Systems and Synthetic Biology

Search results

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

  Diender, M. (Creator), Koehorst, J. J. (Creator) & Machado de Sousa, D. Z. (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. J. (Creator), van Dam, J. C. J. (Contributor), van Heck, R. G. A. (Contributor), Saccenti, E. (Contributor), Martins dos Santos, V. A. P. (Contributor), Suarez Diez, M. (Contributor) & Schaap, P. J. (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. J. (Creator), Schaap, P. J. (Contributor) & Suarez Diez, M. (Contributor), Wageningen University & Research, 24 Oct 2018

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

  Dataset

• Genome sequence of Desulfitobacterium hafniense PCE-S

  Goris, T. (Creator), Hornung, B. V. H. (Creator), Kruse, T. (Creator), Reinhold, A. (Creator), Westermann, M. (Creator), Schaap, P. J. (Creator), Smidt, H. (Creator) & Diekert, G. (Creator), Wageningen University, 15 Oct 2014

  https://www.ebi.ac.uk/ena/data/view/PRJEB6708

  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. J. (Creator), Wageningen University & Research, 7 Jan 2021

  DOI: 10.6084/m9.figshare.13535813

  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 Sept 2009

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

  Dataset

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

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

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

  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

• Ischnura elegans - embryonic development

  Simon, S. (Creator), Sagasser, S. (Creator), Saccenti, E. (Creator), Brugler, M. R. (Creator), Schranz, M. E. (Creator), Hadrys, H. (Creator), Amato, G. (Creator) & DeSalle, R. (Creator), Wageningen University & Research, 5 Sept 2017

  https://www.ncbi.nlm.nih.gov/bioproject/401426

  Dataset

• Genome sequence of Romboutsia str. Frifi

  Gerritsen, J. (Creator), Umanetc, A. (Creator), van Leeuwen-Staneva, I. N. (Creator), Hornung, B. V. H. (Creator), Ritari, J. (Creator), Paulin, L. (Creator), Rijkers, G. T. (Creator), de Vos, W. M. (Creator) & Smidt, H. (Creator), Wageningen University, 17 Mar 2018

  https://www.ebi.ac.uk/ena/data/view/PRJEB7106

  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. A. P. (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/529116744

  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

• 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

• 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

• A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters

  Witjes, L. (Creator), Kooke, R. (Creator), van der Hooft, J. (Creator), de Vos, R. (Creator), Keurentjes, J. (Creator), Medema, M. (Creator) & Nijveen, H. (Creator), Wageningen University & Research, 2 Apr 2019

  DOI: 10.6084/m9.figshare.c.4456952

  Dataset

• Isolation of a novel anaerobic acidophilic sulfate-reducing bacterium, Acididesulfobacillus acetoxydans str. INE

  Sanchez Andrea, I. (Creator), van der Graaf, L. (Creator), Hornung, B. (Creator), Jarzembowska, M. (Creator) & Stams, F. (Creator), Wageningen University and Research Centre, 19 Feb 2022

  https://www.ebi.ac.uk/ena/browser/view/PRJEB7665

  Dataset

• Supplementary Peeking Under the skin: Deciphering enigmas underlying necrotising soft tissue infections

  Jahagirdar, S. (Creator), Wageningen University & Research, 9 Jul 2023

  DOI: 10.5281/zenodo.8128357

  Dataset

• Metagenome analysis reveals yet unexplored reductive dechlorinating potential of Dehalobacter sp. E1 growing in coculture with Sedimentibacter sp.

  Maphosa, F. (Creator), van Passel, M. W. J. (Creator), de Vos, W. M. (Creator) & Smidt, H. (Creator), Wageningen University, 19 Sept 2012

  https://www.ebi.ac.uk/ena/data/view/PRJEB386

  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. A. P. (Creator), de Graaff, L. H. (Creator), Suarez Diez, M. (Creator) & Schaap, P. J. (Creator), Wageningen University, 16 Feb 2017

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

  Dataset

• Novel multi-omics deconfounding variational autoencoders can obtain meaningful disease subtyping

  Katz, S. (Creator) & Li, Z. (Creator), Wageningen University & Research, 4 Jan 2024

  DOI: 10.5281/zenodo.10458940

  Dataset

• Wetland soil incubation treated with sulfate and oxygen

  Wang, D. (Creator), Candry, P. (Creator), Hunt, K. A. (Creator), Flinkstrom, Z. (Creator), Shi, Z. (Creator), Liu, Y. (Creator), Wofford, N. Q. (Creator), McInerney, M. J. (Creator), Tanner, R. S. (Creator), De Leόn, K. B. (Creator), Zhou, J. (Creator), Winkler, M. K. H. (Creator), Stahl, D. A. (Creator) & Pan, C. (Creator), University of Oklahoma, 17 May 2024

  https://www.ncbi.nlm.nih.gov/bioproject/1112840

  Dataset

• Mtb-host model

  Rienksma, R. A. (Creator), Wageningen University & Research, 14 Dec 2018

  DOI: 10.18174/466578, https://edepot.wur.nl/466578

  Dataset

• Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river

  Atashgahi, S. (Creator), Aydin, R. (Creator), Rocha Dimitrov, M. (Creator), Sipkema, D. (Creator), Hamonts, K. (Creator), Lahti, L. (Creator), Maphosa, F. (Creator), Kruse, T. (Creator), Saccenti, E. (Creator), Springael, D. (Creator), Dejonghe, W. (Creator) & Smidt, H. (Creator), Wageningen University, 29 Oct 2015

  https://www.ebi.ac.uk/ena/data/view/PRJEB8703

  Dataset

• Aspergillus niger N402 derivatives grown with different supplements

  Odoni, D. I. (Creator), Vazquez Vilar, M. (Creator), van Gaal, M. (Creator), Schonewille, T. (Creator), Martins dos Santos, V. A. P. (Creator), Tamayo-Ramos, J. A. (Creator), Suarez Diez, M. (Creator) & Schaap, P. J. (Creator), Wageningen University, 29 Jun 2018

  https://www.ebi.ac.uk/ena/data/view/PRJEB24704

  Dataset

• RNA-targeting by the Type III-A CRISPR-Cas complex of Thermus thermophilus

  Staals, R. H. J. (Creator), Zhu, Y. (Creator), Taylor, D. W. (Creator), Kornfeld, J. E. (Creator), Sharma, K. (Creator), Barendregt, A. (Creator), Koehorst, J. J. (Creator), Vlot, M. (Creator), Neupane, N. (Creator), Varossieau, K. (Creator), Sakamoto, K. (Creator), Suzuki, T. (Creator), Schaap, P. J. (Creator), Urlaub, H. (Creator), Heck, A. J. R. (Creator), Nogales, E. (Creator), Doudna, J. A. (Creator), Shinkai, A. (Creator) & van der Oost, J. (Creator), Wageningen University, 9 Oct 2014

  http://www.ebi.ac.uk/ena/data/view/PRJEB7461

  Dataset