Publications

2024

  1. Berkvens, A, Salinas, L, Remeijer, M, Planqué, R, Teusink, B, Bruggeman, FJ et al.. Understanding and computational design of genetic circuits of metabolic networks. Essays Biochem. 2024; :. doi: 10.1042/EBC20230045. PubMed PMID:38662439 .
  2. Botman, D, Kanagasabapathi, S, Rep, MI, van Rossum, K, Tutucci, E, Teusink, B et al.. cAMP in budding yeast: Also a messenger for sucrose metabolism?. Biochim Biophys Acta Mol Cell Res. 2024;1871 (4):119706. doi: 10.1016/j.bbamcr.2024.119706. PubMed PMID:38521467 .
  3. van Otterdijk, S, Motealleh, M, Wang, Z, Visser, TD, Savakis, P, Tutucci, E et al.. Single-Molecule Fluorescent In Situ Hybridization (smFISH) for RNA Detection in the Fungal Pathogen Candida albicans. Methods Mol Biol. 2024;2784 :25-44. doi: 10.1007/978-1-0716-3766-1_2. PubMed PMID:38502476 .
  4. Bexkens, ML, Martin, OMF, van den Heuvel, JM, Schmitz, MGJ, Teusink, B, Bakker, BM et al.. The unusual kinetics of lactate dehydrogenase of Schistosoma mansoni and their role in the rapid metabolic switch after penetration of the mammalian host. Int J Parasitol. 2024; :. doi: 10.1016/j.ijpara.2024.03.005. PubMed PMID:38492780 .
  5. Khartabil, T, van Schaik, RH, Haanstra, JR, Koelewijn, R, Russcher, H, van Hellemond, JJ et al.. The fully automated Sysmex XN-31 hematology analyzer can detect bloodstream form Trypanosoma brucei. Diagn Microbiol Infect Dis. 2024;108 (4):116193. doi: 10.1016/j.diagmicrobio.2024.116193. PubMed PMID:38295683 .
  6. Luzia, L, Battjes, J, Zwering, E, Jansen, D, Melkonian, C, Teusink, B et al.. A fast method to distinguish between fermentative and respiratory metabolisms in single yeast cells. iScience. 2024;27 (1):108767. doi: 10.1016/j.isci.2023.108767. PubMed PMID:38235328 PubMed Central PMC10793178.
  7. Bastola, S, Kort, R, Rajbhandari, P. Publisher Correction: Harnessing a decade of research at the Research Institute for Bioscience and Biotechnology in Kathmandu, Nepal: Proceedings of the Fourth International Conference ICBB-2022. BMC Proc. 2024;18 (1):3. doi: 10.1186/s12919-023-00282-x. PubMed PMID:38195576 PubMed Central PMC10775439.
Search PubMed

2023

  1. Luzia, L, Battjes, J, Zwering, E, Jansen, D, Melkonian, C, Teusink, B et al.. A fast method to distinguish between fermentative and respiratory metabolisms in single yeast cells. iScience. 2024;27 (1):108767. doi: 10.1016/j.isci.2023.108767. PubMed PMID:38235328 PubMed Central PMC10793178.
  2. Douwenga, S, van Olst, B, Boeren, S, Luo, Y, Lai, X, Teusink, B et al.. The hierarchy of sugar catabolization in Lactococcus cremoris. Microbiol Spectr. 2023;11 (6):e0224823. doi: 10.1128/spectrum.02248-23. PubMed PMID:37888986 PubMed Central PMC10715065.
  3. Gralka, M, Pollak, S, Cordero, OX. Genome content predicts the carbon catabolic preferences of heterotrophic bacteria. Nat Microbiol. 2023;8 (10):1799-1808. doi: 10.1038/s41564-023-01458-z. PubMed PMID:37653010 .
  4. Nascimento, JF, O Souza, RO, Alencar, MB, Marsiccobetre, S, Murillo, AM, Damasceno, FS et al.. Correction: How much (ATP) does it cost to build a trypanosome? A theoretical study on the quantity of ATP needed to maintain and duplicate a bloodstream-form Trypanosoma brucei cell. PLoS Pathog. 2023;19 (8):e1011617. doi: 10.1371/journal.ppat.1011617. PubMed PMID:37647328 PubMed Central PMC10468029.
  5. Bendig, T, Ulmer, A, Luzia, L, Müller, S, Sahle, S, Bergmann, FT et al.. The pH-dependent lactose metabolism of Lactobacillus delbrueckii subsp. bulgaricus: An integrative view through a mechanistic computational model. J Biotechnol. 2023;374 :90-100. doi: 10.1016/j.jbiotec.2023.08.001. PubMed PMID:37572793 .
  6. Bruggeman, FJ, Teusink, B, Steuer, R. Trade-offs between the instantaneous growth rate and long-term fitness: Consequences for microbial physiology and predictive computational models. Bioessays. 2023;45 (10):e2300015. doi: 10.1002/bies.202300015. PubMed PMID:37559168 .
  7. van Niekerk, DD, Rust, E, Bruggeman, F, Westerhoff, HV, Snoep, JL. Is distance from equilibrium a good indicator for a reaction's flux control?. Biosystems. 2023;232 :104988. doi: 10.1016/j.biosystems.2023.104988. PubMed PMID:37541333 .
  8. Nascimento, JF, Souza, ROO, Alencar, MB, Marsiccobetre, S, Murillo, AM, Damasceno, FS et al.. How much (ATP) does it cost to build a trypanosome? A theoretical study on the quantity of ATP needed to maintain and duplicate a bloodstream-form Trypanosoma brucei cell. PLoS Pathog. 2023;19 (7):e1011522. doi: 10.1371/journal.ppat.1011522. PubMed PMID:37498954 PubMed Central PMC10409291.
  9. Iturbe-Espinoza, P, Bonte, M, Weedon, JT, Braster, M, Brandt, BW, van Spanning, RJ et al.. Correlating the succession of microbial communities from Nigerian soils to petroleum biodegradation. World J Microbiol Biotechnol. 2023;39 (9):239. doi: 10.1007/s11274-023-03656-7. PubMed PMID:37392206 PubMed Central PMC10314880.
  10. Man, JHK, van Gelder, CAGH, Breur, M, Molenaar, D, Abbink, T, Altelaar, M et al.. Regional vulnerability of brain white matter in vanishing white matter. Acta Neuropathol Commun. 2023;11 (1):103. doi: 10.1186/s40478-023-01599-6. PubMed PMID:37349783 PubMed Central PMC10286497.
  11. Gralka, M. Searching for Principles of Microbial Ecology Across Levels of Biological Organization. Integr Comp Biol. 2023;63 (6):1520-1531. doi: 10.1093/icb/icad060. PubMed PMID:37280177 PubMed Central PMC10755194.
  12. Botman, D, Kanagasabapathi, S, Savakis, P, Teusink, B. Using the AKAR3-EV biosensor to assess Sch9p- and PKA-signalling in budding yeast. FEMS Yeast Res. 2023;23 :. doi: 10.1093/femsyr/foad029. PubMed PMID:37173282 PubMed Central PMC10237333.
  13. Gerber, A, van Otterdijk, S, Bruggeman, FJ, Tutucci, E. Understanding spatiotemporal coupling of gene expression using single molecule RNA imaging technologies. Transcription. 2023;14 (3-5):105-126. doi: 10.1080/21541264.2023.2199669. PubMed PMID:37050882 PubMed Central PMC10807504.
  14. Lao-Martil, D, Schmitz, JPJ, Teusink, B, van Riel, NAW. Elucidating yeast glycolytic dynamics at steady state growth and glucose pulses through kinetic metabolic modeling. Metab Eng. 2023;77 :128-142. doi: 10.1016/j.ymben.2023.03.005. PubMed PMID:36963461 .
  15. Iffland-Stettner, A, Okano, H, Gralka, M, Guessous, G, Amarnath, K, Cordero, OX et al.. A Genome-Scale Metabolic Model of Marine Heterotroph Vibrio splendidus Strain 1A01. mSystems. 2023;8 (2):e0037722. doi: 10.1128/msystems.00377-22. PubMed PMID:36853050 PubMed Central PMC10134806.
  16. de Groot, DH, Tjalma, AJ, Bruggeman, FJ, van Nimwegen, E. Effective bet-hedging through growth rate dependent stability. Proc Natl Acad Sci U S A. 2023;120 (8):e2211091120. doi: 10.1073/pnas.2211091120. PubMed PMID:36780518 PubMed Central PMC9974493.
  17. Jonkers, TJH, Keizers, PHJ, Béen, F, Meijer, J, Houtman, CJ, Al Gharib, I et al.. Identifying antimicrobials and their metabolites in wastewater and surface water with effect-directed analysis. Chemosphere. 2023;320 :138093. doi: 10.1016/j.chemosphere.2023.138093. PubMed PMID:36758810 .
  18. Vincent, F, Gralka, M, Schleyer, G, Schatz, D, Cabrera-Brufau, M, Kuhlisch, C et al.. Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms. Nat Commun. 2023;14 (1):510. doi: 10.1038/s41467-023-36049-3. PubMed PMID:36720878 PubMed Central PMC9889395.
  19. Grigaitis, P, van den Bogaard, SL, Teusink, B. Elevated energy costs of biomass production in mitochondrial respiration-deficient Saccharomyces cerevisia. FEMS Yeast Res. 2023;23 :. doi: 10.1093/femsyr/foad008. PubMed PMID:36694952 PubMed Central PMC9949590.
  20. Baars, T, van Esch, B, van Ooijen, L, Zhang, Z, Dekker, P, Boeren, S et al.. Raw milk kefir: microbiota, bioactive peptides, and immune modulation. Food Funct. 2023;14 (3):1648-1661. doi: 10.1039/d2fo03248a. PubMed PMID:36691758 .
  21. Battjes, J, Melkonian, C, Mendoza, SN, Haver, A, Al-Nakeeb, K, Koza, A et al.. Ethanol-lactate transition of Lachancea thermotolerans is linked to nitrogen metabolism. Food Microbiol. 2023;110 :104167. doi: 10.1016/j.fm.2022.104167. PubMed PMID:36462823 .
Search PubMed

2022

  1. Battjes, J, Melkonian, C, Mendoza, SN, Haver, A, Al-Nakeeb, K, Koza, A et al.. Ethanol-lactate transition of Lachancea thermotolerans is linked to nitrogen metabolism. Food Microbiol. 2023;110 :104167. doi: 10.1016/j.fm.2022.104167. PubMed PMID:36462823 .
  2. Man, JHK, van Gelder, CAGH, Breur, M, Okkes, D, Molenaar, D, van der Sluis, S et al.. Cortical Pathology in Vanishing White Matter. Cells. 2022;11 (22):. doi: 10.3390/cells11223581. PubMed PMID:36429009 PubMed Central PMC9688115.
  3. Brett, BE, Doumbia, HOY, Koko, BK, Koffi, FK, Assa, SE, Zahé, KYAS et al.. Normative cognition and the effects of a probiotic food intervention in first grade children in Côte d'Ivoire. Sci Rep. 2022;12 (1):19491. doi: 10.1038/s41598-022-23797-3. PubMed PMID:36376341 PubMed Central PMC9663712.
  4. van Spanning, RJM, Guan, Q, Melkonian, C, Gallant, J, Polerecky, L, Flot, JF et al.. Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem. Nat Microbiol. 2022;7 (12):2089-2100. doi: 10.1038/s41564-022-01252-3. PubMed PMID:36329197 .
  5. Chauhan, P, van der Meulen, SA, Simões Caetano, JM, Goojani, HG, Botman, D, van Spanning, R et al.. Response of Mycobacterium smegmatis to the Cytochrome bcc Inhibitor Q203. Int J Mol Sci. 2022;23 (18):. doi: 10.3390/ijms231810331. PubMed PMID:36142240 PubMed Central PMC9498996.
  6. Berkvens, A, Chauhan, P, Bruggeman, FJ. Integrative biology of persister cell formation: molecular circuitry, phenotypic diversification and fitness effects. J R Soc Interface. 2022;19 (194):20220129. doi: 10.1098/rsif.2022.0129. PubMed PMID:36099930 PubMed Central PMC9470271.
  7. Nguyen, TLA, Dang, HTC, Dat, TTH, Brandt, BW, Röling, WFM, Brouwer, A et al.. Correlating biodegradation kinetics of 2,3,7,8-tetrachlorodibenzo-p-dioxin to the dynamics of microbial communities originating from soil in Vietnam contaminated with herbicides and dioxins. Front Microbiol. 2022;13 :923432. doi: 10.3389/fmicb.2022.923432. PubMed PMID:36033897 PubMed Central PMC9404497.
  8. Le, NG, van Ulsen, P, van Spanning, R, Brouwer, A, van Straalen, NM, Roelofs, D et al.. A Functional Carbohydrate Degrading Enzyme Potentially Acquired by Horizontal Gene Transfer in the Genome of the Soil Invertebrate Folsomia candida. Genes (Basel). 2022;13 (8):. doi: 10.3390/genes13081402. PubMed PMID:36011312 PubMed Central PMC9460274.
  9. Grigaitis, P, Teusink, B. An excess of glycolytic enzymes under glucose-limited conditions may enable Saccharomyces cerevisiae to adapt to nutrient availability. FEBS Lett. 2022;596 (24):3203-3210. doi: 10.1002/1873-3468.14484. PubMed PMID:36008883 .
  10. Francken, JC, Beerendonk, L, Molenaar, D, Fahrenfort, JJ, Kiverstein, JD, Seth, AK et al.. An academic survey on theoretical foundations, common assumptions and the current state of consciousness science. Neurosci Conscious. 2022;2022 (1):niac011. doi: 10.1093/nc/niac011. PubMed PMID:35975240 PubMed Central PMC9374479.
  11. Grigaitis, P, Grundel, DAJ, van Pelt-KleinJan, E, Isaku, M, Xie, G, Mendoza Farias, S et al.. A Computational Toolbox to Investigate the Metabolic Potential and Resource Allocation in Fission Yeast. mSystems. 2022;7 (4):e0042322. doi: 10.1128/msystems.00423-22. PubMed PMID:35950759 PubMed Central PMC9426579.
  12. Kolbe, L, Molenaar, D, Jak, S, Jorgensen, TD. Assessing measurement invariance with moderated nonlinear factor analysis using the R package OpenMx. Psychol Methods. 2022; :. doi: 10.1037/met0000501. PubMed PMID:35786980 .
  13. Vita, MM, Iturbe-Espinoza, P, Bonte, M, Brandt, BW, Braster, M, Brown, DM et al.. Oil Absorbent Polypropylene Particles Stimulate Biodegradation of Crude Oil by Microbial Consortia. Front Microbiol. 2022;13 :853285. doi: 10.3389/fmicb.2022.853285. PubMed PMID:35677906 PubMed Central PMC9169047.
  14. Hertzberger, R, May, A, Kramer, G, van Vondelen, I, Molenaar, D, Kort, R et al.. Genetic Elements Orchestrating Lactobacillus crispatus Glycogen Metabolism in the Vagina. Int J Mol Sci. 2022;23 (10):. doi: 10.3390/ijms23105590. PubMed PMID:35628398 PubMed Central PMC9141943.
  15. Chen, YH, Molenaar, D, Uyl-de Groot, CA, van Vulpen, M, Blommestein, HM. Medical Resource Use and Medical Costs for Radiotherapy-Related Adverse Effects: A Systematic Review. Cancers (Basel). 2022;14 (10):. doi: 10.3390/cancers14102444. PubMed PMID:35626049 PubMed Central PMC9139402.
  16. Mendoza, SN, Saa, PA, Teusink, B, Agosin, E. Metabolic Modeling of Wine Fermentation at Genome Scale. Methods Mol Biol. 2022;2399 :395-454. doi: 10.1007/978-1-0716-1831-8_16. PubMed PMID:35604565 .
  17. Shaikh, B, Smith, LP, Vasilescu, D, Marupilla, G, Wilson, M, Agmon, E et al.. BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 2022;50 (W1):W108-W114. doi: 10.1093/nar/gkac331. PubMed PMID:35524558 PubMed Central PMC9252793.
  18. Nguyen, TLA, Dao, ATN, Dang, HTC, Koekkoek, J, Brouwer, A, de Boer, TE et al.. Degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) by fungi originating from Vietnam. Biodegradation. 2022;33 (3):301-316. doi: 10.1007/s10532-022-09982-1. PubMed PMID:35499742 PubMed Central PMC9106640.
  19. Luzia, L, Lao-Martil, D, Savakis, P, van Heerden, J, van Riel, N, Teusink, B et al.. pH dependencies of glycolytic enzymes of yeast under in vivo-like assay conditions. FEBS J. 2022;289 (19):6021-6037. doi: 10.1111/febs.16459. PubMed PMID:35429225 PubMed Central PMC9790636.
  20. Iturbe-Espinoza, P, Bonte, M, Gundlach, E, Brandt, BW, Braster, M, van Spanning, RJM et al.. Adaptive changes of sediment microbial communities associated with cleanup of oil spills in Nigerian mangrove forests. Mar Pollut Bull. 2022;176 :113406. doi: 10.1016/j.marpolbul.2022.113406. PubMed PMID:35180540 .
  21. Rabbers, I, Bruggeman, FJ. Escherichia coli robustly expresses ATP synthase at growth rate-maximizing concentrations. FEBS J. 2022;289 (16):4925-4934. doi: 10.1111/febs.16401. PubMed PMID:35175666 PubMed Central PMC9544884.
  22. Elsemman, IE, Rodriguez Prado, A, Grigaitis, P, Garcia Albornoz, M, Harman, V, Holman, SW et al.. Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies. Nat Commun. 2022;13 (1):801. doi: 10.1038/s41467-022-28467-6. PubMed PMID:35145105 PubMed Central PMC8831649.
  23. Chavez-Abiega, S, Grönloh, MLB, Gadella, TWJ, Bruggeman, FJ, Goedhart, J. Single-cell imaging of ERK and Akt activation dynamics and heterogeneity induced by G-protein-coupled receptors. J Cell Sci. 2022;135 (6):. doi: 10.1242/jcs.259685. PubMed PMID:35107584 PubMed Central PMC8977056.
  24. Lao-Martil, D, Verhagen, KJA, Schmitz, JPJ, Teusink, B, Wahl, SA, van Riel, NAW et al.. Kinetic Modeling of Saccharomyces cerevisiae Central Carbon Metabolism: Achievements, Limitations, and Opportunities. Metabolites. 2022;12 (1):. doi: 10.3390/metabo12010074. PubMed PMID:35050196 PubMed Central PMC8779790.
  25. Loghmani, SB, Veith, N, Sahle, S, Bergmann, FT, Olivier, BG, Kummer, U et al.. Inspecting the Solution Space of Genome-Scale Metabolic Models. Metabolites. 2022;12 (1):. doi: 10.3390/metabo12010043. PubMed PMID:35050165 PubMed Central PMC8779308.
  26. Rabbers, I, Gottstein, W, Feist, AM, Teusink, B, Bruggeman, FJ, Bachmann, H et al.. Selection for Cell Yield Does Not Reduce Overflow Metabolism in Escherichia coli. Mol Biol Evol. 2022;39 (1):. doi: 10.1093/molbev/msab345. PubMed PMID:34893866 PubMed Central PMC8789295.
  27. Klein Haneveld, E, Molenaar, D, de Vogel, V, Smid, W, Kamphuis, JH. Do We Hold Males and Females to the Same Standard? A Measurement Invariance Study on the Psychopathy Checklist-Revised. J Pers Assess. 2022;104 (3):368-379. doi: 10.1080/00223891.2021.1947308. PubMed PMID:34269642 .
  28. Pronk, T, Molenaar, D, Wiers, RW, Murre, J. Methods to split cognitive task data for estimating split-half reliability: A comprehensive review and systematic assessment. Psychon Bull Rev. 2022;29 (1):44-54. doi: 10.3758/s13423-021-01948-3. PubMed PMID:34100223 PubMed Central PMC8858277.
Search PubMed

2021

  1. Molenaar, D. A flexible moderated factor analysis approach to test for measurement invariance across a continuous variable. Psychol Methods. 2021;26 (6):660-679. doi: 10.1037/met0000360. PubMed PMID:34978838 .
  2. Slutsky, I, Schratt, G, Stan, GB, Nelson, S, Bruggeman, FJ. Homeostasis. Cell Syst. 2021;12 (12):1124-1126. doi: 10.1016/j.cels.2021.11.002. PubMed PMID:34914902 .
  3. Puebla-Barragan, S, Akouris, PP, Al, KF, Carr, C, Lamb, B, Sumarah, M et al.. The Two-Way Interaction between the Molecules That Cause Vaginal Malodour and Lactobacilli: An Opportunity for Probiotics. Int J Mol Sci. 2021;22 (22):. doi: 10.3390/ijms222212279. PubMed PMID:34830161 PubMed Central PMC8621103.
  4. Prescott, SL, Wegienka, G, Kort, R, Nelson, DH, Gabrysch, S, Hancock, T et al.. Project Earthrise: Proceedings of the Ninth Annual Conference of inVIVO Planetary Health. Int J Environ Res Public Health. 2021;18 (20):. doi: 10.3390/ijerph182010654. PubMed PMID:34682400 PubMed Central PMC8535547.
  5. Lara, EG, van der Windt, I, Molenaar, D, de Vos, MGJ, Melkonian, C. Using Functional Annotations to Study Pairwise Interactions in Urinary Tract Infection Communities. Genes (Basel). 2021;12 (8):. doi: 10.3390/genes12081221. PubMed PMID:34440394 PubMed Central PMC8393552.
  6. Bordel, S, van Spanning, RJM, Santos-Beneit, F. Imaging and modelling of poly(3-hydroxybutyrate) synthesis in Paracoccus denitrificans. AMB Express. 2021;11 (1):113. doi: 10.1186/s13568-021-01273-x. PubMed PMID:34370106 PubMed Central PMC8353029.
  7. Puebla-Barragan, S, Watson, E, van der Veer, C, Chmiel, JA, Carr, C, Burton, JP et al.. Interstrain Variability of Human Vaginal Lactobacillus crispatus for Metabolism of Biogenic Amines and Antimicrobial Activity against Urogenital Pathogens. Molecules. 2021;26 (15):. doi: 10.3390/molecules26154538. PubMed PMID:34361691 PubMed Central PMC8347528.
  8. Henriques, D, Minebois, R, Mendoza, SN, Macías, LG, Pérez-Torrado, R, Barrio, E et al.. A Multiphase Multiobjective Dynamic Genome-Scale Model Shows Different Redox Balancing among Yeast Species of the Saccharomyces Genus in Fermentation. mSystems. 2021;6 (4):e0026021. doi: 10.1128/mSystems.00260-21. PubMed PMID:34342535 PubMed Central PMC8407324.
  9. Klein Haneveld, E, Molenaar, D, de Vogel, V, Smid, W, Kamphuis, JH. Do We Hold Males and Females to the Same Standard? A Measurement Invariance Study on the Psychopathy Checklist-Revised. J Pers Assess. 2022;104 (3):368-379. doi: 10.1080/00223891.2021.1947308. PubMed PMID:34269642 .
  10. Kort, R, Schlösser, J, Vazquez, AR, Atukunda, P, Muhoozi, GKM, Wacoo, AP et al.. Model Selection Reveals the Butyrate-Producing Gut Bacterium Coprococcus eutactus as Predictor for Language Development in 3-Year-Old Rural Ugandan Children. Front Microbiol. 2021;12 :681485. doi: 10.3389/fmicb.2021.681485. PubMed PMID:34149673 PubMed Central PMC8206532.
  11. Melkonian, C, Fillinger, L, Atashgahi, S, da Rocha, UN, Kuiper, E, Olivier, B et al.. Author Correction: High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers. Commun Biol. 2021;4 (1):774. doi: 10.1038/s42003-021-02311-x. PubMed PMID:34145385 PubMed Central PMC8213818.
  12. Lübbers, J, Eveline Li, RJ, Gorki, FS, Bruijns, SCM, Gallagher, A, Kalay, H et al.. α2-3 Sialic acid binding and uptake by human monocyte-derived dendritic cells alters metabolism and cytokine release and initiates tolerizing T cell programming. Immunother Adv. 2021;1 (1):ltab012. doi: 10.1093/immadv/ltab012. PubMed PMID:35919745 PubMed Central PMC9327115.
  13. Pronk, T, Molenaar, D, Wiers, RW, Murre, J. Methods to split cognitive task data for estimating split-half reliability: A comprehensive review and systematic assessment. Psychon Bull Rev. 2022;29 (1):44-54. doi: 10.3758/s13423-021-01948-3. PubMed PMID:34100223 PubMed Central PMC8858277.
  14. Brett, BE, Koko, BK, Doumbia, HOY, Koffi, FK, Assa, SE, Zahé, KYAS et al.. Salivary biomarkers of stress and inflammation in first graders in Côte d'Ivoire: Effects of a probiotic food intervention. Psychoneuroendocrinology. 2021;129 :105255. doi: 10.1016/j.psyneuen.2021.105255. PubMed PMID:34020263 .
  15. Molenaar, D, Rózsa, S, Kõ, N. Modeling Asymmetry in the Time-Distance Relation of Ordinal Personality Items. Appl Psychol Meas. 2021;45 (3):178-194. doi: 10.1177/0146621621990756. PubMed PMID:33953452 PubMed Central PMC8042558.
  16. van Tatenhove-Pel, RJ, de Groot, DH, Bisseswar, AS, Teusink, B, Bachmann, H. Population dynamics of microbial cross-feeding are determined by co-localization probabilities and cooperation-independent cheater growth. ISME J. 2021;15 (10):3050-3061. doi: 10.1038/s41396-021-00986-y. PubMed PMID:33953364 PubMed Central PMC8443577.
  17. Melkonian, C, Fillinger, L, Atashgahi, S, da Rocha, UN, Kuiper, E, Olivier, B et al.. High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers. Commun Biol. 2021;4 (1):530. doi: 10.1038/s42003-021-01948-y. PubMed PMID:33953314 PubMed Central PMC8099898.
  18. Douwenga, S, Janssen, P, Teusink, B, Bachmann, H. A centrifugation-based clearing method allows high-throughput acidification and growth-rate measurements in milk. J Dairy Sci. 2021;104 (8):8530-8540. doi: 10.3168/jds.2020-20108. PubMed PMID:33934870 .
  19. van Pelt-KleinJan, E, de Groot, DH, Teusink, B. Understanding FBA Solutions under Multiple Nutrient Limitations. Metabolites. 2021;11 (5):. doi: 10.3390/metabo11050257. PubMed PMID:33919383 PubMed Central PMC8143296.
  20. Das, S, Vera, M, Gandin, V, Singer, RH, Tutucci, E. Author Correction: Intracellular mRNA transport and localized translation. Nat Rev Mol Cell Biol. 2021;22 (7):505. doi: 10.1038/s41580-021-00374-6. PubMed PMID:33911234 .
  21. Botman, D, O'Toole, TG, Goedhart, J, Bruggeman, FJ, van Heerden, JH, Teusink, B et al.. A yeast FRET biosensor enlightens cAMP signaling. Mol Biol Cell. 2021;32 (13):1229-1240. doi: 10.1091/mbc.E20-05-0319. PubMed PMID:33881352 PubMed Central PMC8351543.
  22. Das, S, Vera, M, Gandin, V, Singer, RH, Tutucci, E. Intracellular mRNA transport and localized translation. Nat Rev Mol Cell Biol. 2021;22 (7):483-504. doi: 10.1038/s41580-021-00356-8. PubMed PMID:33837370 PubMed Central PMC9346928.
  23. Iturbe-Espinoza, P, Brandt, BW, Braster, M, Bonte, M, Brown, DM, van Spanning, RJM et al.. Effects of DNA preservation solution and DNA extraction methods on microbial community profiling of soil. Folia Microbiol (Praha). 2021;66 (4):597-606. doi: 10.1007/s12223-021-00866-0. PubMed PMID:33834428 PubMed Central PMC8298342.
  24. Chen, Y, van Pelt-KleinJan, E, van Olst, B, Douwenga, S, Boeren, S, Bachmann, H et al.. Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments. Mol Syst Biol. 2021;17 (4):e10093. doi: 10.15252/msb.202010093. PubMed PMID:33821549 PubMed Central PMC8022198.
  25. Syvertsson, S, Wang, B, Staal, J, Gao, Y, Kort, R, Hamoen, LW et al.. Different Resource Allocation in a Bacillus subtilis Population Displaying Bimodal Motility. J Bacteriol. 2021;203 (12):e0003721. doi: 10.1128/JB.00037-21. PubMed PMID:33782055 PubMed Central PMC8316123.
  26. Clement, TJ, Baalhuis, EB, Teusink, B, Bruggeman, FJ, Planqué, R, de Groot, DH et al.. Unlocking Elementary Conversion Modes: ecmtool Unveils All Capabilities of Metabolic Networks. Patterns (N Y). 2021;2 (1):100177. doi: 10.1016/j.patter.2020.100177. PubMed PMID:33511367 PubMed Central PMC7815953.
  27. van Tatenhove-Pel, RJ, Zwering, E, Boreel, DF, Falk, M, van Heerden, JH, Kes, MBMJ et al.. Serial propagation in water-in-oil emulsions selects for Saccharomyces cerevisiae strains with a reduced cell size or an increased biomass yield on glucose. Metab Eng. 2021;64 :1-14. doi: 10.1016/j.ymben.2020.12.005. PubMed PMID:33418011 .
  28. Blasche, S, Kim, Y, Mars, RAT, Machado, D, Maansson, M, Kafkia, E et al.. Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community. Nat Microbiol. 2021;6 (2):196-208. doi: 10.1038/s41564-020-00816-5. PubMed PMID:33398099 PubMed Central PMC7610452.
  29. Grigaitis, P, Olivier, BG, Fiedler, T, Teusink, B, Kummer, U, Veith, N et al.. Protein cost allocation explains metabolic strategies in Escherichia coli. J Biotechnol. 2021;327 :54-63. doi: 10.1016/j.jbiotec.2020.11.003. PubMed PMID:33309962 .
  30. Teusink, B, Kuipers, OP, Moineau, S. Symposium on Lactic Acid Bacteria-reading while waiting for a meeting. FEMS Microbiol Rev. 2021;45 (2):. doi: 10.1093/femsre/fuaa049. PubMed PMID:33197931 PubMed Central PMC7968516.
  31. van Tatenhove-Pel, RJ, Rijavec, T, Lapanje, A, van Swam, I, Zwering, E, Hernandez-Valdes, JA et al.. Microbial competition reduces metabolic interaction distances to the low µm-range. ISME J. 2021;15 (3):688-701. doi: 10.1038/s41396-020-00806-9. PubMed PMID:33077887 PubMed Central PMC8027890.
  32. Özcan, E, Seven, M, Şirin, B, Çakır, T, Nikerel, E, Teusink, B et al.. Dynamic co-culture metabolic models reveal the fermentation dynamics, metabolic capacities and interplays of cheese starter cultures. Biotechnol Bioeng. 2021;118 (1):223-237. doi: 10.1002/bit.27565. PubMed PMID:32926401 PubMed Central PMC7971941.
Search PubMed

2020

  1. Molenaar, D. A flexible moderated factor analysis approach to test for measurement invariance across a continuous variable. Psychol Methods. 2021;26 (6):660-679. doi: 10.1037/met0000360. PubMed PMID:34978838 .
  2. Clement, TJ, Baalhuis, EB, Teusink, B, Bruggeman, FJ, Planqué, R, de Groot, DH et al.. Unlocking Elementary Conversion Modes: ecmtool Unveils All Capabilities of Metabolic Networks. Patterns (N Y). 2021;2 (1):100177. doi: 10.1016/j.patter.2020.100177. PubMed PMID:33511367 PubMed Central PMC7815953.
  3. Westerik, N, Nelson, A, Wacoo, AP, Sybesma, W, Kort, R. A Comparative Interrupted Times Series on the Health Impact of Probiotic Yogurt Consumption Among School Children From Three to Six Years Old in Southwest Uganda. Front Nutr. 2020;7 :574792. doi: 10.3389/fnut.2020.574792. PubMed PMID:33363193 PubMed Central PMC7756026.
  4. Frank, SA, Bruggeman, FJ. The Fundamental Equations of Change in Statistical Ensembles and Biological Populations. Entropy (Basel). 2020;22 (12):. doi: 10.3390/e22121395. PubMed PMID:33321870 PubMed Central PMC7764014.
  5. Tamang, JP, Cotter, PD, Endo, A, Han, NS, Kort, R, Liu, SQ et al.. Fermented foods in a global age: East meets West. Compr Rev Food Sci Food Saf. 2020;19 (1):184-217. doi: 10.1111/1541-4337.12520. PubMed PMID:33319517 .
  6. Grigaitis, P, Olivier, BG, Fiedler, T, Teusink, B, Kummer, U, Veith, N et al.. Protein cost allocation explains metabolic strategies in Escherichia coli. J Biotechnol. 2021;327 :54-63. doi: 10.1016/j.jbiotec.2020.11.003. PubMed PMID:33309962 .
  7. Baardman, J, Verberk, SGS, van der Velden, S, Gijbels, MJJ, van Roomen, CPPA, Sluimer, JC et al.. Macrophage ATP citrate lyase deficiency stabilizes atherosclerotic plaques. Nat Commun. 2020;11 (1):6296. doi: 10.1038/s41467-020-20141-z. PubMed PMID:33293558 PubMed Central PMC7722882.
  8. Bruggeman, FJ, Planqué, R, Molenaar, D, Teusink, B. Searching for principles of microbial physiology. FEMS Microbiol Rev. 2020;44 (6):821-844. doi: 10.1093/femsre/fuaa034. PubMed PMID:33099619 PubMed Central PMC7685786.
  9. van Tatenhove-Pel, RJ, Rijavec, T, Lapanje, A, van Swam, I, Zwering, E, Hernandez-Valdes, JA et al.. Microbial competition reduces metabolic interaction distances to the low µm-range. ISME J. 2021;15 (3):688-701. doi: 10.1038/s41396-020-00806-9. PubMed PMID:33077887 PubMed Central PMC8027890.
  10. Ekkers, DM, Branco Dos Santos, F, Mallon, CA, Bruggeman, F, van Doorn, GS. The omnistat: A flexible continuous-culture system for prolonged experimental evolution. Methods Ecol Evol. 2020;11 (8):932-942. doi: 10.1111/2041-210X.13403. PubMed PMID:32999708 PubMed Central PMC7508058.
  11. Kleerebezem, M, Bachmann, H, van Pelt-KleinJan, E, Douwenga, S, Smid, EJ, Teusink, B et al.. Lifestyle, metabolism and environmental adaptation in Lactococcus lactis. FEMS Microbiol Rev. 2020;44 (6):804-820. doi: 10.1093/femsre/fuaa033. PubMed PMID:32990728 .
  12. Özcan, E, Seven, M, Şirin, B, Çakır, T, Nikerel, E, Teusink, B et al.. Dynamic co-culture metabolic models reveal the fermentation dynamics, metabolic capacities and interplays of cheese starter cultures. Biotechnol Bioeng. 2021;118 (1):223-237. doi: 10.1002/bit.27565. PubMed PMID:32926401 PubMed Central PMC7971941.
  13. Keating, SM, Waltemath, D, König, M, Zhang, F, Dräger, A, Chaouiya, C et al.. SBML Level 3: an extensible format for the exchange and reuse of biological models. Mol Syst Biol. 2020;16 (8):e9110. doi: 10.15252/msb.20199110. PubMed PMID:32845085 PubMed Central PMC8411907.
  14. Tsuboi, T, Viana, MP, Xu, F, Yu, J, Chanchani, R, Arceo, XG et al.. Mitochondrial volume fraction and translation duration impact mitochondrial mRNA localization and protein synthesis. Elife. 2020;9 :. doi: 10.7554/eLife.57814. PubMed PMID:32762840 PubMed Central PMC7413667.
  15. Pichon, X, Robert, MC, Bertrand, E, Singer, RH, Tutucci, E. New Generations of MS2 Variants and MCP Fusions to Detect Single mRNAs in Living Eukaryotic Cells. Methods Mol Biol. 2020;2166 :121-144. doi: 10.1007/978-1-0716-0712-1_7. PubMed PMID:32710406 PubMed Central PMC8950302.
  16. Tutucci, E, Singer, RH. Simultaneous Detection of mRNA and Protein in S. cerevisiae by Single-Molecule FISH and Immunofluorescence. Methods Mol Biol. 2020;2166 :51-69. doi: 10.1007/978-1-0716-0712-1_4. PubMed PMID:32710403 .
  17. Hernandez-Valdes, JA, Aan de Stegge, M, Hermans, J, Teunis, J, van Tatenhove-Pel, RJ, Teusink, B et al.. Enhancement of amino acid production and secretion by Lactococcus lactis using a droplet-based biosensing and selection system. Metab Eng Commun. 2020;11 :e00133. doi: 10.1016/j.mec.2020.e00133. PubMed PMID:32551230 PubMed Central PMC7292884.
  18. Reid, G, Sybesma, W, Matovu, W, Onyango, A, Westerik, N, Kort, R et al.. Empowering women through probiotic fermented food in East Africa. J Glob Health. 2020;10 (1):010330. doi: 10.7189/jogh.10.010330. PubMed PMID:32509283 PubMed Central PMC7242885.
  19. Nordholt, N, van Heerden, JH, Bruggeman, FJ. Biphasic Cell-Size and Growth-Rate Homeostasis by Single Bacillus subtilis Cells. Curr Biol. 2020;30 (12):2238-2247.e5. doi: 10.1016/j.cub.2020.04.030. PubMed PMID:32413303 .
  20. Maekiniemi, A, Singer, RH, Tutucci, E. Single molecule mRNA fluorescent in situ hybridization combined with immunofluorescence in S. cerevisiae: Dataset and quantification. Data Brief. 2020;30 :105511. doi: 10.1016/j.dib.2020.105511. PubMed PMID:32368581 PubMed Central PMC7186551.
  21. Iversen, PO, Atukunda, P, Kort, R, Ueland, PM, Westerberg, AC, Muhoozi, GKM et al.. No associations between microbiota signalling substances and cognitive, language and motor development among three-year-old rural Ugandan children. Acta Paediatr. 2020;109 (11):2339-2341. doi: 10.1111/apa.15330. PubMed PMID:32347570 .
  22. Nilsson, A, Haanstra, JR, Engqvist, M, Gerding, A, Bakker, BM, Klingmüller, U et al.. Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis. Proc Natl Acad Sci U S A. 2020;117 (19):10294-10304. doi: 10.1073/pnas.1919250117. PubMed PMID:32341162 PubMed Central PMC7229649.
  23. Lieven, C, Beber, ME, Olivier, BG, Bergmann, FT, Ataman, M, Babaei, P et al.. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020;38 (4):504. doi: 10.1038/s41587-020-0477-4. PubMed PMID:32265554 PubMed Central PMC7138757.
  24. Lieven, C, Beber, ME, Olivier, BG, Bergmann, FT, Ataman, M, Babaei, P et al.. MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020;38 (3):272-276. doi: 10.1038/s41587-020-0446-y. PubMed PMID:32123384 PubMed Central PMC7082222.
  25. Wacoo, AP, Atukunda, P, Muhoozi, G, Braster, M, Wagner, M, Broek, TJVD et al.. Aflatoxins: Occurrence, Exposure, and Binding to Lactobacillus Species from the Gut Microbiota of Rural Ugandan Children. Microorganisms. 2020;8 (3):. doi: 10.3390/microorganisms8030347. PubMed PMID:32121365 PubMed Central PMC7143030.
  26. Botman, D, van Heerden, JH, Teusink, B. An Improved ATP FRET Sensor For Yeast Shows Heterogeneity During Nutrient Transitions. ACS Sens. 2020;5 (3):814-822. doi: 10.1021/acssensors.9b02475. PubMed PMID:32077276 PubMed Central PMC7106129.
  27. Hamers, T, Kortenkamp, A, Scholze, M, Molenaar, D, Cenijn, PH, Weiss, JM et al.. Transthyretin-Binding Activity of Complex Mixtures Representing the Composition of Thyroid-Hormone Disrupting Contaminants in House Dust and Human Serum. Environ Health Perspect. 2020;128 (1):17015. doi: 10.1289/EHP5911. PubMed PMID:32003587 PubMed Central PMC7015555.
  28. de Groot, DH, Hulshof, J, Teusink, B, Bruggeman, FJ, Planqué, R. Elementary Growth Modes provide a molecular description of cellular self-fabrication. PLoS Comput Biol. 2020;16 (1):e1007559. doi: 10.1371/journal.pcbi.1007559. PubMed PMID:31986156 PubMed Central PMC7004393.
  29. Garcia-Albornoz, M, Holman, SW, Antonisse, T, Daran-Lapujade, P, Teusink, B, Beynon, RJ et al.. A proteome-integrated, carbon source dependent genetic regulatory network in Saccharomyces cerevisiae. Mol Omics. 2020;16 (1):59-72. doi: 10.1039/c9mo00136k. PubMed PMID:31868867 .
  30. van Tatenhove-Pel, RJ, Hernandez-Valdes, JA, Teusink, B, Kuipers, OP, Fischlechner, M, Bachmann, H et al.. Microdroplet screening and selection for improved microbial production of extracellular compounds. Curr Opin Biotechnol. 2020;61 :72-81. doi: 10.1016/j.copbio.2019.10.007. PubMed PMID:31770655 .
  31. de Groot, DH, Lischke, J, Muolo, R, Planqué, R, Bruggeman, FJ, Teusink, B et al.. The common message of constraint-based optimization approaches: overflow metabolism is caused by two growth-limiting constraints. Cell Mol Life Sci. 2020;77 (3):441-453. doi: 10.1007/s00018-019-03380-2. PubMed PMID:31758233 PubMed Central PMC7010627.
  32. Poursat, BAJ, van Spanning, RJM, Braster, M, Helmus, R, de Voogt, P, Parsons, JR et al.. Long-term exposure of activated sludge in chemostats leads to changes in microbial communities composition and enhanced biodegradation of 4-chloroaniline and N-methylpiperazine. Chemosphere. 2020;242 :125102. doi: 10.1016/j.chemosphere.2019.125102. PubMed PMID:31669985 .
Search PubMed

2019

  1. Pelicaen, R, Gonze, D, Teusink, B, De Vuyst, L, Weckx, S. Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. Front Microbiol. 2019;10 :2801. doi: 10.3389/fmicb.2019.02801. PubMed PMID:31921009 PubMed Central PMC6915089.
  2. Collombel, I, Melkonian, C, Molenaar, D, Campos, FM, Hogg, T. New Insights Into Cinnamoyl Esterase Activity of Oenococcus oeni. Front Microbiol. 2019;10 :2597. doi: 10.3389/fmicb.2019.02597. PubMed PMID:31781078 PubMed Central PMC6857119.
  3. van Tatenhove-Pel, RJ, Hernandez-Valdes, JA, Teusink, B, Kuipers, OP, Fischlechner, M, Bachmann, H et al.. Microdroplet screening and selection for improved microbial production of extracellular compounds. Curr Opin Biotechnol. 2020;61 :72-81. doi: 10.1016/j.copbio.2019.10.007. PubMed PMID:31770655 .
  4. Rijavec, T, Zrimec, J, van Spanning, R, Lapanje, A. Natural Microbial Communities Can Be Manipulated by Artificially Constructed Biofilms. Adv Sci (Weinh). 2019;6 (22):1901408. doi: 10.1002/advs.201901408. PubMed PMID:31763146 PubMed Central PMC6865284.
  5. de Groot, DH, Lischke, J, Muolo, R, Planqué, R, Bruggeman, FJ, Teusink, B et al.. The common message of constraint-based optimization approaches: overflow metabolism is caused by two growth-limiting constraints. Cell Mol Life Sci. 2020;77 (3):441-453. doi: 10.1007/s00018-019-03380-2. PubMed PMID:31758233 PubMed Central PMC7010627.
  6. Prescott, SL, Hancock, T, Bland, J, van den Bosch, M, Jansson, JK, Johnson, CC et al.. Eighth Annual Conference of inVIVO Planetary Health: From Challenges to Opportunities. Int J Environ Res Public Health. 2019;16 (21):. doi: 10.3390/ijerph16214302. PubMed PMID:31694316 PubMed Central PMC6861902.
  7. Poursat, BAJ, van Spanning, RJM, Braster, M, Helmus, R, de Voogt, P, Parsons, JR et al.. Long-term exposure of activated sludge in chemostats leads to changes in microbial communities composition and enhanced biodegradation of 4-chloroaniline and N-methylpiperazine. Chemosphere. 2020;242 :125102. doi: 10.1016/j.chemosphere.2019.125102. PubMed PMID:31669985 .
  8. Vera, M, Tutucci, E, Singer, RH. Imaging Single mRNA Molecules in Mammalian Cells Using an Optimized MS2-MCP System. Methods Mol Biol. 2019;2038 :3-20. doi: 10.1007/978-1-4939-9674-2_1. PubMed PMID:31407274 PubMed Central PMC8950109.
  9. Abbink, TEM, Wisse, LE, Jaku, E, Thiecke, MJ, Voltolini-González, D, Fritsen, H et al.. Vanishing white matter: deregulated integrated stress response as therapy target. Ann Clin Transl Neurol. 2019;6 (8):1407-1422. doi: 10.1002/acn3.50826. PubMed PMID:31402619 PubMed Central PMC6689685.
  10. Mendoza, SN, Olivier, BG, Molenaar, D, Teusink, B. A systematic assessment of current genome-scale metabolic reconstruction tools. Genome Biol. 2019;20 (1):158. doi: 10.1186/s13059-019-1769-1. PubMed PMID:31391098 PubMed Central PMC6685185.
  11. Patty, CHL, Ten Kate, IL, Buma, WJ, van Spanning, RJM, Steinbach, G, Ariese, F et al.. Circular Spectropolarimetric Sensing of Vegetation in the Field: Possibilities for the Remote Detection of Extraterrestrial Life. Astrobiology. 2019;19 (10):1221-1229. doi: 10.1089/ast.2019.2050. PubMed PMID:31361507 .
  12. Chavez-Abiega, S, Goedhart, J, Bruggeman, FJ. Physical biology of GPCR signalling dynamics inferred from fluorescence spectroscopy and imaging. Curr Opin Struct Biol. 2019;55 :204-211. doi: 10.1016/j.sbi.2019.05.007. PubMed PMID:31319372 .
  13. Poursat, BAJ, van Spanning, RJM, Braster, M, Helmus, R, de Voogt, P, Parsons, JR et al.. Biodegradation of metformin and its transformation product, guanylurea, by natural and exposed microbial communities. Ecotoxicol Environ Saf. 2019;182 :109414. doi: 10.1016/j.ecoenv.2019.109414. PubMed PMID:31301597 .
  14. Melkonian, C, Gottstein, W, Blasche, S, Kim, Y, Abel-Kistrup, M, Swiegers, H et al.. Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture. Front Microbiol. 2019;10 :1347. doi: 10.3389/fmicb.2019.01347. PubMed PMID:31293529 PubMed Central PMC6603220.
  15. Kremer, K, van Teeseling, MCF, Schada von Borzyskowski, L, Bernhardsgrütter, I, van Spanning, RJM, Gates, AJ et al.. Dynamic Metabolic Rewiring Enables Efficient Acetyl Coenzyme A Assimilation in Paracoccus denitrificans. mBio. 2019;10 (4):. doi: 10.1128/mBio.00805-19. PubMed PMID:31289174 PubMed Central PMC6747724.
  16. Hucka, M, Bergmann, FT, Chaouiya, C, Dräger, A, Hoops, S, Keating, SM et al.. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J Integr Bioinform. 2019;16 (2):. doi: 10.1515/jib-2019-0021. PubMed PMID:31219795 PubMed Central PMC6798823.
  17. Aerts, JW, van Spanning, RJM, Flahaut, J, Molenaar, D, Bland, PA, Genge, MJ et al.. Microbial Communities in Sediments From Four Mildly Acidic Ephemeral Salt Lakes in the Yilgarn Craton (Australia) - Terrestrial Analogs to Ancient Mars. Front Microbiol. 2019;10 :779. doi: 10.3389/fmicb.2019.00779. PubMed PMID:31133990 PubMed Central PMC6512757.
  18. Atukunda, P, Muhoozi, GKM, van den Broek, TJ, Kort, R, Diep, LM, Kaaya, AN et al.. Child development, growth and microbiota: follow-up of a randomized education trial in Uganda. J Glob Health. 2019;9 (1):010431. doi: 10.7189/jogh.09.010431. PubMed PMID:31131103 PubMed Central PMC6513500.
  19. Groenenboom, AE, Parker, ME, de Vries, A, de Groot, S, Zobrist, S, Mansen, K et al.. Bacterial community dynamics in lait caillé, a traditional product of spontaneous fermentation from Senegal. PLoS One. 2019;14 (5):e0215658. doi: 10.1371/journal.pone.0215658. PubMed PMID:31075124 PubMed Central PMC6510411.
  20. Sirén, K, Mak, SST, Melkonian, C, Carøe, C, Swiegers, JH, Molenaar, D et al.. Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must. Front Microbiol. 2019;10 :697. doi: 10.3389/fmicb.2019.00697. PubMed PMID:31024486 PubMed Central PMC6465770.
  21. Infantino, V, Tutucci, E, Yeh Martin, N, Zihlmann, A, Garcia-Molinero, V, Silvano, G et al.. The mRNA export adaptor Yra1 contributes to DNA double-strand break repair through its C-box domain. PLoS One. 2019;14 (4):e0206336. doi: 10.1371/journal.pone.0206336. PubMed PMID:30951522 PubMed Central PMC6450643.
  22. van der Veer, C, Hertzberger, RY, Bruisten, SM, Tytgat, HLP, Swanenburg, J, de Kat Angelino-Bart, A et al.. Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota. Microbiome. 2019;7 (1):49. doi: 10.1186/s40168-019-0667-9. PubMed PMID:30925932 PubMed Central PMC6441167.
  23. Molenaar, D, Rózsa, S, Bolsinova, M. A heteroscedastic hidden Markov mixture model for responses and categorized response times. Behav Res Methods. 2019;51 (2):676-696. doi: 10.3758/s13428-019-01229-x. PubMed PMID:30924104 PubMed Central PMC6478648.
  24. de Groot, DH, van Boxtel, C, Planqué, R, Bruggeman, FJ, Teusink, B. The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates. PLoS Comput Biol. 2019;15 (3):e1006858. doi: 10.1371/journal.pcbi.1006858. PubMed PMID:30856167 PubMed Central PMC6428345.
  25. Botman, D, de Groot, DH, Schmidt, P, Goedhart, J, Teusink, B. In vivo characterisation of fluorescent proteins in budding yeast. Sci Rep. 2019;9 (1):2234. doi: 10.1038/s41598-019-38913-z. PubMed PMID:30783202 PubMed Central PMC6381139.
  26. Özcan, E, Selvi, SS, Nikerel, E, Teusink, B, Toksoy Öner, E, Çakır, T et al.. A genome-scale metabolic network of the aroma bacterium Leuconostoc mesenteroides subsp. cremoris. Appl Microbiol Biotechnol. 2019;103 (7):3153-3165. doi: 10.1007/s00253-019-09630-4. PubMed PMID:30712128 .
  27. Wacoo, AP, Mukisa, IM, Meeme, R, Byakika, S, Wendiro, D, Sybesma, W et al.. Probiotic Enrichment and Reduction of Aflatoxins in a Traditional African Maize-Based Fermented Food. Nutrients. 2019;11 (2):. doi: 10.3390/nu11020265. PubMed PMID:30691002 PubMed Central PMC6412935.
  28. Price, CE, Branco Dos Santos, F, Hesseling, A, Uusitalo, JJ, Bachmann, H, Benavente, V et al.. Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength. BMC Evol Biol. 2019;19 (1):15. doi: 10.1186/s12862-018-1331-x. PubMed PMID:30630406 PubMed Central PMC6327505.
  29. Bolsinova, M, Molenaar, D. Nonlinear Indicator-Level Moderation in Latent Variable Models. Multivariate Behav Res. 2019;54 (1):62-84. doi: 10.1080/00273171.2018.1486174. PubMed PMID:30513219 .
  30. Neal, ML, König, M, Nickerson, D, Mısırlı, G, Kalbasi, R, Dräger, A et al.. Harmonizing semantic annotations for computational models in biology. Brief Bioinform. 2019;20 (2):540-550. doi: 10.1093/bib/bby087. PubMed PMID:30462164 PubMed Central PMC6433895.
  31. Patty, CHL, Ariese, F, Buma, WJ, Ten Kate, IL, van Spanning, RJM, Snik, F et al.. Circular spectropolarimetric sensing of higher plant and algal chloroplast structural variations. Photosynth Res. 2019;140 (2):129-139. doi: 10.1007/s11120-018-0572-2. PubMed PMID:30141032 PubMed Central PMC6548066.
Search PubMed

2018

  1. Bolsinova, M, Molenaar, D. Nonlinear Indicator-Level Moderation in Latent Variable Models. Multivariate Behav Res. 2019;54 (1):62-84. doi: 10.1080/00273171.2018.1486174. PubMed PMID:30513219 .
  2. Parker, M, Zobrist, S, Donahue, C, Edick, C, Mansen, K, Hassan Zade Nadjari, M et al.. Naturally Fermented Milk From Northern Senegal: Bacterial Community Composition and Probiotic Enrichment With Lactobacillus rhamnosus. Front Microbiol. 2018;9 :2218. doi: 10.3389/fmicb.2018.02218. PubMed PMID:30298060 PubMed Central PMC6160551.
  3. Bolsinova, M, Molenaar, D. Modeling Nonlinear Conditional Dependence Between Response Time and Accuracy. Front Psychol. 2018;9 :1525. doi: 10.3389/fpsyg.2018.01525. PubMed PMID:30245650 PubMed Central PMC6137682.
  4. Planqué, R, Hulshof, J, Teusink, B, Hendriks, JC, Bruggeman, FJ. Maintaining maximal metabolic flux by gene expression control. PLoS Comput Biol. 2018;14 (9):e1006412. doi: 10.1371/journal.pcbi.1006412. PubMed PMID:30235207 PubMed Central PMC6168163.
  5. Tutucci, E, Vera, M, Singer, RH. Single-mRNA detection in living S. cerevisiae using a re-engineered MS2 system. Nat Protoc. 2018;13 (10):2268-2296. doi: 10.1038/s41596-018-0037-2. PubMed PMID:30218101 .
  6. Westerik, N, Reid, G, Sybesma, W, Kort, R. The Probiotic Lactobacillus rhamnosus for Alleviation of Helicobacter pylori-Associated Gastric Pathology in East Africa. Front Microbiol. 2018;9 :1873. doi: 10.3389/fmicb.2018.01873. PubMed PMID:30154777 PubMed Central PMC6102400.
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  8. Solopova, A, Bachmann, H, Teusink, B, Kok, J, Kuipers, OP. Further Elucidation of Galactose Utilization in Lactococcus lactis MG1363. Front Microbiol. 2018;9 :1803. doi: 10.3389/fmicb.2018.01803. PubMed PMID:30123211 PubMed Central PMC6085457.
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  10. Paul Wacoo, A, Wendiro, D, Nanyonga, S, Hawumba, JF, Sybesma, W, Kort, R et al.. Feasibility of A Novel On-Site Detection Method for Aflatoxin in Maize Flour from Markets and Selected Households in Kampala, Uganda. Toxins (Basel). 2018;10 (8):. doi: 10.3390/toxins10080327. PubMed PMID:30103499 PubMed Central PMC6115733.
  11. Agamennone, V, Krul, CAM, Rijkers, G, Kort, R. A practical guide for probiotics applied to the case of antibiotic-associated diarrhea in The Netherlands. BMC Gastroenterol. 2018;18 (1):103. doi: 10.1186/s12876-018-0831-x. PubMed PMID:30078376 PubMed Central PMC6091175.
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  13. Anton Feenstra, K, Abeln, S, Westerhuis, JA, Brancos Dos Santos, F, Molenaar, D, Teusink, B et al.. Training for translation between disciplines: a philosophy for life and data sciences curricula. Bioinformatics. 2018;34 (13):i4-i12. doi: 10.1093/bioinformatics/bty233. PubMed PMID:29950011 PubMed Central PMC6022589.
  14. Folch-Fortuny, A, Teusink, B, Hoefsloot, HCJ, Smilde, AK, Ferrer, A. Dynamic elementary mode modelling of non-steady state flux data. BMC Syst Biol. 2018;12 (1):71. doi: 10.1186/s12918-018-0589-3. PubMed PMID:29914483 PubMed Central PMC6006576.
  15. Nilsson, A, Haanstra, JR, Teusink, B, Nielsen, J. Metabolite Depletion Affects Flux Profiling of Cell Lines. Trends Biochem Sci. 2018;43 (6):395-397. doi: 10.1016/j.tibs.2018.03.009. PubMed PMID:29656822 .
  16. Bosdriesz, E, Wortel, MT, Haanstra, JR, Wagner, MJ, de la Torre Cortés, P, Teusink, B et al.. Low affinity uniporter carrier proteins can increase net substrate uptake rate by reducing efflux. Sci Rep. 2018;8 (1):5576. doi: 10.1038/s41598-018-23528-7. PubMed PMID:29615663 PubMed Central PMC5883050.
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  18. Overal, GB, Teusink, B, Bruggeman, FJ, Hulshof, J, Planqué, R. Understanding start-up problems in yeast glycolysis. Math Biosci. 2018;299 :117-126. doi: 10.1016/j.mbs.2018.03.007. PubMed PMID:29550298 .
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  20. Patty, CHL, Luo, DA, Snik, F, Ariese, F, Buma, WJ, Ten Kate, IL et al.. Imaging linear and circular polarization features in leaves with complete Mueller matrix polarimetry. Biochim Biophys Acta Gen Subj. 2018;1862 (6):1350-1363. doi: 10.1016/j.bbagen.2018.03.005. PubMed PMID:29526506 PubMed Central PMC5970099.
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  22. Hucka, M, Bergmann, FT, Dräger, A, Hoops, S, Keating, SM, Le Novère, N et al.. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. J Integr Bioinform. 2018;15 (1):. doi: 10.1515/jib-2017-0081. PubMed PMID:29522418 PubMed Central PMC6167032.
  23. Wortel, MT, Noor, E, Ferris, M, Bruggeman, FJ, Liebermeister, W. Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield. PLoS Comput Biol. 2018;14 (2):e1006010. doi: 10.1371/journal.pcbi.1006010. PubMed PMID:29451895 PubMed Central PMC5847312.
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2017

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  4. Teusink, B, Molenaar, D. Systems biology of lactic acid bacteria: For food and thought. Curr Opin Syst Biol. 2017;6 :7-13. doi: 10.1016/j.coisb.2017.07.005. PubMed PMID:32954057 PubMed Central PMC7489361.
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  6. Tutucci, E, Vera, M, Biswas, J, Garcia, J, Parker, R, Singer, RH et al.. An improved MS2 system for accurate reporting of the mRNA life cycle. Nat Methods. 2018;15 (1):81-89. doi: 10.1038/nmeth.4502. PubMed PMID:29131164 PubMed Central PMC5843578.
  7. Molenaar, D, Bolsinova, M, Vermunt, JK. A semi-parametric within-subject mixture approach to the analyses of responses and response times. Br J Math Stat Psychol. 2018;71 (2):205-228. doi: 10.1111/bmsp.12117. PubMed PMID:29044460 .
  8. Branco Dos Santos, F, Olivier, BG, Boele, J, Smessaert, V, De Rop, P, Krumpochova, P et al.. Probing the Genome-Scale Metabolic Landscape of Bordetella pertussis, the Causative Agent of Whooping Cough. Appl Environ Microbiol. 2017;83 (21):. doi: 10.1128/AEM.01528-17. PubMed PMID:28842544 PubMed Central PMC5648915.
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  10. van Boxtel, C, van Heerden, JH, Nordholt, N, Schmidt, P, Bruggeman, FJ. Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments. J R Soc Interface. 2017;14 (132):. doi: 10.1098/rsif.2017.0141. PubMed PMID:28701503 PubMed Central PMC5550968.
  11. Bachmann, H, Molenaar, D, Branco Dos Santos, F, Teusink, B. Experimental evolution and the adjustment of metabolic strategies in lactic acid bacteria. FEMS Microbiol Rev. 2017;41 (Supp_1):S201-S219. doi: 10.1093/femsre/fux024. PubMed PMID:28633473 .
  12. Molenaar, D, Bolsinova, M. A heteroscedastic generalized linear model with a non-normal speed factor for responses and response times. Br J Math Stat Psychol. 2017;70 (2):297-316. doi: 10.1111/bmsp.12087. PubMed PMID:28474768 PubMed Central PMC5434939.
  13. Molenaar, D, Visser, I. Cognitive and psychometric modelling of responses and response times. Br J Math Stat Psychol. 2017;70 (2):185-186. doi: 10.1111/bmsp.12102. PubMed PMID:28474766 .
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  16. Bolsinova, M, Tijmstra, J, Molenaar, D, De Boeck, P. Conditional Dependence between Response Time and Accuracy: An Overview of its Possible Sources and Directions for Distinguishing between Them. Front Psychol. 2017;8 :202. doi: 10.3389/fpsyg.2017.00202. PubMed PMID:28261136 PubMed Central PMC5312167.
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2016

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  5. Brickner, DG, Sood, V, Tutucci, E, Coukos, R, Viets, K, Singer, RH et al.. Subnuclear positioning and interchromosomal clustering of the GAL1-10 locus are controlled by separable, interdependent mechanisms. Mol Biol Cell. 2016;27 (19):2980-93. doi: 10.1091/mbc.E16-03-0174. PubMed PMID:27489341 PubMed Central PMC5042583.
  6. Wortel, MT, Bosdriesz, E, Teusink, B, Bruggeman, FJ. Evolutionary pressures on microbial metabolic strategies in the chemostat. Sci Rep. 2016;6 :29503. doi: 10.1038/srep29503. PubMed PMID:27381431 PubMed Central PMC4933952.
  7. Cvijovic, M, Höfer, T, Aćimović, J, Alberghina, L, Almaas, E, Besozzi, D et al.. Strategies for structuring interdisciplinary education in Systems Biology: an European perspective. NPJ Syst Biol Appl. 2016;2 :16011. doi: 10.1038/npjsba.2016.11. PubMed PMID:28725471 PubMed Central PMC5516850.
  8. Antwi, EB, Haanstra, JR, Ramasamy, G, Jensen, B, Droll, D, Rojas, F et al.. Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression. BMC Genomics. 2016;17 :306. doi: 10.1186/s12864-016-2624-3. PubMed PMID:27118143 PubMed Central PMC4845500.
  9. Dols, JA, Molenaar, D, van der Helm, JJ, Caspers, MP, de Kat Angelino-Bart, A, Schuren, FH et al.. Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity. BMC Infect Dis. 2016;16 :180. doi: 10.1186/s12879-016-1513-3. PubMed PMID:27107961 PubMed Central PMC4841971.
  10. Bachmann, H, Bruggeman, FJ, Molenaar, D, Branco Dos Santos, F, Teusink, B. Public goods and metabolic strategies. Curr Opin Microbiol. 2016;31 :109-115. doi: 10.1016/j.mib.2016.03.007. PubMed PMID:27054480 .
  11. Levering, J, Fiedler, T, Sieg, A, van Grinsven, KW, Hering, S, Veith, N et al.. Genome-scale reconstruction of the Streptococcus pyogenes M49 metabolic network reveals growth requirements and indicates potential drug targets. J Biotechnol. 2016;232 :25-37. doi: 10.1016/j.jbiotec.2016.01.035. PubMed PMID:26970054 .
  12. Gottstein, W, Olivier, BG, Bruggeman, FJ, Teusink, B. Constraint-based stoichiometric modelling from single organisms to microbial communities. J R Soc Interface. 2016;13 (124):. doi: 10.1098/rsif.2016.0627. PubMed PMID:28334697 PubMed Central PMC5134014.
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2015

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  2. Hucka, M, Bergmann, FT, Dräger, A, Hoops, S, Keating, SM, Le Novère, N et al.. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J Integr Bioinform. 2015;12 (2):271. doi: 10.2390/biecoll-jib-2015-271. PubMed PMID:26528569 PubMed Central PMC5457286.
  3. Olivier, BG, Bergmann, FT. The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints. J Integr Bioinform. 2015;12 (2):269. doi: 10.2390/biecoll-jib-2015-269. PubMed PMID:26528567 .
  4. Haanstra, JR, Bakker, BM. Drug target identification through systems biology. Drug Discov Today Technol. 2015;15 :17-22. doi: 10.1016/j.ddtec.2015.06.002. PubMed PMID:26464086 .
  5. Haanstra, JR, González-Marcano, EB, Gualdrón-López, M, Michels, PA. Biogenesis, maintenance and dynamics of glycosomes in trypanosomatid parasites. Biochim Biophys Acta. 2016;1863 (5):1038-48. doi: 10.1016/j.bbamcr.2015.09.015. PubMed PMID:26384872 .
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  7. Roth, S, Kholodenko, BN, Smit, MJ, Bruggeman, FJ. G Protein-Coupled Receptor Signaling Networks from a Systems Perspective. Mol Pharmacol. 2015;88 (3):604-16. doi: 10.1124/mol.115.100057. PubMed PMID:26162865 .
  8. Rabbers, I, van Heerden, JH, Nordholt, N, Bachmann, H, Teusink, B, Bruggeman, FJ et al.. Metabolism at evolutionary optimal States. Metabolites. 2015;5 (2):311-43. doi: 10.3390/metabo5020311. PubMed PMID:26042723 PubMed Central PMC4495375.
  9. Lu, P, Heineke, MH, Koul, A, Andries, K, Cook, GM, Lill, H et al.. The cytochrome bd-type quinol oxidase is important for survival of Mycobacterium smegmatis under peroxide and antibiotic-induced stress. Sci Rep. 2015;5 :10333. doi: 10.1038/srep10333. PubMed PMID:26015371 PubMed Central PMC4450806.
  10. Rybakova, KN, Bruggeman, FJ, Tomaszewska, A, Moné, MJ, Carlberg, C, Westerhoff, HV et al.. Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism. PLoS Comput Biol. 2015;11 (4):e1004236. doi: 10.1371/journal.pcbi.1004236. PubMed PMID:25909187 PubMed Central PMC4409292.
  11. Hanemaaijer, M, Röling, WF, Olivier, BG, Khandelwal, RA, Teusink, B, Bruggeman, FJ et al.. Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure. Front Microbiol. 2015;6 :213. doi: 10.3389/fmicb.2015.00213. PubMed PMID:25852671 PubMed Central PMC4365725.
  12. Bastiaens, P, Birtwistle, MR, Blüthgen, N, Bruggeman, FJ, Cho, KH, Cosentino, C et al.. Silence on the relevant literature and errors in implementation. Nat Biotechnol. 2015;33 (4):336-9. doi: 10.1038/nbt.3185. PubMed PMID:25850052 .
  13. Maarleveld, TR, Wortel, MT, Olivier, BG, Teusink, B, Bruggeman, FJ. Interplay between constraints, objectives, and optimality for genome-scale stoichiometric models. PLoS Comput Biol. 2015;11 (4):e1004166. doi: 10.1371/journal.pcbi.1004166. PubMed PMID:25849486 PubMed Central PMC4388735.
  14. Bosdriesz, E, Magnúsdóttir, S, Bruggeman, FJ, Teusink, B, Molenaar, D. Binding proteins enhance specific uptake rate by increasing the substrate-transporter encounter rate. FEBS J. 2015;282 (12):2394-407. doi: 10.1111/febs.13289. PubMed PMID:25846030 .
  15. Goel, A, Eckhardt, TH, Puri, P, de Jong, A, Branco Dos Santos, F, Giera, M et al.. Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content: does protein investment explain an anaerobic bacterial Crabtree effect?. Mol Microbiol. 2015;97 (1):77-92. doi: 10.1111/mmi.13012. PubMed PMID:25828364 .
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  17. Alemdehy, MF, Haanstra, JR, de Looper, HW, van Strien, PM, Verhagen-Oldenampsen, J, Caljouw, Y et al.. ICL-induced miR139-3p and miR199a-3p have opposite roles in hematopoietic cell expansion and leukemic transformation. Blood. 2015;125 (25):3937-48. doi: 10.1182/blood-2014-11-612507. PubMed PMID:25778535 .
  18. Bosdriesz, E, Molenaar, D, Teusink, B, Bruggeman, FJ. How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization. FEBS J. 2015;282 (10):2029-44. doi: 10.1111/febs.13258. PubMed PMID:25754869 PubMed Central PMC4672707.
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  20. Veith, N, Solheim, M, van Grinsven, KW, Olivier, BG, Levering, J, Grosseholz, R et al.. Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism. Appl Environ Microbiol. 2015;81 (5):1622-33. doi: 10.1128/AEM.03279-14. PubMed PMID:25527553 PubMed Central PMC4325170.
  21. Kempe, H, Schwabe, A, Crémazy, F, Verschure, PJ, Bruggeman, FJ. The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise. Mol Biol Cell. 2015;26 (4):797-804. doi: 10.1091/mbc.E14-08-1296. PubMed PMID:25518937 PubMed Central PMC4325848.
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  23. van Heerden, JH, Bruggeman, FJ, Teusink, B. Multi-tasking of biosynthetic and energetic functions of glycolysis explained by supply and demand logic. Bioessays. 2015;37 (1):34-45. doi: 10.1002/bies.201400108. PubMed PMID:25350875 .
  24. Willemsen, AM, Hendrickx, DM, Hoefsloot, HC, Hendriks, MM, Wahl, SA, Teusink, B et al.. MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis. Mol Biosyst. 2015;11 (1):137-45. doi: 10.1039/c4mb00510d. PubMed PMID:25315283 .
  25. Bachmann, H, Pronk, JT, Kleerebezem, M, Teusink, B. Evolutionary engineering to enhance starter culture performance in food fermentations. Curr Opin Biotechnol. 2015;32 :1-7. doi: 10.1016/j.copbio.2014.09.003. PubMed PMID:25269887 .
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2014

  1. Veith, N, Solheim, M, van Grinsven, KW, Olivier, BG, Levering, J, Grosseholz, R et al.. Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism. Appl Environ Microbiol. 2015;81 (5):1622-33. doi: 10.1128/AEM.03279-14. PubMed PMID:25527553 PubMed Central PMC4325170.
  2. Kempe, H, Schwabe, A, Crémazy, F, Verschure, PJ, Bruggeman, FJ. The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise. Mol Biol Cell. 2015;26 (4):797-804. doi: 10.1091/mbc.E14-08-1296. PubMed PMID:25518937 PubMed Central PMC4325848.
  3. Bergmann, FT, Adams, R, Moodie, S, Cooper, J, Glont, M, Golebiewski, M et al.. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics. 2014;15 (1):369. doi: 10.1186/s12859-014-0369-z. PubMed PMID:25494900 PubMed Central PMC4272562.
  4. Rybakova, KN, Tomaszewska, A, van Mourik, S, Blom, J, Westerhoff, HV, Carlberg, C et al.. Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model. Nucleic Acids Res. 2015;43 (1):153-61. doi: 10.1093/nar/gku1272. PubMed PMID:25477385 PubMed Central PMC4288170.
  5. Kort, R, Caspers, M, van de Graaf, A, van Egmond, W, Keijser, B, Roeselers, G et al.. Shaping the oral microbiota through intimate kissing. Microbiome. 2014;2 :41. doi: 10.1186/2049-2618-2-41. PubMed PMID:25408893 PubMed Central PMC4233210.
  6. Anink-Groenen, LC, Maarleveld, TR, Verschure, PJ, Bruggeman, FJ. Mechanistic stochastic model of histone modification pattern formation. Epigenetics Chromatin. 2014;7 (1):30. doi: 10.1186/1756-8935-7-30. PubMed PMID:25408711 PubMed Central PMC4234852.
  7. van Heerden, JH, Bruggeman, FJ, Teusink, B. Multi-tasking of biosynthetic and energetic functions of glycolysis explained by supply and demand logic. Bioessays. 2015;37 (1):34-45. doi: 10.1002/bies.201400108. PubMed PMID:25350875 .
  8. Willemsen, AM, Hendrickx, DM, Hoefsloot, HC, Hendriks, MM, Wahl, SA, Teusink, B et al.. MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis. Mol Biosyst. 2015;11 (1):137-45. doi: 10.1039/c4mb00510d. PubMed PMID:25315283 .
  9. Bachmann, H, Pronk, JT, Kleerebezem, M, Teusink, B. Evolutionary engineering to enhance starter culture performance in food fermentations. Curr Opin Biotechnol. 2015;32 :1-7. doi: 10.1016/j.copbio.2014.09.003. PubMed PMID:25269887 .
  10. Murabito, E, Verma, M, Bekker, M, Bellomo, D, Westerhoff, HV, Teusink, B et al.. Monte-Carlo modeling of the central carbon metabolism of Lactococcus lactis: insights into metabolic regulation. PLoS One. 2014;9 (9):e106453. doi: 10.1371/journal.pone.0106453. PubMed PMID:25268481 PubMed Central PMC4182131.
  11. Kok, J, Johansen, E, Kleerebezem, M, Teusink, B. Lactic Acid Bacteria: embarking on 30 more years of research. Microb Cell Fact. 2014;13 Suppl 1 (Suppl 1):I1. doi: 10.1186/1475-2859-13-S1-I1. PubMed PMID:25187380 PubMed Central PMC4155817.
  12. Schwabe, A, Bruggeman, FJ. Single yeast cells vary in transcription activity not in delay time after a metabolic shift. Nat Commun. 2014;5 :4798. doi: 10.1038/ncomms5798. PubMed PMID:25178355 .
  13. Roth, S, Bruggeman, FJ. A conformation-equilibrium model captures ligand-ligand interactions and ligand-biased signalling by G-protein coupled receptors. FEBS J. 2014;281 (20):4659-71. doi: 10.1111/febs.12970. PubMed PMID:25145284 .
  14. Boele, J, Persson, H, Shin, JW, Ishizu, Y, Newie, IS, Søkilde, R et al.. PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease. Proc Natl Acad Sci U S A. 2014;111 (31):11467-72. doi: 10.1073/pnas.1317751111. PubMed PMID:25049417 PubMed Central PMC4128123.
  15. Schwabe, A, Bruggeman, FJ. Contributions of cell growth and biochemical reactions to nongenetic variability of cells. Biophys J. 2014;107 (2):301-313. doi: 10.1016/j.bpj.2014.05.004. PubMed PMID:25028872 PubMed Central PMC4104058.
  16. Planqué, R, Bruggeman, FJ, Teusink, B, Hulshof, J. Understanding bistability in yeast glycolysis using general properties of metabolic pathways. Math Biosci. 2014;255 :33-42. doi: 10.1016/j.mbs.2014.06.006. PubMed PMID:24956444 .
  17. Wei, K, Moinat, M, Maarleveld, TR, Bruggeman, FJ. Stochastic simulation of prokaryotic two-component signalling indicates stochasticity-induced active-state locking and growth-rate dependent bistability. Mol Biosyst. 2014;10 (9):2338-46. doi: 10.1039/c4mb00264d. PubMed PMID:24955938 .
  18. Solopova, A, van Gestel, J, Weissing, FJ, Bachmann, H, Teusink, B, Kok, J et al.. Bet-hedging during bacterial diauxic shift. Proc Natl Acad Sci U S A. 2014;111 (20):7427-32. doi: 10.1073/pnas.1320063111. PubMed PMID:24799698 PubMed Central PMC4034238.
  19. Kort, R. Personalized therapy with probiotics from the host by TripleA. Trends Biotechnol. 2014;32 (6):291-3. doi: 10.1016/j.tibtech.2014.04.002. PubMed PMID:24785330 .
  20. Reid, G, Nduti, N, Sybesma, W, Kort, R, Kollmann, TR, Adam, R et al.. Harnessing microbiome and probiotic research in sub-Saharan Africa: recommendations from an African workshop. Microbiome. 2014;2 :12. doi: 10.1186/2049-2618-2-12. PubMed PMID:24739094 PubMed Central PMC3996947.
  21. Mania, D, Heylen, K, van Spanning, RJ, Frostegård, A. The nitrate-ammonifying and nosZ-carrying bacterium Bacillus vireti is a potent source and sink for nitric and nitrous oxide under high nitrate conditions. Environ Microbiol. 2014;16 (10):3196-210. doi: 10.1111/1462-2920.12478. PubMed PMID:24708037 .
  22. Mpofu, A, Linnemann, AR, Sybesma, W, Kort, R, Nout, MJ, Smid, EJ et al.. Development of a locally sustainable functional food based on mutandabota, a traditional food in southern Africa. J Dairy Sci. 2014;97 (5):2591-9. doi: 10.3168/jds.2013-7593. PubMed PMID:24630646 .
  23. Heerden, JH, Wortel, MT, Bruggeman, FJ, Heijnen, JJ, Bollen, YJ, Planqué, R et al.. Fatal attraction in glycolysis: how Saccharomyces cerevisiae manages sudden transitions to high glucose. Microb Cell. 2014;1 (3):103-106. doi: 10.15698/mic2014.01.133. PubMed PMID:28357229 PubMed Central PMC5349229.
  24. Wortel, MT, Peters, H, Hulshof, J, Teusink, B, Bruggeman, FJ. Metabolic states with maximal specific rate carry flux through an elementary flux mode. FEBS J. 2014;281 (6):1547-55. doi: 10.1111/febs.12722. PubMed PMID:24460934 .
  25. van Heerden, JH, Wortel, MT, Bruggeman, FJ, Heijnen, JJ, Bollen, YJ, Planqué, R et al.. Lost in transition: start-up of glycolysis yields subpopulations of nongrowing cells. Science. 2014;343 (6174):1245114. doi: 10.1126/science.1245114. PubMed PMID:24436182 .
  26. Maarleveld, TR, Boele, J, Bruggeman, FJ, Teusink, B. A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803. Plant Physiol. 2014;164 (3):1111-21. doi: 10.1104/pp.113.224394. PubMed PMID:24402049 PubMed Central PMC3938606.
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2013

  1. Maarleveld, TR, Olivier, BG, Bruggeman, FJ. StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes. PLoS One. 2013;8 (11):e79345. doi: 10.1371/journal.pone.0079345. PubMed PMID:24260203 PubMed Central PMC3832486.
  2. Bachmann, H, Fischlechner, M, Rabbers, I, Barfa, N, Branco dos Santos, F, Molenaar, D et al.. Availability of public goods shapes the evolution of competing metabolic strategies. Proc Natl Acad Sci U S A. 2013;110 (35):14302-7. doi: 10.1073/pnas.1308523110. PubMed PMID:23940318 PubMed Central PMC3761572.
  3. Maarleveld, TR, Khandelwal, RA, Olivier, BG, Teusink, B, Bruggeman, FJ. Basic concepts and principles of stoichiometric modeling of metabolic networks. Biotechnol J. 2013;8 (9):997-1008. doi: 10.1002/biot.201200291. PubMed PMID:23893965 PubMed Central PMC4671265.
  4. Zhao, Y, Caspers, MP, Metselaar, KI, de Boer, P, Roeselers, G, Moezelaar, R et al.. Abiotic and microbiotic factors controlling biofilm formation by thermophilic sporeformers. Appl Environ Microbiol. 2013;79 (18):5652-60. doi: 10.1128/AEM.00949-13. PubMed PMID:23851093 PubMed Central PMC3754176.
  5. Schwabe, A, Maarleveld, TR, Bruggeman, FJ. Exploration of the spontaneous fluctuating activity of single enzyme molecules. FEBS Lett. 2013;587 (17):2744-52. doi: 10.1016/j.febslet.2013.07.005. PubMed PMID:23850890 .
  6. Khandelwal, RA, Olivier, BG, Röling, WF, Teusink, B, Bruggeman, FJ. Community flux balance analysis for microbial consortia at balanced growth. PLoS One. 2013;8 (5):e64567. doi: 10.1371/journal.pone.0064567. PubMed PMID:23741341 PubMed Central PMC3669319.
  7. Kolodkin, A, Sahin, N, Phillips, A, Hood, SR, Bruggeman, FJ, Westerhoff, HV et al.. Optimization of stress response through the nuclear receptor-mediated cortisol signalling network. Nat Commun. 2013;4 :1792. doi: 10.1038/ncomms2799. PubMed PMID:23653204 PubMed Central PMC3644104.
  8. Abeln, S, Molenaar, D, Feenstra, KA, Hoefsloot, HC, Teusink, B, Heringa, J et al.. Bioinformatics and systems biology: bridging the gap between heterogeneous student backgrounds. Brief Bioinform. 2013;14 (5):589-98. doi: 10.1093/bib/bbt023. PubMed PMID:23603092 .
  9. Berkhout, J, Bosdriesz, E, Nikerel, E, Molenaar, D, de Ridder, D, Teusink, B et al.. How biochemical constraints of cellular growth shape evolutionary adaptations in metabolism. Genetics. 2013;194 (2):505-12. doi: 10.1534/genetics.113.150631. PubMed PMID:23535382 PubMed Central PMC3664859.
  10. Berkhout, J, Teusink, B, Bruggeman, FJ. Gene network requirements for regulation of metabolic gene expression to a desired state. Sci Rep. 2013;3 :1417. doi: 10.1038/srep01417. PubMed PMID:23475326 PubMed Central PMC3593220.
  11. Caspers, MP, Boekhorst, J, Abee, T, Siezen, RJ, Kort, R. Complete Genome Sequence of Anoxybacillus flavithermus TNO-09.006, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment. Genome Announc. 2013;1 (1):. doi: 10.1128/genomeA.00010-13. PubMed PMID:23469333 PubMed Central PMC3587922.
  12. Sybesma, W, Molenaar, D, van IJcken, W, Venema, K, Kort, R. Genome instability in Lactobacillus rhamnosus GG. Appl Environ Microbiol. 2013;79 (7):2233-9. doi: 10.1128/AEM.03566-12. PubMed PMID:23354703 PubMed Central PMC3623246.
  13. Branco dos Santos, F, de Vos, WM, Teusink, B. Towards metagenome-scale models for industrial applications--the case of Lactic Acid Bacteria. Curr Opin Biotechnol. 2013;24 (2):200-6. doi: 10.1016/j.copbio.2012.11.003. PubMed PMID:23200025 .
  14. Quinton-Tulloch, MJ, Bruggeman, FJ, Snoep, JL, Westerhoff, HV. Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico. FEBS J. 2013;280 (1):160-73. doi: 10.1111/febs.12057. PubMed PMID:23121761 .
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