, K.: Spatio-Temporal Metabolite Profiling of the Barley Germination Process by MALDI MS Imaging. PLOS ONE. 11, : 0150208 (2016).
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905930
Winter, S., Jahn, K., Wehner, S., Kuchenbecker, L., Marz, M., Stoye, J., Böcker, S.: Finding approximate gene clusters with GECKO 3. Nucleic Acids Research. 44, 9600-9610 (2016).
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