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 2019
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Vaccination of carp against SVCV with an oral DNA vaccine or an insect cells-based subunit vaccine
Fish and Shellfish Immunology 85 (2019). - ISSN 1050-4648 - p. 66 - 77.
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Transcriptomics datasets for Clostridium autoethanogenum grown on CO in different environmental conditions
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Transcriptional landscapes of lipid producing microalgae
Wageningen University. Promotor(en): V.A.P. Martins dos Santos; R.H. Wijffels, co-promotor(en): P.J. Schaap; D.E. Martens. - Wageningen : Wageningen University - ISBN 9789463951838 - p.
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Transcriptional and physiological diurnal responses of Tetradesmus obliquus under light-dark cycles and nitrogen limitation
: Wageningen University & Research
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The effect of prebiotic fortified infant formulas on microbiota composition and dynamics in early life
Scientific Reports 9 (2019)1. - ISSN 2045-2322
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The diurnal transcriptional landscape of the microalga Tetradesmus obliquus
Algal Research 40 (2019). - ISSN 2211-9264
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The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation
Scientific Data 6 (2019)1. - ISSN 2052-4463 - 1 p.
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Simulation and reconstruction of metabolite-metabolite association networks using a metabolic dynamic model and correlation based-algorithms
Journal of Proteome Research 18 (2019)3. - ISSN 1535-3893 - p. 1099 - 1113.
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Semi-supervised multivariate statistical network monitoring for learning security threats
IEEE Transactions on Information Forensics and Security 14 (2019)8. - ISSN 1556-6013 - p. 2179 - 2189.
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Semantic systems biology of prokaryotes : heterogeneous data integration to understand bacterial metabolism
Wageningen University. Promotor(en): V.A.P. Martins dos Santos, co-promotor(en): M. Suárez Diez; P.J. Schaap. - Wageningen : Wageningen University - ISBN 9789463435505 - p.
Publications 2018
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Use of proteomics to detect sex-related differences in effects of toxicants : implications for using proteomics in toxicology
Critical Reviews in Toxicology 48 (2018)8. - ISSN 1040-8444 - p. 666 - 681.
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Tools for genome annotation SAPP/GBOL/Empusa
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The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows
Frontiers in Microbiology 9 (2018). - ISSN 1664-302X
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The diurnal transcriptional landscape of the microalga Tetradesmus obliquus
: Wageningen University & Research
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The Role of Endocrine and Dioxin-Like Activity of Extracts of Petroleum Substances in Developmental Toxicity as Detected in a Panel of CALUX Reporter Gene Assays
Toxicological sciences 164 (2018)2. - ISSN 1096-6080 - p. 576 - 591.
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SyNDI : Synchronous network data integration framework
BMC Bioinformatics 19 (2018)1. - ISSN 1471-2105
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Studying microbial functionality within the gut ecosystem by systems biology
Genes & Nutrition 13 (2018)1. - ISSN 1555-8932
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SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles
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SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles
Bioinformatics 34 (2018)8. - ISSN 1367-4803 - p. 1401 - 1403.
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Romboutsia hominis sp. nov., the first human gut-derived representative of the genus Romboutsia, isolated from ileostoma effluent
International Journal of Systematic and Evolutionary Microbiology 68 (2018)11. - ISSN 1466-5026 - p. 3479 - 3486.
Publications 2017
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Zicht op betere vaccins tegen mycoplasma
Zicht op betere vaccins tegen mycoplasma, Resource, jrg. 12, nr. 7, p. 9, 2017-11-16, Tessa Louwerens, http://edepot.wur.nl/427493
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Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity
Scientific Reports 7 (2017)1. - ISSN 2045-2322
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The uptake of carbon sources by Aspergillus niger
Wageningen University. Promotor(en): Vitor Martins dos Santos, co-promotor(en): P.J. Schaap; J.A. Tamayo-Ramos. - Wageningen : Wageningen University - ISBN 9789463432085 - p.
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The effect of Mycobacterium avium subspecies paratuberculosis infection on clinical mastitis occurrence in dairy cows
Journal of Dairy Science 100 (2017)9. - ISSN 0022-0302 - p. 7446 - 7454.
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The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows
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Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production
Wageningen University. Promotor(en): V.A.P. Martins dos Santos, co-promotor(en): P.J. Schaap; J.J.E. Bijlsma. - Wageningen : Wageningen University - ISBN 9789463436519 - p.
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Supplementary data: Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production
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Structure and function of Aspergillus niger laccase McoG
Biocatalysis 3 (2017)1. - ISSN 0886-4454 - p. 1 - 21.
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Stochastic gene expression in Arabidopsis thaliana
Nature Communications 8 (2017)1. - ISSN 2041-1723
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Rhizopus delemar grown under high and low oxygen conditions
: Wageningen University
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)9. - 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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Scenedesmus Obliquus UTEX393 draft genome
: Wageningen University
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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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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
Publications 2015
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NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes
: Wageningen University
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Genome sequencing of one-carbon degrading acetogenic bacteria Sporomusa An4
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Effects of Argonaute on gene expression in Thermus thermophilus
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Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river
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Microbial community response of an organohalide respiring enrichment culture to permanganate oxidation
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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.
Publications 2014
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Listening in on a bacterial/fungal dialog: transcriptional profiling of an antagonistic interaction
: Wageningen UR
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Genome sequence of Desulfitobacterium hafniense PCE-S
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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
: Wageningen University
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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, 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: WO2014207105, verleend: 2014-12-31.
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Anoxic biological production of fuels and of bulk chemicals from second generation feedstocks
Octrooinummer: WO2014207099, 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: WO2014207087, verleend: 2014-12-31.
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). - ISSN 1472-6750
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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
Wageningen 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.
Publications 2012
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Assessment of Dietary Modulation of Inflammatory Tone (ADMIT)
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Metagenome analysis reveals yet unexplored reductive dechlorinating potential of Dehalobacter sp. E1 growing in coculture with Sedimentibacter sp.
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Metagenome analysis reveals yet unexplored reductive dechlorinating potential of Dehalobacter sp. E1 growing in coculture with Sedimentibacter sp.
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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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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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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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Methods for identifying lipoxygenase producing microorganisms on agar plates
AMB Express 2 (2012). - ISSN 2191-0855
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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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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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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.
Publications 2011
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Tracy-Widom statistic for the largest eigenvalue of autoscaled real matrices
Journal of Chemometrics 25 (2011)12. - ISSN 0886-9383 - p. 644 - 652.
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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: EP2562249, 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). - ISSN 1475-2859 - p. 78 - 78.
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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.
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 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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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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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.
Publications 2009
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The metabonomic signature of celiac disease
Journal of Proteome Research 8 (2009)1. - ISSN 1535-3893 - p. 170 - 177.
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Individual human phenotypes in metabolic space and time
Journal of Proteome Research 8 (2009)9. - ISSN 1535-3893 - p. 4264 - 4271.
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The transcriptional response of bioreactor-grown Aspergillus niger cultures towards three oils
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(Re-)construction, characterization and modeling of systems for synthetic biology
Biotechnology Journal 4 (2009)10. - ISSN 1860-6768 - p. 1382 - 1391.