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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 2018

Vaccination of carp against SVCV with an oral DNA vaccine or an insect cells-based subunit vaccine
Embregts, C.W.E. , Rigaudeau, D. , Tacchi, L. , Pijlman, G.P. , Kampers, L. , Veselý, T. , Pokorová, D. , Boudinot, P. , Wiegertjes, G.F. , Forlenza, M. (2018) Fish and Shellfish Immunology (2018). - ISSN 1050-4648
The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows
Vaidya, Jueeli D. , Bogert, Bartholomeus van den , Edwards, J.E. , Boekhorst, Jos , Gastelen, S. van , Saccenti, Edoardo , Plugge, Caroline M. , Smidt, Hauke (2018) Frontiers in Microbiology 9 (2018). - ISSN 1664-302X
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
Kamelia, Lenny , Louisse, Jochem , Haan, Laura de , Maslowska-Gornicz, Anna , Ketelslegers, Hans B. , Brouwer, Abraham , Rietjens, Ivonne M.C.M. , Boogaard, Peter J. (2018) Toxicological sciences 164 (2018)2. - ISSN 1096-6080 - p. 576 - 591.
Studying microbial functionality within the gut ecosystem by systems biology
Hornung, Bastian , Martins dos Santos, Vitor A.P. , Smidt, Hauke , Schaap, Peter J. (2018) Genes & Nutrition 13 (2018)1. - ISSN 1555-8932
SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles
Koehorst, Jasper J. , Dam, Jesse C.J. van , Saccenti, Edoardo , Martins Dos Santos, Vitor A.P. , Suarez-Diez, Maria , Schaap, Peter J. (2018) Bioinformatics 34 (2018)8. - ISSN 1367-4803 - p. 1401 - 1403.
Romboutsia hominis sp. nov., the first human gut-derived representative of the genus Romboutsia, isolated from ileostoma effluent
Gerritsen, Jacoline , Umanets, Alexander , Staneva, Ivelina , Hornung, Bastian , Ritari, Jarmo , Paulin, Lars , Rijkers, Ger T. , Vos, Willem M. de , Smidt, Hauke (2018) International Journal of Systematic and Evolutionary Microbiology 68 (2018)11. - ISSN 1466-5026 - p. 3479 - 3486.
Regulation of three virulence strategies of Mycobacterium tuberculosis : A success story
Zondervan, Niels A. , Dam, Jesse C.J. Van , Schaap, Peter J. , Martins dos Santos, Vitor A.P. , Suarez-Diez, Maria (2018) International Journal of Molecular Sciences 19 (2018)2. - ISSN 1661-6596
Recommended strategies for spectral processing and post-processing of 1D <sup>1</sup>H-NMR data of biofluids with a particular focus on urine
Emwas, Abdul Hamid , Saccenti, Edoardo , Gao, Xin , McKay, Ryan T. , Martins dos Santos, Vitor A.P. , Roy, Raja , Wishart, David S. (2018) Metabolomics 14 (2018)3. - ISSN 1573-3882
Prediction of Metabolic Status of Dairy Cows in Early Lactation Using On-farm Cow Data with Machine Learning Algorithms
Xu, Wei , Saccenti, E. , Vervoort, J.J.M. , Kemp, B. , Knegsel, A.T.M. van (2018) In: Abstract of the WIAS Science Day 2018. - - p. 22 - 22.
Predicting individual differences in viral susceptibility caused by natural genetic variation within species
Sluijs, L. van , Sterken, M.G. , Wang, Yiru , Ritmahan, Wannisa , Gultom, Mitra , Pankok, Frederik , Blokhina, T. , Riksen, J.A.G. , Volkers, J.M. , Snoek, L.B. , Pijlman, G.P. , Kammenga, J.E. (2018)
Population complexity trumps model complexity in understanding trait variation
Sterken, M.G. , Snoek, L.B. , Bevers, R.P.J. , Volkers, J.M. , Riksen, J.A.G. , Kammenga, J.E. (2018)
Phytochrome B dynamics departs from photoequilibrium in the field
Sellaro, Romina , Smith, Robert W. , Legris, Martina , Fleck, Christian , Casal, Jorge J. (2018) Plant, Cell & Environment (2018). - ISSN 0140-7791 - 12 p.
Paracrine mechanisms in early differentiation of human pluripotent stem cells : Insights from a mathematical model
Gaspari, Erika , Franke, Annika , Robles-Diaz, Diana , Zweigerdt, Robert , Roeder, Ingo , Zerjatke, Thomas , Kempf, Henning (2018) Stem Cell Research 32 (2018). - ISSN 1873-5061 - p. 1 - 7.
Neochloris oleoabundans is worth its salt : Transcriptomic analysis under salt and nitrogen stress
Jaeger, Lenny de , Carreres, Benoit M. , Springer, Jan , Schaap, Peter J. , Eggink, Gerrit , Martins dos Santos, Vitor A.P. , Wijffels, Rene H. , Martens, Dirk E. (2018) PLoS One 13 (2018)4. - ISSN 1932-6203
Necrotizing soft tissue infections - a multicentre, prospective observational study (INFECT) : Protocol and statistical analysis plan
Madsen, M.B. , Skrede, S. , Bruun, T. , Arnell, P. , Rosén, A. , Nekludov, M. , Karlsson, Y. , Bergey, F. , Saccenti, E. , Martins dos Santos, V.A.P. , Perner, A. , Norrby-Teglund, A. , Hyldegaard, O. (2018) Acta Anaesthesiologica Scandinavica 62 (2018)2. - ISSN 0001-5172 - p. 272 - 279.
Modeling the Metabolic State of Mycobacterium tuberculosis Upon Infection
Rienksma, Rienk A. , Schaap, Peter J. , Martins Dos Santos, Vitor A.P. , Suarez-Diez, Maria (2018) Frontiers in Cellular and Infection Microbiology 8 (2018). - ISSN 2235-2988
Model-driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation
Ark, Kees C.H. van der , Aalvink, Steven , Suarez-Diez, Maria , Schaap, Peter J. , Vos, Willem M. de , Belzer, Clara (2018) Microbial Biotechnology 11 (2018)3. - ISSN 1751-7907 - p. 476 - 485.
Milk Metabolomics Data Reveal the Energy Balance of Individual Dairy Cows in Early Lactation
Xu, Wei , Vervoort, Jacques , Saccenti, Edoardo , Hoeij, Renny van , Kemp, Bas , Knegsel, Ariette van (2018) Scientific Reports 8 (2018). - ISSN 2045-2322
Metatranscriptome analysis of the microbial fermentation of dietary milk proteins in the murine gut
Hugenholtz, Floor , Davids, Mark , Schwarz, Jessica , Müller, Michael , Tomé, Daniel , Schaap, Peter , Hooiveld, Guido J.E.J. , Smidt, Hauke , Kleerebezem, Michiel (2018) PLoS One 13 (2018)4. - ISSN 1932-6203
Interactive functional networks in microbiota
Hornung, Bastian V.H. (2018) Wageningen University. Promotor(en): Hauke Smidt, co-promotor(en): Peter Schaap. - Wageningen : Wageningen University - ISBN 9789463434867 - p.
Insight into nuclear body formation of phytochromes through stochastic modelling and experiment
Grima, Ramon , Sonntag, Sebastian , Venezia, Filippo , Kircher, Stefan , Smith, Robert W. , Fleck, Christian (2018) Physical Biology 15 (2018)5. - ISSN 1478-3967
Improved functional annotations are key to realize the potential of algal biotechnology
Reijnders, Maarten J.M.F. (2018) Wageningen University. Promotor(en): Vitor Martins dos Santos; Gerrit Eggink, co-promotor(en): Peter Schaap. - Wageningen : Wageningen University - ISBN 9789463435352 - p.
Group-wise partial least square regression
Camacho, José , Saccenti, Edoardo (2018) Journal of Chemometrics 32 (2018)3. - ISSN 0886-9383
Group-wise ANOVA simultaneous component analysis for designed omics experiments
Saccenti, Edoardo , Smilde, Age K. , Camacho, José (2018) Metabolomics 14 (2018)6. - ISSN 1573-3882
Genome sequence of two members of the chloroaromatic-degrading MT community : Pseudomonas reinekei MT1 and Achromobacter xylosoxidans MT3
Gutierrez-Urrutia, Izabook , Miossec, Matthieu J. , Valenzuela, Sandro L. , Meneses, Claudio , Martins dos Santos, Vitor A.P. , Castro-Nallar, Eduardo , Poblete-Castro, Ignacio (2018) Journal of Biotechnology 275 (2018). - ISSN 0168-1656 - p. 13 - 16.
Genetic variation causes differential viral susceptibilities in the model organism Caenorhabditis elegans
Sluijs, L. van , Sterken, M.G. , Wang, Yiru , Ritmahan, Wannisa , Gultom, Mitra , Pankok, Frederik , Blokhina, T. , Riksen, J.A.G. , Volkers, J.M. , Snoek, L.B. , Pijlman, G.P. , Kammenga, J.E. (2018)
From correlation to causation : analysis of metabolomics data using systems biology approaches
Rosato, Antonio , Tenori, Leonardo , Cascante, Marta , Atauri Carulla, Pedro Ramon De , Martins dos Santos, Vitor A.P. , Saccenti, Edoardo (2018) Metabolomics 14 (2018)4. - ISSN 1573-3882
Forward Genetics by Genome Sequencing Uncovers the Central Role of the Aspergillus niger goxB Locus in Hydrogen Peroxide Induced Glucose Oxidase Expression
Laothanachareon, Thanaporn , Tamayo Ramos, J.A. , Nijsse, Bart , Schaap, Peter J. (2018) Frontiers in Microbiology 9 (2018)SEP. - ISSN 1664-302X - 14 p.
Expected and observed genotype complexity in prokaryotes: correlation between 16S-rRNA phylogeny and protein domain content
Koehorst, J.J. , Schaap, P.J. , Suarez Diez, M. (2018)
Engineering Geobacillus thermodenitrificans to introduce cellulolytic activity; expression of native and heterologous cellulase genes
Daas, Martinus J.A. , Nijsse, Bart , Weijer, Antonius H.P. van de , Groenendaal, Bart W.A.J. , Janssen, Fons , Oost, John van der , Kranenburg, Richard van (2018) BMC Biotechnology 18 (2018)1. - ISSN 1472-6750
Diabetes and necrotizing soft tissue infections—A prospective observational cohort study : Statistical analysis plan
Rosén, A. , Arnell, P. , Madsen, M.B. , Nedrebø, B.G. , Norrby-Teglund, A. , Hyldegaard, O. , Santos, V.M. dos , Bergey, F. , Saccenti, E. , Skrede, S. (2018) Acta Anaesthesiologica Scandinavica 62 (2018)8. - ISSN 0001-5172 - p. 1171 - 1177.
Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach
Chia, Loo Wee , Hornung, Bastian V.H. , Aalvink, Steven , Schaap, Peter J. , Vos, Willem M. de , Knol, Jan , Belzer, Clara (2018) Antonie van Leeuwenhoek: : Nederlandsch tijdschrift voor hygiëne, microbiologie en serologie 111 (2018)6. - ISSN 0003-6072 - p. 859 - 873.
Data-Driven Modeling of Intracellular Auxin Fluxes Indicates a Dominant Role of the ER in Controlling Nuclear Auxin Uptake
Middleton, Alistair M. , Bosco, Cristina Dal , Chlap, Phillip , Bensch, Robert , Harz, Hartmann , Ren, Fugang , Bergmann, Stefan , Wend, Sabrina , Weber, Wilfried , Hayashi, Ken Ichiro , Zurbriggen, Matias D. , Uhl, Rainer , Ronneberger, Olaf , Palme, Klaus , Fleck, Christian , Dovzhenko, Alexander (2018) Cell Reports 22 (2018)11. - ISSN 2211-1247 - p. 3044 - 3057.
DNA assembly standards : Setting the low-level programming code for plant biotechnology
Vazquez-Vilar, Marta , Orzaez, Diego , Patron, Nicola (2018) Plant Science 273 (2018). - ISSN 0168-9452 - p. 33 - 41.
DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems
Smith, Robert W. , Rosmalen, Rik P. van , Martins dos Santos, Vitor A.P. , Fleck, Christian (2018) BMC Systems Biology 12 (2018). - ISSN 1752-0509
Comparison of dimensionality assessment methods in Principal Component Analysis based on permutation tests
Vitale, Raffaele , Saccenti, Edoardo (2018) Chemometrics and Intelligent Laboratory Systems 181 (2018). - ISSN 0169-7439 - p. 79 - 94.
Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data
Koehorst, J.J. , Dam, J.C.J. van , Heck, R.G.A. van , Saccenti, E. , Martins dos Santos, V.A.P. , Suarez Diez, M. , Schaap, P.J. (2018)
Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio
Versluis, Dennis , Nijsse, Bart , Naim, Mohd Azrul , Koehorst, Jasper J. , Wiese, Jutta , Imhoff, Johannes F. , Schaap, Peter J. , Passel, Mark W.J. van , Smidt, Hauke , Sipkema, Detmer (2018) Genome Biology and Evolution 10 (2018)1. - ISSN 1759-6653 - p. 125 - 142.
Age and Sex Effects on Plasma Metabolite Association Networks in Healthy Subjects
Vignoli, Alessia , Tenori, Leonardo , Luchinat, Claudio , Saccenti, Edoardo (2018) Journal of Proteome Research 17 (2018)1. - ISSN 1535-3893 - p. 97 - 107.
A constraint-based model analysis of enterocyte mitochondrial adaptation to dietary interventions of lipid type and lipid load
Sinha, Neeraj , Suarez-Diez, Maria , Hooiveld, Guido J.E.J. , Keijer, Jaap , Santos, Vitor Martin dos , Schothorst, Evert M. van (2018) Frontiers in Physiology 9 (2018). - ISSN 1664-042X
A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways
Atashgahi, Siavash , Hornung, Bastian , Waals, Marcelle J. Van Der , Rocha, Ulisses Nunes Da , Hugenholtz, Floor , Nijsse, Bart , Molenaar, Douwe , Spanning, Rob Van , Stams, Alfons J.M. , Gerritse, Jan , Smidt, Hauke (2018) Scientific Reports 8 (2018)1. - ISSN 2045-2322

Publications 2017

Publications 2016

Publications 2015

Publications 2014

Publications 2013

Publications 2012

Publications 2011

Publications 2010

Publications 2009