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414 Publikationen

2019 | Zeitschriftenaufsatz | Im Druck | PUB-ID: 2937712
Rubert, D., Martinez, F. H. V., Stoye, J., & Dörr, D. (In Press). Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants. BMC Genomics
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2019 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2937148
Alanko, J., Bannai, H., Cazaux, B., Peterlongo, P., & Stoye, J. (2019). Finding All Maximal Perfect Haplotype Blocks in Linear Time. Proceedings of WABI 2019, Leibniz International Proceedings in Informatics. LIPIcs, 143, 8:1-8:9. Dagstuhl: Schloss Dagstuhl, Leibniz-Zentrum für Informatik . doi:10.4230/LIPICS.WABI.2019.8
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2019 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2936900
Wittler, R. (2019). Alignment- and reference-free phylogenomics with colored de Bruijn graphs. In K. Huber & D. Gusfield (Eds.), LIPIcs: Vol. 143. Proceedings of WABI 2019 Dagstuhl, Germany: Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik. doi:10.4230/LIPIcs.WABI.2019.2
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2019 | Datenpublikation | PUB-ID: 2936848
Dörr, D., & Rubert, D. (2019). Supplementary Data for "Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants". Bielefeld University. doi:10.4119/unibi/2936848
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2019 | Herausgeber*in Sammelwerk | Veröffentlicht | PUB-ID: 2935998
Setubal J. C., Stoye J., & Dutilh B. E. (Eds.) (2019). Computational Methods for Microbiome Analysis (Frontiers Research Topics). Lausanne: Frontiers Media.
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2019 | Preprint | PUB-ID: 2935604
Wittler, R. (2019). Alignment- and reference-free phylogenomics with colored de-Bruijn graphs. arXiv:1905.04165
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2019 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2932883
Dörr, D., & Stoye, J. (2019). A Perspective on Comparative and Functional Genomics. In T. Warnow (Ed.), Computational Biology: Vol. 29. Bioinformatics and Phylogenetics (pp. 361-372). Cham: Springer . doi:10.1007/978-3-030-10837-3_14
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2933161
Hassan, H., & Shanak, S. (2019). GOTrapper. A tool to navigate through branches of gene ontology hierarchy. BMC Bioinformatics, 20(1), 20. doi:10.1186/s12859-018-2581-8
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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., et al. (2019). Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium. PLOS Pathogens, 15(1), e1007513. doi:10.1371/journal.ppat.1007513
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919005
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. doi:10.1186/s12864-018-4622-0
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919006
Rubert, D., Hoshino, E. A., Dias Vieira Braga, M., Stoye, J., & Martinez, F. H. V. (2018). Computing the family-free DCJ similarity. BMC Bioinformatics, 19(Suppl. 6), 152. doi:10.1186/s12859-018-2130-5
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2018 | Zeitschriftenaufsatz | Veröffentlicht | 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. doi:10.1109/TCBB.2018.2816034
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2932754
Bhatia, S., Feijão, P., & Francis, A. R. (2018). Position and Content Paradigms in Genome Rearrangements. The Wild and Crazy World of Permutations in Genomics. BULLETIN OF MATHEMATICAL BIOLOGY, 80(12), 3227-3246. doi:10.1007/s11538-018-0514-3
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919346
Hagenfeld, D., Koch, R., Jünemann, S., Prior, K., Harks, I., Eickholz, P., Hoffmann, T., et al. (2018). Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis. PLOS ONE, 13(4), e0195534. doi:10.1371/journal.pone.0195534
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Bielefelder E-Dissertation | PUB-ID: 2918485
Holley, G. (2018). Pan-genome Search and Storage. Bielefeld: Universität Bielefeld.
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2018 | Bielefelder E-Dissertation | PUB-ID: 2919356
Willing, E. (2018). On Distance and Sorting of the Double Cut-and-Join and the Inversion-*indel* Model. Bielefeld: Universität Bielefeld.
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2018 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2930445
Cunha, L., Diekmann, Y., Kowada, L., & Stoye, J. (2018). Identifying Maximal Perfect Haplotype Blocks. Proceedings of BSB 2018, LNBI, 11228, 26-37. Springer Verlag. doi:10.1007/978-3-030-01722-4_3
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2018 | Zeitschriftenaufsatz | Veröffentlicht | 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. doi:10.1089/cmb.2018.0068
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913921
Zekic, T., Holley, G., & Stoye, J. (2018). Pan-genome Storage and Analysis Techniques. In J. C. Setubal, P. Stadler, & J. Stoye (Eds.), Methods in Molecular Biology: Vol. 1704. Comparative Genomics. Methods and Protocols (pp. 29-53). New York: Springer Verlag.
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2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913922
Dörr, D., Feijão, P., & Stoye, J. (2018). Family-Free Genome Comparison. In J. C. Setubal, P. Stadler, & J. Stoye (Eds.), Methods in Molecular Biology: Vol. 1704. Comparative Genomics: Methods and Protocols (pp. 331-342). New York: Springer Verlag.
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2018 | Herausgeber*in Sammelwerk | Veröffentlicht | PUB-ID: 2913920
Setubal J. C., Stadler P., & Stoye J. (Eds.) (2018). Comparative Genomics: Methods and Protocols (Methods in Molecular Biology, 1704). New York: Springer Verlag.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | 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, 76. doi:10.1186/s40168-018-0460-1
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Zeitschriftenaufsatz | E-Veröff. vor dem Druck | PUB-ID: 2908574
Luhmann, N., Lafond, M., Thévenin, A., Ouangraoua, A., Wittler, R., & Chauve, C. (2017). The SCJ Small Parsimony Problem for Weighted Gene Adjacencies. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14. doi:10.1109/TCBB.2017.2661761
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2912492
Luhmann, N., Dörr, D., & Chauve, C. (2017). Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes. Microbial Genomics, 3(9). doi:10.1099/mgen.0.000123
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556
Jünemann, S., Kleinbölting, N., Jaenicke, S., Henke, C., Hassa, J., Nelkner, J., Stolze, Y., et al. (2017). Bioinformatics for NGS-based metagenomics and the application to biogas research. Journal of Biotechnology, 261(SI), 10-23. doi:10.1016/j.jbiotec.2017.08.012
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2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913015
Rubert, D., Medeiros, G. L., Hoshino, E. A., Dias Vieira Braga, M., Stoye, J., & Martinez, F. H. V. (2017). Algorithms for Computing the Family-Free Genomic Similarity under DCJ. In J. Meidanis & L. Nakhleh (Eds.), Lecture Notes in Bioinformatics: Vol. 10562. Comparative Genomics. RECOMB-CG 2017 (pp. 76-100). Cham: Springer Verlag. doi:10.1007/978-3-319-67979-2_5
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909057
Rubert, D., Feijão, P., Dias Vieira Braga, M., Stoye, J., & Martinez, F. H. V. (2017). Approximating the DCJ distance of balanced genomes in linear time. Algorithms for Molecular Biology, 12, 3. doi:10.1186/s13015-017-0095-y
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2017 | Bielefelder E-Dissertation | PUB-ID: 2909213
Luhmann, N. (2017). Phylogenetic assembly of paleogenomes integrating ancient DNA data. Bielefeld: Universität Bielefeld.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2916552
da Silva, P. H., Machado, R., Dantas, S., & Dias Vieira Braga, M. (2017). Genomic Distance with High Indel Costs. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14(3), 728-732. doi:10.1109/TCBB.2016.2555301
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Konferenzbeitrag | Veröffentlicht | 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. Proceedings of CPM 2017, LIPIcs, 78, 19:1-19:9. doi:10.4230/LIPIcs.CPM.2017.19
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2911814
Dörr, D., Balaban, M., Feijão, P., & Chauve, C. (2017). The gene family-free median of three. Algorithms for Molecular Biology, 12, 14. doi:10.1186/s13015-017-0106-z
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Preprint | Veröffentlicht | 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
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2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2907587
Holley, G., Wittler, R., Stoye, J., & Hach, F. (2017). Dynamic Alignment-Free and Reference-Free Read Compression. Proceedings of RECOMB 2017, Lecture Notes in Bioinformatics, 10229, 50-65. doi:10.1007/978-3-319-56970-3_4
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2017 | Sammelwerksbeitrag | Im Druck | PUB-ID: 2913924
Anselmetti, Y., Luhmann, N., Bérard, S., Tannier, E., & Chauve, C. (In Press). Comparative Methods for Reconstructing Ancient Genome Organization. In J. C. Setubal, P. Stadler, & J. Stoye (Eds.), Methods in Molecular Biology. Comparative Genomics Springer Verlag.
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2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913016
Schulz, T., Stoye, J., & Dörr, D. (2017). Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery. Proceedings of RECOMB-CG 2017, Lecture Notes in Bioinformatics, 1704, 197-212. Berlin: Springer Verlag. doi:10.1007/978-3-319-67979-2_11
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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. (2017). New Genome Similarity Measures based on Conserved Gene Adjacencies. Journal of Computational Biology, 24(6), 616-634. doi:10.1089/cmb.2017.0065
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901477
Ahmed Raza, S. E., Langenkämper, D., Sirinukunwattana, K., Epstein, D., Nattkemper, T. W., & Rajpoot, N. M. (2016). Robust normalization protocols for multiplexed fluorescence bioimage analysis. BioData Mining, 9(1), 11. doi:10.1186/s13040-016-0088-2
PUB | DOI | WoS | PubMed | Europe PMC
 
2016 | Zeitschriftenaufsatz | Veröffentlicht | 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. doi:10.1093/nar/gkw843
PUB | DOI | WoS | PubMed | Europe PMC
 
2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2903708
Rubert, D., Feijão, P., Dias Vieira Braga, M., Stoye, J., & Martinez, F. H. V. (2016). A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates. In M. Frith & C. N. Storm Pedersen (Eds.), Lecture Notes in Bioinformatics: Vol. 9838. Algorithms in Bioinformatics. WABI 2016 (pp. 293-306). Cham: Springer. doi:10.1007/978-3-319-43681-4_24
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900129
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, 3. doi:10.1186/s13015-016-0066-8
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2016 | Bielefelder E-Dissertation | PUB-ID: 2902049
Dörr, D. (2016). Gene family-free genome comparison. Bielefeld: Universität Bielefeld.
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2016 | Bielefelder E-Dissertation | PUB-ID: 2906743
Bremges, A. (2016). Assembling the microbial dark matter. Bielefeld: Universität Bielefeld.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900943
Langenkämper, D., Jakobi, T., Feld, D., Jelonek, L., Goesmann, A., & Nattkemper, T. W. (2016). Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations. Frontiers in Genetics, 7, 5. doi:10.3389/fgene.2016.00005
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2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2901740
Luhmann, N., Thévenin, A., Ouangraoua, A., Wittler, R., & Chauve, C. (2016). The SCJ small parsimony problem for weighted gene adjacencies. Proceedings 12th International Symposium, ISBRA 2016, 9683, 200-210. doi:10.1007/978-3-319-38782-6_17
PUB | DOI | Download (ext.) | arXiv
 
2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2900111
Kowada, L. A. B., Doerr, D., Dantas, S., & Stoye, J. (2016). New Genome Similarity Measures based on Conserved Gene Adjacencies. In M. Singh (Ed.), Lecture Notes in Bioinformatics (LNBI): Vol. 9649. Research in Computational Molecular Biology. RECOMB 2016 (pp. 204-224). Springer. doi:10.1007/978-3-319-31957-5_15
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900421
Krause, L., Nones, K., Loffler, K. A., Nancarrow, D., Oey, H., Tang, Y. H., Wayte, N. J., et al. (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. doi:10.1093/carcin/bgw018
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2016 | Konferenzband | Veröffentlicht | PUB-ID: 2912258
Hölldobler S. (Ed.) (2016). Genfamilienfreier Genomvergleich. LNI, D-16, 91-100.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2911748
Krahn, T., Wibberg, D., Maus, I., Winkler, A., Pühler, A., Poirel, L., & Schlüter, A. (2015). Complete Genome Sequence ofAcinetobacter baumanniiCIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses. Genome Announcements, 3(4), e00850-15. doi:10.1128/genomea.00850-15
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2015 | Zeitschriftenaufsatz | Veröffentlicht | 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. doi:10.1109/TCBB.2014.2329297
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726366
Viduani Martinez, F. H., Feijão, P., Dias Vieira Braga, M., & Stoye, J. (2015). On the family-free DCJ distance and similarity. Algorithms for Molecular Biology, 10, 13. doi:10.1186/s13015-015-0041-9
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