r2cat: synteny plots and comparative assembly von Husemann, Peter, Stoye, Jens

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Comparative Genomics: Methods and Protocols

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Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing von Jünemann, Sebastian, Prior, Karola, Szczepanowski, Rafael, Harks, Inga, Ehmke, Benjamin, Goesmann, Alexander, Stoye, Jens, Harmsen, Dag

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GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data von Schulz, Tizian, Stoye, Jens, Doerr, Daniel

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HASLR: Fast Hybrid Assembly of Long Reads von Haghshenas, Ehsan, Asghari, Hossein, Stoye, Jens, Chauve, Cedric, Hach, Faraz

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Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants von Rubert, Diego P, Martinez, Fábio V, Stoye, Jens, Doerr, Daniel

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The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110 von Schwientek, Patrick, Szczepanowski, Rafael, Rückert, Christian, Kalinowski, Jörn, Klein, Andreas, Selber, Klaus, Wehmeier, Udo F, Stoye, Jens, Pühler, Alfred

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Sequence-based pangenomic core detection von Schulz, Tizian, Wittler, Roland, Stoye, Jens

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Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms von Mellmann, Alexander, Weniger, Thomas, Berssenbrügge, Christoph, Rothgänger, Jörg, Sammeth, Michael, Stoye, Jens, Harmsen, Dag

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Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium von Oey, Harald, Zakrzewski, Martha, Gravermann, Kerstin, Young, Neil D, Korhonen, Pasi K, Gobert, Geoffrey N, Nawaratna, Sujeevi, Hasan, Shihab, Martínez, David M, You, Hong, Lavin, Martin, Jones, Malcolm K, Ragan, Mark A, Stoye, Jens, Oleaga, Ana, Emery, Aidan M, Webster, Bonnie L, Rollinson, David, Gasser, Robin B, McManus, Donald P, Krause, Lutz

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Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine von Sundermann, Linda K, Wintersinger, Jeff, Rätsch, Gunnar, Stoye, Jens, Morris, Quaid

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Orthology detection combining clustering and synteny for very large datasets von Lechner, Marcus, Hernandez-Rosales, Maribel, Doerr, Daniel, Wieseke, Nicolas, Thévenin, Annelyse, Stoye, Jens, Hartmann, Roland K, Prohaska, Sonja J, Stadler, Peter F

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Phylogenetic classification of short environmental DNA fragments von Krause, Lutz, Diaz, Naryttza N, Goesmann, Alexander, Kelley, Scott, Nattkemper, Tim W, Rohwer, Forest, Edwards, Robert A, Stoye, Jens

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Investigating the complexity of the double distance problems von Braga, Marília D V, Brockmann, Leonie R, Klerx, Katharina, Stoye, Jens

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Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming von BLOM, Jochen, JAKOBI, Tobias, DOPPMEIER, Daniel, JAENICKE, Sebastian, KALINOWSKI, Jorn, STOYE, Jens, GOESMANN, Alexander

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Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor von Krause, Lutz, Diaz, Naryttza N., Edwards, Robert A., Gartemann, Karl-Heinz, Krömeke, Holger, Neuweger, Heiko, Pühler, Alfred, Runte, Kai J., Schlüter, Andreas, Stoye, Jens, Szczepanowski, Rafael, Tauch, Andreas, Goesmann, Alexander

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WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads von Gerlach, Wolfgang, Jünemann, Sebastian, Tille, Felix, Goesmann, Alexander, Stoye, Jens

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Finding all maximal perfect haplotype blocks in linear time von Alanko, Jarno, Bannai, Hideo, Cazaux, Bastien, Peterlongo, Pierre, Stoye, Jens

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Linear time algorithms for finding and representing all the tandem repeats in a string von Gusfield, Dan, Stoye, Jens

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Editorial: Computational Methods for Microbiome Analysis von Setubal, João C, Stoye, Jens, Dutilh, Bas E

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