Go directly to:

Content
Search box
Breadcrumb

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

Publications 2017

Publications 2016

Weight loss predictability by plasma metabolic signatures in adults with obesity and morbid obesity of the DiOGenes study
Stroeve, Johanna H.M. , Saccenti, Edoardo , Bouwman, Jildau , Dane, Adrie , Strassburg, Katrin , Vervoort, Jacques , Hankemeier, Thomas , Astrup, Arne , Smilde, Age K. , Ommen, Ben Van , Saris, Wim H.M. (2016) Obesity 24 (2016)2. - ISSN 1930-7381 - p. 379 - 388.
Unravelling the one-carbon metabolism of the acetogen Sporomusa strain An4 by genome and proteome analysis
Visser, M. , Pieterse, M.M. , Pinkse, M.W.H. , Nijsse, B. , Verhaert, P.D.E.M. , Vos, W.M. de , Schaap, P.J. , Stams, A.J.M. (2016) Environmental Microbiology 18 (2016)9. - ISSN 1462-2912 - p. 2843 - 2855.
Unearthing the transition rates between photoreceptor conformers
Smith, Robert W. , Helwig, Britta , Westphal, Adrie H. , Pel, Eran , Hörner, Maximilian , Beyer, Hannes M. , Samodelov, Sophia L. , Weber, Wilfried , Zurbriggen, Matias D. , Borst, Janwillem , Fleck, Christian (2016) BMC Systems Biology 10 (2016)1. - ISSN 1752-0509
The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis
Belda, Eugeni , Heck, Ruben G.A. van , José Lopez-Sanchez, Maria , Cruveiller, Stéphane , Barbe, Valérie , Fraser, Claire , Klenk, Hans Peter , Petersen, Jörn , Morgat, Anne , Nikel, Pablo I. , Vallenet, David , Rouy, Zoé , Sekowska, Agnieszka , Martins dos Santos, Vitor A.P. , Lorenzo, Víctor de , Danchin, Antoine , Médigue, Claudine (2016) Environmental Microbiology 18 (2016)10. - ISSN 1462-2912 - p. 3403 - 3424.
The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires
Ceapa, C.D. , Davids, M. , Ritari, Jarmo , Lambert, J. , Wels, M. , Douillard, François P. , Smokvina, Tamara , Vos, Willem M. de , Knol, J. , Kleerebezem, M. (2016) Genome Biology and Evolution 8 (2016)6. - ISSN 1759-6653 - p. 1889 - 1905.
Strategies for structuring interdisciplinary education in Systems Biology: an European perspective
Cvijovic, Marija , Höfer, Thomas , Acimovic, Jure , Alberghina, Lilia , Almaas, Eivind , Besozzi, Daniela , Blomberg, Anders , Bretschneider, Till , Cascante, Marta , Collin, Olivier , Atauri, Pedro de , Depner, Cornelia , Dickinson, Robert , Dobrzynski, Maciej , Fleck, C. , Garcia-Ojalvo, Jordi , Gonze, Didier , Hahn, Jens , Hess, Heide Marie , Hollmann, Susanne , Krantz, Marcus , Kummer, Ursula , Lundh, Torbjörn , Martial, Gifta , Martins dos Santos, V.A.P. , Mauer-Oberthür, Angela , Regierer, Babette , Skene, Barbara , Stalidzans, Egils , Stelling, Jörg , Teusink, Bas , Workman, Christopher T. , Hohmann, Stefan (2016) npj Systems Biology and Applications 2 (2016). - ISSN 2056-7189 - 7 p.
Screening and characterization of novel specific peptides targeting MDA-MB-231 claudin-low breast carcinoma by computer-aided phage display methodologies
Nobrega, Franklin L. , Ferreira, Débora , Martins, Ivone M. , Suarez-Diez, Maria , Azeredo, Joana , Kluskens, L.D. , Rodrigues, Lígia R. (2016) BMC Cancer 16 (2016)1. - ISSN 1471-2407
Scenedesmus Obliquus UTEX393 draft genome
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. (2016)
Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics
Koehorst, J.J. , Saccenti, E. , Schaap, P.J. , Martins dos Santos, V.A.P. , Suarez-Diez, M. (2016) F1000 Research 5 (2016). - ISSN 2046-1402 - 28 p.
Organic acids production from starch waste by rumen microorganisms
Palakawong Na Ayudthaya, S. , Hornung, B.V.H. , Ravikumar Varadarajan, Adithi , Plugge, Wendy , Plugge, C.M. (2016)
Natural genetic variation differentially affects the proteome and transcriptome in Caenorhabditis elegans
Kamkina, Polina , Snoek, L.B. , Grossmann, Jonas , Volkers, Rita J.M. , Sterken, Mark G. , Daube, Michael , Roschitzki, Bernd , Fortes, Claudia , Schlapbach, Ralph , Roth, Alexander , Mering, Christian von , Hengartner, Michael O. , Schrimpf, Sabine P. , Kammenga, Jan E. (2016) Molecular and Cellular Proteomics 15 (2016)5. - ISSN 1535-9476 - p. 1670 - 1680.
Integrated in silico analysis of pathway designs for synthetic photo-electro-autotrophy
Volpers, Michael , Claassens, Nico J. , Noor, Elad , Oost, John van der , Vos, Willem M. de , Kengen, Servé W.M. , Martins dos Santos, Vitor (2016) PLoS ONE 11 (2016)6. - ISSN 1932-6203
Industrial potential of lipoxygenases
Heshof, R. , Graaff, L.H. de , Villaverde, J.J. , Silvestre, A.J.D. , Haarmann, T. , Dalsgaard, T.K. , Buchert, J. (2016) Critical Reviews in Biotechnology 36 (2016)4. - ISSN 0738-8551 - p. 665 - 674.
Impact of Dietary Carbohydrate: Lipid ratio modelled in murine Small Intestinal Epithelial Cells
Sinha, N. , Suarez Diez, M. , Schothorst, E.M. van , Keijer, J. , Martins dos Santos, Vitor , Hooiveld, G.J.E.J. (2016)
Identification of a Novel L-rhamnose Uptake Transporter in the Filamentous Fungus Aspergillus niger
Sloothaak, J. , Odoni, D.I. , Martins dos Santos, V.A.P. , Schaap, P.J. , Tamayo Ramos, J.A. (2016) Plos Genetics 12 (2016)12. - ISSN 1553-7404
Identification and functional characterization of novel xylose transporters from the cell factories Aspergillus Niger and Trichoderma reesei
Sloothaak, Jasper , Tamayo-Ramos, Juan Antonio , Odoni, Dorett I. , Laothanachareon, Thanaporn , Derntl, Christian , Mach-Aigner, Astrid R. , Martins Dos Santos, Vitor A.P. , Schaap, Peter J. (2016) Biotechnology for Biofuels 9 (2016)1. - ISSN 1754-6834
Harnessing the power of microbial autotrophy
Claassens, Nico J. , Machado de Sousa, Diana , Martins dos Santos, Vitor , Vos, Willem M. de , Oost, John van der (2016) Nature Reviews Microbiology 14 (2016). - ISSN 1740-1526 - p. 692 - 706.
Genome and proteome analysis of Pseudomonas chloritidismutans AW-1T that grows on n-decane with chlorate or oxygen as electron acceptor
Mehboob, F. , Oosterkamp, M.J. , Koehorst, J.J. , Farrakh, S. , Veuskens, T. , Plugge, C.M. , Boeren, S. , Vos, W.M. de , Schraa, G. , Stams, A.J.M. , Schaap, P.J. (2016) Environmental Microbiology 18 (2016)10. - ISSN 1462-2912 - p. 3247 - 3257.
Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline
Davids, M. , Hugenholtz, F. , Martins dos Santos, V.A.P. , Smidt, H. , Kleerebezem, M. , Schaap, P.J. (2016) PLoS ONE 11 (2016)1. - ISSN 1932-6203 - 18 p.
Entropy-Based Network Representation of the Individual Metabolic Phenotype
Saccenti, Edoardo , Menichetti, Giulia , Ghini, Veronica , Remondini, Daniel , Tenori, Leonardo , Luchinat, Claudio (2016) Journal of Proteome Research 15 (2016)9. - ISSN 1535-3893 - p. 3298 - 3307.
Efficient Reconstruction of Predictive Consensus Metabolic Network Models
Heck, Ruben G.A. van , Ganter, Mathias , Martins dos Santos, Vitor A.P. , Stelling, Joerg (2016) PLoS Computational Biology 12 (2016)8. - ISSN 1553-734X
Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses
Strepis, Nikolaos , Sánchez-Andrea, Irene , Gelder, Ton van , Kruistum, Henri van , Shapiro, Nicole , Kyrpides, Nikos , Göker, Markus , Klenk, H.P. , Schaap, Peter , Stams, Fons , Sousa, Diana Z. (2016) International Journal of Systematic and Evolutionary Microbiology 66 (2016)10. - ISSN 1466-5026 - p. 3957 - 3963.
Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216<sup>T</sup>
Bosma, Elleke F. , Koehorst, Jasper J. , Hijum, Sacha A.F.T. van , Renckens, Bernadet , Vriesendorp, Bastienne , Weijer, Tom van de , Schaap, Peter J. , Vos, Willem M. de , Oost, John van der , Kranenburg, Richard van (2016) Standards in Genomic Sciences 11 (2016). - ISSN 1944-3277 - 11 p.
Complete genome sequence of the Akkermansia glycaniphila strain PytT a mucin-degrading specialist of the reticulated python gut
Ouwerkerk, J.P. , Koehorst, J.J. , Schaap, P.J. , Ritari, Jarmo , Paulin, Lars , Belzer, C. , Vos, W.M. de (2016)
Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data
Koehorst, Jasper J. , Dam, Jesse C.J. van , Heck, Ruben G.A. van , Saccenti, Edoardo , Martins dos Santos, Vitor , Suarez-Diez, Maria , Schaap, Peter J. (2016) Scientific Reports 6 (2016). - ISSN 2045-2322 - 13 p.
Comparative genomic and physiological analysis of Trichococcus species
Strepis, N. , Sanchez Andrea, I. , Gelder, A.H. van , Kruistum, Henri van , Shapiro, Nicole , Kyrpides, Nikos , Göker, Markus , Klenk, H.P. , Schaap, P.J. , Stams, A.J.M. , Machado de Sousa, D.Z. (2016)
Comparative genomic and physiological analysis of Trichococcus species
Strepis, N. , Sanchez Andrea, I. , Gelder, A.H. van , Kruistum, Henri van , Shapiro, Nicole , Kyrpides, Nikos , Göker, Markus , Klenk, H.P. , Schaap, P.J. , Stams, A.J.M. , Machado de Sousa, D.Z. (2016)
Comparative genomic and physiological analysis of Trichococcus species
Strepis, N. , Sanchez Andrea, I. , Gelder, A.H. van , Kruistum, Henri van , Shapiro, Nicole , Kyrpides, Nikos , Göker, Markus , Klenk, H.P. , Schaap, P.J. , Stams, A.J.M. , Machado de Sousa, D.Z. (2016)
Comparative genomic and physiological analysis of Trichococcus species
Strepis, N. , Sanchez Andrea, I. , Gelder, A.H. van , Kruistum, Henri van , Shapiro, Nicole , Kyrpides, Nikos , Göker, Markus , Klenk, H.P. , Schaap, P.J. , Stams, A.J.M. , Machado de Sousa, D.Z. (2016)
Comparative genomic and physiological analysis of Trichococcus species
Strepis, N. , Sanchez Andrea, I. , Gelder, A.H. van , Kruistum, Henri van , Shapiro, Nicole , Kyrpides, Nikos , Göker, Markus , Klenk, H.P. , Schaap, P.J. , Stams, A.J.M. , Machado de Sousa, D.Z. (2016)
Comparative genomic and physiological analysis of Trichococcus species
Strepis, N. , Sanchez Andrea, I. , Gelder, A.H. van , Kruistum, Henri van , Shapiro, Nicole , Kyrpides, Nikos , Göker, Markus , Klenk, H.P. , Schaap, P.J. , Stams, A.J.M. , Machado de Sousa, D.Z. (2016)
Comparative genomic and physiological analysis of Trichococcus species
Strepis, N. , Sanchez Andrea, I. , Gelder, A.H. van , Kruistum, Henri van , Shapiro, Nicole , Kyrpides, Nikos , Göker, Markus , Klenk, H.P. , Schaap, P.J. , Stams, A.J.M. , Machado de Sousa, D.Z. (2016)
Characterizing the optimal flux space of genome-scale metabolic reconstructions through modified latin-hypercube sampling
Chaudhary, N. , Tøndel, K. , Bhatnagar, R. , Martins dos Santos, V.A.P. , Puchalka, J. (2016) Molecular BioSystems 12 (2016)3. - ISSN 1742-206X - p. 994 - 1005.
Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization
Adibi, Milad , Yoshida, Saiko , Weijers, Dolf , Fleck, Christian (2016) PLoS ONE 11 (2016)2. - ISSN 1932-6203
Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation
Künne, Tim , Kieper, Sebastian N. , Bannenberg, Jasper W. , Vogel, Anne , Miellet, Willem R. , Klein, Misha , Depken, Martin , Suarez-Diez, Maria , Brouns, Stan J.J. (2016) Molecular Cell 63 (2016)5. - ISSN 1097-2765 - p. 852 - 864.
CRISPR Cas3 Plasmid degradation assays
Kunne, T.A. , Kieper, Sebastian , Bannenberg, J.W. , Vogel, A.I.M. , Miellet, Willem , Klein, Misha , Depken, Martin , Suarez Diez, M. , Brouns, S.J.J. (2016)
Building pathway graphs from BioPAX data in R
Benis, N. , Schokker, D. , Kramer, F. , Smits, Mari , Suarez-Diez, M. (2016) F1000 Research 5 (2016). - ISSN 2046-1402 - 13 p.
Bacterial antisense RNAs are mainly the product of transcriptional noise
Lloréns-Rico, V. , Cano, J. , Kamminga, T. , Gil, R. , Latorre, A. , Chen, Wei-Hua , Bork, P. , Glass, J.I. , Serrano, L. , Lluch-Senar, M. (2016) Science Advances 2 (2016)3. - ISSN 2375-2548
Approaches to sample size determination for multivariate data : Applications to PCA and PLS-DA of omics data
Saccenti, Edoardo , Timmerman, Marieke E. (2016) Journal of Proteome Research 15 (2016)8. - ISSN 1535-3893 - p. 2379 - 2393.
Adaptation of Akkermansia muciniphila to the oxic-anoxic interface of the mucus layer
Ouwerkerk, Janneke P. , Ark, Kees C.H. van der , Davids, Mark , Claassens, Nico J. , Finestra, Teresa Robert , Vos, Willem M. de , Belzer, Clara (2016) Applied and Environmental Microbiology 82 (2016)23. - ISSN 0099-2240 - p. 6983 - 6993.

Publications 2015

Publications 2014

Publications 2013

Publications 2012

Publications 2011

Publications 2010

Publications 2009