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414 Publikationen

2019 | Zeitschriftenaufsatz | Im Druck | PUB-ID: 2937712
Rubert, D., Martinez, F. H. V., Stoye, J., and 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., and Stoye, J. (2019). “Finding All Maximal Perfect Haplotype Blocks in Linear Time” in Proceedings of WABI 2019 Leibniz International Proceedings in Informatics. LIPIcs, vol. 143, (Dagstuhl: Schloss Dagstuhl, Leibniz-Zentrum für Informatik ), 8:1-8:9.
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2019 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2936900
Wittler, R. (2019). “Alignment- and reference-free phylogenomics with colored de Bruijn graphs” in Proceedings of WABI 2019, Huber, K., and Gusfield, D. eds. LIPIcs, vol. 143, (Dagstuhl, Germany: Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik).
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2019 | Datenpublikation | PUB-ID: 2936848
Dörr, D., and Rubert, D. (2019). Supplementary Data for "Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants". Bielefeld University.
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2019 | Herausgeber*in Sammelwerk | Veröffentlicht | PUB-ID: 2935998
Setubal, J. C., Stoye, J., and 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., and Stoye, J. (2019). “A Perspective on Comparative and Functional Genomics” in Bioinformatics and Phylogenetics, Warnow, T. ed. Computational Biology, vol. 29, (Cham: Springer ), 361-372.
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2933161
Hassan, H., and Shanak, S. (2019). GOTrapper. A tool to navigate through branches of gene ontology hierarchy. BMC Bioinformatics 20:20.
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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., et al. (2019). Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium. PLOS Pathogens 15:e1007513.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919005
Schulz, T., Stoye, J., and Dörr, D. (2018). GraphTeams. A method for discovering spatial gene clusters in Hi-C sequencing data. BMC Genomics 19:308.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919006
Rubert, D., Hoshino, E. A., Dias Vieira Braga, M., Stoye, J., and Martinez, F. H. V. (2018). Computing the family-free DCJ similarity. BMC Bioinformatics 19:152.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918481
Luhmann, N., Chauve, C., Stoye, J., and Wittler, R. (2018). Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. IEEE/ACM Transactions on Computational Biology and Bioinformatics 15, 2094-2100.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2932754
Bhatia, S., Feijão, P., and 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, 3227-3246.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919346
Hagenfeld, D., Koch, R., Jünemann, S., Prior, K., Harks, I., Eickholz, P., Hoffmann, T., Kim, T. - S., Kocher, T., Meyle, J., 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:e0195534.
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., and Stoye, J. (2018). “Identifying Maximal Perfect Haplotype Blocks” in Proceedings of BSB 2018 LNBI, vol. 11228, (Springer Verlag), 26-37.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930268
Holley, G., Wittler, R., Stoye, J., and Hach, F. (2018). Dynamic Alignment-Free and Reference-Free Read Compression. JOURNAL OF COMPUTATIONAL BIOLOGY 25, 825-836.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913921
Zekic, T., Holley, G., and Stoye, J. (2018). “Pan-genome Storage and Analysis Techniques” in Comparative Genomics. Methods and Protocols, Setubal, J. C., Stadler, P., and Stoye, J. eds. Methods in Molecular Biology, vol. 1704, (New York: Springer Verlag), 29-53.
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2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913922
Dörr, D., Feijão, P., and Stoye, J. (2018). “Family-Free Genome Comparison” in Comparative Genomics: Methods and Protocols, Setubal, J. C., Stadler, P., and Stoye, J. eds. Methods in Molecular Biology, vol. 1704, (New York: Springer Verlag), 331-342.
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2018 | Herausgeber*in Sammelwerk | Veröffentlicht | PUB-ID: 2913920
Setubal, J. C., Stadler, P., and 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., and Goesmann, A. (2018). Flexible metagenome analysis using the MGX framework. Microbiome 6:76.
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., and Chauve, C. (2017). The SCJ Small Parsimony Problem for Weighted Gene Adjacencies. IEEE/ACM Transactions on Computational Biology and Bioinformatics 14.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2912492
Luhmann, N., Dörr, D., and Chauve, C. (2017). Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes. Microbial Genomics 3.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556
Jünemann, S., Kleinbölting, N., Jaenicke, S., Henke, C., Hassa, J., Nelkner, J., Stolze, Y., Albaum, S., Schlüter, A., Goesmann, A., et al. (2017). Bioinformatics for NGS-based metagenomics and the application to biogas research. Journal of Biotechnology 261, 10-23.
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2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913015
Rubert, D., Medeiros, G. L., Hoshino, E. A., Dias Vieira Braga, M., Stoye, J., and Martinez, F. H. V. (2017). “Algorithms for Computing the Family-Free Genomic Similarity under DCJ” in Comparative Genomics. RECOMB-CG 2017, Meidanis, J., and Nakhleh, L. eds. Lecture Notes in Bioinformatics, vol. 10562, (Cham: Springer Verlag), 76-100.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909057
Rubert, D., Feijão, P., Dias Vieira Braga, M., Stoye, J., and Martinez, F. H. V. (2017). Approximating the DCJ distance of balanced genomes in linear time. Algorithms for Molecular Biology 12:3.
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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., and Dias Vieira Braga, M. (2017). Genomic Distance with High Indel Costs. IEEE/ACM Transactions on Computational Biology and Bioinformatics 14, 728-732.
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2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2909409
Cunha, L., Dantas, S., Gagie, T., Wittler, R., Kowada, L., and Stoye, J. (2017). “Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings” in Proceedings of CPM 2017 LIPIcs, vol. 78, 19:1-19:9.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2911814
Dörr, D., Balaban, M., Feijão, P., and Chauve, C. (2017). The gene family-free median of three. Algorithms for Molecular Biology 12:14.
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2017 | Preprint | Veröffentlicht | PUB-ID: 2908521
Cunha, L., Dantas, S., Gagie, T., Wittler, R., Kowada, L., and 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., and Hach, F. (2017). “Dynamic Alignment-Free and Reference-Free Read Compression” in Proceedings of RECOMB 2017 Lecture Notes in Bioinformatics, vol. 10229, 50-65.
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2017 | Sammelwerksbeitrag | Im Druck | PUB-ID: 2913924
Anselmetti, Y., Luhmann, N., Bérard, S., Tannier, E., and Chauve, C. (In Press). “Comparative Methods for Reconstructing Ancient Genome Organization” in Comparative Genomics, Setubal, J. C., Stadler, P., and Stoye, J. eds. Methods in Molecular Biology (Springer Verlag).
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2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913016
Schulz, T., Stoye, J., and Dörr, D. (2017). “Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery” in Proceedings of RECOMB-CG 2017 Lecture Notes in Bioinformatics, vol. 1704, (Berlin: Springer Verlag), 197-212.
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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., and Stoye, J. (2017). New Genome Similarity Measures based on Conserved Gene Adjacencies. Journal of Computational Biology 24, 616-634.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901477
Ahmed Raza, S. E., Langenkämper, D., Sirinukunwattana, K., Epstein, D., Nattkemper, T. W., and Rajpoot, N. M. (2016). Robust normalization protocols for multiplexed fluorescence bioimage analysis. BioData Mining 9:11.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905930
Winter, S., Jahn, K., Wehner, S., Kuchenbecker, L., Marz, M., Stoye, J., and Böcker, S. (2016). Finding approximate gene clusters with GECKO 3. Nucleic Acids Research 44, 9600-9610.
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2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2903708
Rubert, D., Feijão, P., Dias Vieira Braga, M., Stoye, J., and Martinez, F. H. V. (2016). “A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates” in Algorithms in Bioinformatics. WABI 2016, Frith, M., and Storm Pedersen, C. N. eds. Lecture Notes in Bioinformatics, vol. 9838, (Cham: Springer), 293-306.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900129
Holley, G., Wittler, R., and Stoye, J. (2016). Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage. Algorithms for Molecular Biology 11:3.
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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 | 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., and Nattkemper, T. W. (2016). Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations. Frontiers in Genetics 7:5.
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2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2900111
Kowada, L. A. B., Doerr, D., Dantas, S., and Stoye, J. (2016). “New Genome Similarity Measures based on Conserved Gene Adjacencies” in Research in Computational Molecular Biology. RECOMB 2016, Singh, M. ed. Lecture Notes in Bioinformatics (LNBI), vol. 9649, (Springer), 204-224.
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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., Patch, A. M., Patel, K., Brosda, S., 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, 356-365.
PUB | DOI | WoS | PubMed | Europe PMC
 
2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2901740
Luhmann, N., Thévenin, A., Ouangraoua, A., Wittler, R., and Chauve, C. (2016). “The SCJ small parsimony problem for weighted gene adjacencies” in Proceedings 12th International Symposium, ISBRA 2016 Lecture Notes in Computer Science, vol. 9683, (Springer International Publishing), 200-210.
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., and Schlüter, A. (2015). Complete Genome Sequence ofAcinetobacter baumanniiCIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses. Genome Announcements 3, e00850-15.
PUB | DOI | WoS | PubMed | Europe PMC
 
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2677844
Dias Vieira Braga, M., and Stoye, J. (2015). Sorting linear genomes with rearrangements and indels. IEEE/ACM Transactions on Computational Biology and Bioinformatics 12, 500-506.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726366
Viduani Martinez, F. H., Feijão, P., Dias Vieira Braga, M., and Stoye, J. (2015). On the family-free DCJ distance and similarity. Algorithms for Molecular Biology 10:13.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2715682
Henning, P., Kuich, J. L., Hoffmann, N., and 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.
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., Teigler-Schlegel, A., Harbott, J., Ginzel, S., et al. (2015). Next-generation-sequencing of recurrent childhood high hyperdiploid acute lymphoblastic leukemia reveals mutations typically associated with high risk patients. Leukemia research.
PUB | DOI | WoS | PubMed | Europe PMC
 
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764612
Wittler, R., Marschall, T., Schönhuth, A., and Makinen, V. (2015). Repeat- and error-aware comparison of deletions. Bioinformatics 31, 2947-2954.
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2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2757497
Holley, G., Wittler, R., and Stoye, J. (2015). “Bloom Filter Trie - a data structure for pan-genome storage” in Proceedings of WABI 2015 LNBI, vol. 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., and Stoye, J. eds. (2015). Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Bioinformatics. BMC Bioinformatics 16.
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2015 | Konferenzband | Veröffentlicht | PUB-ID: 2780232
Meidanis, J., and Stoye, J. eds. (2015). Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Genomics. BMC Genomics 16.
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2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2684241
Viduani Martinez, F. H., Feijão, P., Dias Vieira Braga, M., and Stoye, J. (2014). “On the family-free DCJ distance” in Algorithms in Bioinformatics. WABI 2014, Brown, D., and Morgenstern, B. eds. Lecture Notes in Bioinformatics, vol. 8701, (Berlin ; Heidelberg: Springer Verlag), 174-186.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2687033
Dörr, D., Stoye, J., Böcker, S., and Jahn, K. (2014). Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings. BMC Genomics 15, 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., Prohaska, S. J., and Stadler, P. F. (2014). Orthology Detection Combining Clustering and Synteny for Very Large Datasets. PLoS ONE 9, e105015.
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., and Harmsen, D. (2014). GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers. PLOS ONE 9, e107014.
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., and Goesmann, A. (2014). ReadXplorer - Visualization and Analysis of Mapped Sequences. Bioinformatics 30, 2247-2254.
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., Stoye, J., and Pühler, A. (2014). Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts. Journal of Biotechnology 190, 85-95.
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685988
Jakobi, T., Brinkrolf, K., Tauch, A., Noll, T., Stoye, J., Pühler, A., and Goesmann, A. (2014). Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. Journal of Biotechnology 190, 64-75.
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2690122
Luhmann, N., Chauve, C., Stoye, J., and Wittler, R. (2014). “Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework” in Proc. of BSB 2014, Sérgio, C. ed. LNBI, vol. 8826, (Springer Verlag), 135-143.
PUB | DOI
 
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., and Slany, R. K. (2014). Genomic Inverse PCR for Exploration of Ligated Breakpoints (GIPFEL), a New Method to Detect Translocations in Leukemia. PloS one 9, 104419.
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2693552
Stoye, J. (2014). “Suffix Tree Construction” in Encyclopedia of Algorithms, Kao, M. - Y. ed. (Springer Verlag).
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2693409
Fredrich, E., Ander, C., Stoye, J., Brune, I., and Tauch, A. (2014). Metatranskriptomik der Mikrobiota aus der menschlichen Achselhöhle. BIOspektrum 20, 294-296.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2643941
Hoffmann, N., Wilhelm, M., Doebbe, A., Niehaus, K., and Stoye, J. (2014). BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry. Bioinformatics 30, 988-995.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2691732
Klippel, B., Sahm, K., Basner, A., Wiebusch, S., John, P., Lorenz, U., Peters, A., Abe, F., Takahashi, K., Kaiser, O., et al. (2014). Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria. Extremophiles 18, 853-863.
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2691279
Binder, V., Bartenhagen, C., Okpanyi, V., Gombert, M., Moehlendick, B., Behrens, B., Klein, H. - U., Rieder, H., Krell, P., Dugas, M., et al. (2014). A New Workflow for Whole-Genome Sequencing of Single Human Cells. Human mutation.
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333
Henrich, B., Rumming, M., Sczyrba, A., Velleuer, E., Dietrich, R., Gerlach, W., Gombert, M., Rahn, S., Stoye, J., Borkhardt, A., et al. (2014). Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma. PLoS ONE 9, e92297.
PUB | DOI | WoS | PubMed | Europe PMC
 
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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2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2611641
Dias Vieira Braga, M., and Stoye, J. (2013). “Restricted DCJ-Indel Model Revisited” in Advances in Bioinformatics and Computational Biology. BSB 2013, Setubal, J. C., and Almeida, N. F. eds. Lecture Notes in Bioinformatics, vol. 8213, (Cham: Springer Verlag), 36-46.
PUB | DOI
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611630
Willing, E., Zaccaria, S., Dias Vieira Braga, M., and Stoye, J. (2013). On the Inversion-Indel Distance. BMC Bioinformatics 14:S3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611648
Dias Vieira Braga, M., Chauve, C., Dörr, D., Jahn, K., Stoye, J., Thévenin, A., and Wittler, R. (2013). “The Potential of Family-Free Genome Comparison” in Models and Algorithms for Genome Evolution, Chauve, C., El-Mabrouk, N., and Tannier, E. eds. Computational Biology Series, vol. 19, (Springer Verlag), 287-307.
PUB | DOI
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575011
Ander, C., Schulz-Trieglaff, O. B., Stoye, J., and Cox, A. J. (2013). metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. BMC Bioinformatics 14, S2.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2555342
He, P., Hao, K., Blom, J., Rückert, C., Vater, J., Mao, Z., Wu, Y., Hou, M., He, P., He, 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, 281-291.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641228
Jünemann, S., Sedlazeck, F. J., Prior, K., Albersmeier, A., John, U., Kalinowski, J., Mellmann, A., Goesmann, A., von Haeseler, A., Stoye, J., et al. (2013). Corrigendum: Updating benchtop sequencing performance comparison. Nature biotechnology 31, 1148.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2492825
Reuther, S., Schmetzer, H., Schuster, F. R., Krell, P., Grabrucker, C., Liepert, A., Kroell, T., Kolb, H. - J., Borkhardt, A., and Buhmann, R. (2013). In vitro-induced response patterns of antileukemic T cells: characterization by spectratyping and immunophenotyping. Clinical and Experimental Medicine 13, 29-48.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611643
Bergeron, A., and Stoye, J. (2013). “The Genesis of the DCJ Formula” in Models and Algorithms for Genome Evolution, Chauve, C., El-Mabrouk, N., and Tannier, E. eds. Computational Biology Series, vol. 19, (Springer Verlag), 63-81.
PUB | DOI
 
2013 | Bielefelder E-Dissertation | PUB-ID: 2604883
Blom, J. (2013). Comparative genomics on gene and single nucleotide level. Bielefeld: Universitätsbibliothek.
PUB | PDF
 
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.
PUB | PDF
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575361
Krell, P., Reuther, S., Fischer, U., Keller, T., Weber, S., Gombert, M., Schuster, F. R., Asang, C., Stepensky, P., Strahm, B., 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, 1388-1396.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2577323
Gerlach, W., and Stoye, J. (2013). “Taxonomic classification of metagenomic shotgun sequences with CARMA3” in Encyclopedia of Metagenomics, Nelson, K. E. ed. (Springer Verlag).
PUB | DOI
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2625914
Bergmann, T., Maeder, U., Fiebich, M., Dickob, M., Nattkemper, T. W., and Anselmetti, D. (2013). Categorization of two-photon microscopy images of human cartilage into states of osteoarthritis. Osteoarthritis And Cartilage 21, 1074-1082.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2566922
Jünemann, S., Sedlazeck, F. J., Prior, K., Albersmeier, A., John, U., Kalinowski, J., Mellmann, A., Goesmann, A., von Haeseler, A., Stoye, J., et al. (2013). Updating benchtop sequencing performance comparison. Nature Biotechnology 31, 294-296.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Konferenzband | Veröffentlicht | PUB-ID: 2616537
Darling, A., and Stoye, J. eds. (2013). Algorithms in Bioinformatics. Lecture Notes in Bioinformatics 8126.
PUB | DOI
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611633
Jahn, K., Winter, S., Stoye, J., and Böcker, S. (2013). Statistics for approximate gene clusters. BMC Bioinformatics 14, S14.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2548236
Schwientek, P., Wendler, S., Neshat, A., Eirich, C., Rückert, C., Klein, A., Wehmeier, U. F., Kalinowski, J., Stoye, J., and Pühler, A. (2013). Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media. Journal of Biotechnology 167, 166-177.
PUB | DOI | WoS | PubMed | Europe PMC
 
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., Quesada, A., Huertas, M. J., Blom, J., et al. (2013). Draft whole genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344. Environmental Microbiology 15, 253-270.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2552092
Wittler, R. (2013). Unraveling overlapping deletions by agglomerative clustering. BMC Genomics 14, 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., Vargas, L. K., Wendisch, V. F., and Passaglia, L. (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, 593-601.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659331
Feijão, P., and Meidanis, J. (2013). Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10, 819-831.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2529202
Zakrzewski, M., Bekel, T., Ander, C., Pühler, A., Rupp, O., Stoye, J., Schlüter, A., and Goesmann, A. (2013). MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. Journal of Biotechnology 167, 156-165.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2560353
Dörr, D., Gronau, I., Moran, S., and Yavneh, I. (2012). Stochastic errors vs. modeling errors in distance based phylogenetic reconstructions. Algorithms for Molecular Biology 7, 22.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512642
Dörr, D., Thévenin, A., and Stoye, J. (2012). Gene family assignment-free comparative genomics. BMC Bioinformatics 13, S3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2498160
Schröder, J., Maus, I., Meyer, K., Wördemann, S., Blom, J., Jaenicke, S., Schneider, J., Trost, E., and Tauch, A. (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 13:141.
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