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412 Publikationen

2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900943
Langenkämper, Daniel, Jakobi, Tobias, Feld, Dustin, Jelonek, Lukas, Goesmann, Alexander, and Nattkemper, Tim Wilhelm. “Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations”. Frontiers in Genetics 7 (2016): 5.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900421
Krause, Lutz, Nones, Katia, Loffler, Kelly A., Nancarrow, Derek, Oey, Harald, Tang, Yup Hang, Wayte, Nicola J., Patch, Ann Marie, Patel, Kalpana, Brosda, Sandra, Manning, Suzanne, Lampe, Guy, Clouston, Andrew, Thomas, Janine, Stoye, Jens, Hussey, Damian J., Watson, David I., Lord, Reginald V., Phillips, Wayne A., Gotley, David, Smithers, B. Mark, Whiteman, David C., Hayward, Nicholas K., Grimmond, Sean M., Waddell, Nicola, and Barbour, Andrew P. “Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma”. Carcinogenesis 37.4 (2016): 356-365.
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2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2900111
Kowada, Luis Antonio B., Doerr, Daniel, Dantas, Simone, and Stoye, Jens. “New Genome Similarity Measures based on Conserved Gene Adjacencies”. Research in Computational Molecular Biology. RECOMB 2016. Ed. Mona Singh. Springer, 2016.Vol. 9649. Lecture Notes in Bioinformatics (LNBI). 204-224.
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2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2901740
Luhmann, Nina, Thévenin, Annelyse, Ouangraoua, Aida, Wittler, Roland, and Chauve, Cedric. “The SCJ small parsimony problem for weighted gene adjacencies”. Proceedings 12th International Symposium, ISBRA 2016. Springer International Publishing, 2016.Vol. 9683. Lecture Notes in Computer Science. 200-210.
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2016 | Konferenzband | Veröffentlicht | PUB-ID: 2912258
Steffen Hölldobler, ed. “Genfamilienfreier Genomvergleich”. LNI D-16 (2016): 91-100.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2911748
Krahn, Thomas, Wibberg, Daniel, Maus, Irena, Winkler, Anika, Pühler, Alfred, Poirel, Laurent, and Schlüter, Andreas. “Complete Genome Sequence ofAcinetobacter baumanniiCIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses”. Genome Announcements 3.4 (2015): e00850-15.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2677844
Dias Vieira Braga, Marília, and Stoye, Jens. “Sorting linear genomes with rearrangements and indels”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 12.3 (2015): 500-506.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726366
Viduani Martinez, Fábio Henrique, Feijão, Pedro, Dias Vieira Braga, Marília, and Stoye, Jens. “On the family-free DCJ distance and similarity”. Algorithms for Molecular Biology 10 (2015): 13.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2715682
Henning, Peter, Kuich, Julius Lloyd, Hoffmann, Nils, and Stefan, Kempa. “Maui-VIA: a user-friendly software for visual identification, alignment, correction, and quantification of gas chromatography–mass spectrometry data”. Frontiers in Bioengineering and Biotechnology 2.84 (2015).
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2766708
Chen, Cai, Bartenhagen, Christoph, Gombert, Michael, Okpanyi, Vera, Binder, Vera, Röttgers, Silja, Bradtke, Jutta, Teigler-Schlegel, Andrea, Harbott, Jochen, Ginzel, Sebastian, Thiele, Ralf, Husemann, Peter, Krell, Pina, Borkhardt, Arndt, Dugas, Martin, Hu, Jianda, and Fischer, Ute. “Next-generation-sequencing of recurrent childhood high hyperdiploid acute lymphoblastic leukemia reveals mutations typically associated with high risk patients”. Leukemia research (2015).
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764612
Wittler, Roland, Marschall, Tobias, Schönhuth, Alexander, and Makinen, Veli. “Repeat- and error-aware comparison of deletions”. Bioinformatics 31.18 (2015): 2947-2954.
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2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2757497
Holley, Guillaume, Wittler, Roland, and Stoye, Jens. “Bloom Filter Trie - a data structure for pan-genome storage”. Proceedings of WABI 2015. 2015.Vol. 9289. LNBI. 217-230.
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2015 | Bielefelder E-Dissertation | PUB-ID: 2786037
Hilker, Rolf. Development of a read mapping analysis software and computational pan genome analysis of 20 Pseudomonas aeruginosa strains. Bielefeld: Bielefeld University, 2015.
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2015 | Konferenzband | Veröffentlicht | PUB-ID: 2780229
Joao Meidanis and Jens Stoye, eds. “Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Bioinformatics”. BMC Bioinformatics 16.Supplement 14 (2015).
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2015 | Konferenzband | Veröffentlicht | PUB-ID: 2780232
Joao Meidanis and Jens Stoye, eds. “Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Genomics”. BMC Genomics 16.Supplement 10 (2015).
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2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2684241
Viduani Martinez, Fábio Henrique, Feijão, Pedro, Dias Vieira Braga, Marília, and Stoye, Jens. “On the family-free DCJ distance”. Algorithms in Bioinformatics. WABI 2014. Ed. Dan Brown and Burkhard Morgenstern. Berlin ; Heidelberg: Springer Verlag, 2014.Vol. 8701. Lecture Notes in Bioinformatics. 174-186.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2687033
Dörr, Daniel, Stoye, Jens, Böcker, Sebastian, and Jahn, Katharina. “Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings”. BMC Genomics 15.Suppl. 6: Proc. of RECOMB-CG 2014 (2014): S2.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685362
Lechner, Marcus, Hernandez-Rosales, Maribel, Dörr, Daniel, Wieseke, Nicolas, Thévenin, Annelyse, Stoye, Jens, Hartmann, Roland K., Prohaska, Sonja J., and Stadler, Peter F. “Orthology Detection Combining Clustering and Synteny for Very Large Datasets”. PLoS ONE 9.8 (2014): e105015.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2689773
Jünemann, Sebastian, Prior, Karola, Albersmeier, Andreas, Albaum, Stefan, Kalinowski, Jörn, Goesmann, Alexander, Stoye, Jens, and Harmsen, Dag. “GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers”. PLOS ONE 9.9 (2014): e107014.
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2014 | Bielefelder E-Dissertation | PUB-ID: 2723541
Ander, Christina. Bioinformatic methods for the analysis and comparison of metagenomes and metatranscriptomes. Bielefeld: Universitätsbibliothek Bielefeld, 2014.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2674387
Hilker, Rolf, Stadermann, Kai Bernd, Doppmeier, Daniel, Kalinowski, Jörn, Stoye, Jens, Straube, Jasmin, Winnebald, Jörn, and Goesmann, Alexander. “ReadXplorer - Visualization and Analysis of Mapped Sequences”. Bioinformatics 30.16 (2014): 2247-2254.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665038
Schwientek, Patrick, Neshat, Armin, Kalinowski, Jörn, Klein, Andreas, Rückert, Christian, Schneiker-Bekel, Susanne, Wendler, Sergej, Stoye, Jens, and Pühler, Alfred. “Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts”. Journal of Biotechnology 190 (2014): 85-95.
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2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2690122
Luhmann, Nina, Chauve, Cedric, Stoye, Jens, and Wittler, Roland. “Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework”. Proc. of BSB 2014. Ed. Campos Sérgio. Springer Verlag, 2014.Vol. 8826. LNBI. 135-143.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685988
Jakobi, Tobias, Brinkrolf, Karina, Tauch, Andreas, Noll, Thomas, Stoye, Jens, Pühler, Alfred, and Goesmann, Alexander. “Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing”. Journal of Biotechnology 190 (2014): 64-75.
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2014 | Bielefelder E-Dissertation | PUB-ID: 2677466
Hoffmann, Nils. Computational methods for high-throughput metabolomics. Bielefeld: Universität Bielefeld, 2014.
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2014 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2693552
Stoye, Jens. “Suffix Tree Construction”. Encyclopedia of Algorithms. Ed. M.-Y. Kao. Springer Verlag, 2014.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2691246
Fueller, Elisa, Schaefer, Daniel, Fischer, Ute, Krell, Pina, Stanulla, Martin, Borkhardt, Arndt, and Slany, Robert K. “Genomic Inverse PCR for Exploration of Ligated Breakpoints (GIPFEL), a New Method to Detect Translocations in Leukemia”. PloS one 9.8 (2014): 104419.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2643941
Hoffmann, Nils, Wilhelm, Mathias, Doebbe, Anja, Niehaus, Karsten, and Stoye, Jens. “BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry”. Bioinformatics 30.7 (2014): 988-995.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2693409
Fredrich, Eugenie, Ander, Christina, Stoye, Jens, Brune, Iris, and Tauch, Andreas. “Metatranskriptomik der Mikrobiota aus der menschlichen Achselhöhle”. BIOspektrum 20.5 (2014): 294-296.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2691732
Klippel, Barbara, Sahm, Kerstin, Basner, Alexander, Wiebusch, Sigrid, John, Patrick, Lorenz, Ute, Peters, Anke, Abe, Fumiyoshi, Takahashi, Kyoma, Kaiser, Olaf, Goesmann, Alexander, Jaenicke, Sebastian, Grote, Ralf, Horikoshi, Koki, and Antranikian, Garabed. “Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria”. Extremophiles 18.5 (2014): 853-863.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2691279
Binder, Vera, Bartenhagen, Christoph, Okpanyi, Vera, Gombert, Michael, Moehlendick, Birte, Behrens, Bianca, Klein, Hans-Ulrich, Rieder, Harald, Krell, Pina, Dugas, Martin, Stoecklein, Nikolas Hendrik, and Borkhardt, Arndt. “A New Workflow for Whole-Genome Sequencing of Single Human Cells”. Human mutation (2014).
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2014 | Bielefelder E-Dissertation | PUB-ID: 2673418
Mascher, Martin. POPSEQ Anchoring and ordering contig assemblies from next generation sequencing data by population sequencing. Bielefeld: Universität Bielefeld, 2014.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333
Henrich, Birgit, Rumming, Madis, Sczyrba, Alexander, Velleuer, Eunike, Dietrich, Ralf, Gerlach, Wolfgang, Gombert, Michael, Rahn, Sebastian, Stoye, Jens, Borkhardt, Arndt, and Fischer, Ute. “Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma”. PLoS ONE 9.3 (2014): e92297.
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2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2611641
Dias Vieira Braga, Marília, and Stoye, Jens. “Restricted DCJ-Indel Model Revisited”. Advances in Bioinformatics and Computational Biology. BSB 2013. Ed. João C. Setubal and Nalvo F. Almeida. Cham: Springer Verlag, 2013.Vol. 8213. Lecture Notes in Bioinformatics. 36-46.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611630
Willing, Eyla, Zaccaria, Simone, Dias Vieira Braga, Marília, and Stoye, Jens. “On the Inversion-Indel Distance”. BMC Bioinformatics 14.Suppl 15: Proc. of RECOMB-CG 2013 (2013): S3.
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2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611648
Dias Vieira Braga, Marília, Chauve, Cedric, Dörr, Daniel, Jahn, Katharina, Stoye, Jens, Thévenin, Annelyse, and Wittler, Roland. “The Potential of Family-Free Genome Comparison”. Models and Algorithms for Genome Evolution. Ed. Cedric Chauve, Nadia El-Mabrouk, and Eric Tannier. Springer Verlag, 2013.Vol. 19. Computational Biology Series. 287-307.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575011
Ander, Christina, Schulz-Trieglaff, Ole B., Stoye, Jens, and Cox, Anthony J. “metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences”. BMC Bioinformatics 14.Suppl 5: Proc. of RECOMB-Seq 2013 (2013): S2.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2555342
He, Pengfei, Hao, Kun, Blom, Jochen, Rückert, Christian, Vater, Joachim, Mao, Zichao, Wu, Yixin, Hou, Mingsheng, He, Pengbo, He, Yueqiu, and Borriss, Rainer. “Genome sequence of the plant growth promoting strain Bacillus amyloliquefaciens subsp. plantarum B9601-Y2 and expression of mersacidin and other secondary metabolites”. Journal of biotechnology 164.2 (2013): 281-291.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641228
Jünemann, Sebastian, Sedlazeck, Fritz Joachim, Prior, Karola, Albersmeier, Andreas, John, Uwe, Kalinowski, Jörn, Mellmann, Alexander, Goesmann, Alexander, von Haeseler, Arndt, Stoye, Jens, and Harmsen, Dag. “Corrigendum: Updating benchtop sequencing performance comparison”. Nature biotechnology 31.12 (2013): 1148.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2492825
Reuther, Susanne, Schmetzer, Helga, Schuster, Friedhelm R., Krell, Pina, Grabrucker, Christine, Liepert, Anja, Kroell, Tanja, Kolb, Hans-Jochem, Borkhardt, Arndt, and Buhmann, Raymund. “In vitro-induced response patterns of antileukemic T cells: characterization by spectratyping and immunophenotyping”. Clinical and Experimental Medicine 13.1 (2013): 29-48.
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2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611643
Bergeron, Anne, and Stoye, Jens. “The Genesis of the DCJ Formula”. Models and Algorithms for Genome Evolution. Ed. Cedric Chauve, Nadia El-Mabrouk, and Eric Tannier. Springer Verlag, 2013.Vol. 19. Computational Biology Series. 63-81.
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2013 | Bielefelder E-Dissertation | PUB-ID: 2604883
Blom, Jochen. Comparative genomics on gene and single nucleotide level. Bielefeld: Universitätsbibliothek, 2013.
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2013 | Bielefelder E-Dissertation | PUB-ID: 2594322
Janowski, Sebastian Jan. VANESA - A bioinformatics software application for the modeling, visualization, analysis, and simulation of biological networks in systems biology applications. Bielefeld: Bielefeld University, 2013.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575361
Krell, Pina, Reuther, Susanne, Fischer, Ute, Keller, Thomas, Weber, Stephan, Gombert, Michael, Schuster, Friedhelm R., Asang, Corinna, Stepensky, Polina, Strahm, Birgit, Meisel, Roland, Stoye, Jens, and Borkhardt, Arndt. “Next-generation-sequencing-spectratyping reveals public T-cell receptor repertoires in pediatric very severe aplastic anemia and identifies a beta chain CDR3 sequence associated with hepatitis-induced pathogenesis”. Haematologica 98.9 (2013): 1388-1396.
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2013 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2577323
Gerlach, Wolfgang, and Stoye, Jens. “Taxonomic classification of metagenomic shotgun sequences with CARMA3”. Encyclopedia of Metagenomics. Ed. Karen E. Nelson. Springer Verlag, 2013.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2566922
Jünemann, Sebastian, Sedlazeck, Fritz Joachim, Prior, Karola, Albersmeier, Andreas, John, Uwe, Kalinowski, Jörn, Mellmann, Alexander, Goesmann, Alexander, von Haeseler, Arndt, Stoye, Jens, and Harmsen, Dag. “Updating benchtop sequencing performance comparison”. Nature Biotechnology 31.4 (2013): 294-296.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2625914
Bergmann, Thorsten, Maeder, U., Fiebich, M., Dickob, M., Nattkemper, Tim Wilhelm, and Anselmetti, Dario. “Categorization of two-photon microscopy images of human cartilage into states of osteoarthritis”. Osteoarthritis And Cartilage 21.8 (2013): 1074-1082.
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2013 | Konferenzband | Veröffentlicht | PUB-ID: 2616537
Aaron Darling and Jens Stoye, eds. “Algorithms in Bioinformatics”. Lecture Notes in Bioinformatics 8126 (2013).
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611633
Jahn, Katharina, Winter, Sascha, Stoye, Jens, and Böcker, Sebastian. “Statistics for approximate gene clusters”. BMC Bioinformatics 14.Suppl 15: Proc. of RECOMB-CG 2013 (2013): S14.
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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
Wittler, Roland. “Unraveling overlapping deletions by agglomerative clustering”. BMC Genomics 14.Suppl 1 (2013): S12.
PUB | Dateien verfügbar | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2529309
Bolzan de Campos, Samanta, Youn, Jung-Won, Farina, Roberto, Jaenicke, Sebastian, Jünemann, Sebastian, Szczepanowski, Rafael, Beneduzi, Anelise, Vargas, Luciano K., Wendisch, Volker F., and Passaglia, Luciane. “Changes in Root Bacterial Communities Associated to Two Different Development Stages of Canola (*Brassica napus* L. var oleifera) Evaluated through Next-Generation Sequencing”. Microbial Ecology 65.3 (2013): 593-601.
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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
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
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
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
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
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Bielefelder E-Dissertation | PUB-ID: 2468026
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).
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2486060
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.
PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Konferenzband | Veröffentlicht | PUB-ID: 2510416
Juha Kärkkäinen and Jens Stoye, eds. “Combinatorial Pattern Matching”. Lecture Notes in Computer Science 7354 (2012).
PUB | DOI
 
2012 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2468382
Hoffmann, Nils, and Stoye, Jens. “Generic Software Frameworks for GC-MS Based Metabolomics”. Metabolomics. Ed. Ute Roessner. InTech, 2012. 73-98.
PUB | PDF | DOI | Download (ext.)
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Bielefelder E-Dissertation | PUB-ID: 2533144
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
Schwientek, Patrick. Genomics and transcriptomics of the industrial acarbose producer Actinoplanes sp. SE50/110. Bielefeld: Universität Bielefeld, 2012.
PUB | PDF
 
2012 | Bielefelder E-Dissertation | PUB-ID: 2517237
Bunkowski, Alexander. MCC-IMS data analysis using automated spectra processing and explorative visualisation methods. Bielefeld: Bielefeld University, 2012.
PUB | PDF
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396558
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.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396509
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.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS | PubMed | Europe PMC
 
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.
PUB | DOI | WoS
 
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.
PUB | DOI
 
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.
PUB | DOI
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2401665
Hazelhurst, Scott, and Lipták, Zsuzsanna. “KABOOM! A new suffix-array based algorithm for clustering expression data”. Bioinformatics 27.24 (2011): 3348-3355.
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