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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
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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: 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 | Bielefelder E-Dissertation | PUB-ID: 2918485
Holley, G. (2018). Pan-genome Search and Storage. 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
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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
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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
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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
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2016 | Bielefelder E-Dissertation | PUB-ID: 2906743
Bremges, A. (2016). Assembling the microbial dark matter. Bielefeld: Universität Bielefeld.
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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 | 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: 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
PUB | DOI | WoS | PubMed | Europe PMC
 
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 | 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
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2715682
Henning, P., Kuich, J. L., Hoffmann, N., & Stefan, K. (2015). Maui-VIA: a user-friendly software for visual identification, alignment, correction, and quantification of gas chromatography–mass spectrometry data. Frontiers in Bioengineering and Biotechnology, 2(84). doi:10.3389/fbioe.2014.00084
PUB | DOI | PubMed | Europe PMC
 
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2766708
Chen, C., Bartenhagen, C., Gombert, M., Okpanyi, V., Binder, V., Röttgers, S., Bradtke, J., et al. (2015). Next-generation-sequencing of recurrent childhood high hyperdiploid acute lymphoblastic leukemia reveals mutations typically associated with high risk patients. Leukemia research. doi:10.1016/j.leukres.2015.06.005
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764612
Wittler, R., Marschall, T., Schönhuth, A., & Makinen, V. (2015). Repeat- and error-aware comparison of deletions. Bioinformatics, 31(18), 2947-2954. doi:10.1093/bioinformatics/btv304
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2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2757497
Holley, G., Wittler, R., & Stoye, J. (2015). Bloom Filter Trie - a data structure for pan-genome storage. Proceedings of WABI 2015, 9289, 217-230
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2015 | Bielefelder E-Dissertation | PUB-ID: 2786037
Hilker, R. (2015). Development of a read mapping analysis software and computational pan genome analysis of 20 Pseudomonas aeruginosa strains. Bielefeld: Bielefeld University.
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2015 | Konferenzband | Veröffentlicht | 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)
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2015 | Konferenzband | Veröffentlicht | 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)
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2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2684241
Viduani Martinez, F. H., Feijão, P., Dias Vieira Braga, M., & Stoye, J. (2014). On the family-free DCJ distance. In D. Brown & B. Morgenstern (Eds.), Lecture Notes in Bioinformatics: Vol. 8701. Algorithms in Bioinformatics. WABI 2014 (pp. 174-186). Berlin ; Heidelberg: Springer Verlag. doi:10.1007/978-3-662-44753-6_14
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2687033
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. doi:10.1186/1471-2164-15-S6-S2
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685362
Lechner, M., Hernandez-Rosales, M., Dörr, D., Wieseke, N., Thévenin, A., Stoye, J., Hartmann, R. K., et al. (2014). Orthology Detection Combining Clustering and Synteny for Very Large Datasets. PLoS ONE, 9(8), e105015. doi:10.1371/journal.pone.0105015
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2689773
Jünemann, S., Prior, K., Albersmeier, A., Albaum, S., Kalinowski, J., Goesmann, A., Stoye, J., et al. (2014). GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers. PLOS ONE, 9(9), e107014. doi:10.1371/journal.pone.0107014
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Bielefelder E-Dissertation | PUB-ID: 2723541
Ander, C. (2014). Bioinformatic methods for the analysis and comparison of metagenomes and metatranscriptomes. Bielefeld: Universitätsbibliothek Bielefeld.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2674387
Hilker, R., Stadermann, K. B., Doppmeier, D., Kalinowski, J., Stoye, J., Straube, J., Winnebald, J., et al. (2014). ReadXplorer - Visualization and Analysis of Mapped Sequences. Bioinformatics, 30(16), 2247-2254. doi:10.1093/bioinformatics/btu205
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665038
Schwientek, P., Neshat, A., Kalinowski, J., Klein, A., Rückert, C., Schneiker-Bekel, S., Wendler, S., et al. (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. doi:10.1016/j.jbiotec.2014.03.013
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2690122
Luhmann, N., Chauve, C., Stoye, J., & Wittler, R. (2014). Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. In C. Sérgio (Ed.), LNBI: Vol. 8826. Proc. of BSB 2014 (pp. 135-143). Springer Verlag. doi:10.1007/978-3-319-12418-6_17
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2014 | Zeitschriftenaufsatz | Veröffentlicht | 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. doi:10.1016/j.jbiotec.2014.07.437
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Bielefelder E-Dissertation | PUB-ID: 2677466
Hoffmann, N. (2014). Computational methods for high-throughput metabolomics. Bielefeld: Universität Bielefeld.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2691246
Fueller, E., Schaefer, D., Fischer, U., Krell, P., Stanulla, M., Borkhardt, A., & Slany, R. K. (2014). Genomic Inverse PCR for Exploration of Ligated Breakpoints (GIPFEL), a New Method to Detect Translocations in Leukemia. PloS one, 9(8), 104419. doi:10.1371/journal.pone.0104419
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2693552
Stoye, J. (2014). Suffix Tree Construction. In M. - Y. Kao (Ed.), Encyclopedia of Algorithms Springer Verlag. doi:10.1007/978-3-642-27848-8_414-2
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2014 | Zeitschriftenaufsatz | Veröffentlicht | 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. doi:10.1093/bioinformatics/btt738
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2014 | Zeitschriftenaufsatz | Veröffentlicht | 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. doi:10.1007/s12268-014-0468-4
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2691732
Klippel, B., Sahm, K., Basner, A., Wiebusch, S., John, P., Lorenz, U., Peters, A., et al. (2014). Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria. Extremophiles, 18(5), 853-863. doi:10.1007/s00792-014-0676-3
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2691279
Binder, V., Bartenhagen, C., Okpanyi, V., Gombert, M., Moehlendick, B., Behrens, B., Klein, H. - U., et al. (2014). A New Workflow for Whole-Genome Sequencing of Single Human Cells. Human mutation. doi:10.1002/humu.22625
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2014 | Bielefelder E-Dissertation | PUB-ID: 2673418
Mascher, M. (2014). POPSEQ Anchoring and ordering contig assemblies from next generation sequencing data by population sequencing. Bielefeld: Universität Bielefeld.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333
Henrich, B., Rumming, M., Sczyrba, A., Velleuer, E., Dietrich, R., Gerlach, W., Gombert, M., et al. (2014). Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma. PLoS ONE, 9(3), e92297. doi:10.1371/journal.pone.0092297
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2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2611641
Dias Vieira Braga, M., & Stoye, J. (2013). Restricted DCJ-Indel Model Revisited. In J. C. Setubal & N. F. Almeida (Eds.), Lecture Notes in Bioinformatics: Vol. 8213. Advances in Bioinformatics and Computational Biology. BSB 2013 (pp. 36-46). Cham: Springer Verlag. doi:10.1007/978-3-319-02624-4_4
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611630
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. doi:10.1186/1471-2105-14-S15-S3
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2013 | Sammelwerksbeitrag | Veröffentlicht | 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 C. Chauve, N. El-Mabrouk, & E. Tannier (Eds.), Computational Biology Series: Vol. 19. Models and Algorithms for Genome Evolution (pp. 287-307). Springer Verlag. doi:10.1007/978-1-4471-5298-9_13
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575011
Ander, C., Schulz-Trieglaff, O. B., Stoye, J., & Cox, A. J. (2013). metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. BMC Bioinformatics, 14(Suppl 5: Proc. of RECOMB-Seq 2013), S2. doi:10.1186/1471-2105-14-S5-S2
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2555342
He, P., Hao, K., Blom, J., Rückert, C., Vater, J., Mao, Z., Wu, Y., et al. (2013). Genome sequence of the plant growth promoting strain Bacillus amyloliquefaciens subsp. plantarum B9601-Y2 and expression of mersacidin and other secondary metabolites. Journal of biotechnology, 164(2), 281-291. doi:10.1016/j.jbiotec.2012.12.014
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641228
Jünemann, S., Sedlazeck, F. J., Prior, K., Albersmeier, A., John, U., Kalinowski, J., Mellmann, A., et al. (2013). Corrigendum: Updating benchtop sequencing performance comparison. Nature biotechnology, 31(12), 1148. doi:10.1038/nbt1213-1148e
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2492825
Reuther, S., Schmetzer, H., Schuster, F. R., Krell, P., Grabrucker, C., Liepert, A., Kroell, T., et al. (2013). In vitro-induced response patterns of antileukemic T cells: characterization by spectratyping and immunophenotyping. Clinical and Experimental Medicine, 13(1), 29-48. doi:10.1007/s10238-012-0180-y
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2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611643
Bergeron, A., & Stoye, J. (2013). The Genesis of the DCJ Formula. In C. Chauve, N. El-Mabrouk, & E. Tannier (Eds.), Computational Biology Series: Vol. 19. Models and Algorithms for Genome Evolution (pp. 63-81). Springer Verlag. doi:10.1007/978-1-4471-5298-9_5
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2013 | Bielefelder E-Dissertation | PUB-ID: 2604883
Blom, J. (2013). Comparative genomics on gene and single nucleotide level. Bielefeld: Universitätsbibliothek.
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2013 | Bielefelder E-Dissertation | PUB-ID: 2594322
Janowski, S. J. (2013). VANESA - A bioinformatics software application for the modeling, visualization, analysis, and simulation of biological networks in systems biology applications. Bielefeld: Bielefeld University.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575361
Krell, P., Reuther, S., Fischer, U., Keller, T., Weber, S., Gombert, M., Schuster, F. R., et al. (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. doi:10.3324/haematol.2012.069708
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2013 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2577323
Gerlach, W., & Stoye, J. (2013). Taxonomic classification of metagenomic shotgun sequences with CARMA3. In K. E. Nelson (Ed.), Encyclopedia of Metagenomics Springer Verlag. doi:10.1007/978-1-4614-6418-1_751-2
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2625914
Bergmann, T., Maeder, U., Fiebich, M., Dickob, M., Nattkemper, T. W., & Anselmetti, D. (2013). Categorization of two-photon microscopy images of human cartilage into states of osteoarthritis. Osteoarthritis And Cartilage, 21(8), 1074-1082. doi:10.1016/j.joca.2013.04.019
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2566922
Jünemann, S., Sedlazeck, F. J., Prior, K., Albersmeier, A., John, U., Kalinowski, J., Mellmann, A., et al. (2013). Updating benchtop sequencing performance comparison. Nature Biotechnology, 31(4), 294-296. doi:10.1038/nbt.2522
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Konferenzband | Veröffentlicht | PUB-ID: 2616537
Darling A., & Stoye J. (Eds.) (2013). Algorithms in Bioinformatics. Lecture Notes in Bioinformatics, 8126. doi:10.1007/978-3-642-40453-5
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611633
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. doi:10.1186/1471-2105-14-S15-S14
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2548236
Schwientek, P., Wendler, S., Neshat, A., Eirich, C., Rückert, C., Klein, A., Wehmeier, U. F., et al. (2013). Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media. Journal of Biotechnology, 167(2), 166-177. doi:10.1016/j.jbiotec.2012.10.019
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2548286
Luque-Almagro, V. M., Acera, F., Igeño, M. I., Wibberg, D., Roldán, M. D., Sáez, L. P., Hennig, M., et al. (2013). Draft whole genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344. Environmental Microbiology, 15(1), 253-270. doi:10.1111/j.1462-2920.2012.02875.x
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2552092
Wittler, R. (2013). Unraveling overlapping deletions by agglomerative clustering. BMC Genomics, 14(Suppl 1), S12. doi:10.1186/1471-2164-14-S1-S12
PUB | Dateien verfügbar | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2529309
Bolzan de Campos, S., Youn, J. - W., Farina, R., Jaenicke, S., Jünemann, S., Szczepanowski, R., Beneduzi, A., et al. (2013). Changes in Root Bacterial Communities Associated to Two Different Development Stages of Canola (*Brassica napus* L. var oleifera) Evaluated through Next-Generation Sequencing. Microbial Ecology, 65(3), 593-601. doi:10.1007/s00248-012-0132-9
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659331
Feijão, P., & Meidanis, J. (2013). Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(4), 819-831. doi:10.1109/TCBB.2012.161
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2529202
Zakrzewski, M., Bekel, T., Ander, C., Pühler, A., Rupp, O., Stoye, J., Schlüter, A., et al. (2013). MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. Journal of Biotechnology, 167(2), 156-165. doi:10.1016/j.jbiotec.2012.09.013
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2560353
Dörr, D., Gronau, I., Moran, S., & Yavneh, I. (2012). Stochastic errors vs. modeling errors in distance based phylogenetic reconstructions. Algorithms for Molecular Biology, 7(1), 22. doi:10.1186/1748-7188-7-22
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512642
Dörr, D., Thévenin, A., & Stoye, J. (2012). Gene family assignment-free comparative genomics. BMC Bioinformatics, 13(Suppl 19: Proc. of RECOMB-CG 2012), S3. doi:10.1186/1471-2105-13-S19-S3
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2498160
Schröder, J., Maus, I., Meyer, K., Wördemann, S., Blom, J., Jaenicke, S., Schneider, J., et al. (2012). Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient. BMC Genomics, 13(1), 141. doi:10.1186/1471-2164-13-141
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