Systems Biology

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• Naturally Fermented Milk from Northern Senegal

  Molenaar, D. (Creator), Diallo, A. M. (Contributor) & Kort, R. (Contributor), VU, 2022

  DOI: 10.48338/vu01-2lt5v4, https://publication.yoda.vu.nl/full/VU01/2LT5V4.html

  Dataset / Software: Dataset

• The Python Simulator for Cellular Systems: PySCeS (1.0.1)

  Olivier, B. (Creator) & Rohwer, J. M. (Creator), Zenodo, 24 Feb 2022

  DOI: 10.5281/zenodo.6260080, https://github.com/PySCeS/pysces/tree/1.0.1

  Dataset / Software: Dataset

• Single molecule mRNA Fluorescent In Situ Hybridization combined to Immunofluorescence in S. cerevisiae: Dataset and quantification

  Tutucci, E. (Creator), Singer, R. H. (Contributor) & Maekiniemi, A. (Contributor), Elsevier, 13 Apr 2020

  DOI: 10.17632/bcmn9cxyzs.4

  Dataset / Software: Dataset

• The Python Simulator for Cellular Systems: PySCeS

  Olivier, B. (Creator) & Rohwer, J. (Creator), Zenodo, 25 Jul 2023

  DOI: 10.5281/zenodo.8187854, https://zenodo.org/record/8187854

  Dataset / Software: Dataset

• libSBML-5.19.0

  Keating, S. M. (Creator), Bergmann, F. T. (Creator), Olivier, B. (Creator), Smith, L. P. (Creator) & Hucka, M. (Creator), Zenodo, 27 Nov 2020

  DOI: 10.5281/zenodo.4293358, https://zenodo.org/record/4293358

  Dataset / Software: Dataset

• CBMPy release 0.8.8 update 1

  Olivier, B. (Creator), Gottstein, W. (Creator), Teusink, B. (Creator) & Molenaar, D. (Creator), Zenodo, 2 Nov 2023

  DOI: 10.5281/zenodo.10067017, https://zenodo.org/records/10067017

  Dataset / Software: Dataset

• MetaDraft Release: 0.9.5

  Olivier, B. (Creator), Mendoza, S. (Creator), Molenaar, D. (Creator) & Teusink, B. (Creator), Zenodo, 25 Nov 2020

  DOI: 10.5281/zenodo.4291058, https://zenodo.org/record/4291058

  Dataset / Software: Dataset

• Additional file 18: Table S4. of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

  Antwi, E. B. (Creator), Haanstra, J. R. (Creator), Ramasamy, G. (Contributor), Jensen, B. (Creator), Droll, D. (Creator), Rojas, F. (Creator), Minia, I. (Creator), Terrao, M. (Creator), Mercé, C. (Creator), Matthews, K. (Creator), Myler, P. J. (Creator), Parsons, M. (Creator) & Clayton, C. (Creator), Figshare, 2016

  DOI: 10.6084/m9.figshare.c.3636047_d11, https://figshare.com/articles/Additional_file_18_Table_S4_of_Integrative_analysis_of_the_Trypanosoma_brucei_gene_expression_cascade_predicts_differential_regulation_of_mRNA_processing_and_unusual_control_of_ribosomal_protein_expression/4440332

  Dataset / Software: Dataset

• Additional file 1: of A practical guide for probiotics applied to the case of antibiotic-associated diarrhea in The Netherlands

  Agamennone, V. (Contributor), Krul, C. (Contributor), Rijkers, G. (Contributor) & Kort, R. (Contributor), Unknown Publisher, 6 Aug 2018

  DOI: 10.6084/m9.figshare.6935087.v1, https://springernature.figshare.com/articles/Additional_file_1_of_A_practical_guide_for_probiotics_applied_to_the_case_of_antibiotic-associated_diarrhea_in_The_Netherlands/6935087/1

  Dataset / Software: Dataset

• Additional file 3: of A practical guide for probiotics applied to the case of antibiotic-associated diarrhea in The Netherlands

  Agamennone, V. (Creator), Krul, C. A. M. (Creator), Rijkers, G. (Creator) & Kort, R. (Creator), Figshare, 2018

  DOI: 10.6084/m9.figshare.6935105, https://figshare.com/articles/Additional_file_3_of_A_practical_guide_for_probiotics_applied_to_the_case_of_antibiotic-associated_diarrhea_in_The_Netherlands/6935105

  Dataset / Software: Dataset

• Additional file 1: of Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity

  Dols, J. A. M. (Creator), Molenaar, D. (Creator), van der Helm, J. J. (Contributor), Caspers, M. P. M. (Creator), Angelino-Bart, A. D. K. (Creator), Schuren, F. H. J. (Creator), Speksnijder, A. G. C. L. (Creator), Westerhoff, H. V. (Creator), Richardus, J. H. (Creator), Boon, M. E. (Creator), Reid, G. (Creator), de Vries, H. J. C. (Contributor) & Kort, R. (Creator), Figshare, 2016

  DOI: 10.6084/m9.figshare.c.3615860_d1, https://figshare.com/articles/Additional_file_1_of_Molecular_assessment_of_bacterial_vaginosis_by_Lactobacillus_abundance_and_species_diversity/4377728

  Dataset / Software: Dataset

• Additional file 14: Table S2. of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

  Antwi, E. (Contributor), Haanstra, J. (Contributor), Ramasamy, G. (Contributor), Jensen, B. (Contributor), Droll, D. (Contributor), Rojas, F. (Contributor), Minia, I. (Contributor), Terrao, M. (Contributor), Mercé, C. (Contributor), Matthews, K. (Contributor), Myler, P. (Contributor), Parsons, M. (Contributor) & Clayton, C. (Contributor), Unknown Publisher, 26 Apr 2016

  DOI: 10.6084/m9.figshare.c.3636047_d3.v1, https://springernature.figshare.com/articles/dataset/Additional_file_14_Table_S2_of_Integrative_analysis_of_the_Trypanosoma_brucei_gene_expression_cascade_predicts_differential_regulation_of_mRNA_processing_and_unusual_control_of_ribosomal_protein_expression/4440308/1

  Dataset / Software: Dataset

• Additional file 1: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

  Antwi, E. B. (Creator), Haanstra, J. R. (Creator), Ramasamy, G. (Contributor), Jensen, B. (Creator), Droll, D. (Creator), Rojas, F. (Creator), Minia, I. (Creator), Terrao, M. (Creator), Mercé, C. (Contributor), Matthews, K. (Creator), Myler, P. J. (Creator), Parsons, M. (Creator) & Clayton, C. (Creator), Figshare, 2016

  DOI: 10.6084/m9.figshare.c.3636047_d18, https://figshare.com/articles/Additional_file_1_of_Integrative_analysis_of_the_Trypanosoma_brucei_gene_expression_cascade_predicts_differential_regulation_of_mRNA_processing_and_unusual_control_of_ribosomal_protein_expression/4440353

  Dataset / Software: Dataset

• Steering microbiomes by organic amendments towards climate-smart agricultural soils

  Brenzinger, K. (Contributor), Costa, O. Y. A. (Contributor), Ho, A. (Contributor), Koorneef, G. (Contributor), Robroek, B. (Contributor), Molenaar, D. (Contributor), Korthals, G. (Contributor) & Bodelier, P. L. E. (Contributor), DRYAD, 1 Jan 2021

  DOI: 10.5061/dryad.4qrfj6q9n, http://datadryad.org/stash/dataset/doi:10.5061/dryad.4qrfj6q9n

  Dataset / Software: Dataset

• Additional file 2: of Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity

  Dols, J. (Contributor), Molenaar, D. (Contributor), Helm, J. V. D. (Contributor), Caspers, M. (Contributor), Angelino-Bart, A. D. K. (Contributor), Schuren, F. (Contributor), Speksnijder, A. (Contributor), Westerhoff, H. (Contributor), Richardus, J. (Contributor), Boon, M. (Contributor), Reid, G. (Contributor), Vries, H. D. (Contributor) & Kort, R. (Contributor), Unknown Publisher, 1 Jan 2016

  DOI: 10.6084/m9.figshare.c.3615860_d3.v1, https://springernature.figshare.com/articles/dataset/Additional_file_2_of_Molecular_assessment_of_bacterial_vaginosis_by_Lactobacillus_abundance_and_species_diversity/4377770/1

  Dataset / Software: Dataset

• Additional file 13: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

  Antwi, E. (Contributor), Haanstra, J. (Contributor), Ramasamy, G. (Contributor), Jensen, B. (Contributor), Droll, D. (Contributor), Rojas, F. (Contributor), Minia, I. (Contributor), Terrao, M. (Contributor), MercĂŠ, C. (Contributor), Matthews, K. (Contributor), Myler, P. (Contributor), Parsons, M. (Contributor) & Clayton, C. (Contributor), Unknown Publisher, 26 Apr 2016

  DOI: 10.6084/m9.figshare.c.3636047_d16.v1, https://springernature.figshare.com/articles/dataset/Additional_file_13_of_Integrative_analysis_of_the_Trypanosoma_brucei_gene_expression_cascade_predicts_differential_regulation_of_mRNA_processing_and_unusual_control_of_ribosomal_protein_expression/4440347/1

  Dataset / Software: Dataset

• Additional file 13: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

  Antwi, E. B. (Creator), Haanstra, J. R. (Creator), Ramasamy, G. (Contributor), Jensen, B. (Creator), Droll, D. (Creator), Rojas, F. (Creator), Minia, I. (Creator), Terrao, M. (Creator), Mercé, C. (Contributor), Matthews, K. (Creator), Myler, P. J. (Creator), Parsons, M. (Creator) & Clayton, C. (Creator), Figshare, 2016

  DOI: 10.6084/m9.figshare.c.3636047_d16, https://figshare.com/articles/Additional_file_13_of_Integrative_analysis_of_the_Trypanosoma_brucei_gene_expression_cascade_predicts_differential_regulation_of_mRNA_processing_and_unusual_control_of_ribosomal_protein_expression/4440347

  Dataset / Software: Dataset

• Additional file 8: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

  Antwi, E. B. (Creator), Haanstra, J. R. (Creator), Ramasamy, G. (Contributor), Jensen, B. (Creator), Droll, D. (Creator), Rojas, F. (Creator), Minia, I. (Creator), Terrao, M. (Creator), Mercé, C. (Contributor), Matthews, K. (Creator), Myler, P. J. (Creator), Parsons, M. (Creator) & Clayton, C. (Creator), Figshare, 2016

  DOI: 10.6084/m9.figshare.c.3636047_d15, https://figshare.com/articles/Additional_file_8_of_Integrative_analysis_of_the_Trypanosoma_brucei_gene_expression_cascade_predicts_differential_regulation_of_mRNA_processing_and_unusual_control_of_ribosomal_protein_expression/4440344

  Dataset / Software: Dataset

• Additional file 2: of Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity

  Dols, J. A. M. (Creator), Molenaar, D. (Creator), van der Helm, J. J. (Contributor), Caspers, M. P. M. (Creator), Angelino-Bart, A. D. K. (Creator), Schuren, F. H. J. (Creator), Speksnijder, A. G. C. L. (Creator), Westerhoff, H. V. (Creator), Richardus, J. H. (Creator), Boon, M. E. (Creator), Reid, G. (Creator), de Vries, H. J. C. (Contributor) & Kort, R. (Creator), Figshare, 2016

  DOI: 10.6084/m9.figshare.c.3615860_d3, https://figshare.com/articles/Additional_file_2_of_Molecular_assessment_of_bacterial_vaginosis_by_Lactobacillus_abundance_and_species_diversity/4377770

  Dataset / Software: Dataset

• Additional file 1: of A systematic assessment of current genome-scale metabolic reconstruction tools

  Mendoza, S. N. (Creator), Olivier, B. G. (Creator), Molenaar, D. (Creator) & Teusink, B. (Creator), Figshare, 2019

  DOI: 10.6084/m9.figshare.9350297, https://springernature.figshare.com/articles/Additional_file_1_of_A_systematic_assessment_of_current_genome-scale_metabolic_reconstruction_tools/9350297

  Dataset / Software: Dataset

• A computational toolbox to investigate the metabolic potential and resource allocation in fission yeast

  Grigaitis, P. (Creator), Grundel, D. A. J. (Creator), van Pelt-KleinJan, E. (Creator), Isaku, M. (Creator), Xie, G. (Creator), Mendoza Farias, S. (Creator), Olivier, B. G. (Creator), Teusink, B. (Creator) & van Heerden, J. H. (Creator), Zenodo, 2022

  DOI: 10.5281/zenodo.6513463, https://zenodo.org/record/6513463

  Dataset / Software: Dataset

• Additional file 8: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

  Antwi, E. (Contributor), Haanstra, J. (Contributor), Ramasamy, G. (Contributor), Jensen, B. (Contributor), Droll, D. (Contributor), Rojas, F. (Contributor), Minia, I. (Contributor), Terrao, M. (Contributor), MercĂŠ, C. (Contributor), Matthews, K. (Contributor), Myler, P. (Contributor), Parsons, M. (Contributor) & Clayton, C. (Contributor), Unknown Publisher, 26 Apr 2016

  DOI: 10.6084/m9.figshare.c.3636047_d15.v1, https://springernature.figshare.com/articles/dataset/Additional_file_8_of_Integrative_analysis_of_the_Trypanosoma_brucei_gene_expression_cascade_predicts_differential_regulation_of_mRNA_processing_and_unusual_control_of_ribosomal_protein_expression/4440344/1

  Dataset / Software: Dataset

• Additional file 6: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

  Antwi, E. B. (Creator), Haanstra, J. R. (Creator), Ramasamy, G. (Contributor), Jensen, B. (Creator), Droll, D. (Creator), Rojas, F. (Creator), Minia, I. (Creator), Terrao, M. (Creator), Mercé, C. (Contributor), Matthews, K. (Creator), Myler, P. J. (Creator), Parsons, M. (Creator) & Clayton, C. (Creator), Figshare, 2016

  DOI: 10.6084/m9.figshare.c.3636047_d1, https://figshare.com/articles/Additional_file_6_of_Integrative_analysis_of_the_Trypanosoma_brucei_gene_expression_cascade_predicts_differential_regulation_of_mRNA_processing_and_unusual_control_of_ribosomal_protein_expression/4440302

  Dataset / Software: Dataset

• Additional file 3: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

  Antwi, E. (Contributor), Haanstra, J. (Contributor), Ramasamy, G. (Contributor), Jensen, B. (Contributor), Droll, D. (Contributor), Rojas, F. (Contributor), Minia, I. (Contributor), Terrao, M. (Contributor), MercĂŠ, C. (Contributor), Matthews, K. (Contributor), Myler, P. (Contributor), Parsons, M. (Contributor) & Clayton, C. (Contributor), Unknown Publisher, 26 Apr 2016

  DOI: 10.6084/m9.figshare.c.3636047_d10.v1, https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Integrative_analysis_of_the_Trypanosoma_brucei_gene_expression_cascade_predicts_differential_regulation_of_mRNA_processing_and_unusual_control_of_ribosomal_protein_expression/4440329/1

  Dataset / Software: Dataset

• Additional file 5: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

  Antwi, E. (Contributor), Haanstra, J. (Contributor), Ramasamy, G. (Contributor), Jensen, B. (Contributor), Droll, D. (Contributor), Rojas, F. (Contributor), Minia, I. (Contributor), Terrao, M. (Contributor), MercĂŠ, C. (Contributor), Matthews, K. (Contributor), Myler, P. (Contributor), Parsons, M. (Contributor) & Clayton, C. (Contributor), Unknown Publisher, 26 Apr 2016

  DOI: 10.6084/m9.figshare.c.3636047_d9.v1, https://springernature.figshare.com/articles/dataset/Additional_file_5_of_Integrative_analysis_of_the_Trypanosoma_brucei_gene_expression_cascade_predicts_differential_regulation_of_mRNA_processing_and_unusual_control_of_ribosomal_protein_expression/4440326/1

  Dataset / Software: Dataset