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419 Publikationen

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., Passaglia, L.: 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 (2013).
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659331
Feijão, P., Meidanis, J.: Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 10, 819-831 (2013).
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2529202
Zakrzewski, M., Bekel, T., Ander, C., Pühler, A., Rupp, O., Stoye, J., Schlüter, A., Goesmann, A.: MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. Journal of Biotechnology. 167, 156-165 (2013).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2560353 OA
Dörr, D., Gronau, I., Moran, S., Yavneh, I.: Stochastic errors vs. modeling errors in distance based phylogenetic reconstructions. Algorithms for Molecular Biology. 7, 22 (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512642 OA
Dörr, D., Thévenin, A., Stoye, J.: Gene family assignment-free comparative genomics. BMC Bioinformatics. 13, S3 (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2498160 OA
Schröder, J., Maus, I., Meyer, K., Wördemann, S., Blom, J., Jaenicke, S., Schneider, J., Trost, E., Tauch, A.: 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 (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517239 OA
Hoffmann, N., Keck, M., Neuweger, H., Wilhelm, M., Högy, P., Niehaus, K., Stoye, J.: Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinformatics. 13, 21 (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512644 OA
Jahn, K., Sudek, H., Stoye, J.: Multiple genome comparison based on overlap regions of pairwise local alignments. BMC Bioinformatics. 13, S7 (2012).
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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., Azevedo, V., Schneider, M.P., Silva, A., Camello, T.C., Sabbadini, P.S., Santos, C.S., Santos, L.S., Hirata, R.J., Mattos-Guaraldi, A.L., Efstratiou, A., Schmitt, M.P., Ton-That, H., Tauch, A.: 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 (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2490949
Zschuttig, A., Zimmermann, K., Blom, J., Goesmann, A., Pohlmann, C., Gunzer, F.: Identification and Characterization of Microcin S, a New Antibacterial Peptide Produced by Probiotic Escherichia coli G3/10. PLoS ONE. 7, e33351 (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2709879
Doerr, D., Hu, K., Renly, S., Edlund, S., Davis, M.: 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 (2012).
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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., Derveaux, S., Hellemans, J., Vandesompele, J.: 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 (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2553484
Marschall, T., Herms, I., Kaltenbach, H.-M., Rahmann, S.: Probabilistic Arithmetic Automata and Their Applications. Ieee/Acm Transactions On Computational Biology And Bioinformatics. 9, 1737-1750 (2012).
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2012 | Bielefelder E-Dissertation | PUB-ID: 2468026 OA
Gerlach, W.: Taxonomic classification of metagenomic sequences. Universität, Bielefeld (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2553300
Manuch, J., Patterson, M., Wittler, R., Chauve, C., Tannier, E.: Linearization of ancestral multichromosomal genomes. BMC Bioinformatics. 13, (2012).
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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., Camara-Lopes, L.H.: Genome Sequence and Assembly of Bos indicus. Journal of Heredity. 103, 342-348 (2012).
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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., Freitas, I.T.: A GRASP-based Heuristic for the Project Portfolio Selection Problem. 2012 IEEE 15th International Conference on Computational Science and Engineering. p. 36-41. (2012).
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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., Coutinho, T.A.: The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification. Bmc Genomics. 13, 625 (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2486060 OA
Schwientek, P., Szczepanowski, R., Rückert, C., Kalinowski, J., Klein, A., Selber, K., Wehmeier, U.F., Stoye, J., Pühler, A.: The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. BMC Genomics. 13, : 112 (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659280
Biller, P., Feijão, P., Meidanis, J.: Rearrangement-Based Phylogeny Using the Single-Cut-or-Join Operation. IEEE/ACM transactions on computational biology and bioinformatics. 10, 122-134 (2012).
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2012 | Konferenzband | Veröffentlicht | PUB-ID: 2510416
Kärkkäinen, J., Stoye, J. eds: Combinatorial Pattern Matching. Lecture Notes in Computer Science. 7354, (2012).
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2012 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2468382 OA
Hoffmann, N., Stoye, J.: Generic Software Frameworks for GC-MS Based Metabolomics. In: Roessner, U. (ed.) Metabolomics. p. 73-98. InTech (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2510984
Hilker, R., Sickinger, C., Pedersen, C.N.S., Stoye, J.: UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ. Bioinformatics. 28, 2509-2511 (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2542210
Parreira, V.R., Costa, M., Eikmeyer, F.G., Blom, J., Prescott, J.F.: Sequence of Two Plasmids from Clostridium perfringens Chicken Necrotic Enteritis Isolates and Comparison with C. perfringens Conjugative Plasmids. PLoS ONE. 7, e49753 (2012).
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2012 | Bielefelder E-Dissertation | PUB-ID: 2533144 OA
Zakrzewski, M.: Development of computational methods for the analysis of metagenome and metatranscriptome data. Universität Bielefeld, Bielefeld (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2493233
Burcsi, P., Cicalese, F., Fici, G., Lipták, Z.: ALGORITHMS FOR JUMBLED PATTERN MATCHING IN STRINGS. International Journal of Foundations of Computer Science. 23, 357-374 (2012).
PUB | DOI | WoS | arXiv
 
2012 | Bielefelder E-Dissertation | PUB-ID: 2484427 OA
Schwientek, P.: Genomics and transcriptomics of the industrial acarbose producer Actinoplanes sp. SE50/110. Universität Bielefeld, Bielefeld (2012).
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2012 | Bielefelder E-Dissertation | PUB-ID: 2517237 OA
Bunkowski, A.: MCC-IMS data analysis using automated spectra processing and explorative visualisation methods. Bielefeld University, Bielefeld (2012).
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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., Witte, W., Werner, G.: Complete Genome Sequence of the Porcine Isolate Enterococcus faecalis D32. Journal of Bacteriology. 194, 5490-5491 (2012).
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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., Pühler, A., Schlüter, A.: Complete Genome Sequence of the Hydrogenotrophic, Methanogenic Archaeon Methanoculleus bourgensis Strain MS2T, Isolated from a Sewage Sludge Digester. Journal of Bacteriology. 194, 5487-5488 (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2526933
Dohrmann, A.B., Küting, M., Jünemann, S., Jaenicke, S., Schlüter, A., Tebbe, C.C.: Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties. The ISME journal. 7, 37-49 (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517230
Jünemann, S., Prior, K., Szczepanowski, R., Harks, I., Ehmke, B., Goesmann, A., Stoye, J., Harmsen, D.: Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing. PLoS ONE. 7, e41606 (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2501312
Gorzolka, K., Lissel, M., Kessler, N., Loch-Ahring, S., Niehaus, K.: Metabolite fingerprinting of barley whole seeds, endosperms, and embryos during industrial malting. Journal of Biotechnology. 159, 177-187 (2012).
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2490286
Vogel, U., Szczepanowski, R., Claus, H., Jünemann, S., Prior, K., Harmsen, D.: 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 (2012).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897974
Erdős, P.L., Soukup, L., Stoye, J.: Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance. Applied Mathematics Letters. 24, 82-86 (2011).
PUB | DOI | WoS | arXiv
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396558 OA
Dias Vieira Braga, M., Machado, R., Ribeiro, L.C., Stoye, J.: On the weight of indels in genomic distances. BMC Bioinformatics. 12, : S13 (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396509 OA
Dias Vieira Braga, M., Machado, R., Ribeiro, L.C., Stoye, J.: Genomic distance under gene substitutions. BMC Bioinformatics. 12, : S8 (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091794
Dias Vieira Braga, M., Willing, E., Stoye, J.: Double Cut and Join with Insertions and Deletions. Journal of Computational Biology. 18, 1167-1184 (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091790
Kovac, J., Warren, R., Dias Vieira Braga, M., Stoye, J.: Restricted DCJ Model. Rearrangement Problems with Chromosome Reincorporation. Journal of Computational Biology. 18, 1231-1241 (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2354746
Schwientek, P., Szczepanowski, R., Rückert, C., Stoye, J., Pühler, A.: Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology. Journal of Biotechnology. 155, 68-77 (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2375634
Pothier, J.F., Vorhölter, F.-J., Blom, J., Goesmann, A., Pühler, A., Smits, T.H., Duffy, B.: The ubiquitous plasmid pXap41 in the invasive phytopathogen Xanthomonas arboricola pv. pruni: complete sequence and comparative genomic analysis. FEMS Microbiology Letters. 323, 52-60 (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2404767
Niu, B., Rückert, C., Blom, J., Wang, Q., Borriss, R.: 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 (2011).
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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., Schmitt, R., Pühler, A., Schlüter, A.: 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 (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659339
Feijão, P., Meidanis, J.: SCJ: A Breakpoint-Like Distance that Simplifies Several Rearrangement Problems. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8, 1318-1329 (2011).
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2326511
Rückert, C., Blom, J., Chen, X.H., Reva, O., Borriss, R.: Genome sequence of B. amyloliquefaciens type strain DSM7(T) reveals differences to plant-associated B. amyloliquefaciens FZB42. Journal of Biotechnology. 155, 78-85 (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2373808
Herold, J., Loyek, C., Nattkemper, T.W.: Multivariate Image Mining. Wiley Interdisciplinary Reviews: DATA MINING AND KNOWLEDGE DISCOVERY. 1, 2-13 (2011).
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2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2659373
Mira, C., Feijão, P., Duque-Estrada, T., Meidanis, J., Joly, C.A.: The SinBiota 2.0 Biodiversity Information System. 2011 IEEE Seventh International Conference on eScience. p. 142-149. (2011).
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2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2401639
Fici, G., Lipták, Z.: On prefix normal words. In: Mauri, G. and Leporati, A. (eds.) Development in Language Theory. 15th International Conference (DLT 2011). Proceedings. Lecture Notes in Computer Science. 6795, p. 228-238. Springer, Berlin ; Heidelberg (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2401665
Hazelhurst, S., Lipták, Z.: KABOOM! A new suffix-array based algorithm for clustering expression data. Bioinformatics. 27, 3348-3355 (2011).
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., Junge, H., Vater, J., Pühler, A., Klenk, H.-P.: 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 (2011).
PUB | DOI | WoS | PubMed | Europe PMC
 
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., Lopez, M.M.: Erwinia amylovora novel plasmid pEI70: Complete sequence, biogeography, and role in aggressiveness in the fire blight phytopathogen. PLoS one. 6, e28651 (2011).
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2423955
Cicalese, F., Erdős, P.L.P., Lipták, Z.: Efficient Reconstruction of RC-Equivalent Strings. Proc. WOCA. 6460, p. 349-362. (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2326445
Schneider, J., Blom, J., Jaenicke, S., Linke, B., Brinkrolf, K., Neuweger, H., Tauch, A., Goesmann, A.: RAPYD - Rapid Annotation Platform for Yeast Data. Journal of Biotechnology. 155, 118-126 (2011).
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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., Duffy, B.: Metabolic Versatility and Antibacterial Metabolite Biosynthesis Are Distinguishing Genomic Features of the Fire Blight Antagonist Pantoea vagans C9-1. PLoS ONE. 6, e22247 (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2448409
Imperi, F., Antunes, L., Blom, J., Villa, L., Iacono, M., Visca, P., Carattoli, A.: The genomics of Acinetobacter baumannii: Insights into genome plasticity, antimicrobial resistance and pathogenicity. IUBMB life. 63, 1068-1074 (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2326455
Krol, E., Blom, J., Winnebald, J., Berhoerster, A., Barnett, M.J., Goesmann, A., Baumbach, J., Becker, A.: RhizoRegNet-A database of rhizobial transcription factors and regulatory networks. Journal of Biotechnology. 155, 127-134 (2011).
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., Schlüter, A.: 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 (2011).
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2329973
Wittler, R., Chauve, C.: Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes. BMC Bioinformatics. 12, S21 (2011).
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2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2425344
Cicalese, F., Erdős, P.L.P., Lipták, Z.: Efficient Reconstruction of RC-Equivalent Strings. Combinatorial Algorithms : 21st International Workshop, IWOCA 2010, London, UK, July 26-28, 2010, Revised Selected Papers. Lecture Notes in Computer Science. 6460, p. 349-362. Springer, Berlin, Heidelberg (2011).
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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., Schoen, C.: Virulence Evolution of the Human Pathogen Neisseria meningitidis by Recombination in the Core and Accessory Genome. PLoS ONE. 6, e18441 (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2093389
Schoen, C., Weber-Lehmann, J., Blom, J., Joseph, B., Goesmann, A., Strittmatter, A., Frosch, M.: Whole-Genome Sequence of the Transformable Neisseria meningitidis Serogroup A Strain WUE2594. Journal of Bacteriology. 193, 2064-2065 (2011).
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., Dreier, J.: Complete Genome Analysis of Streptococcus gallolyticus subsp gallolyticus, an Emerging Pathogen of Infective Endocarditis. Clinical Chemistry and Laboratory Medicine. 49, S837 (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2289952
Blom, J., Jakobi, T., Doppmeier, D., Jaenicke, S., Kalinowski, J., Stoye, J., Goesmann, A.: Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics. 27, 1351-1358 (2011).
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Bielefelder E-Dissertation | PUB-ID: 2324501 OA
Husemann, P., Tauch, A.: Bioinformatic approaches for genome finishing. Universitätsbibliothek Bielefeld, Bielefeld (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2425310
Wolfsheimer, S., Herms, I., Rahmann, S., Hartmann, A.K.: Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling. BMC Bioinformatics. 12, 47-2105 (2011).
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2310613
Chauve, C., Maňuch, J., Patterson, M., Wittler, R.: Tractability results for the Consecutive-Ones Property with multiplicity. Proceedings of CPM 2011. 6661, p. 90-103. (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2289928
Kant, R., Blom, J., Palva, A., Siezen, R.J., de Vos, W.M.: Comparative genomics of Lactobacillus. Microbial Biotechnology. 4, 323-332 (2011).
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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., Borkhardt, A.: 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 (2011).
PUB | DOI | WoS | PubMed | Europe PMC
 
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., Pühler, A., Schlüter, A.: The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome. Journal of Biotechnology. 155, 20-33 (In Press).
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918550
Heber, S., Mayr, R., Stoye, J.: Common Intervals of Multiple Permutations. Algorithmica. 60, 175-206 (2011).
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., Vinardell, J.M., Weidner, S.: 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 (2011).
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., Kunert, R., Jeffs, S., Hofacker, I.L., Goesmann, A., Pühler, A., Borth, N., Grillari, J.: 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 (2011).
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2298170 OA
Gerlach, W., Stoye, J.: Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res. 39, e91 (2011).
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., Rodoni, B.: Genome Sequence of an Erwinia amylovora Strain with Pathogenicity Restricted to Rubus Plants. Journal of Bacteriology. 193, 785-786 (2011).
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091787
Wittler, R., Maňuch, J., Patterson, M., Stoye, J.: Consistency of Sequence-Based Gene Clusters. Journal of Computational Biology. 18, 1023-1039 (2011).
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2093398
Brankatschk, K., Blom, J., Goesmann, A., Smits, T.H.M., Duffy, B.: Genome of a European Fresh-Vegetable Food Safety Outbreak Strain of Salmonella enterica subsp enterica Serovar Weltevreden. Journal of Bacteriology. 193, 2066 (2011).
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091779
Hufsky, F., Kuchenbecker, L., Jahn, K., Stoye, J., Böcker, S.: Swiftly Computing Center Strings. BMC Bioinformatics. 12, 106 (2011).
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Bielefelder E-Dissertation | PUB-ID: 2301939 OA
Wittler, R.: Phylogeny-based analysis of gene clusters. Bielefeld University, Bielefeld (Germany) (2010).
PUB | PDF | Download (ext.)
 
2010 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2907492
Bergeron, A., Mixtacki, J., Stoye, J.: A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance. In: Apostolico, A., Dress, A., and Parida, L. (eds.) Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings. 10231, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, Dagstuhl, Germany (2010).
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2010 | Bielefelder E-Dissertation | PUB-ID: 2303705 OA
Jahn, K.: Approximate common intervals based gene cluster models. Bielefeld University, Bielefeld (Germany) (2010).
PUB | PDF
 
2010 | Bielefelder E-Dissertation | PUB-ID: 2301975 OA
Wittkop, T.: Clustering biological data by unraveling hidden transitive substructures. Bielefeld University, Bielefeld (Germany) (2010).
PUB | PDF
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2308298
Bunkowski, A., Maddula, S., Davies, A.N., Westhoff, M., Litterst, P., Bödeker, B., Baumbach, J.I.: One-year time series of investigations of analytes within human breath using ion mobility spectrometry. Int. J. Ion Mobility Spectrometry. 13, 141-148 (2010).
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2425329
Bunkowski, A.: Software tool for coupling chromatographic total ion current dependencies of GC/MSD and MCC/IMS. Int. J. Ion Mobil. Spectrom. 13, 169-175 (2010).
PUB | DOI
 
2010 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2445157
Bergeron, A., Mixtacki, J., Stoye, J.: Computing the Genomic Distance in Linear Time. In: Apostolico, A., Dress, A., and Parida, L. (eds.) Dagstuhl Seminar Proceedings: 10231 Abstracts Collection : Structure Discovery in Biology: Motifs, Networks & Phylogenies. 10231, p. 18. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Dagstuhl (2010).
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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., Goesmann, A.: CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks. Genetics and Molecular Research. 9, 1660-1672 (2010).
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2425332
Burcsi, P., Cicalese, F., Fici, G., Lipták, Z.: On Table Arrangements, Scrabble Freaks, and Jumbled Pattern Matching. In: Boldi, P. (ed.) Fun with Algorithms: 5th International Conference, FUN 2010, Ischia, Italy, June 2-4, 2010. Proceedings. Lecture Notes in Computer Science. 6099, p. 89-101. Springer, Berlin, Heidelberg (2010).
PUB | DOI
 
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2425351
Jahn, K.: Efficient Computation of Approximate Gene Clusters Based on Reference Occurrences. Proc. RECOMB-CG. 6398, p. 264-277. (2010).
PUB
 
2010 | Bielefelder E-Dissertation | PUB-ID: 2302499 OA
Quitzau, J.A.A.: Biological applications for de Bruijn subgraphs and interval group testing. Bielefeld University, Bielefeld (Germany) (2010).
PUB | PDF
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1893893 OA
Husemann, P., Stoye, J.: Phylogenetic Comparative Assembly. Algorithms for Molecular Biology. 5, 3 (2010).
PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
2010 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918836
Besenbacher, S., Schwikowski, B., Stoye, J.: Indexing and Searching a Mass Spectrometry Database. In: Elomaa, T., Mannila, H., and Orponen, P. (eds.) Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday. LNCS. 6060, p. 62-76. (2010).
PUB | DOI
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1966439
Trost, E., Ott, L., Schneider, J., Schröder, J., Jaenicke, S., Goesmann, A., Husemann, P., Stoye, J., Alves Dorella, F., Souza Rocha, F., de Castro Soares, S., D'Afonseca, V., Miyoshi, A., Ruiz, J., Silva, A., Azevedo, V., Burkovski, A., Guiso, N., Join-Lambert, O.F., Kayal, S., Tauch, A.: The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence. BMC Genomics. 11, : 728 (2010).
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1785275 OA
Trost, E., Götker, S., Schneider, J., Schneiker-Bekel, S., Szczepanowski, R., Tilker, A., Viehöver, P., Arnold, W., Bekel, T., Blom, J., Gartemann, K.-H., Linke, B., Goesmann, A., Pühler, A., Shukla, S.K., Tauch, A.: Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion. BMC Genomics. 11, : 91 (2010).
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1795670
Wittkop, T., Emig, D., Lange, S.J., Rahmann, S., Albrecht, M., Morris, J.H., Böcker, S., Stoye, J., Baumbach, J.: Partitioning Biological Data with Transitivity Clustering. Nature Methods. 7, 419-420 (2010).
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1796445
Smits, T.H.M., Rezzonico, F., Kamber, T., Blom, J., Goesmann, A., Frey, J.E., Duffy, B.: Complete Genome Sequence of the Fire Blight Pathogen Erwinia amylovora CFBP 1430 and Comparison to Other Erwinia spp. MOLECULAR PLANT-MICROBE INTERACTIONS. 23, 384-393 (2010).
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898012
Blin, G., Faye, D., Stoye, J.: Finding Nested Common Intervals Efficiently. Journal of Computational Biology. 17, 1183-1194 (2010).
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1894907
Mittard-Runte, V., Bekel, T., Blom, J., Dondrup, M., Henckel, K., Jaenicke, S., Krause, L., Linke, B., Neuweger, H., Schneiker-Bekel, S., Goesmann, A.: Practical Guide: Genomic Techniques and How to Apply Them to Marine Questions. In: Cock, J.M., Tessmar-Raible, K., Boyen, C., and Viard, F. (eds.) Introduction to Marine Genomics (Advances in Marine Genomics). 1, p. 315-396. Springer Netherlands, Netherlands (2010).
PUB | DOI
 
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919217
Wittler, R., Stoye, J.: Consistency of Sequence-based Gene Clusters. Proc. of Recomb-CG 2010. LNBI. 6398, p. 252-263. Springer Verlag (2010).
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1893890
Husemann, P., Stoye, J.: Repeat-aware Comparative Genome Assembly. Proc. of GCB 2010. LNI. P-173, p. 61-70. (2010).
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588556
Husemann, P., Stoye, J.: r2cat: Synteny Plots and Comparative Assembly. Bioinformatics. 26, 570-571 (2010).
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897997
Bergeron, A., Medvedev, P., Stoye, J.: Rearrangement Models and Single-Cut Operations. Journal of Computational Biology. 17, 1213-1225 (2010).
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