Search Results - "STOYE, Jens"

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

“…Recent parallel pyrosequencing methods and the increasing number of finished genomes encourage the sequencing and investigation of closely related strains…”
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Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing by Jünemann, Sebastian, Prior, Karola, Szczepanowski, Rafael, Harks, Inga, Ehmke, Benjamin, Goesmann, Alexander, Stoye, Jens, Harmsen, Dag

“…Periodontitis, one of the most common diseases in the world, is caused by a mixture of pathogenic bacteria and inflammatory host responses and often treated by…”
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GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data by Schulz, Tizian, Stoye, Jens, Doerr, Daniel

“…Hi-C sequencing offers novel, cost-effective means to study the spatial conformation of chromosomes. We use data obtained from Hi-C experiments to provide new…”
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HASLR: Fast Hybrid Assembly of Long Reads by Haghshenas, Ehsan, Asghari, Hossein, Stoye, Jens, Chauve, Cedric, Hach, Faraz

“…Third-generation sequencing technologies from companies such as Oxford Nanopore and Pacific Biosciences have paved the way for building more contiguous and…”
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Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants by Rubert, Diego P, Martinez, Fábio V, Stoye, Jens, Doerr, Daniel

“…Computationally inferred ancestral genomes play an important role in many areas of genome research. We present an improved workflow for the reconstruction from…”
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Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine by Sundermann, Linda K, Wintersinger, Jeff, Rätsch, Gunnar, Stoye, Jens, Morris, Quaid

“…Tumors contain multiple subpopulations of genetically distinct cancer cells. Reconstructing their evolutionary history can improve our understanding of how…”
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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 by Mellmann, Alexander, Weniger, Thomas, Berssenbrügge, Christoph, Rothgänger, Jörg, Sammeth, Michael, Stoye, Jens, Harmsen, Dag

“…For typing of Staphylococcus aureus, DNA sequencing of the repeat region of the protein A (spa) gene is a well established discriminatory method for outbreak…”
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Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium by 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

“…Mesenteric infection by the parasitic blood fluke Schistosoma bovis is a common veterinary problem in Africa and the Middle East and occasionally in the…”
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Orthology detection combining clustering and synteny for very large datasets by Lechner, Marcus, Hernandez-Rosales, Maribel, Doerr, Daniel, Wieseke, Nicolas, Thévenin, Annelyse, Stoye, Jens, Hartmann, Roland K, Prohaska, Sonja J, Stadler, Peter F

“…The elucidation of orthology relationships is an important step both in gene function prediction as well as towards understanding patterns of sequence…”
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The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110 by Schwientek, Patrick, Szczepanowski, Rafael, Rückert, Christian, Kalinowski, Jörn, Klein, Andreas, Selber, Klaus, Wehmeier, Udo F, Stoye, Jens, Pühler, Alfred

“…Actinoplanes sp. SE50/110 is known as the wild type producer of the alpha-glucosidase inhibitor acarbose, a potent drug used worldwide in the treatment of…”
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Sequence-based pangenomic core detection by Schulz, Tizian, Wittler, Roland, Stoye, Jens

“…One of the most basic kinds of analysis to be performed on a pangenome is the detection of its core, i.e., the information shared among all members. Pangenomic…”
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Phylogenetic classification of short environmental DNA fragments by Krause, Lutz, Diaz, Naryttza N, Goesmann, Alexander, Kelley, Scott, Nattkemper, Tim W, Rohwer, Forest, Edwards, Robert A, Stoye, Jens

“…Metagenomics is providing striking insights into the ecology of microbial communities. The recently developed massively parallel 454 pyrosequencing technique…”
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Investigating the complexity of the double distance problems by Braga, Marília D V, Brockmann, Leonie R, Klerx, Katharina, Stoye, Jens

“…Two genomes [Formula: see text] and [Formula: see text] over the same set of gene families form a canonical pair when each of them has exactly one gene from…”
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Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming by BLOM, Jochen, JAKOBI, Tobias, DOPPMEIER, Daniel, JAENICKE, Sebastian, KALINOWSKI, Jorn, STOYE, Jens, GOESMANN, Alexander

“…The introduction of next-generation sequencing techniques and especially the high-throughput systems Solexa (Illumina Inc.) and SOLiD (ABI) made the mapping of…”
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WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads by Gerlach, Wolfgang, Jünemann, Sebastian, Tille, Felix, Goesmann, Alexander, Stoye, Jens

“…Metagenomics is a new field of research on natural microbial communities. High-throughput sequencing techniques like 454 or Solexa-Illumina promise new…”
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Finding all maximal perfect haplotype blocks in linear time by Alanko, Jarno, Bannai, Hideo, Cazaux, Bastien, Peterlongo, Pierre, Stoye, Jens

“…Recent large-scale community sequencing efforts allow at an unprecedented level of detail the identification of genomic regions that show signatures of natural…”
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Editorial: Computational Methods for Microbiome Analysis by Setubal, João C, Stoye, Jens, Dutilh, Bas E

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GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers by Jünemann, Sebastian, Prior, Karola, Albersmeier, Andreas, Albaum, Stefan, Kalinowski, Jörn, Goesmann, Alexander, Stoye, Jens, Harmsen, Dag

“…De novo genome assembly is the process of reconstructing a complete genomic sequence from countless small sequencing reads. Due to the complexity of this task,…”
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Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor by 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

“…A total community DNA sample from an agricultural biogas reactor continuously fed with maize silage, green rye, and small proportions of chicken manure has…”
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MeltDB: a software platform for the analysis and integration of metabolomics experiment data by Neuweger, Heiko, Albaum, Stefan P., Dondrup, Michael, Persicke, Marcus, Watt, Tony, Niehaus, Karsten, Stoye, Jens, Goesmann, Alexander

“…Motivation: The recent advances in metabolomics have created the potential to measure the levels of hundreds of metabolites which are the end products of…”
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