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Metabolic Engineering in the -omics Era: Elucidating and Modulating Regulatory Networks

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Metabolomics or metabolite profiles?

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The food metabolome: a window over dietary exposure

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Analytical strategies for LC–MS-based targeted metabolomics

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Metabolic flux analysis and pharmaceutical production

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A Metabolomic View of Staphylococcus aureus and Its Ser/Thr Kinase and Phosphatase Deletion Mutants: Involvement in Cell Wall Biosynthesis

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From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

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Metabolite Profiling Reveals YihU as a Novel Hydroxybutyrate Dehydrogenase for Alternative Succinic Semialdehyde Metabolism in Escherichia coli

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The benefits of being transient: isotope-based metabolic flux analysis at the short time scale

Nöh, K., & Wiechert, W. (2011) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-011-3390-4 · Cited by 69 · see citing works

Evaluation of Sampling and Extraction Methodologies for the Global Metabolic Profiling ofSaccharophagus degradans

Shin, M. H., Lee, D. Y., Liu, K., Fiehn, O., & Kim, K. H. (2010) · Analytical Chemistry · doi:10.1021/ac1012656 · Cited by 68 · see citing works

Qualitative Alterations of Bacterial Metabolome after Exposure to Metal Nanoparticles with Bactericidal Properties: A Comprehensive Workflow Based on 1H NMR, UHPLC-HRMS, and Metabolic Databases

Chatzimitakos, T. G., & Stalikas, C. D. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00489 · Cited by 68 · see citing works

Phenotypic and metabolic profiling of colony morphology variants evolved from Pseudomonas fluorescens biofilms

Workentine, M. L., Harrison, J. J., Weljie, A. M., Tran, V. A., Stenroos, P. U., Tremaroli, V., Vogel, H. J., Ceri, H., & Turner, R. J. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02185.x · Cited by 62 · see citing works

Looking back into the future: 30 years of metabolomics at TNO

van der Greef, J., van Wietmarschen, H., van Ommen, B., & Verheij, E. R. (2013) · Mass Spectrometry Reviews · doi:10.1002/mas.21370 · Cited by 60 · see citing works

Sample preparation procedures utilized in microbial metabolomics: An overview

Patejko, M., Jacyna, J., & Markuszewski, M. J. (2016) · Journal of Chromatography B · doi:10.1016/j.jchromb.2016.09.029 · Cited by 60 · see citing works

Systems biology perspectives on minimal and simpler cells

Xavier, J. C., Patil, K. R., & Rocha, I. (2014) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00050-13 · Cited by 58 · see citing works

Direct enantioseparation of underivatized aliphatic 3-hydroxyalkanoic acids with a quinine-based zwitterionic chiral stationary phase

Ianni, F., Pataj, Z., Gross, H., Sardella, R., Natalini, B., Lindner, W. F., & Lämmerhofer, M. (2014) · Journal of Chromatography A · doi:10.1016/j.chroma.2014.03.060 · Cited by 58 · see citing works

Comprehensive analysis of the metabolome of Pseudomonas putida S12 grown on different carbon sources

WERF, M. J. V. D., Overkamp, K. M., Muilwijk, B., Koek, M. M., der Vat, B. J. C. V. D. W.-V., Jellema, R. H., Coulier, L., & Hankemeier, T. (2008) · Molecular BioSystems · doi:10.1039/b717340g · Cited by 58 · see citing works

Global metabolic analyses identify key differences in metabolite levels between polymyxin-susceptible and polymyxin-resistant Acinetobacter baumannii

Maifiah, M. H. M., Cheah, S.-E., Johnson, M. D., Han, M., Boyce, J. D., Thamlikitkul, V., Forrest, A., Kaye, K. S., Hertzog, P. J., Purcell, A. W., et al. (2016) · Scientific Reports · doi:10.1038/srep22287 · Cited by 58 · see citing works

Chemometric evaluation of Saccharomyces cerevisiae metabolic profiles using LC–MS

Farrés, M., Piña, B., & Tauler, R. (2014) · Metabolomics · doi:10.1007/s11306-014-0689-z · Cited by 56 · see citing works

Simple Data-Reduction Method for High-Resolution LC–MS Data in Metabolomics

Scheltema, R. A., Decuypere, S., Dujardin, J., Watson, D., Jansen, R., & Rainer Breitling, A. (2009) · Bioanalysis · doi:10.4155/bio.09.146 · Cited by 55 · see citing works

Metabolic profiling of human urine by CE-MS using a positively charged capillary coating and comparison with UPLC-MS

Ramautar, R., Nevedomskaya, E., Mayboroda, O. A., Deelder, A. M., Wilson, I. D., Gika, H., Theodoridis, G. A., Somsen, G. W., & de Jong, G. J. (2010) · Molecular BioSystems · doi:10.1039/c0mb00032a · Cited by 55 · see citing works

Mass Spectrometry-Based Metabolomics of Yeast

Crutchfield, C. A., Lu, W., Melamud, E., & Rabinowitz, J. D. (2010) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(10)70016-1 · Cited by 55 · see citing works

Metabolic engineering of Bacillus subtilis for terpenoid production

Guan, Z., Xue, D., Abdallah, I. I., Dijkshoorn, L., Setroikromo, R., Lv, G., & Quax, W. J. (2015) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-015-6950-1 · Cited by 54 · see citing works

A flexible framework for sparse simultaneous component based data integration

Deun, K. V., Wilderjans, T. F., van den Berg, R. A., Antoniadis, A., & Mechelen, I. V. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-448 · Cited by 52 · see citing works

Key Challenges in Plant Microbiome Research in the Next Decade

Fadiji, A. E., Adeniji, A. A., Lanrewaju, A. A., Adedayo, A. A., Chukwuneme, C. F., Nwachukwu, B. C., Aderibigbe, J., & Omomowo, I. O. (2025) · Microorganisms · doi:10.3390/microorganisms13112546 · Cited by 51 · see citing works

Genome-enabled plant metabolomics

Tohge, T., de Souza, L. P., & Fernie, A. R. (2014) · Journal of Chromatography B · doi:10.1016/j.jchromb.2014.04.003 · Cited by 49 · see citing works

TiO2-Assisted Laser Desorption/Ionization Mass Spectrometry for Rapid Profiling of Candidate Metabolite Biomarkers from Antimicrobial-Resistant Bacteria

Zhang, R., Qin, Q., Liu, B., & Qiao, L. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.7b04565 · Cited by 49 · see citing works

Metabolite damage and repair in metabolic engineering design

Sun, J., Jeffryes, J. G., Henry, C. S., Bruner, S. D., & Hanson, A. D. (2017) · Metabolic Engineering · doi:10.1016/j.ymben.2017.10.006 · Cited by 48 · see citing works

The potential of metabolomics for Leishmania research in the post-genomics era

Scheltema, R. A., Decuypere, S., t’Kindt, R., Dujardin, J., Coombs, G. H., & Rainer Breitling, A. (2010) · Parasitology · doi:10.1017/s0031182009992022 · Cited by 45 · see citing works

Intracellular Metabolite Pool Changes in Response to Nutrient Depletion Induced Metabolic Switching in Streptomyces coelicolor

Wentzel, A., Sletta, H., Ellingsen, T. E., & Bruheim, P. (2012) · Metabolites · doi:10.3390/metabo2010178 · Cited by 44 · see citing works

In vivo dynamics of glycolysis in Escherichia coli shows need for growth‐rate dependent metabolome analysis

Schaub, J., & Reuß, M. (2008) · Biotechnology Progress · doi:10.1002/btpr.59 · Cited by 44 · see citing works

Integrative Approaches to Enhance Understanding of Plant Metabolic Pathway Structure and Regulation

Tohge, T., Scossa, F., & Fernie, A. R. (2015) · PLANT PHYSIOLOGY · doi:10.1104/pp.15.01006 · Cited by 43 · see citing works

Sampling and analysis of metabolomes in biological fluids

de Paiva, M. J. N., Menezes, H. C., & Cardeal, Z. D. L. (2014) · The Analyst · doi:10.1039/c4an00583j · Cited by 43 · see citing works

A complex matrix characterization approach, applied to cigarette smoke, that integrates multiple analytical methods and compound identification strategies for non‐targeted liquid chromatography with high‐resolution mass spectrometry

Arndt, D., Wachsmuth, C. J., Buchholz, C., & Bentley, M. C. (2019) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.8571 · Cited by 41 · see citing works

Optimization of a sample preparation method for the metabolomic analysis of clinically relevant bacteria

Marcinowska, R., Trygg, J., Wolf‐Watz, H., Möritz, T., & Surowiec, I. (2011) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2011.07.001 · Cited by 40 · see citing works

Complementing reversed-phase selectivity with porous graphitized carbon to increase the metabolome coverage in an on-line two-dimensional LC-MS setup for metabolomics

Ortmayr, K., Hann, S., & Koellensperger, G. (2015) · The Analyst · doi:10.1039/c5an00206k · Cited by 40 · see citing works

Towards a platform for the metabonomic profiling of different strains of Drosophila melanogaster using liquid chromatography–Fourier transform mass spectrometry

Kamleh, M. A., Hobani, Y. H., Dow, J. A. T., Zheng, L., & Watson, D. G. (2009) · FEBS Journal · doi:10.1111/j.1742-4658.2009.07397.x · Cited by 40 · see citing works

Advancing Biopharmaceutical Process Development by System-Level Data Analysis and Integration of Omics Data

Schaub, J., Clemens, C., Kaufmann, H., & Schulz, T. W. (2011) · Springer eBooks · doi:10.1007/10_2010_98 · Cited by 39 · see citing works

DISCO-SCA and Properly Applied GSVD as Swinging Methods to Find Common and Distinctive Processes

Deun, K. V., Mechelen, I. V., Thorrez, L., Schouteden, M., Moor, B. D., WERF, M. J. V. D., Lathauwer, L. D., Smilde, A. K., & Kiers, H. A. L. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037840 · Cited by 39 · see citing works

Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis

Redestig, H., Kusano, M., Fukushima, A., Matsuda, F., Saito, K., & Arita, M. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-214 · Cited by 39 · see citing works

Metabolomic profiling of CHO fed-batch growth phases at 10, 100 and 1, 000 L

Vodopivec, M., Lah, L., Narat, M., & Curk, T. (2019) · Biotechnology and Bioengineering · doi:10.1002/bit.27087 · Cited by 37 · see citing works

Application of GC–MS metabolic profiling to ‘blue-green water’ from microbial influenced corrosion in copper pipes

Beale, D. J., Dunn, M. S., & Marney, D. (2010) · Corrosion Science · doi:10.1016/j.corsci.2010.04.039 · Cited by 37 · see citing works

Simultaneous Analysis of Organic Acids, Glycerol and Phenolic Acids in Wines Using Gas Chromatography-Mass Spectrometry

García-Viñola, V., Ruiz-de-Villa, C., Gombau, J., Poblet, M., Bordons, A., Reguant, C., & Rozés, N. (2024) · Foods · doi:10.3390/foods13020186 · Cited by 35 · see citing works

Analyzing Longitudinal Microbial Metabolomics Data

Rubingh, C. M., Bijlsma, S., Jellema, R. H., Overkamp, K. M., WERF, M. J. V. D., & Smilde, A. K. (2009) · Journal of Proteome Research · doi:10.1021/pr900126e · Cited by 35 · see citing works

A proper metabolomics strategy supports efficient food quality improvement: A case study on tomato sensory properties

Thissen, U., Coulier, L., Overkamp, K. M., Jetten, J. M., der Vat, B. J. C. V. D. W.-V., van de Ven, T., & WERF, M. J. V. D. (2010) · Food Quality and Preference · doi:10.1016/j.foodqual.2010.12.001 · Cited by 34 · see citing works

Coupled metabolic‐hydrodynamic modeling enabling rational scale‐up of industrial bioprocesses

Wang, G., Haringa, C., Tang, W., Noorman, H. J., Chu, J., Zhuang, Y., & Zhang, S. (2019) · Biotechnology and Bioengineering · doi:10.1002/bit.27243 · Cited by 34 · see citing works

Current status, strategies, and potential for the metabolic engineering of heterologous polyketides in Escherichia coli

Boghigian, B. A., & Pfeifer, B. A. (2008) · Biotechnology Letters · doi:10.1007/s10529-008-9689-2 · Cited by 34 · see citing works

Large-scale metabolome analysis and quantitative integration with genomics and proteomics data in Mycoplasma pneumoniae

Maier, T., Marcos, J., Wodke, J. A. H., Paetzold, B., Liebeke, M., Gallego, R. G., & Serrano, L. G. (2013) · Molecular BioSystems · doi:10.1039/c3mb70113a · Cited by 34 · see citing works

From fluxes and isotope labeling patterns towards in silico cells

Dauner, M. (2010) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2010.01.014 · Cited by 33 · see citing works

Development and validation of a systematic platform for broad-scale profiling of microbial metabolites

Wang, X.-N., Yin, Y., Cheng, X. S., Chen, L., Chen, M., Zheng, J., Jin, Y., Liu, J., Liu, L., & Xin, G.-Z. (2019) · Talanta · doi:10.1016/j.talanta.2019.03.087 · Cited by 2 · see citing works

Microbial Metabolomics with Gas Chromatography/Mass Spectrometry

Koek, M. M., Muilwijk, B., WERF, M. J. V. D., & Hankemeier, T. (2006) · Analytical Chemistry · doi:10.1021/ac051683+ · Cited by 316 · see citing works

Comprehensive analysis of the metabolome of Pseudomonas putida S12 grown on different carbon sources

WERF, M. J. V. D., Overkamp, K. M., Muilwijk, B., Koek, M. M., der Vat, B. J. C. V. D. W.-V., Jellema, R. H., Coulier, L., & Hankemeier, T. (2008) · Molecular BioSystems · doi:10.1039/b717340g · Cited by 58 · see citing works

Multiple metabolomics of uropathogenic E. coli reveal different information content in terms of metabolic potential compared to virulence factors

Alrabiah, H. K., Yun Xu, A., Rattray, N. J. W., Vaughan, A. A., Gibreel, T. M., Sayqal, A. A., Upton, M., Allwood, J. W., & Goodacre, R. (2014) · The Analyst · doi:10.1039/c4an00176a · Cited by 14 · see citing works

Metabolomics and the techniques applicable

Zargar, S. M., Farooq, A., Sofi, P. A., Sudan, J., Urwat, U., & Hussain, K. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-21923-8.00005-4