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 Sep 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

• The transcriptional response of bioreactor-grown Aspergillus niger cultures towards three oils

  van der Veen, D. (Creator), van den Berg, R. A. (Creator) & de Graaff, L. (Creator), Wageningen University and Research Centre, 1 Sep 2009

  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14285

  Dataset

• The diurnal transcriptional landscape of the microalga Tetradesmus obliquus

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

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

  Dataset

• Rhizopus delemar grown under high and low oxygen conditions

  Odoni, D. I. (Creator), Tamayo Ramos, J. A. (Creator), Sloothaak, J. (Creator), van Heck, R. G. A. (Creator), Martins dos Santos, V. (Creator), de Graaff, L. H. (Creator), Suarez Diez, M. (Creator) & Schaap, P. (Creator), Wageningen University, 16 Feb 2017

  https://www.ebi.ac.uk/ena/data/view/PRJEB14210

  Dataset

• Neochloris oleoabundans RNA sequencing of 5 growth conditions, 8 samples

  Carreres, B. M. (Creator) & Martens, D. (Creator), Wageningen University & Research, 1 Feb 2019

  https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3651/

  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

• Assessment of Dietary Modulation of Inflammatory Tone (ADMIT)

  Saccenti, E. (Creator), Ernst, R. (Creator) & Coolen, J. (Creator), Wageningen UR, 13 Dec 2012

  http://studies.dbnp.org/study/show/96239

  Dataset

• In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions

  Kampers, L. F. C. (Creator), van Heck, R. G. A. (Creator), Donati, S. (Creator), Saccenti, E. (Creator), Volkers, R. J. M. (Creator), Schaap, P. (Creator), Suarez Diez, M. (Creator), Nikel, P. I. (Creator) & Martins dos Santos, V. (Creator), Wageningen University & Research, 23 Oct 2019

  DOI: 10.6084/m9.figshare.c.4708994

  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

• Genome-scale metabolic modeling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production

  Pham, N. (Creator), Reijnders, M. (Creator), Suarez Diez, M. (Creator), Nijsse, B. (Creator), Springer, J. (Creator), Eggink, G. (Creator) & Schaap, P. (Creator), Wageningen University & Research, 7 Jan 2021

  DOI: 10.6084/m9.figshare.13535813

  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

• 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/PRJEB12704

  Dataset

• Effects of Argonaute on gene expression in Thermus thermophilus

  Swarts, D. (Creator), Koehorst, J. (Creator), Westra, E. R. (Creator), Schaap, P. (Creator) & van der Oost, J. (Creator), Wageningen University, 23 Apr 2015

  https://www.ebi.ac.uk/ena/data/view/PRJEB8709

  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. (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/PRJEB12707

  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

• CRISPR Cas3 Plasmid degradation assays

  Kunne, T. A. (Creator), Kieper, S. (Creator), Bannenberg, J. (Creator), Vogel, A. I. M. (Creator), Miellet, W. (Creator), Klein, M. (Creator), Depken, M. (Creator), Suarez Diez, M. (Creator) & Brouns, S. J. J. (Creator), Wageningen University, 16 Aug 2016

  https://www.ebi.ac.uk/ena/data/view/PRJEB13999

  Dataset

• Genome sequencing of one-carbon degrading acetogenic bacteria Sporomusa An4

  Visser, M. (Creator), Pieterse, M. M. (Creator), Pinkse, M. W. H. (Creator), Nijsse, B. (Creator), Verhaert, P. D. E. M. (Creator), de Vos, W. (Creator) & Stams, A. J. M. (Creator), Wageningen University, 28 Feb 2015

  https://www.ebi.ac.uk/ena/data/view/PRJEB8443

  Dataset

• Long-chain fatty acids degradation by Desulfomonile species, proposal of “Candidatus Desulfomonile palmitatoxidans” and emended description of the genus Desulfomonile

  Alves, J. I. (Creator), Salvador, A. F. (Creator), Castro, A. R. (Creator), Zheng, Y. (Creator), Nijsse, B. (Creator), Atashgahi, S. (Creator), Machado de Sousa, D. (Creator), Stams, F. (Creator), Alves, M. M. (Creator) & Cavaleiro, A. J. (Creator), Wageningen University, 17 Feb 2020

  https://www.ebi.ac.uk/ena/browser/view/PRJEB35900

  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 Sep 2016

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

  Dataset

• Transcriptomics Profiles of Eight Cancers From GEO

  Saccenti, E. (Creator), Wageningen University & Research, 10 Dec 2020

  DOI: 10.5281/zenodo.4314604

  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

• Akkermansia transcriptome response to mucin and/or glucose growth medium

  Ottman, N. A. (Creator), Davids, M. (Creator), Suarez Diez, M. (Creator), Boeren, S. (Creator), Schaap, P. (Creator), Martins dos Santos, V. (Creator), Smidt, H. (Creator), Belzer, C. (Creator) & de Vos, W. (Creator), Wageningen University, 9 May 2017

  https://www.ebi.ac.uk/ena/data/view/PRJEB9527

  Dataset