Prof. Dr. Aljoscha Wahl

2025

• Verhagen KJA., Pardijs IH., van Klaveren HM., Wahl SA.:
  A Dive Into Yeast's Sugar Diet—Comparing the Metabolic Response of Glucose, Fructose, Sucrose, and Maltose Under Dynamic Feast/Famine Conditions
  In: Biotechnology and Bioengineering (2025)
  ISSN: 0006-3592
  DOI: 10.1002/bit.28935

2023

• Arevalo Villa C., Marienhagen J., Noack S., Wahl SA.:
  Achieving net zero CO2 emission in the biobased production of reduced platform chemicals using defined co-feeding of methanol
  In: Current Opinion in Biotechnology 82 (2023), Article No.: 102967
  ISSN: 0958-1669
  DOI: 10.1016/j.copbio.2023.102967
• Gallego-Murillo JS., Yağcı N., Pinho EM., Wahl SA., van den Akker E., von Lindern M.:
  Iron-loaded deferiprone can support full hemoglobinization of cultured red blood cells
  In: Scientific Reports 13 (2023), Article No.: 6960
  ISSN: 2045-2322
  DOI: 10.1038/s41598-023-32706-1
• Lao-Martil D., Verhagen KJ., Valdeira Caetano AH., Pardijs IH., van Riel NA., Wahl SA.:
  Using Kinetic Modelling to Infer Adaptations in Saccharomyces cerevisiae Carbohydrate Storage Metabolism to Dynamic Substrate Conditions
  In: Metabolites 13 (2023), Article No.: 88
  ISSN: 2218-1989
  DOI: 10.3390/metabo13010088
• Olavarria K., Becker MV., Sousa DZ., van Loosdrecht MC., Wahl SA.:
  Design and thermodynamic analysis of a pathway enabling anaerobic production of poly-3-hydroxybutyrate in Escherichia coli
  In: Synthetic and Systems Biotechnology 8 (2023), p. 629-639
  ISSN: 2405-805X
  DOI: 10.1016/j.synbio.2023.09.005
• Paez-Watson T., Van Loosdrecht MCM., Wahl SA.:
  Predicting the impact of temperature on metabolic fluxes using resource allocation modelling: Application to polyphosphate accumulating organisms
  In: Water Research 228 (2023)
  ISSN: 0043-1354
  DOI: 10.1016/j.watres.2022.119365
• Soares Rodrigues CI., den Ridder M., Pabst M., Gombert AK., Wahl SA.:
  Comparative proteome analysis of different Saccharomyces cerevisiae strains during growth on sucrose and glucose
  In: Scientific Reports 13 (2023), Article No.: 2126
  ISSN: 2045-2322
  DOI: 10.1038/s41598-023-29172-0

2022

• Gallego-Murillo JS., Iacono G., van der Wielen LA., van den Akker E., von Lindern M., Wahl SA.:
  Expansion and differentiation of ex vivo cultured erythroblasts in scalable stirred bioreactors
  In: Biotechnology and Bioengineering (2022)
  ISSN: 0006-3592
  DOI: 10.1002/bit.28193
• Lao-Martil D., Verhagen KJA., Schmitz JP., Teusink B., Wahl SA., van Riel NA.:
  Kinetic Modeling of Saccharomyces cerevisiae Central Carbon Metabolism: Achievements, Limitations, and Opportunities
  In: Metabolites 12 (2022), Article No.: 74
  ISSN: 2218-1989
  DOI: 10.3390/metabo12010074
• Verhagen KJA., Eerden SA., Sikkema BJ., Wahl SA.:
  Predicting Metabolic Adaptation Under Dynamic Substrate Conditions Using a Resource-Dependent Kinetic Model: A Case Study Using Saccharomyces cerevisiae
  In: Frontiers in Molecular Biosciences 9 (2022), Article No.: 863470
  ISSN: 2296-889X
  DOI: 10.3389/fmolb.2022.863470

2021

• Evers B., Gerding A., Boer T., Heiner-Fokkema MR., Jalving M., Reijngoud DJ., Bakker BM., Wahl SA.:
  Simultaneous quantification of the concentration and carbon isotopologue distribution of polar metabolites in a single analysis by gas chromatography and mass spectrometry
  In: Analytical Chemistry 93 (2021), p. 8248-8256
  ISSN: 0003-2700
  DOI: 10.1021/acs.analchem.1c01040
• Mcdaniel EA., Wahl SA., Ishii SI., Pinto A., Ziels R., Nielsen PH., Mcmahon KD., Williams RBH.:
  Prospects for multi-omics in the microbial ecology of water engineering
  In: Water Research 205 (2021), Article No.: 117608
  ISSN: 0043-1354
  DOI: 10.1016/j.watres.2021.117608
• Olavarria K., Carnet A., Van Renselaar J., Quakkelaar C., Cabrera R., Da Silva LG., Smids AL., Andres Villalobos P., Van Loosdrecht MCM., Wahl SA.:
  An NADH preferring acetoacetyl-CoA reductase is engaged in poly-3-hydroxybutyrate accumulation in Escherichia coli
  In: Journal of Biotechnology 325 (2021), p. 207-216
  ISSN: 0168-1656
  DOI: 10.1016/j.jbiotec.2020.10.022
• Regueira A., Rombouts JL., Mauricio-Iglesias M., Lema JM., Kleerebezem R., Wahl SA.:
  Resource allocation explains lactic acid production in mixed-culture anaerobic fermentations
  In: Biotechnology and bioengineering 118 (2021), p. 745-758
  ISSN: 1097-0290
  DOI: 10.1002/bit.27605
• Soares Rodrigues CI., Gombert AK., Wahl SA.:
  Aerobic growth physiology of Saccharomyces cerevisiae on sucrose is strain-dependent
  In: Fems Yeast Research 21 (2021), Article No.: foab021
  ISSN: 1567-1356
  DOI: 10.1093/femsyr/foab021

2020

• Ferreira S., Pereira R., Wahl SA., Rocha I.:
  Metabolic engineering strategies for butanol production in Escherichia coli
  In: Biotechnology and Bioengineering 117 (2020), p. 2571-2587
  ISSN: 0006-3592
  DOI: 10.1002/bit.27377
• Olavarria K., Quakkelaar C., Van Renselaar J., Langerak D., Van Loosdrecht MCM., Wahl SA.:
  NADH-driven poly-3-hydroxybutyrate accumulation in Escherichia coli: Data from enzymatic assays and oxygen-limited continuous cultures
  In: Data in Brief 33 (2020), Article No.: 106588
  ISSN: 2352-3409
  DOI: 10.1016/j.dib.2020.106588
• Vasilakou E., Van Loosdrecht MCM., Wahl SA.:
  Escherichia coli metabolism under short-Term repetitive substrate dynamics: Adaptation and trade-offs
  In: Microbial Cell Factories 19 (2020), Article No.: 116
  ISSN: 1475-2859
  DOI: 10.1186/s12934-020-01379-0
• Verhagen KJA., Van Gulik WM., Wahl SA.:
  Dynamics in redox metabolism, from stoichiometry towards kinetics
  In: Current Opinion in Biotechnology 64 (2020), p. 116-123
  ISSN: 0958-1669
  DOI: 10.1016/j.copbio.2020.01.002
• Zhang J., Van Den Herik BM., Wahl SA.:
  Alpha-ketoglutarate utilization in Saccharomyces cerevisiae: transport, compartmentation and catabolism
  In: Scientific Reports 10 (2020), Article No.: 12838
  ISSN: 2045-2322
  DOI: 10.1038/s41598-020-69178-6
• da Silva LG., Gamez KO., Gomes JC., Akkermans K., Welles L., Abbas B., Loosdrecht MC., Wahl SA.:
  Revealing the Metabolic Flexibility of “Candidatus Accumulibacter phosphatis” through Redox Cofactor Analysis and Metabolic Network Modeling
  In: Applied and Environmental Microbiology 86 (2020), p. 1-17
  ISSN: 0099-2240
  DOI: 10.1128/AEM.0808-20

2019

• Doerr A., De Reus E., Van Nies P., Van Der Haar M., Wei K., Kattan J., Danelon C., Wahl SA.:
  Modelling cell-free RNA and protein synthesis with minimal systems
  In: Physical Biology 16 (2019), Article No.: 025001
  ISSN: 1478-3967
  DOI: 10.1088/1478-3975/aaf33d
• Giordano G., De Graaf LM., Vasilakou E., Wahl SA.:
  Unraveling energy homeostasis in a dynamic model of glycolysis in Escherichia coli
  18th European Control Conference, ECC 2019 (Naples, 25th June 2019 - 28th June 2019)
  In: 2019 18th European Control Conference, ECC 2019 2019
  DOI: 10.23919/ECC.2019.8795884
• Olavarria K., Fina A., Velasco MI., Van Loosdrecht MCM., Wahl SA.:
  Metabolism of sucrose in a non-fermentative Escherichia coli under oxygen limitation
  In: Applied Microbiology and Biotechnology 103 (2019), p. 6245-6256
  ISSN: 0175-7598
  DOI: 10.1007/s00253-019-09909-6
• Straathof AJJ., Benjamin KR., Takors R., Wierckx N., Noorman HJ., Wahl SA.:
  Grand Research Challenges for Sustainable Industrial Biotechnology
  In: Trends in Biotechnology 37 (2019), p. 1042-1050
  ISSN: 0167-7799
  DOI: 10.1016/j.tibtech.2019.04.002
• Zhang J., Martinez-Gomez K., Heinzle E., Wahl SA.:
  Metabolic switches from quiescence to growth in synchronized Saccharomyces cerevisiae
  In: Metabolomics 15 (2019), Article No.: 121
  ISSN: 1573-3882
  DOI: 10.1007/s11306-019-1584-4

2017

• Cueto-Rojas HF., Milne N., Van Helmond W., Pieterse MM., Van Maris AJA., Daran JM., Wahl SA.:
  Membrane potential independent transport of NH3 in the absence of ammonium permeases in Saccharomyces cerevisiae
  In: BMC Systems Biology 11 (2017), Article No.: 49
  ISSN: 1752-0509
  DOI: 10.1186/s12918-016-0381-1

2016

• Cueto-Rojas HF., Seifar RM., Ten Pierick A., Heijnen SJ., Wahl SA.:
  Accurate measurement of the in vivo ammonium concentration in Saccharomyces cerevisiae
  In: Metabolites 6 (2016), Article No.: 12
  ISSN: 2218-1989
  DOI: 10.3390/metabo6020012
• Cueto-Rojas HF., Seifar RM., Ten Pierick A., Van Helmond W., Pieterse MM., Heijnen JJ., Wahl SA.:
  In vivo analysis of NH4+ transport and central nitrogen metabolism in Saccharomyces cerevisiae during aerobic nitrogen-limited growth
  In: Applied and Environmental Microbiology 82 (2016), p. 6831-6845
  ISSN: 0099-2240
  DOI: 10.1128/AEM.01547-16
• Milne N., van Maris AJ., Pronk JT., Daran JM., Wahl SA.:
  Excessive by-product formation: A key contributor to low isobutanol yields of engineered Saccharomyces cerevisiae strains
  In: Metabolic Engineering Communications 3 (2016), p. 39-51
  ISSN: 2214-0301
  DOI: 10.1016/j.meteno.2016.01.002
• Niedenfuehr S., Ten Pierick A., Van Dam PTN., Suarez-Mendez CA., Noeh K., Wahl SA.:
  Natural isotope correction of MS/MS measurements for metabolomics and 13C fluxomics
  In: Biotechnology and Bioengineering 113 (2016), p. 1137-1147
  ISSN: 0006-3592
  DOI: 10.1002/bit.25859
• Suarez-Mendez CA., Hanemaaijer M., ten Pierick A., Wolters JC., Heijnen JJ., Wahl SA.:
  Interaction of storage carbohydrates and other cyclic fluxes with central metabolism: A quantitative approach by non-stationary 13C metabolic flux analysis
  In: Metabolic Engineering Communications 3 (2016), p. 52-63
  ISSN: 2214-0301
  DOI: 10.1016/j.meteno.2016.01.001
• Vasilakou E., Machado D., Theorell A., Rocha I., Noeh K., Oldiges M., Wahl SA.:
  Current state and challenges for dynamic metabolic modeling
  In: Current Opinion in Microbiology 33 (2016), p. 97-104
  ISSN: 1369-5274
  DOI: 10.1016/j.mib.2016.07.008

2015

• Cueto-Rojas HF., Van Maris AJA., Heijnen JJ., Wahl SA.:
  Thermodynamics-based design of microbial cell factories for anaerobic product formation
  In: Trends in Biotechnology 33 (2015), p. 534-546
  ISSN: 0167-7799
  DOI: 10.1016/j.tibtech.2015.06.010
• Milne N., Luttik MAH., Rojas HFC., Van Maris AJA., Pronk JT., Daran JM., Wahl SA.:
  Functional expression of a heterologous nickel-dependent, ATP-independent urease in Saccharomyces cerevisiae
  In: Metabolic Engineering 30 (2015), p. 130-140
  ISSN: 1096-7176
  DOI: 10.1016/j.ymben.2015.05.003
• Willemsen AM., Hendrickx DM., Hoefsloot HCJ., Hendriks MMWB., Teusink B., Smilde AK., Van Kampen AHC., Wahl SA.:
  MetDFBA: Incorporating time-resolved metabolomics measurements into dynamic flux balance analysis
  In: Molecular bioSystems 11 (2015), p. 137-145
  ISSN: 1742-2051
  DOI: 10.1039/c4mb00510d
• Zhang J., Sassen T., Ten Pierick A., Ras C., Heijnen JJ., Wahl SA.:
  A fast sensor for in vivo quantification of cytosolic phosphate in Saccharomyces cerevisiae
  In: Biotechnology and Bioengineering 112 (2015), p. 1033-1046
  ISSN: 0006-3592
  DOI: 10.1002/bit.25516
• Zhang J., Ten Pierick A., Van Rossum HM., Seifar RM., Ras C., Daran JM., Heijnen JJ., Wahl SA.:
  Determination of the Cytosolic NADPH/NADP Ratio in Saccharomyces cerevisiae using Shikimate Dehydrogenase as Sensor Reaction
  In: Scientific Reports 5 (2015), Article No.: 12846
  ISSN: 2045-2322
  DOI: 10.1038/srep12846

2014

• De Jonge L., Buijs NAA., Heijnen JJ., Van Gulik WM., Abate A., Wahl SA.:
  Flux response of glycolysis and storage metabolism during rapid feast/famine conditions in Penicillium chrysogenum using dynamic 13C labeling
  In: Biotechnology Journal 9 (2014), p. 372-385
  ISSN: 1860-6768
  DOI: 10.1002/biot.201200260
• Romagnoli G., Verhoeven MD., Mans R., Rey YF., Bel-Rhlid R., Van Den Broek M., Seifar RM., Ten Pierick A., Thompson M., Mueller V., Pronk JT., Daran JM., Wahl SA.:
  An alternative, arginase-independent pathway for arginine metabolism in Kluyveromyces lactis involves guanidinobutyrase as a key enzyme
  In: Molecular Microbiology 93 (2014), p. 369-389
  ISSN: 0950-382X
  DOI: 10.1111/mmi.12666
• Van Heerden JH., Wortel MT., Bruggeman FJ., Heijnen JJ., Bollen YJM., Planque R., Hulshof J., O'Toole TG., Teusink B., Wahl SA.:
  Lost in transition: Start-up of glycolysis yields subpopulations of nongrowing cells
  In: Science 343 (2014), Article No.: 1245114
  ISSN: 0036-8075
  DOI: 10.1126/science.1245114
• Wahl SA.:
  Flux response of glycolysis and storage metabolism during rapid feast/famine conditions in penicillium chrysogenum using dynamic 13C labeling
  Metabolic Engineering X (Vancouver, BC, 15th June 2014 - 19th June 2014)
  In: Metabolic Engineering X 2014
• Wahl SA., Seifar RM., ten Pierick A., Ras C., van Dam JC., Heijnen JJ., van Gulik WM.:
  Quantitative metabolomics using ID-MS
  In: Jens O. Krömer, Lars K. Nielsen, Lars M. Blank (ed.): Metabolic Flux Analysis, Humana Press Inc., 2014, p. 91-105 (Methods in Molecular Biology, Vol.1191)
  DOI: 10.1007/978-1-4939-1170-7_6

2013

• Jorda J., Suarez C., Carnicer M., Ten Pierick A., Heijnen JJ., Van Gulik W., Ferrer P., Albiol J., Wahl SA.:
  Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary 13C flux analysis
  In: Bmc Systems Biology 7 (2013), Article No.: 17
  ISSN: 1752-0509
  DOI: 10.1186/1752-0509-7-17

2012

• Abate A., Hillen RC., Wahl SA.:
  Piecewise affine approximations of fluxes and enzyme kinetics from in vivo 13C labeling experiments
  In: International Journal of Robust and Nonlinear Control 22 (2012), p. 1120-1139
  ISSN: 1049-8923
  DOI: 10.1002/rnc.2798
• Brinkman EK., Schipper K., Bongaerts N., Voges MJ., Abate A., Wahl SA.:
  A toolkit to enable hydrocarbon conversion in aqueous environments
  In: Journal of Visualized Experiments (2012)
  ISSN: 1940-087X
  DOI: 10.3791/4182
• Cruz ALB., Hebly M., Duong GH., Pronk JT., Heijnen JJ., Daran-Lapujade P., Van Gulik WM., Wahl SA.:
  Similar temperature dependencies of glycolytic enzymes: An evolutionary adaptation to temperature dynamics?
  In: BMC Systems Biology 6 (2012), Article No.: 151
  ISSN: 1752-0509
  DOI: 10.1186/1752-0509-6-151
• Veiga T., Solis-Escalante D., Romagnoli G., Ten Pierick A., Hanemaaijer M., Deshmuhk A., Pronk JT., Daran JM., Wahl SA.:
  Resolving phenylalanine metabolism sheds light on natural synthesis of penicillin G in Penicillium chrysogenum
  In: Eukaryotic Cell 11 (2012), p. 238-249
  ISSN: 1535-9778
  DOI: 10.1128/EC.05285-11
• Zhao Z., Ten Pierick A., De Jonge L., Heijnen JJ., Wahl SA.:
  Substrate cycles in Penicillium chrysogenum quantified by isotopic non-stationary flux analysis
  In: Microbial Cell Factories 11 (2012), Article No.: 140
  ISSN: 1475-2859
  DOI: 10.1186/1475-2859-11-140

2011

• Janke R., Genzel Y., Handel N., Reichl U., Wahl SA.:
  Metabolic adaptation of MDCK cells to different growth conditions: Effects on catalytic activities of central metabolic enzymes
  In: Biotechnology and Bioengineering 108 (2011), p. 2691-2704
  ISSN: 0006-3592
  DOI: 10.1002/bit.23215

2010

• Janke R., Genzel Y., Freund S., Wolff MW., Grammel H., Ruehmkorf C., Seidemann J., Reichl U., Wahl SA.:
  Expression, purification, and characterization of a His6-tagged glycerokinase from Pichia farinosa for enzymatic cycling assays in mammalian cells
  In: Journal of Biotechnology 150 (2010), p. 396-403
  ISSN: 0168-1656
  DOI: 10.1016/j.jbiotec.2010.09.963
• Janke R., Genzel Y., Reichl U., Wahl SA.:
  Measurement of key metabolic enzyme activities in mammalian cells using rapid and sensitive microplate-based assays
  In: Biotechnology and Bioengineering 107 (2010), p. 566-581
  ISSN: 0006-3592
  DOI: 10.1002/bit.22817
• Ritter JB., Freund S., Genzel Y., Reichl U., Wahl SA.:
  Metabolic effects of influenza virus infection in cultured animal cells: Intra- and extracellular metabolite profiling
  In: Bmc Systems Biology 4 (2010), Article No.: 61
  ISSN: 1752-0509
  DOI: 10.1186/1752-0509-4-61