Publications of the Laboratory of Systems and Synthetic Biology
Researchers of the Laboratory of Systems and Synthetic Biology publish on a regular basis in scientific journals, professional journals, scientific and popular books, and proceedings.
For publication lists, we refer to Staff Publications. The provided lists can be searched by author, year, etc. by clicking ‘Search within results’.
Publications 2017
- Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol Atashgahi, Siavash ; Lu, Yue ; Zheng, Ying ; Saccenti, Edoardo ; Suarez-Diez, Maria ; Ramiro-Garcia, Javier ; Eisenmann, Heinrich ; Elsner, Martin ; J.M. Stams, Alfons ; Springael, Dirk ; Dejonghe, Winnie ; Smidt, Hauke (2017) Environmental Microbiology 19 (3). - p. 968 - 981.
- Draft genome sequence of the oleaginous green alga Tetradesmus obliquus UTEX 393 Carreres, B.M. ; Jaeger, L. de; Springer, J. ; Barbosa, M.J. ; Breuer, G. ; End, E.J. van den; Kleinegris, D.M.M. ; Schäffers, I. ; Wolbert, E.J.H. ; Zhang, H. ; Lamers, P.P. ; Martins dos Santos, V.A.P. ; Wijffels, R.H. ; Eggink, G. ; Schaap, P.J. ; Martens, D.E. (2017) Genome announcements 5 (3).
- Persistence of functional protein domains in mycoplasma species and their role in host specificity and synthetic minimal life Kamminga, Tjerko ; Koehorst, Jasper J. ; Vermeij, Paul ; Slagman, Simen Jan ; Santos, Vitor A.P.M. dos; Bijlsma, Jetta J.E. ; Schaap, Peter J. (2017) Frontiers in Cellular and Infection Microbiology 7 (FEB).
- Diurnal dynamics of gaseous and dissolved metabolites and microbiota composition in the bovine rumen Lingen, Henk J. van; Edwards, Joan E. ; Vaidya, Jueeli D. ; Gastelen, Sanne van; Saccenti, Edoardo ; Bogert, Bartholomeus van den; Bannink, André ; Smidt, Hauke ; Plugge, Caroline M. ; Dijkstra, Jan (2017) Frontiers in Microbiology 8 (MAR).
- Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation Odoni, Dorett I. ; Tamayo-Ramos, Juan A. ; Sloothaak, Jasper ; Heck, Ruben van; Martins dos Santos, Vitor A.P. ; Graaff, Leo H. de; Suarez-Diez, Maria ; Schaap, Peter J. (2017) PeerJ 2017 (3).
- Complete genome sequence of Akkermansia glycaniphila strain Pyt<sup>T</sup>, a mucin-degrading specialist of the reticulated python gut Ouwerkerk, Janneke P. ; Koehorst, Jasper J. ; Schaap, Peter J. ; Ritari, Jarmo ; Paulin, Lars ; Belzer, Clara ; Vos, Willem M. de (2017) Genome announcements 5 (1).
- Concurrent haloalkanoate degradation and chlorate reduction by Pseudomonas chloritidismutans AW-1<sup>T</sup> Peng, Peng ; Zheng, Ying ; Koehorst, Jasper J. ; Schaap, Peter J. ; Stams, Fons ; Smidt, Hauke ; Atashgahi, Siavash (2017) Applied and Environmental Microbiology 83 (12). - 11 p.
- Correlation Patterns in Experimental Data Are Affected by Normalization Procedures: Consequences for Data Analysis and Network Inference Saccenti, E. (2017) Journal of Proteome Research 16 (2). - p. 619 - 634.
- Considering Horn’s Parallel Analysis from a Random Matrix Theory Point of View Saccenti, Edoardo ; Timmerman, Marieke E. (2017) Psychometrika 82 (1). - p. 186 - 209.
- Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans Snoek, Basten L. ; Sterken, Mark G. ; Bevers, Roel P.J. ; Volkers, Rita J.M. ; Hof, Arjen van 't; Brenchley, Rachel ; Riksen, Joost A.G. ; Cossins, Andrew ; Kammenga, Jan E. (2017) BMC Genomics 18 . - 15 p.
- Reverse Methanogenesis and Respiration in Methanotrophic Archaea Timmers, Peer H.A. ; Welte, Cornelia U. ; Koehorst, Jasper J. ; Plugge, Caroline M. ; Jetten, Mike S.M. ; Stams, Alfons J.M. (2017) Archaea : an international microbiological journal 2017.
- Monascus ruber as cell factory for lactic acid production at low pH Weusthuis, Ruud A. ; Mars, Astrid E. ; Springer, Jan ; Wolbert, Emil J.H. ; Wal, Hetty van der; Vrije, Truus G. de; Levisson, Mark ; Leprince, Audrey ; Houweling-Tan, Bwee ; Moers, Antoine ; Hendriks, Sjon N.A. ; Mendes, Odette ; Griekspoor, Yvonne ; Werten, Marc W.T. ; Schaap, Peter J. ; Oost, John van der; Eggink, Gerrit (2017) Metabolic Engineering 42 . - p. 66 - 73.
- Multi-level integration of environmentally perturbed internal phenotypes reveals key points of connectivity between them Benis, Nirupama , Kar, Soumya K. , Martins dos Santos, Vitor A.P. , Smits, Mari A. , Schokker, Dirkjan , Suarez-Diez, Maria (2017) Frontiers in Physiology 8 (2017). - ISSN 1664-042X - 11 p.
Publications 2016
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Weight loss predictability by plasma metabolic signatures in adults with obesity and morbid obesity of the DiOGenes study
Obesity 24 (2016)2. - ISSN 1930-7381 - p. 379 - 388.
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Unravelling the one-carbon metabolism of the acetogen Sporomusa strain An4 by genome and proteome analysis
Environmental Microbiology 18 (2016). - ISSN 1462-2912 - p. 2843 - 2855.
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Unearthing the transition rates between photoreceptor conformers
BMC Systems Biology 10 (2016)1. - ISSN 1752-0509
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The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis
Environmental Microbiology 18 (2016)10. - ISSN 1462-2912 - p. 3403 - 3424.
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The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires
Genome Biology and Evolution 8 (2016)6. - ISSN 1759-6653 - p. 1889 - 1905.
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Strategies for structuring interdisciplinary education in Systems Biology: an European perspective
npj Systems Biology and Applications 2 (2016). - ISSN 2056-7189 - 7 p.
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Screening and characterization of novel specific peptides targeting MDA-MB-231 claudin-low breast carcinoma by computer-aided phage display methodologies
BMC Cancer 16 (2016)1. - ISSN 1471-2407
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Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics
F1000 Research 5 (2016). - ISSN 2046-1402 - 28 p.
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Natural genetic variation differentially affects the proteome and transcriptome in Caenorhabditis elegans
Molecular and Cellular Proteomics 15 (2016)5. - ISSN 1535-9476 - p. 1670 - 1680.
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Integrated in silico analysis of pathway designs for synthetic photo-electro-autotrophy
PLoS One 11 (2016)6. - ISSN 1932-6203
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Industrial potential of lipoxygenases
Critical Reviews in Biotechnology 36 (2016)4. - ISSN 0738-8551 - p. 665 - 674.
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Impact of Dietary Carbohydrate: Lipid ratio modelled in murine Small Intestinal Epithelial Cells
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Identification of a Novel L-rhamnose Uptake Transporter in the Filamentous Fungus Aspergillus niger
Plos Genetics 12 (2016)12. - ISSN 1553-7404
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Identification and functional characterization of novel xylose transporters from the cell factories Aspergillus Niger and Trichoderma reesei
Biotechnology for Biofuels 9 (2016)1. - ISSN 1754-6834
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Harnessing the power of microbial autotrophy
Nature Reviews Microbiology 14 (2016). - ISSN 1740-1526 - p. 692 - 706.
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Genome and proteome analysis of Pseudomonas chloritidismutans AW-1T that grows on n-decane with chlorate or oxygen as electron acceptor
Environmental Microbiology 18 (2016)10. - ISSN 1462-2912 - p. 3247 - 3257.
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Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline
PLoS One 11 (2016)1. - ISSN 1932-6203 - 18 p.
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Entropy-Based Network Representation of the Individual Metabolic Phenotype
Journal of Proteome Research 15 (2016)9. - ISSN 1535-3893 - p. 3298 - 3307.
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Efficient Reconstruction of Predictive Consensus Metabolic Network Models
PLoS Computational Biology 12 (2016)8. - ISSN 1553-734X
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Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses
International Journal of Systematic and Evolutionary Microbiology 66 (2016)10. - ISSN 1466-5026 - p. 3957 - 3963.
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Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216<sup>T</sup>
Standards in Genomic Sciences 11 (2016). - ISSN 1944-3277 - 11 p.
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Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data
Scientific Reports 6 (2016). - ISSN 2045-2322 - 13 p.
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Characterizing the optimal flux space of genome-scale metabolic reconstructions through modified latin-hypercube sampling
Molecular BioSystems 12 (2016)3. - ISSN 1742-206X - p. 994 - 1005.
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Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization
PLoS One 11 (2016)2. - ISSN 1932-6203
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Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation
Molecular Cell 63 (2016)5. - ISSN 1097-2765 - p. 852 - 864.
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Building pathway graphs from BioPAX data in R
F1000 Research 5 (2016). - ISSN 2046-1402 - 13 p.
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Bacterial antisense RNAs are mainly the product of transcriptional noise
Science Advances 2 (2016)3. - ISSN 2375-2548
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Approaches to sample size determination for multivariate data
Journal of Proteome Research 15 (2016)8. - ISSN 1535-3893 - p. 2379 - 2393.
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Adaptation of Akkermansia muciniphila to the oxic-anoxic interface of the mucus layer
Applied and Environmental Microbiology 82 (2016)23. - ISSN 0099-2240 - p. 6983 - 6993.
Publications 2015
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Genome sequencing of one-carbon degrading acetogenic bacteria Moorella glycerini Strain NMP
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Systematic analysis of how phytochrome B dimerization determines its specificity
Nature Plants 1 (2015). - ISSN 2055-026X - 8 p.
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Algal Omics: The Functional Annotation Challenge
Current Biotechnology 4 (2015)4. - ISSN 2211-5501 - p. 457 - 463.
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Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river
Scientific Reports 5 (2015). - ISSN 2045-2322
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Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains
BMC Genomics 16 (2015)1. - ISSN 1471-2164 - 27 p.
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Erratum to
Trends in Biotechnology 33 (2015)5. - ISSN 0167-7799 - p. 315 - 315.
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Comparative and Functional Metagenomics of Akkermansia muciniphila
In: Encyclopedia of Metagenomics: Environmental Metagenomics. - : Springer - p. 99 - 102.
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Effects of bowel cleansing on the intestinal microbiota
Gut 64 (2015)10. - ISSN 0017-5749 - p. 1562 - 1568.
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Effects of Argonaute on Gene Expression in Thermus thermophilus
PLoS One 10 (2015)4. - ISSN 1932-6203 - 13 p.
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Comparative genomics of Streptococcus pyogenes M1 isolates differing in virulence and propensity to cause systemic infection in mice
International Journal of Medical Microbiology 305 (2015)6. - ISSN 1438-4221 - p. 532 - 543.
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Proteomics of Syntrophomonas zehnderi and Methanobacterium formicicum growing on long-chain fatty acids
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Wageningen can become Synth City
Wageningen : Wageningen UR
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RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource
Journal of Biomedical Semantics 6 (2015). - ISSN 2041-1480 - 12 p.
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Perchlorate and chlorate reduction by the Crenarchaeon Aeropyrum pernix and two thermophilic Firmicutes
Environmental Microbiology Reports 7 (2015)6. - ISSN 1758-2229 - p. 936 - 945.
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Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S
Standards in Genomic Sciences 10 (2015). - ISSN 1944-3277 - 8 p.
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Effects of Sample Size and Dimensionality on the Performance of Four Algorithms for Inference of Association Networks in Metabonomics
Journal of Proteome Research 14 (2015)12. - ISSN 1535-3893 - p. 5119 - 5130.
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Jasmonate signalling drives time-of-day differences in susceptibility of Arabidopsis to the fungal pathogen Botrytis cinerea
The Plant Journal 84 (2015)5. - ISSN 0960-7412 - p. 937 - 948.
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Determining the number of components in principal components analysis: A comparison of statistical, crossvalidation and approximated methods
Chemometrics and Intelligent Laboratory Systems 149 (2015)part A. - ISSN 0169-7439 - p. 99 - 116.
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Aspergillus niger membrane-associated proteome analysis for the identification of glucose transporters
Biotechnology for Biofuels 8 (2015). - ISSN 1754-6834 - 15 p.
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Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions
Scientific Reports 5 (2015). - ISSN 2045-2322 - 10 p.
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EU invests 16 million in synthetic biology
EU invests 16 million in synthetic biology, Resource: weekblad voor Wageningen UR, 2015-01-01, V.A.P. Martins dos Santos, http://resource.wageningenur.nl/en/show/EU-invests-16-million-in-synthetic-biology.htm
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Organisms on the drawing board
Organisms on the drawing board, WageningenWorld, 2015-01-01, V.A.P. Martins dos Santos, http://issuu.com/wageningenur/docs/wageningen_world_2015-03_eng_web/34
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Synthetic biology is in the picture
Synthetic biology is in the picture, Resource: weekblad voor Wageningen UR, 2015-01-01, V.A.P. Martins dos Santos, http://resource.wageningenur.nl/en/show/Synthetic-biology-is-in-the-picture.htm
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Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets
BMC Genomics 16 (2015). - ISSN 1471-2164
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Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation
PLoS One 10 (2015)8. - ISSN 1932-6203
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Allostasis and Resilience of the Human Individual Metabolic Phenotype
Journal of Proteome Research 14 (2015)7. - ISSN 1535-3893 - p. 2951 - 2962.
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On the use of the observation-wise k-fold operation in PCA cross-validation
Journal of Chemometrics 29 (2015)8. - ISSN 0886-9383 - p. 467 - 478.
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Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View
PLoS One 10 (2015)9. - ISSN 1932-6203
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Draft genome sequence of Talaromyces (Penicillium) islandicus WF-38-12, a neglected mold with significant biotechnological potential - Genome announcement
Journal of Biotechnology 211 (2015). - ISSN 0168-1656 - p. 101 - 102.
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High yields of active Thermus thermophilus proline dehydrogenase are obtained using maltose-binding protein as a solubility tag.
Biotechnology Journal 10 (2015)3. - ISSN 1860-6768 - p. 395 - 403.
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Proteomic analysis of nitrate-dependent acetone degradation by Alicycliphilus denitrificans strain BC
FEMS Microbiology Letters 362 (2015)11. - ISSN 0378-1097 - 7 p.
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Synthetische biologie komende jaren in het vizier
Resource: weekblad voor Wageningen UR 9 (2015)20. - ISSN 1874-3625 - p. 12 - 13.
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EU steekt 16 miljoen in synthetische biologie
EU steekt 16 miljoen in synthetische biologie, Resource: nieuwssite voor studenten en medewerkers van Wageningen UR, 2015-01-01, V.A.P. Martins dos Santos, http://edepot.wur.nl/345773
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Lipoxygenase : a game-changing enzyme
University. Promotor(en): Willem de Vos; Vitor Martins dos Santos, co-promotor(en): Leo de Graaff. - Wageningen : Wageningen University - ISBN 9789462571761 - p.
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Strategies for individual phenotyping of linoleic and arachidonic Acid metabolism using an oral glucose tolerance test
PLoS One 10 (2015)3. - ISSN 1932-6203 - 16 p.
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Hypothesis: the sound of the individual metabolic phenotype? Acoustic detection of NMR experiments
OMICS - A Journal of Integrative Biology 19 (2015)3. - ISSN 1536-2310 - p. 147 - 156.
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Covariances Simultaneous Component Analysis: a new method within a framework for modeling covariances
Journal of Chemometrics 29 (2015)5. - ISSN 0886-9383 - p. 277 - 288.
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Method for the single step introduction of a plurality of genes in microbial cells
Octrooinummer: EP2840139 A1, verleend: 2015-02-25.
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Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing
BMC Genomics 16 (2015). - ISSN 1471-2164 - 31 p.
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Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature
Molecular Systems Biology 11 (2015)1. - ISSN 1744-4292
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Application of the Human Intestinal Tract Chip to the non-human primate gut microbiota
Beneficial Microbes 6 (2015)3. - ISSN 1876-2883 - p. 271 - 276.
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Probabilistic networks of blood metabolites in healthy subjects as indicators of latent cardiovascular risk
Journal of Proteome Research 14 (2015)2. - ISSN 1535-3893 - p. 1101 - 1111.
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Multivariate Modeling of the collaboration between Luigi Illica and Giuseppe Giacosa for the librettos of three operas by Giacomo Puccini
Digital Scholarship in the Humanities 30 (2015)3. - ISSN 2055-7671 - p. 405 - 422.
Publications 2014
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RNA-targeting by the Type III-A CRISPR-Cas complex of Thermus thermophilus
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Microbe enriched dual RNA sequencing of Mycobacterium bovis BCG infecting macrophage-like THP-1 cells
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Gut microbiota disturbance during antibiotic therapy: a multi-omic approach
Gut Microbes 5 (2014)1. - ISSN 1949-0976 - p. 64 - 70.
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Fungals strains with improved citric acid and itaconic acid production
Octrooinummer: WO2014142647 A1, verleend: 2014-09-18.
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Identification and production of recombinant Culicoides obsoletus allergens for diagnosis and immunotherapy of insect bite hypersensitive horses
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Yeast engineered for the production of 1-alcohols from sugars under anoxic conditions
Octrooinummer: WO/2014/207105, verleend: 2014-12-31.
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Anoxic biological production of fuels and of bulk chemicals from second generation feedstocks
Octrooinummer: WO/2014/207099, verleend: 2014-12-31.
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Production of advanced fuels and of chemicals by yeasts on the basis of second generation feedstocks
Octrooinummer: WO/2014/207087 A1, verleend: 2014-12-31.
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Of Monkeys and Men: A Metabolomic Analysis of Static and Dynamic Urinary Metabolic Phenotypes in Two Species
PLoS One 9 (2014)9. - ISSN 1932-6203
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Toolkit for Visualization of the Cellular Structure and Organelles in Aspergillus niger
ACS synthetic biology 3 (2014)12. - ISSN 2161-5063 - p. 995 - 998.
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RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus
Molecular Cell 56 (2014)4. - ISSN 1097-2765 - p. 518 - 530.
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Overexpression of the Aspergillus niger GatA transporter leads to preferential use of D-galacturonic acid over D-xylose
AMB Express 4 (2014). - ISSN 2191-0855 - 9 p.
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Heterologous expression of Gaeumannomyces graminis lipoxygenase in Aspergillus nidulans
AMB Express 4 (2014). - ISSN 2191-0855 - 6 p.
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Mathematical Models Light Up Plant Signaling
The Plant Cell 26 (2014)1. - ISSN 1040-4651 - p. 5 - 20.
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Birth, death, and diversification of mobile promoters in prokaryotes
Genetics 197 (2014)1. - ISSN 0016-6731 - p. 291 - 299.
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System size expansion using Feynman rules and diagrams
Journal of Physics. A, Mathematical and Theoretical 47 (2014)45. - ISSN 1751-8113
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Systems-level modeling of mycobacterial metabolism for the identification of new (multi-)drug targets
Seminars in Immunology 26 (2014)6. - ISSN 1044-5323 - p. 610 - 622.
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Green genes: bioinformatics and systems-biology innovations drive algal biotechnology
Trends in Biotechnology 32 (2014)12. - ISSN 0167-7799 - p. 617 - 626.
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Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium
Standards in Genomic Sciences 9 (2014)3. - ISSN 1944-3277
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Quantification of variability in trichome patterns
Frontiers in Plant Science 5 (2014). - ISSN 1664-462X
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Pathway transfer in fungi: Transporters are the key to success
Bioengineered 5 (2014)5. - ISSN 1949-1018 - p. 335 - 339.
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A genomic view on syntrophic versus non-syntrophic lifestyle in anaerobic fatty acid degrading communities
Biochimica et Biophysica Acta. B, Bioenergetics 1837 (2014)12. - ISSN 0005-2728 - p. 2004 - 2016.
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Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis
BMC Systems Biology 8 (2014). - ISSN 1752-0509 - 21 p.
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Synthetic Biology in Health and Disease
In: Synbio and Human Health - A Challenge to the Current IP Framework?. - Dordrecht : Springer Science + Business Media - ISBN 9789401791960
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The ratio of the lateral correlation length and particle radius determines the density profile of spherical molecules near a fluctuating membrane
Soft Matter 10 (2014). - ISSN 1744-683X - p. 8475 - 8481.
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Effects of ß-Lactam Antibiotics and Fluoroquinolones on Human Gut Microbiota in Relation to Clostridium difficile Associated Diarrhea
PLoS One 9 (2014)2. - ISSN 1932-6203
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Delineating the effect of host environmental signals on a fully virulent strain of Bacillus anthracis using an integrated transcriptomics and proteomics approach
Journal of Proteomics 105 (2014). - ISSN 1874-3919 - p. 242 - 265.
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Integration of growth and patterning during vascular tissue formation in Arabidopsis
Science 345 (2014)6197. - ISSN 0036-8075 - 9 p.
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A lipid zipper triggers bacterial invasion
Proceedings of the National Academy of Sciences of the United States of America 111 (2014)35. - ISSN 0027-8424 - p. 12895 - 12900.
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A continuum approximation to an off-lattice individual-cell based model of cell migration and adhesion
Journal of Theoretical Biology 359 (2014). - ISSN 0022-5193 - p. 220 - 232.
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Effects of selective digestive decontamination (SDD) on the gut resistome
Journal of Antimicrobial Chemotherapy 69 (2014)8. - ISSN 0305-7453 - p. 2215 - 2223.
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Degenerate target sites mediate rapid primed CRISPR adaptation
Proceedings of the National Academy of Sciences of the United States of America 111 (2014)16. - ISSN 0027-8424 - p. E1629 - E1638.
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Flavin dependent monooxygenases
Archives of Biochemistry and Biophysics 544 (2014). - ISSN 0003-9861 - p. 2 - 17.
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Understanding the antimicrobial mechanism of TiO2-based nanocomposite films in a pathogenic bacterium
Scientific Reports 4 (2014)4134. - ISSN 2045-2322
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From the Environment to the Host: Re-Wiring of the Transcriptome of Pseudomonas aeruginosa from 22°C to 37°C
PLoS One 9 (2014)2. - ISSN 1932-6203
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A Metabolomic Perspective on Coeliac Disease
Autoimmune Diseases 2014 (2014). - ISSN 2090-0422 - 13 p.
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Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans
Standards in Genomic Sciences 9 (2014)3. - ISSN 1944-3277 - p. 655 - 675.
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Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage
ISME Journal 8 (2014). - ISSN 1751-7362 - p. 1259 - 1274.
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Expression of the Aspergillus terreus itaconic acid biosynthesis cluster in Aspergillus niger
Microbial Cell Factories 13 (2014). - ISSN 1475-2859 - 9 p.
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Improved production of medium-chain-length Polyhydroxyalkanotes in glucose-based fed-batch cultivations of metabolically engineered Pseudomonas putida strains
Journal of Microbiology and Biotechnology 24 (2014)1. - ISSN 1017-7825 - p. 59 - 69.
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Shedding (far-red) light on phytochrome mechanisms and responses in land plants
Plant Science 217-218 (2014). - ISSN 0168-9452 - p. 36 - 46.
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A novel class of fungal lipoxygenases
Applied Microbiology and Biotechnology 98 (2014)3. - ISSN 0175-7598 - p. 1261 - 1270.
Publications 2013
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ISBE – set out for a Systems Biology Infrastructure for Europe
EMBnet.journal 19 (2013)1. - ISSN 2226-6089 - p. 3 - 4.
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Differential translation tunes uneven production of operon-encoded proteins
Cell Reports 4 (2013)5. - ISSN 2211-1247 - p. 938 - 944.
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Potential of proton-pumping rhodopsins: engineering photosystems into microorganisms
Trends in Biotechnology 31 (2013)11. - ISSN 0167-7799 - p. 633 - 642.
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Ex vivo transcriptional profiling reveals a common set of genes important for the adaptation of Pseudomonas aeruginosa to chronically infected host sites
Environmental Microbiology 15 (2013)2. - ISSN 1462-2912 - p. 570 - 587.
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Reconciling in vivo and in silico key biological parameters of Pseudomonas putida KT2440 during growth on glucose under carbon-limited condition
BMC Biotechnology 13 (2013)93. - ISSN 1472-6750 - 13 p.
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Signatures of nonlinearity in single cell noise-induced oscillations
Journal of Theoretical Biology 335 (2013). - ISSN 0022-5193 - p. 222 - 234.
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Overexpression of a modified 6-phosphofructo-1-kinase results in an increased itaconic acid productivity in Aspergillus niger
AMB Express 3 (2013). - ISSN 2191-0855
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Physiology and biochemistry of aromatic hydrocarbon-degrading bacteria that use chlorate and/or nitrate as electron acceptor
University. Promotor(en): Fons Stams, co-promotor(en): Caroline Plugge; Peter Schaap. - Wageningen : Wageningen University - ISBN 9789461737779 - p.
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Design and analysis of a tunable synchronized oscillator
Journal of Biological Engineering 7 (2013). - ISSN 1754-1611 - 10 p.
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Structure and Activity of the RNA-Targeting Type III-B CRISPR-Cas Complex of Thermus thermophilus
Molecular Cell 52 (2013)1. - ISSN 1097-2765 - p. 135 - 145.
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Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation
Applied Microbiology and Biotechnology 97 (2013)19. - ISSN 0175-7598 - p. 8729 - 8739.
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Computational protein design with electrostatic focusing: experimental characterization of a conditionally folded helical domain with a reduced amino acid alphabet
Biotechnology Journal 8 (2013)7. - ISSN 1860-6768 - p. 855 - 864.
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A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
BMC Genomics 14 (2013). - ISSN 1471-2164 - 14 p.
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Metabolic response of Alicycliphilus denitrificans strain BC towards electron acceptor variation
Proteomics 13 (2013)18-19. - ISSN 1615-9853 - p. 2886 - 2894.
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Genome Analysis and Physiological Comparison of Alicycliphilus denitrificans Strains BC and K601(T.)
PLoS One 8 (2013)6. - ISSN 1932-6203
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Functional consequences of microbial shifts in the human gastrointestinal tract linked to antibiotic treatment and obesity
Gut Microbes 12 (2013)4. - ISSN 1949-0976 - p. 306 - 315.
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ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes
PLoS One 8 (2013)5. - ISSN 1932-6203
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Genome analysis of Desulfotomaculum kuznetsovii strain 17T reveals a physiological similarity with Pelotomaculum thermopropionicum SIT
Standards in Genomic Sciences 8 (2013)1. - ISSN 1944-3277 - p. 69 - 87.
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Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling
Molecular Systems Biology 9 (2013). - ISSN 1744-4292 - 19 p.
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Cloning and expression of candidate allergens from Culicoides obsoletus for diagnosis of insect bite hypersensitivity in horses
Veterinary Immunology and Immunopathology 153 (2013)3-4. - ISSN 0165-2427 - p. 227 - 239.
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Archaeal (Per)Chlorate Reduction at High Temperature: An Interplay of Biotic and Abiotic Reactions
Science 340 (2013)85. - ISSN 0036-8075 - p. 85 - 87.
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Hydroperoxide production from linoleic acid by heterologous Gaeumannomyces graminis tritici lipoxygenase: Optimization and scale-up
Chemical Engineering Journal 217 (2013). - ISSN 1385-8947 - p. 82 - 90.
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Immunoglobulins drive terminal maturation of splenic dendritic cells
Proceedings of the National Academy of Sciences of the United States of America 110 (2013)6. - ISSN 0027-8424 - p. 2282 - 2287.
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Proteomics of Filamentous Fungi
In: Proteomics in Foods. - New York : Springer (Food Microbiology and Food Safety 2) - p. 563 - 578.
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Protoanemonin: a natural quorum sensing inhibitor that selectively activates iron starvation response
Environmental Microbiology 15 (2013)1. - ISSN 1462-2912 - p. 111 - 120.
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In-silico-driven metabolic engineering of Pseudomonas putida for enhanced production of poly-hydroxyalkanoates
Metabolic Engineering 15 (2013). - ISSN 1096-7176 - p. 113 - 123.
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Gut microbiota disturbance during antibiotic therapy: a multi-omic approach
Gut 62 (2013)11. - ISSN 0017-5749 - p. 1591 - 1601.
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Enhanced production of Aspergillus niger laccase-like multicopper oxidases through mRNA optimization of the glucoamylase expression system
Biotechnology and Bioengineering 110 (2013)2. - ISSN 0006-3592 - p. 543 - 551.
Publications 2012
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Using semantic web technology to accelerate plant breeding
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Promoter propagation in prokaryotes
Nucleic Acids Research 40 (2012)20. - ISSN 0305-1048 - p. 10032 - 10040.
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Metagenome analysis reveals yet unexplored reductive dechlorinating potential of Dehalobacter sp. E1 growing in coculture with Sedimentibacter sp
Environmental Microbiology Reports 4 (2012)6. - ISSN 1758-2229 - p. 604 - 616.
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The Constructor: a web application optimizing cloning strategies based on modules from the registry of standard biological parts
Journal of Biological Engineering 6 (2012). - ISSN 1754-1611 - 6 p.
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Production of cyanophycin in Rhizopus oryzae through the expression of a cyanophycin synthetase encoding gene
Applied Microbiology and Biotechnology 93 (2012)3. - ISSN 0175-7598 - p. 1167 - 1174.
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Programmable bacterial catalysis – designing cells for biosynthesis of value-added compounds
FEBS Letters 586 (2012)15. - ISSN 0014-5793 - p. 2184 - 2190.
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The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: Highlights from a multi-level omics approach
Microbial Cell Factories 11 (2012)34. - ISSN 1475-2859
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Random and cyclical deletion of large DNA segments in the genome of Pseudomonas putida
Environmental Microbiology 14 (2012)6. - ISSN 1462-2912 - p. 1444 - 1453.
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pH-stat fed-batch process to enhance the production of cis, cis-muconate from benzoate by Pseudomonas putida KT2440-JD1
Biotechnology Progress 28 (2012)1. - ISSN 8756-7938 - p. 85 - 92.
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Industrial biotechnology of Pseudomonas putida and related species
Applied Microbiology and Biotechnology 93 (2012)6. - ISSN 0175-7598 - p. 2279 - 2290.
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Methods for identifying lipoxygenase producing microorganisms on agar plates
AMB Express 26 (2012)2. - ISSN 2191-0855
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Metabolic engineering of Rhizopus oryzae for the production of platform chemicals
Applied Microbiology and Biotechnology 94 (2012)4. - ISSN 0175-7598 - p. 875 - 886.
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D-Xylose Concentration-Dependent Hydrolase Expression Profiles and the Function of CreA and XlnR in Aspergillus niger
Applied and Environmental Microbiology 78 (2012)9. - ISSN 0099-2240 - p. 3145 - 3155.
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Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands
BMC Genomics 13 (2012). - ISSN 1471-2164 - 35 p.
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CRISPR Interference Directs Strand Specific Spacer Acquisition
PLoS One 7 (2012)4. - ISSN 1932-6203
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A Multi-Platform Flow Device for Microbial (Co-) Cultivation and Microscopic Analysis
PLoS One 7 (2012)5. - ISSN 1932-6203
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Streamlining genomes: toward the generation of simplified and stabilized microbial systems
Current Opinion in Biotechnology 23 (2012)5. - ISSN 0958-1669 - p. 651 - 658.
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Evaluation of Design Strategies for Time Course Experiments in Genetic Networks: Case Study of the XlnR Regulon in Aspergillus niger
IEEE/ACM Transactions on Computational Biology and Bioinformatics 9 (2012)5. - ISSN 1545-5963 - p. 1316 - 1325.
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Streamlining of a Pseudomonas putida Genome using a Combinatorial Deletion Method Based on Mini-transposon Insertion and the Flp-FRT Recombination System
In: Synthetic Gene Networks / , Weber, W., Fussenegger, M.. - Heidelberg : Springer (Methods in Molecular Biology 813) - ISBN 9781617794117 - p. Part III - chapter 15.
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Biocatalytic potential of laccase-like multicopper oxidases from Aspergillus niger
Microbial Cell Factories 11 (2012)165. - ISSN 1475-2859 - 11 p.
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Modeling and analysis of flux distributions in the two branches of the phosphotransferase system in Pseudomonas putida
BMC Systems Biology 6 (2012). - ISSN 1752-0509 - 25 p.
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Promoter reuse in prokaryotes
Mobile Genetic Elements 2 (2012)6. - ISSN 2159-2543 - p. 1 - 3.
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The Arabidopsis thaliana SERK1 kinase domain spontaneously refolds to an active state in vitro
PLoS One 7 (2012)12. - ISSN 1932-6203
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Influence of cell-to-cell variability on spatial pattern formation
IET Systems Biology 6 (2012)4. - ISSN 1751-8849 - p. 143 - 153.
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Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT)
Standards in Genomic Sciences 7 (2012). - ISSN 1944-3277 - p. 304 - 319.
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Assessment of Dietary Modulation of Inflammatory Tone (ADMIT)
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From existing data to novel hypotheses : design and application of structure-based Molecular Class Specific Information Systems
University. Promotor(en): Vitor Martins dos Santos; G. Vriend, co-promotor(en): Peter Schaap. - S.l. : s.n. - ISBN 9789461733504 - p.
Publications 2011
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Genomic approaches for identification of the biopolymer degrading enzyme network of Aspergillus niger
In: Industrial Applications / , Hofrichter, M.. - Berlin Heidelberg : Springer (The Mycota 10) - ISBN 9783642114571 - p. 407 - 424.
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Engineered host cells and methods for the production of cis, cis-muconic acid
Octrooinummer: EP11178713.1, verleend: 2011-08-24.
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Predicting microbial growth kinetics with the use of genetic circuit models
In: 21st European Symposium on Computer Aided Process Engineering. - : Elsevier (Computer Aided Chemical Engineering ) - ISBN 9780444538956 - p. 1321 - 1325.
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The ten grand challenges of synthetic life
Systems and synthetic biology 5 (2011)1-2. - ISSN 1872-5325 - p. 1 - 9.
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The Aspergillus niger multicopper oxidase family: analysis and overexpression of laccase-like encoding genes
Microbial Cell Factories 10 (2011)78. - ISSN 1475-2859
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A comprehensive metatranscriptomics analysis pipeline
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Systems biology of Host-Food-Microbe interactions in the mammalian gut
In: Systems Biology and Livestock Science / , te Pas, M.. - : John Wiley and Sons - ISBN 9780813811741 - p. 109 - 135.
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Generation of a catR deficient mutant of P. putida KT2440 that produces cis, cis-muconate from benzoate at high rate and yield
Journal of Biotechnology 156 (2011)3. - ISSN 0168-1656 - p. 163 - 172.
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Tracing common origins of Genomic Islands in prokaryotes based on genome signature analyses
Mobile Genetic Elements 1 (2011)3. - ISSN 2159-2543 - p. 247 - 249.
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Parameter estimation in genetic networks using a constrained stochastic space search method
In: 30th Benelux Meeting on Systems and Control, Lommel, Belgium, 15 - 17 March, 2011. - - p. 129 - 129.
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Proteomic analysis of the secretory response of Aspergillus niger to D-maltose and D-xylose
PLoS One 6 (2011)6. - ISSN 1932-6203
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Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction
BMC Systems Biology 5 (2011). - ISSN 1752-0509 - 16 p.
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Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis
PLoS Computational Biology 7 (2011)3. - ISSN 1553-734X - 18 p.
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Improving the prediction of Pseudomonas putida mt-2 growth kinetics with the use of a gene expression regulation model of the TOL plasmid
Biochemical Engineering Journal 55 (2011)2. - ISSN 1369-703X - p. 108 - 118.
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The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms
Environmental Microbiology 13 (2011)9. - ISSN 1462-2912 - p. 2389 - 2402.
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Linking genes to microbial growth kinetics: an integrated biochemical systems engineering approach
Metabolic Engineering 13 (2011)4. - ISSN 1096-7176 - p. 401 - 413.
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Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
Genome Research 21 (2011)6. - ISSN 1088-9051 - p. 885 - 897.
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In-Vivo Expression Profiling of Pseudomonas aeruginosa Infections Reveals Niche-Specific and Strain-Independent Transcriptional Programs
PLoS One 6 (2011). - ISSN 1932-6203 - 11 p.
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Dual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger
ISME Journal 5 (2011)9. - ISSN 1751-7362 - p. 1494 - 1504.
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A quantitative account of genomic island acquisitions in prokaryotes
BMC Genomics 12 (2011). - ISSN 1471-2164 - p. 427 - 427.
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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
Journal of Bacteriology 193 (2011)9. - ISSN 0021-9193 - p. 2373 - 2374.
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Genome sequence of the verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems
Journal of Bacteriology 193 (2011)9. - ISSN 0021-9193 - p. 2367 - 2368.
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Genome sequence of "Pedosphaera parvula" Ellin514, an aerobic Verrucomicrobial isolate from pasture soil
Journal of Bacteriology 193 (2011)11. - ISSN 0021-9193 - p. 2900 - 2901.
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Genome sequence of Chthoniobacter flavus Ellin428, an aerobic heterotrophic soil bacterium
Journal of Bacteriology 193 (2011)11. - ISSN 0021-9193 - p. 2902 - 2903.
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Optimization of Pseudomonas putida KT2440 as host for the production of cis, cis-muconate from benzoate
University. Promotor(en): Gerrit Eggink; Vitor Martins dos Santos, co-promotor(en): Astrid Mars. - {S.l.] : S.n. - ISBN 9789085859901 - p.
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A limited LCA of bio-adipic acid: Manufacturing the nylon-6,6 precursor adipic acid using the benzoic acid degradation pathway from different feedstocks
Biotechnology and Bioengineering 108 (2011)6. - ISSN 0006-3592 - p. 1298 - 1306.
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Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma
Genome Biology 12 (2011)4. - ISSN 1474-7596 - p. R40 - R40.
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Modeling and analysis of the dynamic behavior of the XlnR regulon in Aspergillus niger
BMC Systems Biology 5 (2011)Suppl. 1. - ISSN 1752-0509 - 14 p.
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Redefining plant systems biology: from cell to ecosystem
Trends in Plant Science 16 (2011)4. - ISSN 1360-1385 - p. 183 - 190.
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An iterative workflow for mining the human intestinal metaproteome
BMC Genomics 12 (2011). - ISSN 1471-2164 - p. 6 - 6.
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Proteomics of industrial fungi: trends and insights for biotechnology
Applied Microbiology and Biotechnology 89 (2011)2. - ISSN 0175-7598 - p. 225 - 237.
Publications 2010
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Exploring Networks at the genome scale
European Biotechnology Science and Industry News 9 (2010)1-2. - ISSN 1618-8276 - p. 40 - 42.
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Combining Genetic Circuit and Microbial Growth Kinetic Models: A Challenge for Biological Modelling
In: Computer Aided Process Engineering. - : Elsevier - p. 301 - 306.
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Consortia modulation of the stress response: proteomic analysis of single strain versus mixed culture
Environmental Microbiology 12 (2010)9. - ISSN 1462-2912 - p. 2436 - 2449.
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The alpha/beta-Hydrolase Fold 3DM Database (ABHDB) as a Tool for Protein Engineering
ChemBioChem 11 (2010)12. - ISSN 1439-4227 - p. 1635 - 1643.
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The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid
Environmental Microbiology 12 (2010)6. - ISSN 1462-2912 - p. 1705 - 1718.
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Systems biology of the gut: the interplay of food, microbiota and host at the mucosal interface
Current Opinion in Biotechnology 21 (2010)4. - ISSN 0958-1669 - p. 539 - 550.
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Modeling the dynamics of the XlnR Regulon network in Aspergillus Niger The Fourth International Conference on Computational Systems Biology (ISB2010), Suzhou, China, Sep 9-11, 2010, Publisher: ORSC & APORC, p. 128-138
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Novel tools for extraction and validation of disease-related mutations applied to fabry disease
Human Mutation 31 (2010)9. - ISSN 1059-7794 - p. 1026 - 1032.