Systems and Synthetic Biology

Search results

• Transcriptomics datasets for Clostridium autoethanogenum grown on CO in different environmental conditions

  Diender, M. (Creator), Koehorst, J. (Creator) & Machado de Sousa, D. (Creator), Wageningen University & Research, 25 Jan 2019

  DOI: 10.4121/uuid:b6bd64a9-5bdb-4655-9829-520aa4600987

  Dataset

• Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data

  Koehorst, J. (Creator), van Dam, J. C. J. (Contributor), van Heck, R. G. A. (Contributor), Saccenti, E. (Contributor), Martins dos Santos, V. (Contributor), Suarez Diez, M. (Contributor) & Schaap, P. (Contributor), Wageningen University & Research, 25 Sept 2018

  DOI: 10.4121/uuid:948c10fe-7ea5-47f3-bdb2-d5b0f908820b

  Dataset

• Expected and observed genotype complexity in prokaryotes: correlation between 16S-rRNA phylogeny and protein domain content

  Koehorst, J. (Creator), Schaap, P. (Contributor) & Suarez Diez, M. (Contributor), Wageningen University & Research, 24 Oct 2018

  DOI: 10.4121/uuid:37346f1e-f8cf-4112-ba4b-1223a3e4edda

  Dataset

• Host and pathogen gene expression profiles in Necrotizing Soft Tissue Infections

  Saccenti, E. (Creator), Wageningen University & Research, 30 Nov 2021

  DOI: 10.5281/zenodo.5744186

  Dataset

• Determination of variability of fermentor-grown Aspergillus niger

  van der Veen, D. (Creator), Pimenta Ferreira De Oliveira, J. (Creator), van den Berg, W. (Creator) & de Graaff, L. (Creator), Wageningen University and Research Centre, 31 Dec 2008

  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11405

  Dataset

• uncultured bacterium 16S ribosomal RNA gene, partial sequence

  Méndez-Garcia, C. (Creator), Mesa, V. (Creator), Sprenger, R. R. (Creator), Richter, M. (Creator), Suarez Diez, M. (Creator), Solano, J. (Creator), Bargiela, R. (Creator), Golyshina, O. V. (Creator), Manteca, A. (Creator), Ramos, J. L. (Creator), Gallego, J. R. (Creator), Llorente, I. (Creator), Martins dos Santos, V. (Creator), Jensen, O. N. (Creator), Paláez, A. I. (Creator), Sánchez, J. (Creator) & Ferrer, M. (Creator), 24 Mar 2014

  https://www.ncbi.nlm.nih.gov/popset/529116721

  Dataset

• Transcriptional and physiological diurnal responses of Tetradesmus obliquus under light-dark cycles and nitrogen limitation

  Carreres, B. M. (Creator) & Martens, D. (Creator), Wageningen University & Research, 30 May 2019

  https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-7016/

  Dataset

• The diurnal transcriptional landscape of the microalga Tetradesmus obliquus

  Carreres, B. M. (Creator) & Martens, D. (Creator), Wageningen University & Research, 24 Sept 2018

  https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-7009/

  Dataset

• Microbe enriched dual RNA sequencing of Mycobacterium bovis BCG infecting macrophage-like THP-1 cells

  Rienksma, R. A. (Creator), Suarez Diez, M. (Creator), Mollenkopf, H. J. (Creator), Dolganov, G. M. (Creator), Dorhoi, A. (Creator), Schoolnik, G. K. (Creator), Martins dos Santos, V. (Creator), Kaufmann, S. (Creator), Schaap, P. (Creator) & Gengenbacher, M. (Creator), Wageningen University, 17 Jun 2014

  http://www.ebi.ac.uk/ena/data/view/PRJEB6552

  Dataset

• A high quality Draft genome of Aspergillus niger N402 (ATCC 64974)

  Laothanachareon, T. (Creator), Tamayo Ramos, J. A. (Creator), Nijsse, B. (Creator) & Schaap, P. (Creator), Wageningen University, 8 Jan 2018

  https://www.ebi.ac.uk/ena/data/view/PRJEB21769

  Dataset

• RNA sequencing of Cutaneotrichosporon curvatum ATCC 20509 in two conditions. C/N of 2.8 and 28

  Pham, N. (Creator), Reijnders, M. (Creator), Suarez Diez, M. (Creator), Nijsse, B. (Creator), Springer, J. (Creator), Eggink, G. (Creator) & Schaap, P. (Creator), Wageningen University, 14 Apr 2020

  https://www.ebi.ac.uk/ena/browser/view/PRJEB34237

  Dataset

• Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism

  Sinha, N. (Creator), van Schothorst, E. (Creator), Hooiveld, G. (Creator), Keijer, J. (Creator), Martins dos Santos, V. (Creator) & Suarez Diez, M. (Creator), Wageningen University & Research, 29 Nov 2021

  DOI: 10.6084/m9.figshare.c.5726679

  Dataset

• Complete genome sequence of the Akkermansia glycaniphila strain PytT a mucin-degrading specialist of the reticulated python gut

  Ouwerkerk, J. P. (Creator), Koehorst, J. (Creator), Schaap, P. (Creator), Ritari, J. (Creator), Paulin, L. (Creator), Belzer, C. (Creator) & de Vos, W. (Creator), Wageningen University, 2 Sept 2016

  https://www.ebi.ac.uk/ena/data/view/PRJEB15121

  Dataset

• Annotated genomes used in the publication: Machine learning approaches to predict the plant-associated phenotype of Xanthomonas strains

  Koehorst, J. (Creator), Poncheewin, W. (Creator), Schaap, P. (Creator) & te Molder, D. (Creator), Wageningen University & Research, 8 Jul 2021

  DOI: 10.4121/14546625

  Dataset

• A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration

  Martens, L. (Creator), Koehorst, J. (Creator), van Heck, R. (Creator), Suarez Diez, M. (Creator), Stams, F. (Creator) & Schaap, P. (Creator), Wageningen University & Research, 7 Jan 2021

  DOI: 10.6084/m9.figshare.13533055

  Dataset

• The effect of Clostridium difficile toxins on gene expression profiles in intestinal Caco-2 cells

  de Wit, N. (Creator), Venkatasubramanian, P. B. (Creator), Saccenti, E. (Creator) & Mes, J. (Creator), Wageningen University & Research, 30 Apr 2021

  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100541

  Dataset

• Classification of the plant-associated phenotype of Pseudomonas strains using genome properties

  Poncheewin, W. (Creator), van Diepeningen, A. (Creator), van der Lee, T. (Creator), Suarez Diez, M. (Creator) & Schaap, P. (Creator), Wageningen University & Research, 20 Jul 2021

  https://www.ncbi.nlm.nih.gov/bioproject/PRJEB45033

  Dataset

• Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

  Strepis, N. (Creator), Naranjo, H. D. (Creator), Meier-Kolthoff, J. P. (Creator), Göker, M. (Creator), Shapiro, N. (Creator), Kyrpides, N. C. (Creator), Klenk, H. P. (Creator), Schaap, P. (Creator), Stams, F. (Creator) & Machado de Sousa, D. (Creator), Wageningen University & Research, 9 Jan 2020

  DOI: 10.6084/m9.figshare.c.4810569

  Dataset

• Genome sequencing of one-carbon degrading acetogenic bacteria Moorella glycerini Strain NMP

  Liebensteiner, M. (Creator), Pinkse, M. W. H. (Creator), Nijsse, B. (Creator), Verhaert, P. D. E. M. (Creator), Tsesmetzis, N. (Creator), Stams, A. J. M. (Creator) & Lomans, B. P. (Creator), Wageningen University, 5 Feb 2015

  http://www.ebi.ac.uk/ena/data/view/PRJEB8377

  Dataset

• Comparative genomic and physiological analysis of Trichococcus species

  Strepis, N. (Creator), Sanchez Andrea, I. (Creator), van Gelder, T. (Creator), van Kruistum, H. (Creator), Shapiro, N. (Creator), Kyrpides, N. (Creator), Göker, M. (Creator), Klenk, H. P. (Creator), Schaap, P. (Creator), Stams, A. J. M. (Creator) & Machado de Sousa, D. (Creator), Wageningen University, 10 Apr 2016

  https://www.ebi.ac.uk/ena/data/view/PRJEB12709

  Dataset

• Comparative genomic and physiological analysis of Trichococcus species

  Strepis, N. (Creator), Sanchez Andrea, I. (Creator), van Gelder, T. (Creator), van Kruistum, H. (Creator), Shapiro, N. (Creator), Kyrpides, N. (Creator), Göker, M. (Creator), Klenk, H. P. (Creator), Schaap, P. (Creator), Stams, A. J. M. (Creator) & Machado de Sousa, D. (Creator), Wageningen University, 10 Apr 2016

  https://www.ebi.ac.uk/ena/data/view/PRJEB12706

  Dataset

• Comparative genomic and physiological analysis of Trichococcus species

  Strepis, N. (Creator), Sanchez Andrea, I. (Creator), van Gelder, T. (Creator), van Kruistum, H. (Creator), Shapiro, N. (Creator), Kyrpides, N. (Creator), Göker, M. (Creator), Klenk, H. P. (Creator), Schaap, P. (Creator), Stams, A. J. M. (Creator) & Machado de Sousa, D. (Creator), Wageningen University, 10 Apr 2016

  https://www.ebi.ac.uk/ena/data/view/PRJEB12707

  Dataset

• Microbial community response of an organohalide respiring enrichment culture to permanganate oxidation

  Sutton, N. (Creator), Atashgahi, S. (Creator), Saccenti, E. (Creator), Grotenhuis, T. (Creator), Smidt, H. (Creator) & Rijnaarts, H. (Creator), Wageningen University, 29 May 2015

  https://www.ebi.ac.uk/ena/data/view/PRJEB8632

  Dataset

• Genome sequence of organohalide-respiring Desulfoluna spongiiphila DBB and Desulfoluna butyratoxydans MSL71T

  Peng, P. (Creator), Goris, T. (Creator), Lu, Y. (Creator), Nijsse, B. (Creator), Burrichter, A. (Creator), Schleheck, D. (Creator), Koehorst, J. (Creator), Liu, J. (Creator), Sipkema, D. (Creator), Sinninghe Damste, J. S. (Creator), Stams, F. (Creator), Häggblom, M. M. (Creator), Smidt, H. (Creator) & Atashgahi, S. (Creator), Wageningen University, 15 May 2019

  https://www.ebi.ac.uk/ena/data/view/PRJEB31368

  Dataset

• Diversity of tryptophan halogenases in sponges of the genus Aplysina

  Gutleben, J. (Creator), Koehorst, J. (Creator), Mcpherson, K. (Creator), Pomponi, S. (Creator), Wijffels, R. (Creator), Smidt, H. (Creator) & Sipkema, D. (Creator), Wageningen University, 17 Sept 2018

  https://www.ncbi.nlm.nih.gov/bioproject/PRJNA491469/

  Dataset