Systems and Synthetic Biology

2025

YeastFab Cloning of Toxic Genes and Protein Expression Optimization in Yeast

Hoffmann, S. A., 4 Oct 2025, Golden Gate Cloning: Methods and Protocols. Schindler, D. (ed.). New York: Humana Press, p. 435-450 16 p. (Methods in molecular biology; vol. 2850).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

2024

A gentle introduction to principal component analysis using tea-pots, dinosaurs, and pizza

Saccenti, E., Jan 2024, In: Teaching Statistics. 46, 1, p. 38-52

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

3 Citations (Scopus)

Amplified seasonality in western Europe in a warmer world

de Winter, N. J., Tindall, J., Johnson, A. L. A., Goudsmit-Harzevoort, B., Wichern, N., Kaskes, P., Claeys, P., Huygen, F., van Leeuwen, S., Metcalfe, B., Bakker, P., Goolaerts, S., Wesselingh, F. & Ziegler, M., 15 May 2024, In: Science Advances. 10, 20, eadl6717.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

1 Citation (Scopus)

Biobased short chain fatty acid production - Exploring microbial community dynamics and metabolic networks through kinetic and microbial modeling approaches

Atasoy, M., Scott, W. T., Regueira, A., Mauricio-Iglesias, M., Schaap, P. J. & Smidt, H., 1 Jul 2024, In: Biotechnology Advances. 73, 108363.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

2 Citations (Scopus)

Bridging the gap in precision medicine: TranSYS training programme for next-generation scientists

Andreoli, L., Berca, C., Katz, S., Korshevniuk, M., Head, R. M. & Van Steen, K., 24 May 2024, In: Frontiers in Medicine. 11, 1348148.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

1 Citation (Scopus)

Combinatorial optimization of pathway, process and media for the production of p-coumaric acid by Saccharomyces cerevisiae

Moreno Paz, S., van der Hoek, R., Eliana, E., Martins dos Santos, V. A. P., Schmitz, J. & Suarez Diez, M., 25 Mar 2024, In: Microbial Biotechnology. 17, 3, e14424.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomics

Stelloo, S., Alejo-Vinogradova, M. T., van Gelder, C. A. G. H., Zijlmans, D. W., van Oostrom, M. J., Valverde, J. M., Lamers, L. A., Rus, T., Sobrevals Alcaraz, P., Schäfers, T., Furlan, C., Jansen, P. W. T. C., Baltissen, M. P. A., Sonnen, K. F., Burgering, B., Altelaar, M. A. F. M., Vos, H. R. & Vermeulen, M., 2024, In: Cell Stem Cell. 31, 7, p. 1072-1090.e8 28 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

1 Citation (Scopus)

Designing interpretable deep learning applications for functional genomics: A quantitative analysis

Van Hilten, A., Katz, S., Saccenti, E., Niessen, W. J. & Roshchupkin, G. V., Sept 2024, In: Briefings in Bioinformatics. 25, 5, bbae449.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Discrimination of Lipogenic or Glucogenic Diet Effects in Early-Lactation Dairy Cows Using Plasma Metabolite Abundances and Ratios in Combination with Machine Learning

Wang, X., Jahagirdar, S., Bakker, W., Lute, C., Kemp, B., van Knegsel, A. & Saccenti, E., Apr 2024, In: Metabolites. 14, 4, 230.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Exploring RNA-seq data normalization methods using principal component analysis and KEGG pathway enrichment

van Lingen, H. J., Suarez Diez, M. & Saccenti, E., 18 Jan 2024.

Research output: Contribution to conference › Poster › Academic

Open Access

From bytes to bedside and back: Enhancing clinical decision support with explainable AI

Katz, S., 20 Sept 2024, Wageningen: Wageningen University. 305 p.

Research output: Thesis › internal PhD, WU

Open Access

Genes controlling hydrolysate toxin tolerance identified by QTL analysis of the natural Saccharomyces cerevisiae BCC39850

Sornlek, W., Sonthirod, C., Tangphatsornruang, S., Ingsriswang, S., Runguphan, W., Eurwilaichtr, L., Champreda, V., Tanapongpipat, S., Schaap, P. J. & Martins dos Santos, V. A. P., Jan 2024, In: Applied Microbiology and Biotechnology. 108, 1, p. 1-13 13 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

2 Citations (Scopus)

Identification of genes associated with the high-temperature fermentation trait in the Saccharomyces cerevisiae natural isolate BCC39850

Sornlek, W., Suwanakitti, N., Sonthirod, C., Tangphatsornruang, S., Ingsriswang, S., Runguphan, W., Eurwilaichtr, L., Tanapongpipat, S., Champreda, V., Roongsawang, N., Schaap, P. J. & Martins dos Santos, V. A. P., 4 Sept 2024, In: Archives of Microbiology. 206, 391.

Research output: Contribution to journal › Article › Academic › peer-review

Innovative genetic tools and metabolic engineering strategies for advanced biomanufacturing: A focus on Pseudomonas putida

Martín Pascual, M., 19 Apr 2024, Wageningen: Wageningen University. 446 p.

Research output: Thesis › internal PhD, WU

In silico analysis of design of experiment methods for metabolic pathway optimization

Moreno-Paz, S., Schmitz, J. & Suarez-Diez, M., 1 May 2024, In: Computational and Structural Biotechnology Journal. 23, p. 1959-1967 9 p.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Integrative protocol for quantifying cholesterol-related sterols in human serum samples and building decision support systems

Kočar, E., Katz, S., Pušnik, Ž., Skubic, C., Režen, T., Martins dos Santos, V. A. P., Mraz, M., Moškon, M. & Rozman, D., 20 Sept 2024, In: STAR Protocols. 5, 3, 103213.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

iSO1949_N.oceanica, Genome-scale metabolic model of Nannochloropsis oceanica

van Oossanen, S., Ferrer Ledo, N. (Other), Martins dos Santos, V. A. P. (Other), Barbosa, M. J. (Other), Suarez Diez, M. (Other) & D'Adamo, S. (Other), 14 Feb 2024

Research output: Non-textual form › Software

Open Access

Machine Learning-Guided Optimization of p-Coumaric Acid Production in Yeast

Moreno Paz, S., Van der Hoek, R., Eliana, E., Zwartjens, P., Gosiewska, S., Martins dos Santos, V. A. P., Schmitz, J. & Suarez Diez, M., 2024, In: ACS synthetic biology. 13, 4, p. 1312-1322

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

1 Citation (Scopus)

Metagenomic clustering links specific metabolic functions to globally relevant ecosystems

Flinkstrom, Z., Bryson, S., Candry, P. & Winkler, M. K. H., 1 Aug 2024, In: mSystems. 9, 8

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Metaproteomics-informed stoichiometric modeling reveals the responses of wetland microbial communities to oxygen and sulfate exposure

Wang, D., Candry, P., Hunt, K. A., Flinkstrom, Z., Shi, Z., Liu, Y., Wofford, N. Q., McInerney, M. J., Tanner, R. S., De Leόn, K. B., Zhou, J., Winkler, M. K. H., Stahl, D. A. & Pan, C., 3 Jul 2024, In: npj Biofilms and Microbiomes. 10, 55.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Metatranscriptomic analysis indicates prebiotic effect of isomalto/malto-polysaccharides on human colonic microbiota in-vitro

Borewicz, K., Hornung, B., Gu, F., van der Zaal, P. H., Schols, H. A., Schaap, P. J. & Smidt, H., 14 Aug 2024, In: Scientific Reports. 14, 18866.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Microbe-cellulose hydrogels as a model system for particulate carbon degradation in soil aggregates

Candry, P., Godfrey, B. & Winkler, M., 8 Jan 2024, In: ISME Communications. 4, 1, ycae068.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Model-driven engineering of Cutaneotrichosporon oleaginosus ATCC 20509 for improved microbial oil production

Duman, Z. E., Julsing, M. K., Verbokkem, J. A. C., Wolbert, E. J. H., Martins dos Santos, V. A. P., Hugenholtz, J. & Suarez Diez, M., 19 Mar 2024, BioRxiv.

Research output: Working paper › Preprint

Model-guided strain engineering: bridges between design and learning in bioprocess development

Moreno Paz, S., 31 May 2024, Wageningen: Wageningen University.

Research output: Thesis › internal PhD, WU

Open Access

Network analysis of the proteome and peptidome sheds light on human milk as a biological system

Dekker, P. M., Boeren, S., Saccenti, E. & Hettinga, K. A., 30 Mar 2024, In: Scientific Reports. 14, 1, 7569.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

1 Citation (Scopus)

Normalization of gene counts affects principal components-based exploratory analysis of RNA-sequencing data

van Lingen, H. J., Suarez-Diez, M. & Saccenti, E., Dec 2024, In: Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1867, 4, 195058.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

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

Li, Z., Katz, S. M., Saccenti, E., Fardo, D. W., Claes, P., Martins dos Santos, V. A. P., Van Steen, K. & Roshchupkin, G. V., 7 Mar 2024, BioRxiv.

Research output: Working paper › Preprint

Open Access

Omics-based analysis of Akkermansia muciniphila cultivation in food-grade media

Geerlings, S. Y., van der Ark, K., Nijsse, B., Boeren, S., van Loosdrecht, M., Belzer, C. & de Vos, W. M., 16 Jun 2024, In: Microbiome Research Reports. 3, 36.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Proteomics-based identification of biomarkers reflecting endogenous and exogenous exposure to the advanced glycation end product precursor methylglyoxal in SH-SY5Y human neuroblastoma cells

Zheng, L., Boeren, S., Liu, C., Bakker, W., Wang, H., Rietjens, I. M. C. M. & Saccenti, E., Jun 2024, In: International Journal of Biological Macromolecules. 272, 132859.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Putting Algae on the map: improving lipid productivity of Nannochloropsis oceanica through Genome-Scale Metabolic Modelling

van Oossanen, S., 21 May 2024, Wageningen: Wageningen University. 192 p.

Research output: Thesis › internal PhD, WU

RAF-like protein kinases mediate a deeply conserved, rapid auxin response

Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren, S., Monzer, A., Koehorst, J., Kohchi, T., Nishihama, R., Fendrych, M., Sprakel, J., Friml, J. & Weijers, D., 4 Jan 2024, In: Cell. 187, 1, p. 130-148.e17

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

18 Citations (Scopus)

The rise of scientific machine learning: a perspective on combining mechanistic modelling with machine learning for systems biology

Noordijk, B., Garcia Gomez, M. L., ten Tusscher, K. H. W. J., de Ridder, D., van Dijk, A. D. J. & Smith, R. W., 2 Aug 2024, In: Frontiers in Systems Biology. 4, 1407994.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass

Lyu, X., Nuhu, M., Candry, P., Wolfanger, J., Betenbaugh, M., Saldivar, A., Zuniga, C., Wang, Y. & Shrestha, S., 2024, In: Journal of Industrial Microbiology and Biotechnology. 51, kuae025.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

2023

A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem

Katoh, T., Yamada, C., Wallace, M. D., Yoshida, A., Gotoh, A., Arai, M., Maeshibu, T., Kashima, T., Hagenbeek, A., Ojima, M. N., Takada, H., Sakanaka, M., Shimizu, H., Nishiyama, K., Ashida, H., Hirose, J., Suarez-Diez, M., Nishiyama, M., Kimura, I. & Stubbs, K. A. & 2 others, Fushinobu, S. & Katayama, T., 2 Mar 2023, In: Nature Chemical Biology. 19, p. 778-789 12 p.

Research output: Contribution to journal › Article › Academic › peer-review

17 Citations (Scopus)

A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia

Scott, W. T., Benito-Vaquerizo, S., Zimmermann, J., Bajić, D., Heinken, A., Suarez-Diez, M. & Schaap, P. J., Aug 2023, In: PLoS Computational Biology. 19, 8 August, e1011363.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

15 Citations (Scopus)

A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia

Scott, T. W., Benito Vaquerizo, S., Zimmerman, J., Bajić, D., Heinken, A., Suarez Diez, M. & Schaap, P. J., 16 Feb 2023, BioRxiv, 32 p. (bioRxiv (Cold Spring Harbor Laboratory)).

Research output: Working paper › Preprint

Open Access

A tunable metabolic valve for precise growth control and increased product formation in Pseudomonas putida

Batianis, C., van Rosmalen, R. P., Major, M., van Ee, C., Kasiotakis, A., Weusthuis, R. A. & Martins dos Santos, V. A. P., Jan 2023, In: Metabolic Engineering. 75, p. 47-57

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

4 Citations (Scopus)

Author Correction: A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses

Waagmeester, A., Willighagen, E. L., Su, A. I., Kutmon, M., Gayo, J. E. L., Fernández-Álvarez, D., Groom, Q., Schaap, P. J., Verhagen, L. M. & Koehorst, J. J., 16 Nov 2023, In: BMC Biology. 21, 261.

Research output: Contribution to journal › Comment/Letter to the editor › Academic

Open Access

Author Correction: Corruption of the Pearson correlation coefficient by measurement error and its estimation, bias, and correction under different error models

Saccenti, E., Hendriks, M. H. W. B. & Smilde, A. K., Dec 2023, In: Scientific Reports. 13, 1, 22748.

Research output: Contribution to journal › Comment/Letter to the editor › Academic

Open Access

1 Citation (Scopus)

Classifying lipogenic and glucogenic diets in dairy cows based on metabolomics profiles

Wang, X., Jahagirdar, S. R., Bakker, W., Lute, C., Kemp, B., Saccenti, E. & van Knegsel, A. T. M., 20 Apr 2023, Program book The 45th animal nutrition research forum: Bridging expertise: advances in animal nutrition through interdisciplinary research. Wageningen: Wageningen University & Research, p. 35-35 P9

Research output: Chapter in Book/Report/Conference proceeding › Abstract

Classifying lipogenic and glucogenic diets in dairy cows based on metabolomics profiles

Wang, X., Jahagirdar, S. R., Bakker, W., Lute, C., Kemp, B., Saccenti, E. & van Knegsel, A. T. M., 28 Aug 2023, Book of Abstracts of the 74th Annual Meeting of the European Federation of Animal Science. Wageningen: Wageningen Academic Publishers, p. 569-569 1 p. (Book of Abstracts; no. 29).

Research output: Chapter in Book/Report/Conference proceeding › Abstract

Computational Approaches for Peroxisomal Protein Localization

Anteghini, M. & Martins dos Santos, V. A. P., 24 Mar 2023, Peroxisomes: Methods and protocols. Schrader, M. (ed.). 2 ed. Humana Press, p. 405-411 7 p. (Methods in Molecular Biology; vol. 2643).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

Open Access

Corrigendum: The human milk proteome and allergy of mother and child: exploring associations with protein abundances and protein network connectivity

Dekker, P. M., Azad, M. B., Boeren, S., Mandhane, P. J., Moraes, T. J., Simons, E., Subbarao, P., Turvey, S. E., Saccenti, E. & Hettinga, K. A., 2023, In: Frontiers in Immunology. 14, 1276180.

Research output: Contribution to journal › Comment/Letter to the editor › Academic

Open Access

COVID-19 and cholesterol biosynthesis: Towards innovative decision support systems

Kočar, E., Katz, S., Pušnik, Ž., Bogovič, P., Turel, G., Skubic, C., Režen, T., Strle, F., Martins dos Santos, V. A. P., Mraz, M., Moškon, M. & Rozman, D., 20 Oct 2023, In: iScience. 26, 10, 107799.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

3 Citations (Scopus)

Digital twin maturity levels: a theoretical framework for defining capabilities and goals in the life and environmental sciences

Metcalfe, B., Boshuizen, H. C., Bulens, J. D. & Koehorst, J. J., 10 Aug 2023, In: F1000Research. 12, 961

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Editorial Education in systems biology 2022

Saccenti, E., 13 Mar 2023, In: Frontiers in Systems Biology. 3, 1176588.

Research output: Contribution to journal › Editorial › Academic

Open Access

Energy balance clusters in relation to metabolic and inflammatory status and disease in dairy cows

Ma, J., Kok, A., Bruckmaier, R., Burgers, E. E. A., Goselink, R. M. A., Gross, J., Lam, T., Minuti, A., Saccenti, E., Trevisi, E. & van Knegsel, A. T. M., 28 Aug 2023, Book of Abstracts of the 74th Annual Meeting of the European Federation of Animal Science. Wageningen: Wageningen Academic Publishers, p. 994-994 1 p. (Book of Abstracts; no. 29).

Research output: Chapter in Book/Report/Conference proceeding › Abstract