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414 Publikationen

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.
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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., 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.
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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.
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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., 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.
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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).
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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.
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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., Goesmann, A., von Haeseler, A., Stoye, J., et al. (2013). Updating benchtop sequencing performance comparison. Nature Biotechnology 31, 294-296.
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2013 | Konferenzband | Veröffentlicht | PUB-ID: 2616537
Darling, A., and Stoye, J. eds. (2013). Algorithms in Bioinformatics. Lecture Notes in Bioinformatics 8126.
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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.
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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., 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.
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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., 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.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2552092
Wittler, R. (2013). Unraveling overlapping deletions by agglomerative clustering. BMC Genomics 14, S12.
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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.
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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.
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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.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512642
Dörr, D., Thévenin, A., and Stoye, J. (2012). Gene family assignment-free comparative genomics. BMC Bioinformatics 13, 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., 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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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517239
Hoffmann, N., Keck, M., Neuweger, H., Wilhelm, M., Högy, P., Niehaus, K., and Stoye, J. (2012). Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinformatics 13, 21.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512644
Jahn, K., Sudek, H., and Stoye, J. (2012). Multiple genome comparison based on overlap regions of pairwise local alignments. BMC Bioinformatics 13, S7.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2513347
Trost, E., Blom, J., de Castro Soares, S., Huang, I. - H., Al-Dilaimi, A., Schröder, J., Jaenicke, S., Dorella, F. A., Rocha, F. S., Miyoshi, A., et al. (2012). Pangenomic Study of Corynebacterium diphtheriae That Provides Insights into the Genomic Diversity of Pathogenic Isolates from Cases of Classical Diphtheria, Endocarditis, and Pneumonia. Journal of bacteriology 194, 3199-3215.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2490949
Zschuttig, A., Zimmermann, K., Blom, J., Goesmann, A., Pohlmann, C., and Gunzer, F. (2012). Identification and Characterization of Microcin S, a New Antibacterial Peptide Produced by Probiotic Escherichia coli G3/10. PLoS ONE 7, e33351.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2527519
Ruijter, J. M., Pfaffl, M. W., Zhao, S., Spiess, A. N., Boggy, G., Blom, J., Rutledge, R. G., Sisti, D., Lievens, A., De Preter, K., et al. (2012). Evaluation of qPCR curve analysis methods for reliable biomarker discovery: Bias, resolution, precision, and implications. Methods. A companion to methods in enzymology (San Diego, Calif.) 59, 32-46.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2709879
Doerr, D., Hu, K., Renly, S., Edlund, S., and Davis, M. (2012). Accelerating investigation of food-borne disease outbreaks using pro-active geospatial modeling of food supply chains. HealthGIS '12: Proceedings of the First ACM SIGSPATIAL International Workshop on Use of GIS in Public Health, 44-47.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2553484
Marschall, T., Herms, I., Kaltenbach, H. - M., and Rahmann, S. (2012). Probabilistic Arithmetic Automata and Their Applications. Ieee/Acm Transactions On Computational Biology And Bioinformatics 9, 1737-1750.
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2012 | Bielefelder E-Dissertation | PUB-ID: 2468026
Gerlach, W. (2012). Taxonomic classification of metagenomic sequences. Bielefeld: Universität.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2553300
Manuch, J., Patterson, M., Wittler, R., Chauve, C., and Tannier, E. (2012). Linearization of ancestral multichromosomal genomes. BMC Bioinformatics 13.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659289
Canavez, F. C., Luche, D. D., Stothard, P., Leite, K. R. M., Sousa-Canavez, J. M., Plastow, G., Meidanis, J., Souza, M. A., Feijão, P., Moore, S. S., et al. (2012). Genome Sequence and Assembly of Bos indicus. Journal of Heredity 103, 342-348.
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2012 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2659385
Mira, C., Feijão, P., Souza, M. A., Moura, A., Meidanis, J., Lima, G., Schmitz, R., Bossolan, R. P., and Freitas, I. T. (2012). “A GRASP-based Heuristic for the Project Portfolio Selection Problem” in 2012 IEEE 15th International Conference on Computational Science and Engineering 36-41.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2553455
De Maayer, P., Chan, W. - Y., Blom, J., Venter, S. N., Duffy, B., Smits, T. H. M., and Coutinho, T. A. (2012). The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification. Bmc Genomics 13, 625.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2486060
Schwientek, P., Szczepanowski, R., Rückert, C., Kalinowski, J., Klein, A., Selber, K., Wehmeier, U. F., Stoye, J., and Pühler, A. (2012). The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. BMC Genomics 13:112.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659280
Biller, P., Feijão, P., and Meidanis, J. (2012). Rearrangement-Based Phylogeny Using the Single-Cut-or-Join Operation. IEEE/ACM transactions on computational biology and bioinformatics 10, 122-134.
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2012 | Konferenzband | Veröffentlicht | PUB-ID: 2510416
Kärkkäinen, J., and Stoye, J. eds. (2012). Combinatorial Pattern Matching. Lecture Notes in Computer Science 7354.
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2012 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2468382
Hoffmann, N., and Stoye, J. (2012). “Generic Software Frameworks for GC-MS Based Metabolomics” in Metabolomics, Roessner, U. ed. (InTech), 73-98.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2510984
Hilker, R., Sickinger, C., Pedersen, C. N. S., and Stoye, J. (2012). UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ. Bioinformatics 28, 2509-2511.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2542210
Parreira, V. R., Costa, M., Eikmeyer, F. G., Blom, J., and Prescott, J. F. (2012). Sequence of Two Plasmids from Clostridium perfringens Chicken Necrotic Enteritis Isolates and Comparison with C. perfringens Conjugative Plasmids. PLoS ONE 7, e49753.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Bielefelder E-Dissertation | PUB-ID: 2533144
Zakrzewski, M. (2012). Development of computational methods for the analysis of metagenome and metatranscriptome data. Bielefeld: Universität Bielefeld.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2493233
Burcsi, P., Cicalese, F., Fici, G., and Lipták, Z. (2012). ALGORITHMS FOR JUMBLED PATTERN MATCHING IN STRINGS. International Journal of Foundations of Computer Science 23, 357-374.
PUB | DOI | WoS | arXiv
 
2012 | Bielefelder E-Dissertation | PUB-ID: 2484427
Schwientek, P. (2012). Genomics and transcriptomics of the industrial acarbose producer Actinoplanes sp. SE50/110. Bielefeld: Universität Bielefeld.
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2012 | Bielefelder E-Dissertation | PUB-ID: 2517237
Bunkowski, A. (2012). MCC-IMS data analysis using automated spectra processing and explorative visualisation methods. Bielefeld: Bielefeld University.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2526281
Zischka, M., Kuenne, C., Blom, J., Dabrowski, P. W., Linke, B., Hain, T., Nitsche, A., Goesmann, A., Larsen, J., Jensen, L. B., et al. (2012). Complete Genome Sequence of the Porcine Isolate Enterococcus faecalis D32. Journal of Bacteriology 194, 5490-5491.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2526298
Maus, I., Wibberg, D., Stantscheff, R., Eikmeyer, F. G., Seffner, A., Boelter, J., Szczepanowski, R., Blom, J., Jaenicke, S., König, H., et al. (2012). Complete Genome Sequence of the Hydrogenotrophic, Methanogenic Archaeon Methanoculleus bourgensis Strain MS2T, Isolated from a Sewage Sludge Digester. Journal of Bacteriology 194, 5487-5488.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2526933
Dohrmann, A. B., Küting, M., Jünemann, S., Jaenicke, S., Schlüter, A., and Tebbe, C. C. (2012). Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties. The ISME journal 7, 37-49.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517230
Jünemann, S., Prior, K., Szczepanowski, R., Harks, I., Ehmke, B., Goesmann, A., Stoye, J., and Harmsen, D. (2012). Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing. PLoS ONE 7, e41606.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2501312
Gorzolka, K., Lissel, M., Kessler, N., Loch-Ahring, S., and Niehaus, K. (2012). Metabolite fingerprinting of barley whole seeds, endosperms, and embryos during industrial malting. Journal of Biotechnology 159, 177-187.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2490286
Vogel, U., Szczepanowski, R., Claus, H., Jünemann, S., Prior, K., and Harmsen, D. (2012). Ion Torrent PGM sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information. Journal of clinical microbiology 50, 1889-1894.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396558
Dias Vieira Braga, M., Machado, R., Ribeiro, L. C., and Stoye, J. (2011). On the weight of indels in genomic distances. BMC Bioinformatics 12:S13.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396509
Dias Vieira Braga, M., Machado, R., Ribeiro, L. C., and Stoye, J. (2011). Genomic distance under gene substitutions. BMC Bioinformatics 12:S8.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091794
Dias Vieira Braga, M., Willing, E., and Stoye, J. (2011). Double Cut and Join with Insertions and Deletions. Journal of Computational Biology 18, 1167-1184.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091790
Kovac, J., Warren, R., Dias Vieira Braga, M., and Stoye, J. (2011). Restricted DCJ Model. Rearrangement Problems with Chromosome Reincorporation. Journal of Computational Biology 18, 1231-1241.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2354746
Schwientek, P., Szczepanowski, R., Rückert, C., Stoye, J., and Pühler, A. (2011). Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology. Journal of Biotechnology 155, 68-77.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2375634
Pothier, J. F., Vorhölter, F. - J., Blom, J., Goesmann, A., Pühler, A., Smits, T. H., and Duffy, B. (2011). The ubiquitous plasmid pXap41 in the invasive phytopathogen Xanthomonas arboricola pv. pruni: complete sequence and comparative genomic analysis. FEMS Microbiology Letters 323, 52-60.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2404767
Niu, B., Rückert, C., Blom, J., Wang, Q., and Borriss, R. (2011). The Genome of the Plant Growth-Promoting Rhizobacterium Paenibacillus polymyxa M-1 Contains Nine Sites Dedicated to Nonribosomal Synthesis of Lipopeptides and Polyketides. Journal of Bacteriology 193, 5862-5863.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2354731
Wibberg, D., Blom, J., Jaenicke, S., Kollin, F., Rupp, O., Scharf, B., Schneiker-Bekel, S., Szczepanowski, R., Goesmann, A., Setubal, J. C., et al. (2011). Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. Journal of Biotechnology 155, 50-62.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659339
Feijão, P., and Meidanis, J. (2011). SCJ: A Breakpoint-Like Distance that Simplifies Several Rearrangement Problems. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8, 1318-1329.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2326511
Rückert, C., Blom, J., Chen, X. H., Reva, O., and Borriss, R. (2011). Genome sequence of B. amyloliquefaciens type strain DSM7(T) reveals differences to plant-associated B. amyloliquefaciens FZB42. Journal of Biotechnology 155, 78-85.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2373808
Herold, J., Loyek, C., and Nattkemper, T. W. (2011). Multivariate Image Mining. Wiley Interdisciplinary Reviews: DATA MINING AND KNOWLEDGE DISCOVERY 1, 2-13.
PUB | DOI | WoS
 
2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2659373
Mira, C., Feijão, P., Duque-Estrada, T., Meidanis, J., and Joly, C. A. (2011). “The SinBiota 2.0 Biodiversity Information System” in 2011 IEEE Seventh International Conference on eScience 142-149.
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2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2401639
Fici, G., and Lipták, Z. (2011). “On prefix normal words” in Development in Language Theory. 15th International Conference (DLT 2011). Proceedings, Mauri, G., and Leporati, A. eds. Lecture Notes in Computer Science, vol. 6795, (Berlin ; Heidelberg: Springer), 228-238.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2401665
Hazelhurst, S., and Lipták, Z. (2011). KABOOM! A new suffix-array based algorithm for clustering expression data. Bioinformatics 27, 3348-3355.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2375954
Borriss, R., Chen, X. - H., Rückert, C., Blom, J., Becker, A., Baumgarth, B., Fan, B., Pukall, R., Schumann, P., Sproer, C., et al. (2011). Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons. Int J Syst Evol Microbiol 61, 1786-1801.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2472468
Llop, P., Cabrefiga, J., Smits, T. H. M., Dreo, T., Barbé, S., Pulawska, J., Bultreys, A., Blom, J., Duffy, B., Montesinos, E., et al. (2011). Erwinia amylovora novel plasmid pEI70: Complete sequence, biogeography, and role in aggressiveness in the fire blight phytopathogen. PLoS one 6, e28651.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2423955
Cicalese, F., Erdős, P. L. P., and Lipták, Z. (2011). “Efficient Reconstruction of RC-Equivalent Strings” in Proc. WOCA, vol. 6460, 349-362.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2326445
Schneider, J., Blom, J., Jaenicke, S., Linke, B., Brinkrolf, K., Neuweger, H., Tauch, A., and Goesmann, A. (2011). RAPYD - Rapid Annotation Platform for Yeast Data. Journal of Biotechnology 155, 118-126.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2307104
Smits, T. H. M., Rezzonico, F., Kamber, T., Blom, J., Goesmann, A., Ishimaru, C. A., Frey, J. E., Stockwell, V. O., and Duffy, B. (2011). Metabolic Versatility and Antibacterial Metabolite Biosynthesis Are Distinguishing Genomic Features of the Fire Blight Antagonist Pantoea vagans C9-1. PLoS ONE 6, e22247.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2448409
Imperi, F., Antunes, L., Blom, J., Villa, L., Iacono, M., Visca, P., and Carattoli, A. (2011). The genomics of Acinetobacter baumannii: Insights into genome plasticity, antimicrobial resistance and pathogenicity. IUBMB life 63, 1068-1074.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2326455
Krol, E., Blom, J., Winnebald, J., Berhoerster, A., Barnett, M. J., Goesmann, A., Baumbach, J., and Becker, A. (2011). RhizoRegNet-A database of rhizobial transcription factors and regulatory networks. Journal of Biotechnology 155, 127-134.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2326518
Szczepanowski, R., Eikmeyer, F. G., Harfmann, J., Blom, J., Rogers, L. M., Top, E. M., and Schlüter, A. (2011). Sequencing and comparative analysis of IncP-1 alpha antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions. Journal of Biotechnology 155, 95-103.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2329973
Wittler, R., and Chauve, C. (2011). Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes. BMC Bioinformatics 12, S21.
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2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2425344
Cicalese, F., Erdős, P. L. P., and Lipták, Z. (2011). “Efficient Reconstruction of RC-Equivalent Strings” in Combinatorial Algorithms : 21st International Workshop, IWOCA 2010, London, UK, July 26-28, 2010, Revised Selected Papers Lecture Notes in Computer Science, vol. 6460, (Berlin, Heidelberg: Springer), 349-362.
PUB | DOI
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2290032
Joseph, B., Schwarz, R. F., Linke, B., Blom, J., Becker, A., Claus, H., Goesmann, A., Frosch, M., Mueller, T., Vogel, U., et al. (2011). Virulence Evolution of the Human Pathogen Neisseria meningitidis by Recombination in the Core and Accessory Genome. PLoS ONE 6, e18441.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2093389
Schoen, C., Weber-Lehmann, J., Blom, J., Joseph, B., Goesmann, A., Strittmatter, A., and Frosch, M. (2011). Whole-Genome Sequence of the Transformable Neisseria meningitidis Serogroup A Strain WUE2594. Journal of Bacteriology 193, 2064-2065.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2289887
Hinse, D., Vollmer, T., Rückert, C., Blom, J., Kalinowski, J., Knabbe, C., and Dreier, J. (2011). Complete Genome Analysis of Streptococcus gallolyticus subsp gallolyticus, an Emerging Pathogen of Infective Endocarditis. Clinical Chemistry and Laboratory Medicine 49, S837.
PUB | WoS
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2289952
Blom, J., Jakobi, T., Doppmeier, D., Jaenicke, S., Kalinowski, J., Stoye, J., and Goesmann, A. (2011). Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics 27, 1351-1358.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Bielefelder E-Dissertation | PUB-ID: 2324501
Husemann, P., and Tauch, A. (2011). Bioinformatic approaches for genome finishing. Bielefeld: Universitätsbibliothek Bielefeld.
PUB | PDF
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2425310
Wolfsheimer, S., Herms, I., Rahmann, S., and Hartmann, A. K. (2011). Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling. BMC Bioinformatics 12, 47-2105.
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2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2310613
Chauve, C., Maňuch, J., Patterson, M., and Wittler, R. (2011). “Tractability results for the Consecutive-Ones Property with multiplicity” in Proceedings of CPM 2011, vol. 6661, 90-103.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2289928
Kant, R., Blom, J., Palva, A., Siezen, R. J., and de Vos, W. M. (2011). Comparative genomics of Lactobacillus. Microbial Biotechnology 4, 323-332.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2492807
Schuster, F. R., Hubner, B., Führer, M., Eckermann, O., Gombert, M., Dornmair, K., Binder, V., Reuther, S., Krell, P., Keller, T., et al. (2011). Highly skewed T-cell receptor V-beta chain repertoire in the bone marrow is associated with response to immunosuppressive drug therapy in children with very severe aplastic anemia. Blood Cancer Journal 1, e8.
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2011 | Zeitschriftenaufsatz | Im Druck | PUB-ID: 2017892
Schneiker-Bekel, S., Wibberg, D., Bekel, T., Blom, J., Linke, B., Neuweger, H., Stiens, M., Vorhölter, F. - J., Weidner, S., Goesmann, A., et al. (In Press). The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome. Journal of Biotechnology 155, 20-33.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918550
Heber, S., Mayr, R., and Stoye, J. (2011). Common Intervals of Multiple Permutations. Algorithmica 60, 175-206.
PUB | DOI | WoS
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2036058
Margaret, I., Becker, A., Blom, J., Bonilla, I., Goesmann, A., Göttfert, M., Lloret, J., Mittard-Runte, V., Rückert, C., Ruiz-Sainz, J. - E., et al. (2011). Symbiotic properties and first analyses of the genomic sequence of the fast growing model strain Sinorhizobium fredii HH103 nodulating soybean. Journal of Biotechnology 155, 11-19.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2087955
Hackl, M., Jakobi, T., Blom, J., Doppmeier, D., Brinkrolf, K., Szczepanowski, R., Bernhart, S. H., Höner zu Siederdissen, C., Bort, J. A. H., Wieser, M., et al. (2011). Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of Biotechnology 153, 62-75.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2298170
Gerlach, W., and Stoye, J. (2011). Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res 39, e91.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2003418
Powney, R., Smits, T. H. M., Sawbridge, T., Frey, B., Blom, J., Frey, J. E., Plummer, K. M., Beer, S. V., Luck, J., Duffy, B., et al. (2011). Genome Sequence of an Erwinia amylovora Strain with Pathogenicity Restricted to Rubus Plants. Journal of Bacteriology 193, 785-786.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897974
Erdős, P. L., Soukup, L., and Stoye, J. (2011). Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance. Applied Mathematics Letters 24, 82-86.
PUB | DOI | WoS
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091787
Wittler, R., Maňuch, J., Patterson, M., and Stoye, J. (2011). Consistency of Sequence-Based Gene Clusters. Journal of Computational Biology 18, 1023-1039.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2093398
Brankatschk, K., Blom, J., Goesmann, A., Smits, T. H. M., and Duffy, B. (2011). Genome of a European Fresh-Vegetable Food Safety Outbreak Strain of Salmonella enterica subsp enterica Serovar Weltevreden. Journal of Bacteriology 193, 2066.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091779
Hufsky, F., Kuchenbecker, L., Jahn, K., Stoye, J., and Böcker, S. (2011). Swiftly Computing Center Strings. BMC Bioinformatics 12, 106.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Bielefelder E-Dissertation | PUB-ID: 2301939
Wittler, R. (2010). Phylogeny-based analysis of gene clusters. Bielefeld (Germany): Bielefeld University.
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2010 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2907492
Bergeron, A., Mixtacki, J., and Stoye, J. (2010). “A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance” in Structure Discovery in Biology: Motifs, Networks & Phylogenies, Apostolico, A., Dress, A., and Parida, L. eds. Dagstuhl Seminar Proceedings, vol. 10231, (Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany).
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2010 | Bielefelder E-Dissertation | PUB-ID: 2303705
Jahn, K. (2010). Approximate common intervals based gene cluster models. Bielefeld (Germany): Bielefeld University.
PUB | PDF
 
2010 | Bielefelder E-Dissertation | PUB-ID: 2301975
Wittkop, T. (2010). Clustering biological data by unraveling hidden transitive substructures. Bielefeld (Germany): Bielefeld University.
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2308298
Bunkowski, A., Maddula, S., Davies, A. N., Westhoff, M., Litterst, P., Bödeker, B., and Baumbach, J. I. (2010). One-year time series of investigations of analytes within human breath using ion mobility spectrometry. Int. J. Ion Mobility Spectrometry 13, 141-148.
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2425329
Bunkowski, A. (2010). Software tool for coupling chromatographic total ion current dependencies of GC/MSD and MCC/IMS. Int. J. Ion Mobil. Spectrom. 13, 169-175.
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2010 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2445157
Bergeron, A., Mixtacki, J., and Stoye, J. (2010). “Computing the Genomic Distance in Linear Time” in Dagstuhl Seminar Proceedings: 10231 Abstracts Collection : Structure Discovery in Biology: Motifs, Networks & Phylogenies, Apostolico, A., Dress, A., and Parida, L. eds., vol. 10231, (Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik), 18.
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1929692
Schneider, J., Vorhölter, F. - J., Trost, E., Blom, J., Musa, Y. R., Neuweger, H., Niehaus, K., Schatschneider, S., Tauch, A., and Goesmann, A. (2010). CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks. Genetics and Molecular Research 9, 1660-1672.
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2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2425332
Burcsi, P., Cicalese, F., Fici, G., and Lipták, Z. (2010). “On Table Arrangements, Scrabble Freaks, and Jumbled Pattern Matching” in Fun with Algorithms: 5th International Conference, FUN 2010, Ischia, Italy, June 2-4, 2010. Proceedings, Boldi, P. ed. Lecture Notes in Computer Science, vol. 6099, (Berlin, Heidelberg: Springer), 89-101.
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