Publications
2025
Application of a Deep Learning Model to Predict Liquid Chromatography Retention Times of Food Peptides Across Chromatographic Conditions, B Hollebrands, J Hageman, HG Janssen, Journal of Separation Science 48 (9), e70270.
JK Kampen, JA Hageman, M Breuer, H Tobi, (2025) The validity of concept mapping: let’s call a spade a spade, Quality & Quantity, 1-17.
Barallat-Pérez, C., Hollebrands, B., Janssen, H.-G., Martins, S., Fogliano, V., Hageman, J., & Oliviero, T. (2025). Development of a QSAR model to predict protein-flavor binding in protein-rich food systems, Food Chemistry, 467, 142268.
N Köllmann, J Hageman, DG Nibbelink, L Zhang, AJ van der Goot, (2024), Wavelength selection enables robust quantification of oil content with near-infrared spectroscopy in pea protein gels produced under varying heating conditions, Food Control, 110995
2024
Giovana P.F. Macan, Davi R. Munhoz, Leo A.J. Willems, Charlie Monkley, Charlotte E.M. Lloyd, Jos Hageman, Violette Geissen, Blanca B. Landa, Paula Harkes (2024), Macro- and microplastics leachates: Characterization and impact on seed germination, Journal of Hazardous Materials, 480, 136013.
Lazaridi, E., Hennebelle, M., Hollebrands, B., Hageman, J., Vincken, J.P., & Janssen, H.G. (2024). Selective ionization of oxidized lipid species using different solvent additives in flow injection mass spectrometry. Analytical and Bioanalytical Chemistry, 416(3), 787–799.
Jin, G., Boeschoten, S., Hageman, J., Zhu, Y., Wijffels, R., Rinzema, A., & Xu, Y. (2024). Identifying Variables Influencing Traditional Food Solid-State Fermentation by Statistical Modeling. Foods, 13(9), 1317.
2023
Ditzler, L., Rossing, W., Schulte, R., Hageman, J., & Apeldoorn, D. (2023). Prospects for increasing the resolution of crop diversity for agroecosystem service delivery in a Dutch arable system. Agriculture, Ecosystems & Environment, 351, 108472.
Hollebrands, B., Hageman, J., Sande, J., Albada, B., & Janssen, H.G. (2023). Improved LC–MS identification of short homologous peptides using sequence-specific retention time predictors. Analytical and Bioanalytical Chemistry, 415(14), 2715–2726.
Lie-Piang, A., Hageman, J., Vreenegoor, I., Kolk, K., Leeuw, S., Padt, A., & Boom, R. (2023). Quantifying techno-functional properties of ingredients from multiple crops using machine learning. Current Research in Food Science, 7, 100601.
2022
Pandeirada, C., Hageman, J., Janssen, H.G., Westphal, Y., & Schols, H. (2022). Identification of plant polysaccharides by MALDI-TOF MS fingerprinting after periodate oxidation and thermal hydrolysis. Carbohydrate Polymers, 292, 119685.
2021
Marr, S., Hageman, J., Wehrens, R., Dam, N., Bruelheide, H., & Neumann, S. (2021). LC-MS based plant metabolic profiles of thirteen grassland species grown in diverse neighbourhoods. Scientific data, 8(1), 52.
Andini, S., Araya-Cloutier, C., Lay, B., Vreeke, G., Hageman, J., & Vincken, J.P. (2021). QSAR-based physicochemical properties of isothiocyanate antimicrobials against gram-negative and gram-positive bacteria. LWT, 144, 111222.
Kouzounis, D., Hageman, J., Soares, N., Michiels, J., & Schols, H. (2021). Impact of xylanase and glucanase on oligosaccharide formation, carbohydrate fermentation patterns, and nutrient utilization in the gastrointestinal tract of broilers. Animals, 11(5), 1285.
Kalli, S., Araya-Cloutier, C., Hageman, J., & Vincken, J.P. (2021). Insights into the molecular properties underlying antibacterial activity of prenylated (iso) flavonoids against MRSA. Scientific Reports, 11(1), 14180.
Hageman, J., & Engel, J.. (2021). Development and application of statistical methods for analyzing metabolomics data.
2020
Melandri, G., AbdElgawad, H., Riewe, D., Hageman, J., Asard, H., Beemster, G., Kadam, N., Jagadish, K., Altmann, T., Ruyter-Spira, C., & others (2020). Biomarkers for grain yield stability in rice under drought stress. Journal of Experimental Botany, 71(2), 669–683.
Bijlsma, J., Bruijn, W., Hageman, J., Goos, P., Velikov, K., & Vincken, J.P. (2020). Revealing the main factors and two-way interactions contributing to food discolouration caused by iron-catechol complexation. Scientific Reports, 10(1), 8288.
Flood, P., Theeuwen, T., Schneeberger, K., Keizer, P., Kruijer, W., Severing, E., Kouklas, E., Hageman, J., Wijfjes, R., Calvo-Baltanas, V., & others (2020). Reciprocal cybrids reveal how organellar genomes affect plant phenotypes. Nature Plants, 6(1), 13–21.
2019
Pan, X., Alsayyari, A., Dalm, C., Hageman, J., Wijffels, R., & Martens, D. (2019). Transcriptome analysis of CHO cell size increase during a fed-batch process. Biotechnology journal, 14(3), 1800156.
Elwakiel, M., Boeren, S., Hageman, J., Szeto, I., Schols, H., & Hettinga, K. (2019). Variability of serum proteins in Chinese and Dutch human milk during lactation. Nutrients, 11(3), 499.
Hageman, J., Nieuwenhuizen, A., Ruth, S., Hageman, J., & Keijer, J. (2019). Application of volatile organic compound analysis in a nutritional intervention study: differential responses during five hours following consumption of a high-and a low-fat dairy Drink. Molecular nutrition & food research, 63(20), 1900189.
2018
Alsayyari, A., Pan, X., Dalm, C., Veen, J., Vriezen, N., Hageman, J., Wijffels, R., & Martens, D. (2018). Transcriptome analysis for the scale-down of a CHO cell fed-batch process. Journal of Biotechnology, 279, 61–72.
Elwakiel, M., Hageman, J., Wang, W., Szeto, I., Van Goudoever, J., Hettinga, K., & Schols, H. (2018). Human milk oligosaccharides in colostrum and mature milk of Chinese mothers: Lewis positive secretor subgroups. Journal of Agricultural and Food Chemistry, 66(27), 7036–7043.
Araya-Cloutier, C., Vincken, J.P., Schans, M., Hageman, J., Schaftenaar, G., Besten, H., & Gruppen, H. (2018). QSAR-based molecular signatures of prenylated (iso) flavonoids underlying antimicrobial potency against and membrane-disruption in Gram positive and Gram negative bacteria. Scientific Reports, 8(1), 9267.
Bruijn, W., Hageman, J., Araya-Cloutier, C., Gruppen, H., & Vincken, J.P. (2018). QSAR of 1, 4-benzoxazin-3-one antimicrobials and their drug design perspectives. Bioorganic & Medicinal Chemistry, 26(23-24), 6105–6114.
Nyarukowa, C., Koech, R., Loots, T., Hageman, J., & Apostolides, Z. (2018). Prioritising the replanting schedule of seedling tea fields on tea estates for drought susceptibility measured by the SWAPDT method in the absence of historical in-filling records. Journal of Agricultural Science, 10(7), 26.
2017
Calingacion, M., Mumm, R., Tan, K., Quiatchon-Baeza, L., Concepcion, J., Hageman, J., Prakash, S., Fitzgerald, M., & Hall, R. (2017). A multidisciplinary phenotyping and genotyping analysis of a mapping population enables quality to be combined with yield in rice. Frontiers in Molecular Biosciences, 4, 32.
2016
Mumm, R., Hageman, J., Calingacion, M., De Vos, R., Jonker, H., Erban, A., Kopka, J., Hansen, T., Laursen, K., Schjoerring, J., & others (2016). Multi-platform metabolomics analyses of a broad collection of fragrant and non-fragrant rice varieties reveals the high complexity of grain quality characteristics. Metabolomics, 12, 1–19.
Zhang, L., Waard, M., Verheijen, H., Boeren, S., Hageman, J., Van Hooijdonk, T., Vervoort, J., Van Goudoever, J., & Hettinga, K. (2016). Changes over lactation in breast milk serum proteins involved in the maturation of immune and digestive system of the infant. Journal of Proteomics, 147, 40–47.
Wehrens, R., Hageman, J., Eeuwijk, F., Kooke, R., Flood, P., Wijnker, E., Keurentjes, J., Lommen, A., Eekelen, H., Hall, R., & others (2016). Improved batch correction in untargeted MS-based metabolomics. Metabolomics, 12, 1–12.
Donkelaar, L., Hageman, J., Oguz, S., Noordman, T., Boom, R., & Goot, A.J. (2016). Combining unmalted barley and pearling gives good quality brewing. Journal of the Institute of Brewing, 122(2), 228–236.
2015
Zhang, L., Boeren, S., Hageman, J., Hooijdonk, T., Vervoort, J., & Hettinga, K. (2015). Bovine milk proteome in the first 9 days: protein interactions in maturation of the immune and digestive system of the newborn. PloS one, 10(2), e0116710.
Zhang, L., Boeren, S., Hageman, J., Hooijdonk, T., Vervoort, J., & Hettinga, K. (2015). Perspective on calf and mammary gland development through changes in the bovine milk proteome over a complete lactation. Journal of dairy science, 98(8), 5362–5373.
2014
Gupta, A., Hageman, J., Wierenga, P., Boots, J.W., & Gruppen, H. (2014). Chemometric analysis of soy protein hydrolysates used in animal cell culture for IgG production–An untargeted metabolomics approach. Process Biochemistry, 49(2), 309–317.
2012
Hageman, J., Malosetti, M., & Van Eeuwijk, F. (2012). Two-mode clustering of genotype by trait and genotype by environment data. Euphytica, 183(3), 349–359.
2011
Saccenti, E., Westerhuis, J., Smilde, A., Werf, M., Hageman, J., & Hendriks, M. (2011). Simplivariate models: uncovering the underlying biology in functional genomics data. PloS one, 6(6), e20747.
Doeswijk, T., Smilde, A., Hageman, J., Westerhuis, J., & Van Eeuwijk, F. (2011). On the increase of predictive performance with high-level data fusion. Analytica chimica acta, 705(1-2), 41–47.
Doeswijk, T., Hageman, J., Westerhuis, J., Tikunov, Y., Bovy, A., & Eeuwijk, F. (2011). Canonical correlation analysis of multiple sensory directed metabolomics data blocks reveals corresponding parts between data blocks. Chemometrics and Intelligent Laboratory Systems, 107(2), 371–376.
2010
Zakrzewska, A., Boorsma, A., Beek, A., Hageman, J., Westerhuis, J., Hellingwerf, K., Brul, S., Klis, F., & Smits, G. (2010). Comparative analysis of transcriptome and fitness profiles reveals general and condition-specific cellular functions involved in adaptation to environmental change in Saccharomyces cerevisiae. Omics: a journal of integrative biology, 14(5), 603–614.
2009
Maldonado, A., Hageman, J., Mastroianni, S., & Rothenberg, G. (2009). Backbone diversity analysis in catalyst design. Advanced Synthesis & Catalysis, 351(3), 387–396.
Lindinger, C., Pollien, P., Vos, R., Tikunov, Y., Hageman, J., Lambot, C., Fumeaux, R., Voirol-Baliguet, E., & Blank, I. (2009). Identification of ethyl formate as a quality marker of the fermented off-note in coffee by a nontargeted chemometric approach. Journal of agricultural and food chemistry, 57(21), 9972–9978.
2008
Hageman, J., Berg, R., Westerhuis, J., Werf, M., & Smilde, A. (2008). Genetic algorithm based two-mode clustering of metabolomics data. Metabolomics, 4, 141–149.
Tonneijck, F., Hageman, J., Sevink, J., & Verstraten, J. (2008). Tephra stratification of volcanic ash soils in Northern Ecuador. Geoderma, 144(1-2), 231–247.
Hageman, J., Hendriks, M., Westerhuis, J., Werf, M., Berger, R., & Smilde, A. (2008). Simplivariate models: ideas and first examples. PLoS One, 3(9), e3259.
2007
Westerhuis, J., Hageman, J., Fruhauf, H.W., Rothenberg, G., & others (2007). Understanding ligand diversity. Chimica Oggi, 25.
2006
Jansen, B., Nierop, K., Hageman, J., Cleef, A., & Verstraten, J. (2006). The straight-chain lipid biomarker composition of plant species responsible for the dominant biomass production along two altitudinal transects in the Ecuadorian Andes. Organic Geochemistry, 37(11), 1514–1536.
Hageman, J., Westerhuis, J., Frühauf, H.W., & Rothenberg, G. (2006). Design and assembly of virtual homogeneous catalyst libraries–towards in silico catalyst optimisation. Advanced Synthesis & Catalysis, 348(3), 361–369.
Nierop, K., Jansen, B., Hageman, J., & Verstraten, J. (2006). The complementarity of extractable and ester-bound lipids in a soil profile under pine. Plant and Soil, 286, 269–285.
Hageman, J., Van Den Berg, R., Westerhuis, J., Hoefsloot, H., & Smilde, A. (2006). Bagged K-means clustering of metabolome data. Critical reviews in analytical chemistry, 36(3-4), 211–220.
2005
Hageman, J., Westerhuis, J., & Smilde, A. (2005). Temperature robust multivariate calibration: an overview of methods for dealing with temperature influences on near infrared spectra. Journal of near infrared spectroscopy, 13(2), 53.
2003
Hageman, J., Streppel, M., Wehrens, R., & Buydens, L. (2003). Wavelength selection with Tabu search. Journal of Chemometrics: A Journal of the Chemometrics Society, 17(8-9), 427–437.
Hageman, J., Wehrens, R., Van Sprang, H., & Buydens, L. (2003). Hybrid genetic algorithm–tabu search approach for optimising multilayer optical coatings. Analytica Chimica Acta, 490(1-2), 211–222.
Hageman, J., Wehrens, R., De Gelder, R., & Buydens, L. (2003). Powder pattern indexing using the weighted crosscorrelation and genetic algorithms. Journal of computational chemistry, 24(9), 1043–1051.
2001
Gelder, R., Wehrens, R., & Hageman, J. (2001). A generalized expression for the similarity of spectra: application to powder diffraction pattern classifica
2000
Van Acker, F., Hageman, J., Haenen, G., Vijgh, W., Bast, A., & Menge, W. (2000). Synthesis of novel 3, 7-substituted-2-(3 ‘, 4 ‘-dihydroxyphenyl) flavones with improved antioxidant activity. Journal of medicinal chemistry, 43(20), 3752–3760.
Hageman, J., Wehrens, R., Gelder, R., Leo Meerts, W., & Buydens, L. (2000). Direct determination of molecular constants from rovibronic spectra with genetic algorithms. The Journal of Chemical Physics, 113(18), 7955–7962.
Hageman, J., Wehrens, R., Gelder, R., Meerts, W., & Buydens, L. (2000). Fitting fluorescence spectra with genetic algorithms. In Parallel Problem Solving from Nature PPSN VI: 6th International Conference Paris, France, September 18–20, 2000 Proceedings 6 (pp. 702–711).
Hageman, J., & Wehrens, R. (2000). de R. Gelder, WL Meerts, LMC Buydens. J. Chem. Phys, 113, 7955–7962.
Book Chapters
Relevant metabolites’ selection strategies, (2022), Jos Hageman, Metabolomics Perspectives, 381-398
Hageman, J., Engel, B., Vos, R., Mumm, R., Hall, R., Jwanro, H., Crouzillat, D., Spadone, J., & Eeuwijk, F. (2017). Robust and confident predictor selection in metabolomics. Statistical analysis of proteomics, metabolomics, and lipidomics data using mass spectrometry, 239–257.
Veer, G., Ruth, S., & Hageman, J. (2014). An integral approach to validation of analytical fingerprinting methods in combination with chemometric modelling for food quality assurance
How to find the best homogeneous catalyst, G Rothenberg, JA Hageman, F Clerc, HWFJA Westerhuis, (2006), Catalysis of Organic Reactions, 287-296