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421 Publikationen

2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2548236
Schwientek, Patrick, Wendler, Sergej, Neshat, Armin, Eirich, Christina, Rückert, Christian, Klein, Andreas, Wehmeier, Udo F, Kalinowski, Jörn, Stoye, Jens, and Pühler, Alfred. “Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media”. Journal of Biotechnology 167.2 (2013): 166-177.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2548286
Luque-Almagro, Víctor M, Acera, Felipe, Igeño, Ma Isabel, Wibberg, Daniel, Roldán, Ma Dolores, Sáez, Lara P, Hennig, Magdalena, Quesada, Alberto, Huertas, Ma José, Blom, Jochen, Merchán, Faustino, Escribano, Ma Paz, Jaenicke, Sebastian, Estepa, Jessica, Guijo, Ma Isabel, Martínez-Luque, Manuel, Macías, Daniel, Szczepanowski, Rafael, Becerra, Gracia, Ramirez, Silvia, Carmona, Ma Isabel, Gutiérrez, Oscar, Manso, Isabel, Pühler, Alfred, Castillo, Francisco, Moreno-Vivián, Conrado, Schlüter, Andreas, and Blasco, Rafael. “Draft whole genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344”. Environmental Microbiology 15.1 (2013): 253-270.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2552092 OA
Wittler, Roland. “Unraveling overlapping deletions by agglomerative clustering”. BMC Genomics 14.Suppl 1 (2013): S12.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659331
Feijão, Pedro, and Meidanis, Joao. “Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10.4 (2013): 819-831.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2529202
Zakrzewski, Martha, Bekel, Thomas, Ander, Christina, Pühler, Alfred, Rupp, Oliver, Stoye, Jens, Schlüter, Andreas, and Goesmann, Alexander. “MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets”. Journal of Biotechnology 167.2 (2013): 156-165.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2560353 OA
Dörr, Daniel, Gronau, Ilan, Moran, Shlomo, and Yavneh, Irad. “Stochastic errors vs. modeling errors in distance based phylogenetic reconstructions”. Algorithms for Molecular Biology 7.1 (2012): 22.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512642 OA
Dörr, Daniel, Thévenin, Annelyse, and Stoye, Jens. “Gene family assignment-free comparative genomics”. BMC Bioinformatics 13.Suppl 19: Proc. of RECOMB-CG 2012 (2012): S3.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2498160 OA
Schröder, Jasmin, Maus, Irena, Meyer, Katja, Wördemann, Stephanie, Blom, Jochen, Jaenicke, Sebastian, Schneider, Jessica, Trost, Eva, and Tauch, Andreas. “Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient”. BMC Genomics 13.1 (2012): 141.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517239 OA
Hoffmann, Nils, Keck, Matthias, Neuweger, Heiko, Wilhelm, Mathias, Högy, Petra, Niehaus, Karsten, and Stoye, Jens. “Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets”. BMC Bioinformatics 13.1 (2012): 21.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512644 OA
Jahn, Katharina, Sudek, Henner, and Stoye, Jens. “Multiple genome comparison based on overlap regions of pairwise local alignments”. BMC Bioinformatics 13.Suppl. 19: Proc. of RECOMB-CG 2012 (2012): S7.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2513347
Trost, Eva, Blom, Jochen, de Castro Soares, Siomar, Huang, I-Hsiu, Al-Dilaimi, Arwa, Schröder, Jasmin, Jaenicke, Sebastian, Dorella, Fernanda A, Rocha, Flavia S, Miyoshi, Anderson, Azevedo, Vasco, Schneider, Maria P, Silva, Artur, Camello, Thereza C, Sabbadini, Priscila S, Santos, Cintia S, Santos, Louisy S, Hirata, Raphael Jr, Mattos-Guaraldi, Ana L, Efstratiou, Androulla, Schmitt, Michael P, Ton-That, Hung, and Tauch, Andreas. “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 194.12 (2012): 3199-3215.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2490949
Zschuttig, Anke, Zimmermann, Kurt, Blom, Jochen, Goesmann, Alexander, Pohlmann, Christoph, and Gunzer, Florian. “Identification and Characterization of Microcin S, a New Antibacterial Peptide Produced by Probiotic Escherichia coli G3/10”. PLoS ONE 7.3 (2012): e33351.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2709879
Doerr, D, Hu, K, Renly, S, Edlund, S, and 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 (2012): 44-47.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2527519
Ruijter, Jan M, Pfaffl, Michael W, Zhao, Sheng, Spiess, Andrej N, Boggy, Gregory, Blom, Jochen, Rutledge, Robert G, Sisti, Davide, Lievens, Antoon, De Preter, Katleen, Derveaux, Stefaan, Hellemans, Jan, and Vandesompele, Jo. “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.) 59.1 (2012): 32-46.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2553484
Marschall, T., Herms, Inke, Kaltenbach, Hans-Michael, and Rahmann, Sven. “Probabilistic Arithmetic Automata and Their Applications”. Ieee/Acm Transactions On Computational Biology And Bioinformatics 9.6 (2012): 1737-1750.
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2012 | Bielefelder E-Dissertation | PUB-ID: 2468026 OA
Gerlach, Wolfgang. Taxonomic classification of metagenomic sequences. Bielefeld: Universität, 2012.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2553300
Manuch, Jan, Patterson, Murray, Wittler, Roland, Chauve, Cedric, and Tannier, Eric. “Linearization of ancestral multichromosomal genomes”. BMC Bioinformatics 13.Proc. of RECOMB-CG 2012 (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, Pedro, Moore, S. S., and Camara-Lopes, L. H. “Genome Sequence and Assembly of Bos indicus”. Journal of Heredity 103.3 (2012): 342-348.
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2012 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2659385
Mira, Cleber, Feijão, Pedro, Souza, Maria Angelica, Moura, Arnaldo, Meidanis, Joao, Lima, Gabriel, Schmitz, Rafael, Bossolan, Renato P., and Freitas, Italo T. “A GRASP-based Heuristic for the Project Portfolio Selection Problem”. 2012 IEEE 15th International Conference on Computational Science and Engineering. 2012. 36-41.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2553455
De Maayer, Pieter, Chan, Wai-Yin, Blom, Jochen, Venter, Stephanus N., Duffy, Brion, Smits, Theo H. M., and Coutinho, Teresa A. “The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification”. Bmc Genomics 13.1 (2012): 625.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2486060 OA
Schwientek, Patrick, Szczepanowski, Rafael, Rückert, Christian, Kalinowski, Jörn, Klein, Andreas, Selber, Klaus, Wehmeier, Udo F., Stoye, Jens, and Pühler, Alfred. “The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110”. BMC Genomics 13.1 (2012): 112.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659280
Biller, Priscilla, Feijão, Pedro, and Meidanis, João. “Rearrangement-Based Phylogeny Using the Single-Cut-or-Join Operation.”. IEEE/ACM transactions on computational biology and bioinformatics 10.1 (2012): 122-134.
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2012 | Konferenzband | Veröffentlicht | PUB-ID: 2510416
Juha Kärkkäinen and Jens Stoye, eds. “Combinatorial Pattern Matching”. Lecture Notes in Computer Science 7354 (2012).
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2012 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2468382 OA
Hoffmann, Nils, and Stoye, Jens. “Generic Software Frameworks for GC-MS Based Metabolomics”. Metabolomics. Ed. Ute Roessner. InTech, 2012. 73-98.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2510984
Hilker, Rolf, Sickinger, Corinna, Pedersen, Christian N. S., and Stoye, Jens. “UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ”. Bioinformatics 28.19 (2012): 2509-2511.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2542210
Parreira, Valeria R., Costa, Marcio, Eikmeyer, Felix Gregor, Blom, Jochen, and Prescott, John F. “Sequence of Two Plasmids from Clostridium perfringens Chicken Necrotic Enteritis Isolates and Comparison with C. perfringens Conjugative Plasmids”. PLoS ONE 7.11 (2012): e49753.
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2012 | Bielefelder E-Dissertation | PUB-ID: 2533144 OA
Zakrzewski, Martha. Development of computational methods for the analysis of metagenome and metatranscriptome data. Bielefeld: Universität Bielefeld, 2012.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2493233
Burcsi, Peter, Cicalese, Ferdinando, Fici, Gabriele, and Lipták, Zsuzsanna. “ALGORITHMS FOR JUMBLED PATTERN MATCHING IN STRINGS”. International Journal of Foundations of Computer Science 23.02 (2012): 357-374.
PUB | DOI | WoS | arXiv
 
2012 | Bielefelder E-Dissertation | PUB-ID: 2484427 OA
Schwientek, Patrick. Genomics and transcriptomics of the industrial acarbose producer Actinoplanes sp. SE50/110. Bielefeld: Universität Bielefeld, 2012.
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2012 | Bielefelder E-Dissertation | PUB-ID: 2517237 OA
Bunkowski, Alexander. MCC-IMS data analysis using automated spectra processing and explorative visualisation methods. Bielefeld: Bielefeld University, 2012.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2526281
Zischka, M., Kuenne, C., Blom, Jochen, Dabrowski, P. W., Linke, Burkhard, Hain, T., Nitsche, A., Goesmann, Alexander, Larsen, J., Jensen, L. B., Witte, W., and Werner, G. “Complete Genome Sequence of the Porcine Isolate Enterococcus faecalis D32”. Journal of Bacteriology 194.19 (2012): 5490-5491.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2526298
Maus, Irena, Wibberg, Daniel, Stantscheff, R., Eikmeyer, Felix Gregor, Seffner, A., Boelter, J., Szczepanowski, Rafael, Blom, Jochen, Jaenicke, Sebastian, König, H., Pühler, Alfred, and Schlüter, Andreas. “Complete Genome Sequence of the Hydrogenotrophic, Methanogenic Archaeon Methanoculleus bourgensis Strain MS2T, Isolated from a Sewage Sludge Digester”. Journal of Bacteriology 194.19 (2012): 5487-5488.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2526933
Dohrmann, Anja B, Küting, Meike, Jünemann, Sebastian, Jaenicke, Sebastian, Schlüter, Andreas, and Tebbe, Christoph C. “Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties”. The ISME journal 7.1 (2012): 37-49.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517230
Jünemann, Sebastian, Prior, Karola, Szczepanowski, Rafael, Harks, Inga, Ehmke, Benjamin, Goesmann, Alexander, Stoye, Jens, and Harmsen, Dag. “Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing”. PLoS ONE 7.8 (2012): e41606.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2501312
Gorzolka, Karin, Lissel, Manfred, Kessler, Nikolas, Loch-Ahring, S., and Niehaus, Karsten. “Metabolite fingerprinting of barley whole seeds, endosperms, and embryos during industrial malting”. Journal of Biotechnology 159.3 (2012): 177-187.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2490286
Vogel, Ulrich, Szczepanowski, Rafael, Claus, Heike, Jünemann, Sebastian, Prior, Karola, and Harmsen, Dag. “Ion Torrent PGM sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information”. Journal of clinical microbiology 50.6 (2012): 1889-1894.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897974
Erdős, Péter L., Soukup, Lajos, and Stoye, Jens. “Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance”. Applied Mathematics Letters 24.1 (2011): 82-86.
PUB | DOI | WoS | arXiv
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396558 OA
Dias Vieira Braga, Marília, Machado, Raphael, Ribeiro, Leonardo C., and Stoye, Jens. “On the weight of indels in genomic distances”. BMC Bioinformatics 12.Suppl 9: RECOMB-CG 2011 (2011): S13.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396509 OA
Dias Vieira Braga, Marília, Machado, Raphael, Ribeiro, Leonardo C., and Stoye, Jens. “Genomic distance under gene substitutions”. BMC Bioinformatics 12.Suppl 9: Proc. of RECOMB-CG 2011 (2011): S8.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091794
Dias Vieira Braga, Marília, Willing, Eyla, and Stoye, Jens. “Double Cut and Join with Insertions and Deletions”. Journal of Computational Biology 18.9 (2011): 1167-1184.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091790
Kovac, Jakub, Warren, Robert, Dias Vieira Braga, Marília, and Stoye, Jens. “Restricted DCJ Model. Rearrangement Problems with Chromosome Reincorporation”. Journal of Computational Biology 18.9 (2011): 1231-1241.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2354746
Schwientek, Patrick, Szczepanowski, Rafael, Rückert, Christian, Stoye, Jens, and Pühler, Alfred. “Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology”. Journal of Biotechnology 155.1 (2011): 68-77.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2375634
Pothier, Joël F., Vorhölter, Frank-Jörg, Blom, Jochen, Goesmann, Alexander, Pühler, Alfred, Smits, TH, and Duffy, B. “The ubiquitous plasmid pXap41 in the invasive phytopathogen Xanthomonas arboricola pv. pruni: complete sequence and comparative genomic analysis”. FEMS Microbiology Letters 323.1 (2011): 52-60.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2404767
Niu, Ben, Rückert, Christian, Blom, Jochen, Wang, Qi, and Borriss, Rainer. “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 193.20 (2011): 5862-5863.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2354731
Wibberg, Daniel, Blom, Jochen, Jaenicke, Sebastian, Kollin, Florian, Rupp, Oliver, Scharf, Birgit, Schneiker-Bekel, Susanne, Szczepanowski, Rafael, Goesmann, Alexander, Setubal, Joao Carlos, Schmitt, Rüdiger, Pühler, Alfred, and Schlüter, Andreas. “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 155.1 (2011): 50-62.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659339
Feijão, Pedro, and Meidanis, J. “SCJ: A Breakpoint-Like Distance that Simplifies Several Rearrangement Problems”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8.5 (2011): 1318-1329.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2326511
Rückert, Christian, Blom, Jochen, Chen, XiaoHua, Reva, Oleg, and Borriss, Rainer. “Genome sequence of B. amyloliquefaciens type strain DSM7(T) reveals differences to plant-associated B. amyloliquefaciens FZB42”. Journal of Biotechnology 155.1 (2011): 78-85.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2373808
Herold, Julia, Loyek, Christian, and Nattkemper, Tim Wilhelm. “Multivariate Image Mining”. Wiley Interdisciplinary Reviews: DATA MINING AND KNOWLEDGE DISCOVERY 1.1 (2011): 2-13.
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2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2659373
Mira, Cleber, Feijão, Pedro, Duque-Estrada, Tiago, Meidanis, Joao, and Joly, Carlos A. “The SinBiota 2.0 Biodiversity Information System”. 2011 IEEE Seventh International Conference on eScience. 2011. 142-149.
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2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2401639
Fici, Gabriele, and Lipták, Zsuzsanna. “On prefix normal words”. Development in Language Theory. 15th International Conference (DLT 2011). Proceedings. Ed. Giancarlo Mauri and Alberto Leporati. Berlin ; Heidelberg: Springer, 2011.Vol. 6795. Lecture Notes in Computer Science. 228-238.
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