Search Results - "van Passel, Mark Wj"

A quantitative account of genomic island acquisitions in prokaryotes by Roos, T.E, Passel, M.W.J. van

“…Microbial genomes do not merely evolve through the slow accumulation of mutations, but also, and often more dramatically, by taking up new DNA in a process…”
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The reach of the genome signature in prokaryotes by van Passel, Mark W J, Kuramae, Eiko E, Luyf, Angela C M, Bart, Aldert, Boekhout, Teun

“…With the increased availability of sequenced genomes there have been several initiatives to infer evolutionary relationships by whole genome characteristics…”
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Compositional discordance between prokaryotic plasmids and host chromosomes by van Passel, Mark W J, Bart, Aldert, Luyf, Angela C M, van Kampen, Antoine H C, van der Ende, Arie

“…Most plasmids depend on the host replication machinery and possess partitioning genes. These properties confine plasmids to a limited range of hosts, yielding…”
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Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands by Bohlin, Jon, van Passel, Mark W J, Snipen, Lars, Kristoffersen, Anja B, Ussery, David, Hardy, Simon P

“…We sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in…”
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Mononucleotide repeats are asymmetrically distributed in fungal genes by Passel, M.W.J. van, Graaff, L.H. de

“…Systematic analyses of sequence features have resulted in a better characterisation of the organisation of the genome. A previous study in prokaryotes on the…”
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An intragenic distribution bias of DNA uptake sequences in Pasteurellaceae and Neisseriae by Passel, M.W.J. van

“…Most sequenced strains from Pasteurellaceae and Neisseriae contain hundreds to thousands of uptake sequence (US) motifs in their genome, which are associated…”
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Rates of Lateral Gene Transfer in Prokaryotes: High but Why? by Vos, Michiel, Hesselman, Matthijn C, te Beek, Tim A, van Passel, Mark W.J, Eyre-Walker, Adam

“…Lateral gene transfer is of fundamental importance to the evolution of prokaryote genomes and has important practical consequences, as evidenced by the rapid…”
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The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes by Passel, M.W.J. van, Kant, R, Zoetendal, E.G, Plugge, C.M, Derrien, M.M.N, Malfatti, S.A, Palva, A, Vos, W.M. de, Smidt, H

“…The human gastrointestinal tract contains a complex community of microbes, fulfilling important health-promoting functions. However, this vast complexity of…”
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Mucin-bacterial interactions in the human oral cavity and digestive tract by Derrien, Muriel, van Passel, Mark W.J., van de Bovenkamp, Jeroen H.B., Schipper, Raymond, de Vos, Willem, Dekker, Jan

“…Mucins are a family of heavily glycosylated proteins that are the major organic components of the mucus layer, the protective layer covering the epithelial…”
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Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions by Versluis, Dennis, D’Andrea, Marco Maria, Ramiro Garcia, Javier, Leimena, Milkha M., Hugenholtz, Floor, Zhang, Jing, Öztürk, Başak, Nylund, Lotta, Sipkema, Detmer, Schaik, Willem van, de Vos, Willem M., Kleerebezem, Michiel, Smidt, Hauke, Passel, Mark W.J. van

“…Antibiotic resistance genes are found in a broad range of ecological niches associated with complex microbiota. Here we investigated if resistance genes are…”
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Promoter propagation in prokaryotes by Matus-Garcia, Mariana, Nijveen, Harm, van Passel, Mark W J

“…Transcriptional activation or 'rewiring' of silent genes is an important, yet poorly understood, phenomenon in prokaryotic genomes. Anecdotal evidence coming…”
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Streamlining genomes: toward the generation of simplified and stabilized microbial systems by Leprince, Audrey, van Passel, Mark WJ, dos Santos, Vitor AP Martins

“…Graphical abstract Highlights ► Top-down and bottom-up approaches to genome streamlining. ► Computational support for constructing and refactoring streamlined…”
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Genome Sequence of the Verrucomicrobium Opitutus terrae PB90-1, an Abundant Inhabitant of Rice Paddy Soil Ecosystems by VAN PASSEL, Mark W. J, KANT, Ravi, HUI SUN, SCHMUTZ, Jeremy, LARIMER, Frank W, LAND, Miriam L, HAUSER, Loren, KYRPIDES, Nikolaos, MIKHAILOVA, Natalia, RICHARDSON, P. Paul, JANSSEN, Peter H, DE VOS, Willem M, PALVA, Airi, SMIDT, Hauke, COPELAND, Alex, LUCAS, Susan, LAPIDUS, Alia, DEL RIO, Tijana Glavina, PITLUCK, Sam, GOLTSMAN, Eugene, CLUM, Alicia

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Shotgun Proteomics of Aspergillus niger Microsomes upon D-Xylose Induction by de Oliveira, José Miguel P. Ferreira, van Passel, Mark W.J, Schaap, Peter J, de Graaff, Leo H

“…Protein secretion plays an eminent role in cell maintenance and adaptation to the extracellular environment of microorganisms. Although protein secretion is an…”
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Tracing common origins of Genomic Islands in prokaryotes based on genome signature analyses by van Passel, Mark WJ

“…Horizontal gene transfer constitutes a powerful and innovative force in evolution, but often little is known about the actual origins of transferred genes…”
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Genome Sequence of Victivallis vadensis ATCC BAA-548, an Anaerobic Bacterium from the Phylum Lentisphaerae, Isolated from the Human Gastrointestinal Tract by VAN PASSEL, Mark W. J, KANT, Ravi, GOODWIN, Lynne, PITLUCK, Sam, WALSTON DAVENPORT, Karen, SIMS, David, BRETTIN, Thomas S, DETTER, John C, SHUNSHENG HAN, LARIMER, Frank W, LAND, Miriam L, HAUSER, Loren, PALVA, Airi, KYRPIDES, Nikolaos, OVCHINNIKOVA, Galina, RICHARDSON, P. Paul, DE VOS, Willem M, SMIDT, Hauke, ZOETENDAL, Erwin G, LUCAS, Susan, COPELAND, Alex, LAPIDUS, Alia, DEL RIO, Tijana Glavina, DALIN, Eileen, TICE, Hope, BRUCE, David

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Design and analysis of a tunable synchronized oscillator by Ryback, Brendan M, Odoni, Dorett I, van Heck, Ruben Ga, van Nuland, Youri, Hesselman, Matthijn C, Martins Dos Santos, Vítor Ap, van Passel, Mark Wj, Hugenholtz, Floor

“…The use of in silico simulations as a basis for designing artificial biological systems (and experiments to characterize them) is one of the tangible…”
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Tracing common origins of Genomic Islands in prokaryotes based on genome signature analyses by van Passel, Mark W.J.

“…Horizontal gene transfer constitutes a powerful and innovative force in evolution, but often little is known about the actual origins of transferred genes…”
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Plasmid Diversity in Neisseriae by Passel, Mark W.J. van, Ende, Arie van der, Bart, Aldert

“…Horizontal gene transfer constitutes an important force in prokaryotic genome evolution, and it is well-known that plasmids are vehicles for DNA transfer…”
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Identification of acquired DNA in Neisseria lactamica by Van Passel, Mark W.J., Bart, Aldert, Luyf, Angela C.M., Van Kampen, Antoine H.C., Van Der Ende, Arie

“…Abstract Anomalous DNA (aDNA) in prokaryotic genomes, identified by its aberrant nucleotide composition, generally represents horizontally acquired DNA…”
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