BT/Industriele Microbiologie

Scott, W. T., Benito-Vaquerizo, S., Zimmermann, J., Bajić, D., Heinken, A., Suarez-Diez, M. & Schaap, P. J., 2023, In: PLoS Computational Biology. 19, 8 August, 32 p., e1011363.

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Co-cultivation of Saccharomyces cerevisiae strains combines advantages of different metabolic engineering strategies for improved ethanol yield

van Aalst, A. C. A., van der Meulen, I. S., Jansen, M. L. A., Mans, R. & Pronk, J. T., 2023, In: Metabolic Engineering. 80, p. 151-162

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Comparative proteome analysis of different Saccharomyces cerevisiae strains during growth on sucrose and glucose

Soares Rodrigues, C. I., den Ridder, M., Pabst, M., Gombert, A. K. & Wahl, S. A., 2023, In: Scientific Reports. 13, 1, 10 p., 2126.

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CRI-SPA: a high-throughput method for systematic genetic editing of yeast libraries

Cachera, P., Olsson, H., Coumou, H., Jensen, M. L., Sánchez, B. J., Strucko, T., van den Broek, M., Daran, J. M., Jensen, M. K., Sonnenschein, N., Lisby, M. & Mortensen, U. H., 2023, In: Nucleic Acids Research. 51, 17, 14 p., e91.

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Emergent coexistence in multispecies microbial communities

Chang, C. Y., Bajić, D., Vila, J. C. C., Estrela, S. & Sanchez, A., 2023, In: Science (New York, N.Y.). 381, 6655, p. 343-348 6 p.

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Expanding the genome editing toolbox of Saccharomyces cerevisiae with the endonuclease ErCas12a

Bennis, N. X., Anderson, J. P., Kok, S. M. C. & Daran, J. M. G., 2023, In: FEMS Yeast Research. 23, p. 1-14 14 p., foad043.

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Improving CRISPR-Cas9 mediated genome integration in interspecific hybrid yeasts

Bennis, N. X., Kostanjšek, M., van den Broek, M. & Daran, J. M. G., 2023, In: New Biotechnology. 76, p. 49-62 14 p.

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Iron-loaded deferiprone can support full hemoglobinization of cultured red blood cells

Gallego-Murillo, J. S., Yağcı, N., Pinho, E. M., Wahl, S. A., van den Akker, E. & von Lindern, M., 2023, In: Scientific Reports. 13, 1, 34 p., 6960.

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Long-read direct RNA sequencing of the mitochondrial transcriptome of Saccharomyces cerevisiae reveals condition-dependent intron abundance

Koster, C. C., Kleefeldt, A. A., van den Broek, M., Luttik, M., Daran, J. M. & Daran-Lapujade, P., 2023, In: Yeast. 23 p.

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Optimizing the balance between heterologous acetate- and CO2-reduction pathways in anaerobic cultures of Saccharomyces cerevisiae strains engineered for low-glycerol production

van Aalst, A. C. A., Geraats, E. H., Jansen, M. L. A., Mans, R. & Pronk, J. T., 2023, In: FEMS yeast research. 23, 11 p.

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Predicting the impact of temperature on metabolic fluxes using resource allocation modelling: Application to polyphosphate accumulating organisms

Páez-Watson, T., van Loosdrecht, M. C. M. & Wahl, S. A., 2023, In: Water Research. 228, 9 p., 119365.

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Predicting the influence of combined oxygen and glucose gradients based on scale-down and modelling approaches for the scale-up of penicillin fermentations

Janoska, A., Buijs, J. & van Gulik, W. M., 2023, In: Process Biochemistry. 124, p. 100-112

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Proteome Dynamics During Transition From Exponential to Stationary Phase Under Aerobic and Anaerobic Conditions in Yeast

Ridder, M. D., van den Brandeler, W., Altiner, M., Daran-Lapujade, P. & Pabst, M., 2023, In: Molecular & cellular proteomics : MCP. 22, 6, p. 100552 1 p., 100552.

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Quantification and mitigation of byproduct formation by low-glycerol-producing Saccharomyces cerevisiae strains containing Calvin-cycle enzymes

van Aalst, A. C. A., Jansen, M. L. A., Mans, R. & Pronk, J. T., 2023, In: Biotechnology for Biofuels and Bioproducts. 16, 1, 17 p., 81.

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The Architecture of Metabolic Networks Constrains the Evolution of Microbial Resource Hierarchies

Takano, S., Vila, J. C. C., Miyazaki, R., Sánchez, Á. & Bajić, D., 2023, In: Molecular Biology and Evolution. 40, 9, 14 p., msad187.

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Trichlorobacter ammonificans, a dedicated acetate-dependent ammonifier with a novel module for dissimilatory nitrate reduction to ammonia

Sorokin, D. Y., Tikhonova, T. V., Koch, H., van den Berg, E. M., Hinderks, R. S., Pabst, M., Kuenen, G. J., van Loosdrecht, M. C. M., Lücker, S. & More Authors, 2023, In: ISME Journal. 17, 10, p. 1639-1648 10 p.

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Using Kinetic Modelling to Infer Adaptations in Saccharomyces cerevisiae Carbohydrate Storage Metabolism to Dynamic Substrate Conditions

Lao-Martil, D., Verhagen, K. J. A., Valdeira Caetano, A. H., Pardijs, I. H., van Riel, N. A. W. & Wahl, S. A., 2023, In: Metabolites. 13, 1, 20 p., 88.

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2022

An engineered non-oxidative glycolytic bypass based on Calvin-cycle enzymes enables anaerobic co-fermentation of glucose and sorbitol by Saccharomyces cerevisiae

van Aalst, A. C. A., Mans, R. & Pronk, J. T., 2022, In: Biotechnology for Biofuels and Bioproducts. 15, 1, 112.

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A systematic evaluation of yeast sample preparation protocols for spectral identifications, proteome coverage and post-isolation modifications

den Ridder, M., Knibbe, E., van den Brandeler, W., Daran-Lapujade, P. & Pabst, M., 2022, In: Journal of Proteomics. 261, 13 p., 104576.

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5 Citations (Scopus)

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Automated Evolutionary Engineering of Yeasts

de Hulster, E., Mooiman, C., Timmermans, R. & Mans, R., 2022, In: Methods in molecular biology (Clifton, N.J.). 2513, p. 255-270

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Beyond Saccharomyces pastorianus for modern lager brews: Exploring non-cerevisiae Saccharomyces hybrids with heterotic maltotriose consumption and novel aroma profile

Gyurchev, N. Y., Coral-Medina, Á., Weening, S. M., Almayouf, S., Kuijpers, N. G. A., Nevoigt, E. & Louis, E. J., 2022, In: Frontiers in Microbiology. 13, 14 p., 1025132.

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Carbon dioxide fixation via production of succinic acid from glycerol in engineered Saccharomyces cerevisiae

Malubhoy, Z., Bahia, F. M., de Valk, S. C., de Hulster, E., Rendulić, T., Ortiz, J. P. R., Xiberras, J., Klein, M., Mans, R. & Nevoigt, E., 2022, In: Microbial Cell Factories. 21, 1, 15 p., 102.

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Engineering an acetoacetyl-CoA reductase from Cupriavidus necator toward NADH preference under physiological conditions

Olavarria, K., Pijman, Y. O., Cabrera, R., van Loosdrecht, M. C. M. & Wahl, S. A., 2022, In: Scientific Reports. 12, 1, 10 p., 3757.

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Engineering proton-coupled hexose uptake in Saccharomyces cerevisiae for improved ethanol yield

de Valk, S. C., Bouwmeester, S. E., de Hulster, E. & Mans, R., 2022, In: Biotechnology for Biofuels and Bioproducts. 15, 1, 16 p., 47.

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Expansion and differentiation of ex vivo cultured erythroblasts in scalable stirred bioreactors

Gallego-Murillo, J. S., Iacono, G., van der Wielen, L. A. M., van den Akker, E., von Lindern, M. & Wahl, S. A., 2022, In: Biotechnology and Bioengineering. 119, 11, p. 3096-3116

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Full humanization of the glycolytic pathway in Saccharomyces cerevisiae

Boonekamp, F. J., Knibbe, E., Vieira-Lara, M. A., Wijsman, M., Luttik, M. A. H., van Eunen, K., Ridder, M. D., Pabst, M., Daran, J. M. & Daran-Lapujade, P., 2022, In: Cell Reports. 39, 13, p. 111010 32 p., 111010.

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Genetic bases for the metabolism of the DMS precursor S-methylmethionine by Saccharomyces cerevisiae

Eder, M., Sanchez, I., Camarasa, C., Daran, J. M., Legras, J. L. & Dequin, S., 2022, In: Food Microbiology. 106, 9 p., 104041.

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Genome-wide effect of non-optimal temperatures under anaerobic conditions on gene expression in Saccharomyces cerevisiae

García-Ríos, E., Alonso-del-Real, J., Lip, K. Y. F., Pinheiro, T., Teixeira, J., van Gulik, W., Domingues, L., Querol, A. & Guillamón, J. M., 2022, In: Genomics. 114, 4, 14 p., 110386.

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Identification of fungal dihydrouracil-oxidase genes by expression in Saccharomyces cerevisiae

Bouwknegt, J., Vos, A. M., Ortiz Merino, R. A., van Cuylenburg, D. C., Luttik, M. A. H. & Pronk, J. T., 2022, In: Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology. 115, 11, p. 1363-1378

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Influence of oxygen concentration on the metabolism of Penicillium chrysogenum

Janoska, A., Verheijen, J. J., Tang, W., Lee, Q., Sikkema, B. & van Gulik, W. M., 2022, In: Engineering in Life Sciences. 23, 1, 17 p., e2100139.

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Modular, synthetic chromosomes as new tools for large scale engineering of metabolism

Postma, E. D., Hassing, E. J., Mangkusaputra, V., Geelhoed, J., de la Torre, P., van den Broek, M., Mooiman, C., Pabst, M., Daran, J. M. & Daran-Lapujade, P., 2022, In: Metabolic Engineering. 72, p. 1-13

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Monitoring Intracellular Metabolite Dynamics in Saccharomyces cerevisiae during Industrially Relevant Famine Stimuli

Minden, S., Aniolek, M., Sarkizi Shams Hajian, C., Teleki, A., Zerrer, T., Delvigne, F., van Gulik, W., Deshmukh, A., Noorman, H. & Takors, R., 2022, In: Metabolites. 12, 3, 263.

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Novel Evolutionary Engineering Approach to Alter Substrate Specificity of Disaccharide Transporter Mal11 in Saccharomyces cerevisiae

de Valk, S. C. & Mans, R., 2022, In: Journal of Fungi. 8, 4, 15 p., 358.

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Pathway engineering strategies for improved product yield in yeast-based industrial ethanol production

van Aalst, A. C. A., de Valk, S. C., van Gulik, W. M., Jansen, M. L. A., Pronk, J. T. & Mans, R., 2022, In: Synthetic and Systems Biotechnology. 7, 1, p. 554-566

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Predicting Metabolic Adaptation Under Dynamic Substrate Conditions Using a Resource-Dependent Kinetic Model: A Case Study Using Saccharomyces cerevisiae

Verhagen, K. J. A., Eerden, S. A., Sikkema, B. J. & Wahl, S. A., 2022, In: Frontiers in Molecular Biosciences. 9, 12 p., 863470.

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Respiratory reoxidation of NADH is a key contributor to high oxygen requirements of oxygen-limited cultures of Ogataea parapolymorpha

Dekker, W. J. C., Jürgens, H., Ortiz-Merino, R. A., Mooiman, C., van den Berg, R., Kaljouw, A., Mans, R. & Pronk, J. T., 2022, In: FEMS Yeast Research. 22, 1, 15 p., foac007.

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Top-Down, Knowledge-Based Genetic Reduction of Yeast Central Carbon Metabolism

Postma, E. D., Couwenberg, L. G. F., van Roosmalen, R. N., Geelhoed, J., de Groot, P. A. & Daran-Lapujade, P., 2022, In: mBio. 13, 5, p. e0297021

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Towards closed carbon loop fermentations: Cofeeding of Yarrowia lipolytica with glucose and formic acid

van Winden, W. A., Mans, R., Breestraat, S., Verlinden, R. A. J., Mielgo-Gómez, Á., de Hulster, E. A. F., de Bruijn, H. M. C. J. & Noorman, H. J., 2022, In: Biotechnology and Bioengineering. 119, 8, p. 2142-2151 10 p.

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Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

Elsemman, I. E., Rodriguez Prado, A., Grigaitis, P., Garcia Albornoz, M., Harman, V., Holman, S. W., van Heerden, J., Bisschops, M. M. M., Daran-Lapujade, P. & More Authors, 2022, In: Nature Communications. 13, 1, 12 p., 801.

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2021

Aerobic growth physiology of Saccharomyces cerevisiae on sucrose is strain-dependent

Rodrigues, C. I. S., Wahl, A. & Gombert, A. K., 2021, In: FEMS Yeast Research. 21, 3, 13 p., foab021.

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A possible influence of extracellular polysaccharides on the analysis of intracellular metabolites from Trichoderma harzianum grown under carbon-limited conditions

Gelain, L., Geraldo da Cruz Pradella, J., Carvalho da Costa, A., van der Wielen, L. & van Gulik, W. M., 2021, In: Fungal Biology. 125, 5, p. 368-377

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A squalene-hopene cyclase in Schizosaccharomyces japonicus represents a eukaryotic adaptation to sterol-limited anaerobic environments

Bouwknegt, J., Wiersma, S. J., Ortiz-Merino, R. A., Doornenbal, E. S. R., Buitenhuis, P., Giera, M., Müller, C. & Pronk, J. T., 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 32, e2105225118.

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A supernumerary designer chromosome for modular in vivo pathway assembly in Saccharomyces cerevisiae

Postma, E. D., Dashko, S., van Breemen, L., Taylor Parkins, S. K., van den Broek, M., Daran, J. M. & Daran-Lapujade, P., 2021, In: Nucleic Acids Research. 49, 3, p. 1769-1783 15 p.

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Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis

Bouwknegt, J., Koster, C. C., Vos, A. M., Ortiz-Merino, R. A., Wassink, M., Luttik, M. A. H., van den Broek, M., Hagedoorn, P. L. & Pronk, J. T., 2021, In: Fungal Biology and Biotechnology. 8, 1, 18 p., 10.

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Co-fermentation of sugarcane bagasse hydrolysate and molasses by Clostridium saccharoperbutylacetonicum: Effect on sugar consumption and butanol production

Zetty-Arenas, A. M., Tovar, L. P., Alves, R. F., Mariano, A. P., van Gulik, W., Maciel Filho, R. & Freitas, S., 2021, In: Industrial Crops and Products. 167, 10 p., 113512.

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BT/Industriele Microbiologie

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