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410 Publikationen

2019 | Herausgeber Sammelwerk | Veröffentlicht | PUB-ID: 2935998
Setubal, João C., Stoye, Jens, and Dutilh, Bas E., eds. 2019. Computational Methods for Microbiome Analysis. Frontiers Research Topics. Lausanne: Frontiers Media.
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2019 | Preprint | PUB-ID: 2935604
Wittler, Roland. 2019. “Alignment- and reference-free phylogenomics with colored de-Bruijn graphs”. arXiv:1905.04165.
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2019 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2932883
Dörr, Daniel, and Stoye, Jens. 2019. “A Perspective on Comparative and Functional Genomics”. In Bioinformatics and Phylogenetics, ed. Tandy Warnow, 29:361-372. Computational Biology. Cham: Springer .
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2933161
Hassan, Hezha, and Shanak, Siba. 2019. “GOTrapper. A tool to navigate through branches of gene ontology hierarchy”. BMC Bioinformatics 20 (1): 20.
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2932884
Oey, Harald, Zakrzewski, Martha, Gravermann, Kerstin, Young, Neil D., Korhonen, Pasi K., Gobert, Geoffrey N., Nawaratna, Sujeevi, et al. 2019. “Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium”. PLOS Pathogens 15 (1): e1007513.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919005
Schulz, Tizian, Stoye, Jens, and Dörr, Daniel. 2018. “GraphTeams. A method for discovering spatial gene clusters in Hi-C sequencing data”. BMC Genomics 19 (Suppl. 5): 308.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919006
Rubert, Diego, Hoshino, Edna A., Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. 2018. “Computing the family-free DCJ similarity”. BMC Bioinformatics 19 (Suppl. 6): 152.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918481
Luhmann, Nina, Chauve, Cedric, Stoye, Jens, and Wittler, Roland. 2018. “Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 15 (6): 2094-2100.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2932754
Bhatia, Sangeeta, Feijão, Pedro, and Francis, Andrew R. 2018. “Position and Content Paradigms in Genome Rearrangements. The Wild and Crazy World of Permutations in Genomics”. BULLETIN OF MATHEMATICAL BIOLOGY 80 (12): 3227-3246.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919346
Hagenfeld, Daniel, Koch, Raphael, Jünemann, Sebastian, Prior, Karola, Harks, Inga, Eickholz, Peter, Hoffmann, Thomas, et al. 2018. “Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis”. PLOS ONE 13 (4): e0195534.
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2018 | Bielefelder E-Dissertation | PUB-ID: 2918485
Holley, Guillaume. 2018. Pan-genome Search and Storage. Bielefeld: Universität Bielefeld.
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2018 | Bielefelder E-Dissertation | PUB-ID: 2919356
Willing, Eyla. 2018. On Distance and Sorting of the Double Cut-and-Join and the Inversion-*indel* Model. Bielefeld: Universität Bielefeld.
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2018 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2930445
Cunha, Luís, Diekmann, Yoan, Kowada, Luis, and Stoye, Jens. 2018. “Identifying Maximal Perfect Haplotype Blocks”. In Proceedings of BSB 2018, 11228:26-37. LNBI. Springer Verlag.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930268
Holley, Guillaume, Wittler, Roland, Stoye, Jens, and Hach, Faraz. 2018. “Dynamic Alignment-Free and Reference-Free Read Compression”. JOURNAL OF COMPUTATIONAL BIOLOGY 25 (7): 825-836.
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2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913921
Zekic, Tina, Holley, Guillaume, and Stoye, Jens. 2018. “Pan-genome Storage and Analysis Techniques”. In Comparative Genomics. Methods and Protocols, ed. João C. Setubal, Peter Stadler, and Jens Stoye, 1704:29-53. Methods in Molecular Biology. New York: Springer Verlag.
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2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913922
Dörr, Daniel, Feijão, Pedro, and Stoye, Jens. 2018. “Family-Free Genome Comparison”. In Comparative Genomics: Methods and Protocols, ed. João C. Setubal, Peter Stadler, and Jens Stoye, 1704:331-342. Methods in Molecular Biology. New York: Springer Verlag.
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2018 | Herausgeber Sammelwerk | Veröffentlicht | PUB-ID: 2913920
Setubal, João C, Stadler, Peter, and Stoye, Jens, eds. 2018. Comparative Genomics: Methods and Protocols. Vol. 1704. Methods in Molecular Biology. New York: Springer Verlag.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919012
Jaenicke, Sebastian, Albaum, Stefan, Blumenkamp, Patrick, Linke, Burkhard, Stoye, Jens, and Goesmann, Alexander. 2018. “Flexible metagenome analysis using the MGX framework”. Microbiome 6: 76.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2912492
Luhmann, Nina, Dörr, Daniel, and Chauve, Cedric. 2017. “Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes”. Microbial Genomics 3 (9).
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556
Jünemann, Sebastian, Kleinbölting, Nils, Jaenicke, Sebastian, Henke, Christian, Hassa, Julia, Nelkner, Johanna, Stolze, Yvonne, et al. 2017. “Bioinformatics for NGS-based metagenomics and the application to biogas research”. Journal of Biotechnology 261 (SI): 10-23.
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2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913015
Rubert, Diego, Medeiros, Gabriel L., Hoshino, Edna A., Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. 2017. “Algorithms for Computing the Family-Free Genomic Similarity under DCJ”. In Comparative Genomics. RECOMB-CG 2017, ed. Joao Meidanis and Luay Nakhleh, 10562:76-100. Lecture Notes in Bioinformatics. Cham: Springer Verlag.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909057
Rubert, Diego, Feijão, Pedro, Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. 2017. “Approximating the DCJ distance of balanced genomes in linear time”. Algorithms for Molecular Biology 12: 3.
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2017 | Bielefelder E-Dissertation | PUB-ID: 2909213
Luhmann, Nina. 2017. Phylogenetic assembly of paleogenomes integrating ancient DNA data. Bielefeld: Universität Bielefeld.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2916552
da Silva, Poly H., Machado, Raphael, Dantas, Simone, and Dias Vieira Braga, Marília. 2017. “Genomic Distance with High Indel Costs”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 14 (3): 728-732.
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2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2909409
Cunha, Luis, Dantas, Simone, Gagie, Travis, Wittler, Roland, Kowada, Luis, and Stoye, Jens. 2017. “Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings”. In Proceedings of CPM 2017, 78:19:1-19:9. LIPIcs.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2911814
Dörr, Daniel, Balaban, Metin, Feijão, Pedro, and Chauve, Cedric. 2017. “The gene family-free median of three”. Algorithms for Molecular Biology 12: 14.
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2017 | Preprint | Veröffentlicht | PUB-ID: 2908521
Cunha, Luís, Dantas, Simone, Gagie, Travis, Wittler, Roland, Kowada, Luis, and Stoye, Jens. 2017. “Faster Jumbled Indexing for Binary Run-Length Encoded Strings”. arXiv: 1702.01280.
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2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2907587
Holley, Guillaume, Wittler, Roland, Stoye, Jens, and Hach, Faraz. 2017. “Dynamic Alignment-Free and Reference-Free Read Compression”. In Proceedings of RECOMB 2017, 10229:50-65. Lecture Notes in Bioinformatics.
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2017 | Sammelwerksbeitrag | Im Druck | PUB-ID: 2913924
Anselmetti, Yoan, Luhmann, Nina, Bérard, Sèverine, Tannier, Eric, and Chauve, Cedric. In Press. “Comparative Methods for Reconstructing Ancient Genome Organization”. In Comparative Genomics, ed. João C. Setubal, Peter Stadler, and Jens Stoye. Methods in Molecular Biology. Springer Verlag.
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2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913016
Schulz, Tizian, Stoye, Jens, and Dörr, Daniel. 2017. “Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery”. In Proceedings of RECOMB-CG 2017, 1704:197-212. Lecture Notes in Bioinformatics. Berlin: Springer Verlag.
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2017 | Zeitschriftenaufsatz | E-Veröff. vor dem Druck | PUB-ID: 2908574
Luhmann, Nina, Lafond, Manuel, Thévenin, Annelyse, Ouangraoua, Aida, Wittler, Roland, and Chauve, Cedric. 2017. “The SCJ Small Parsimony Problem for Weighted Gene Adjacencies”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 14.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909967
Dörr, Daniel, Kowada, Luis Antonio B., Soares de Araujo, Francisco Eloi, Deshpande, Shachi, Dantas, Simone, Moret, Bernard M. E., and Stoye, Jens. 2017. “New Genome Similarity Measures based on Conserved Gene Adjacencies”. Journal of Computational Biology 24 (6): 616-634.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901477
Ahmed Raza, Shan E, Langenkämper, Daniel, Sirinukunwattana, Korsuk, Epstein, David, Nattkemper, Tim Wilhelm, and Rajpoot, Nasir M. 2016. “Robust normalization protocols for multiplexed fluorescence bioimage analysis”. BioData Mining 9 (1): 11.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905930
Winter, Sascha, Jahn, Katharina, Wehner, Stefanie, Kuchenbecker, Leon, Marz, Manja, Stoye, Jens, and Böcker, Sebastian. 2016. “Finding approximate gene clusters with GECKO 3”. Nucleic Acids Research 44 (20): 9600-9610.
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2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2903708
Rubert, Diego, Feijão, Pedro, Dias Vieira Braga, Marília, Stoye, Jens, and Martinez, Fábio Henrique Viduani. 2016. “A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates”. In Algorithms in Bioinformatics. WABI 2016, ed. Martin Frith and Christian Nørgaard Storm Pedersen, 9838:293-306. Lecture Notes in Bioinformatics. Cham: Springer.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900129
Holley, Guillaume, Wittler, Roland, and Stoye, Jens. 2016. “Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage”. Algorithms for Molecular Biology 11: 3.
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2016 | Bielefelder E-Dissertation | PUB-ID: 2902049
Dörr, Daniel. 2016. Gene family-free genome comparison. Bielefeld: Universität Bielefeld.
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2016 | Bielefelder E-Dissertation | PUB-ID: 2906743
Bremges, Andreas. 2016. Assembling the microbial dark matter. Bielefeld: Universität Bielefeld.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900943
Langenkämper, Daniel, Jakobi, Tobias, Feld, Dustin, Jelonek, Lukas, Goesmann, Alexander, and Nattkemper, Tim Wilhelm. 2016. “Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations”. Frontiers in Genetics 7: 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., et al. 2016. “Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma”. Carcinogenesis 37 (4): 356-365.
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2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2900111
Kowada, Luis Antonio B., Doerr, Daniel, Dantas, Simone, and Stoye, Jens. 2016. “New Genome Similarity Measures based on Conserved Gene Adjacencies”. In Research in Computational Molecular Biology. RECOMB 2016, ed. Mona Singh, 9649:204-224. Lecture Notes in Bioinformatics (LNBI). Springer.
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2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2901740
Luhmann, Nina, Thévenin, Annelyse, Ouangraoua, Aida, Wittler, Roland, and Chauve, Cedric. 2016. “The SCJ small parsimony problem for weighted gene adjacencies”. In Proceedings 12th International Symposium, ISBRA 2016, 9683:200-210. Lecture Notes in Computer Science. Springer International Publishing.
PUB | DOI | Download (ext.) | arXiv
 
2016 | Konferenzband | Veröffentlicht | PUB-ID: 2912258
Hölldobler, Steffen, ed. 2016. “Genfamilienfreier Genomvergleich”, LNI, D-16: 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. 2015. “Complete Genome Sequence ofAcinetobacter baumanniiCIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses”. Genome Announcements 3 (4): e00850-15.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2677844
Dias Vieira Braga, Marília, and Stoye, Jens. 2015. “Sorting linear genomes with rearrangements and indels”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 12 (3): 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. 2015. “On the family-free DCJ distance and similarity”. Algorithms for Molecular Biology 10: 13.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2715682
Henning, Peter, Kuich, Julius Lloyd, Hoffmann, Nils, and Stefan, Kempa. 2015. “Maui-VIA: a user-friendly software for visual identification, alignment, correction, and quantification of gas chromatography–mass spectrometry data”. Frontiers in Bioengineering and Biotechnology 2 (84).
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2766708
Chen, Cai, Bartenhagen, Christoph, Gombert, Michael, Okpanyi, Vera, Binder, Vera, Röttgers, Silja, Bradtke, Jutta, et al. 2015. “Next-generation-sequencing of recurrent childhood high hyperdiploid acute lymphoblastic leukemia reveals mutations typically associated with high risk patients”. Leukemia research.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764612
Wittler, Roland, Marschall, Tobias, Schönhuth, Alexander, and Makinen, Veli. 2015. “Repeat- and error-aware comparison of deletions”. Bioinformatics 31 (18): 2947-2954.
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2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2757497
Holley, Guillaume, Wittler, Roland, and Stoye, Jens. 2015. “Bloom Filter Trie - a data structure for pan-genome storage”. In Proceedings of WABI 2015, 9289:217-230. LNBI.
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