Pimentel, D.; Amaro, R.; Erban, A.; Mauri, N.; Soares, F.; Rego, C.; Martıńez-Zapater, J.M.; Mithöfer, A.; Kopka, J.; Fortes, A.M.: Transcriptome, hormonome, and metabolome of susceptible grape berries under powdery mildew infection. In: Acta Horticulturae, Bd. 1390, (1390), S. 1 - 14. International Society for Horticultural Science., The Hague (2024)

Tang, J.; Chung, K. P.; Zeng, Y.: An Overview of Protein Secretion in Plant Cells. In: Plant Protein Secretion, Bd. 2841, S. 19 - 36 (Hg. Jiang, L.; Shen, J.; Gao, C.; Wang, X.) (2024)

Mariette, A.; Curry, T. M.; Urbanowicz, B. R.; Ebert, B.: Plant Cell Wall Glycosyltransferases. In: Plant Cell Walls: Research 2023 Milestones and Conceptual Insights, S. 29 - 60 (Hg. Geitmann, A.). CRC Press, Boca Raton (2023)

de Souza, L. P.; Fernie, A. R.: Databases and Tools to Investigate Protein-Metabolite Interactions. In: Methods in Molecular Biology (Hg. Walker, J. M.) (2023)

Luzarowski, M.; Skirycz, A.: Parallel Analysis of Protein–Protein and Protein–Metabolite Complexes Using a Single-Step Affinity Purification. In: Methods in Molecular Biology, Bd. 2554 (Hg. Walker, J. M.) (2023)

Luzarowski, M.; Sokolowska, E.; Schlossarek, D.; Skirycz, A.: PROMIS: Co-fractionation Mass Spectrometry for Analysis of Protein–Metabolite Interactions. In: Methods in Molecular Biology (Hg. Walker, J. M.). Springer, US (2023)

Walther, D.: Specifics of Metabolite-Protein Interactions and Their Computational Analysis and Prediction. In: Methods in Molecular Biology (Hg. Walker, J. M.) (2023)

Zhu, F.; Bulut, M.; Cheng, Y.; Alseekh, S.; Fernie, A. R.: Metabolite-Based Genome-Wide Association Studies of Large-Scale Metabolome Analysis to Illustrate Alterations in the Metabolite Landscape of Plants upon Responses to Stresses. In: Methods in Molecular Biology, Bd. 2642, S. 241 - 255 (2023)

Wen, W.; Jia, X.; Zhang, W.; Jiang, X.; Fernie, A. R.: Understanding carotenoid biosynthetic pathway control points using metabolomic analysis and natural genetic variation. In: Methods in Enzymology, Bd. 671, S. 127 - 151 (2022)

Zhu, F.; Fernie, A. R.; Scossa, F.: Preparation and Curation of Omics Data for Genome-Wide Association Studies. In: Methods in Molecular Biology, Bd. 2481 (Hg. Torkamabeh, D.; Belzile, F.). Humana, New York, NY (2022)

Machin, F.; Hasbioğlu, Y.; Kragler, F.: An Arabidopsis Callus Grafting Method to Test Cell-to-Cell Mobility of Proteins. In: Plasmodesmata, Bd. 2457, S. 299 - 312 (Hg. Benitez-Alfonso, Y.; Heinlein, M.) (2022)

Borghi, M.; de Souza, L. P.; Fernie, A. R.: Measurement of Flower Metabolite Concentrations Using Gas Chromatography–Mass Spectrometry and High-Performance Liquid Chromatography–Mass Spectrometry. In: Methods in Molecular Biology, Bd. 2484 (Hg. Lambing, C.) (2022)

Claassens, N. J.; Satanowski, A.; Bysani, V.R.; Dronsella, B.; Orsi, E.; Rainaldi, V.; Yilmaz, S.; Wenk, S.; Lindner, S. N.: Engineering the Reductive Glycine Pathway: A Promising Synthetic Metabolism Approach for C1-Assimilation. In: Advances in Biochemical Engineering/Biotechnology (Hg. Scheper, T.; Ulber, R.). Springer, Cham (2022)

Martins, M.C.M.; Mafra, V.; Monte-Bello, C.C.; Caldana, C.: The Contribution of Metabolomics to Systems Biology: Current Applications Bridging Genotype and Phenotype in Plant Science. In: Advances in experimental medicine and biology, Bd. 1346, S. 91 - 105 (Hg. Winck, F. W.) (2022)

Winck, F.V.; Dos Santos, A.L.W.; Calderan-Rodrigues, M.J.: Plant Proteomics and Systems Biology. In: Advances in Plant Omics and Systems Biology Approaches, Bd. 1346, S. 51 - 66 (Hg. Winck, F. W.) (2022)

Ting, M. K. Y.; Zoschke, R.; Haydon, M. J.: Agrobacterium-Mediated Seedling Transformation to Measure Circadian Rhythms in Arabidopsis. In: Plant Circadian Networks, 2. Aufl. (Hg. Staiger, D.; Davis, S.) (2021)

Allwood, J. W.; Gibon, Y.; Osorio, S.; Araújo, W. L.; Vallarino, J. G.; Pétriacq, P.; Moing, A.: Developmental metabolomics to decipher and improve fleshy fruit quality. In: Advances in Botanical Research, Bd. 98, S. 3 - 34 (Hg. Pétriacq, P.; Bouchereau, A.). Academic Press (2021)

Alseekh, S.; Fernie, A. R.: Using Metabolomics to Assist Plant Breeding. In: Crop Breeding: Genetic Improvement Methods, Bd. 2264, S. 33 - 46 (Hg. Tripodi, P.). Springer US, New York, NY (2021)

Annunziata, M. G.; Lunn, J. E.: Regulation of Assimilatory Starch Metabolism by Cellular Carbohydrate Status. In: Enzymology of Complex Alpha-Glucans, 1st Aufl. (Hg. Nitschke, F.). CRC Press, Boca Raton (2021)

Bauwe, H.; Fernie, A. R.: With a Little Help from My Friends: The Central Role of Photorespiration and Related Metabolic Processes in the Acclimation and Adaptation of Plants to Oxygen and to Low-CO2 Stress. In: Photosynthesis, Respiration, and Climate Change, Bd. 48, S. 355 - 385 (Hg. Becklin, K. M.; Ward, J. K.; Way, D. A.). Springer, Cham (2021)

Bock, R.: Engineering Chloroplasts for High-Level Constitutive or Inducible Transgene Expression. In: Chloroplast Biotechnology: Methods and Protocols, Bd. 2317, S. 77 - 94 (Hg. Maliga, P.). Springer US, New York, NY (2021)

Nieva, A.S.; Ruiz, O. A.: Lotus spp.: A Foreigner that Came to Stay Forever: Economic and Environmental Changes Caused by Its Naturalization in the Salado River Basin (Argentina). In: Saline and Alkaline Soils in Latin America: Natural Resources, Management and Productive Alternatives, S. 431 - 446 (Hg. Taleisnik, E.; Lavado, R. S.). Springer International Publishing, Cham (2021)

Ruf, S.; Bock, R.: Plastid Transformation in Tomato: A Vegetable Crop and Model Species. In: Chloroplast Biotechnology: Methods and Protocols, Bd. 2317, S. 217 - 228 (Hg. Maliga, P.). Springer US, New York, NY (2021)

Torabi, S.; Varshney, K.; Villaecija-Aguilar, J.; Keymer, A.; Gutjahr, C.: Controlled Assays for Phenotyping the Effects of Strigolactone-Like Molecules on Arbuscular Mycorrhiza Development. In: STRIGOLACTONES: Methods and Protocols, S. 157 - 177 (2021)

Villaecija-Aguilar, J.; Struk, S.; Goormachtig, S.; Gutjahr, C.: Bioassays for the Effects of Strigolactones and Other Small Molecules on Root and Root Hair Development. In: STRIGOLACTONES: Methods and Protocols, S. 129 - 142 (2021)

Wu, S.; Alseekh, S.; Brotman, Y.; Fernie, A. R.: Metabolomic Analysis of Natural Variation in Arabidopsis. In: ARABIDOPSIS PROTOCOLS, 4 EDITION, Bd. 2200, S. 393 - 411 (Hg. Sanchez-Serrano, J.; Salinas, J.) (2021)

Erban, A.; Martinez-Seidel, F.; Rajarathinam, Y.; Dethloff, F.; Orf, I.; Fehrle, I.; Alpers, J.; Beine-Golovchuk, O.; Kopka, J.: Multiplexed Profiling and Data Processing Methods to Identify Temperature-Regulated Primary Metabolites Using Gas Chromatography Coupled to Mass Spectrometry. In: Plant Cold Acclimation: Methods in molecular biology, Bd. 2156, S. 203 - 239 (Hg. Hincha, D. K.; Zuther, E.) (2020)

Forner, J.: Germline-Transmitted Genome Editing Methodology in Arabidopsis thaliana Using TAL Effector Nucleases. In: Plant Stem Cells: Methods and Protocols, S. 23 - 30 (Hg. Naseem, M.; Dandekar, T.). Springer US, New York, NY (2020)

Hincha, D. K.; Zuther, E.: Introduction: Plant Cold Acclimation and Winter Survival. In: Plant Cold Acclimation: Methods and Protocols, Bd. 2156, S. 1 - 7 (Hg. Hincha, D. K.; Zuther, E.). Springer US, New York, NY (2020)

Incarbone, M.; Ritzenthaler, C.: Double-Stranded RNA Pull-Down to Characterize Viral Replication Complexes in Plants. In: RNA TAGGING: Methods and Protocols, Bd. 2166, S. 307 - 327 (Hg. Heinlein, M.) (2020)

Naake, T.; Gaquerel, E.; Fernie, A. R.: Annotation of Specialized Metabolites from High-Throughput and High Resolution Mass Spectrometry Metabolomics. In: Computational Methods and Data Analysis for Metabolomics, S. 209 - 225 (Hg. Li, S.). Springer US, New York, NY (2020)

Naseri, G.; Mueller-Roeber, B.: A Step-by-Step Protocol for COMPASS, a Synthetic Biology Tool for Combinatorial Gene Assembly. In: DNA Cloning and Assembly: Methods and Protocols, S. 277 - 303 (Hg. Chandran, S.; George, K. W.). Springer US, New York, NY (2020)

Seerangan, K.; van Spoordonk, R.; Sampathkumar, A.; Eng, R.C.: Long-term live-cell imaging techniques for visualizing pavement cell morphogenesis. In: Methods in cell biology, Bd. 160, S. 365 - 380 (2020)

Takahashi, D.; Zuther, E.; Hincha, D. K.: Analysis of Changes in Plant Cell Wall CompositionCell wallcompositions and Structure During Cold Acclimation. In: Plant Cold Acclimation: Methods and Protocols, Bd. 2156, S. 255 - 268 (Hg. Hincha, D. K.; Zuther, E.). Springer US, New York, NY (2020)

Thalhammer, A.; Pagter, M.; Hincha, D. K.; Zuther, E.: Measuring Freezing Tolerance of Leaves and Rosettes: Electrolyte Leakage and Chlorophyll Fluorescence Assays. In: Plant Cold Acclimation: Methods in Molecular Biology, Bd. 2156, S. 9 - 21 (Hg. Hincha, D. K.; Zuther, E.). Springer, US (2020)

Das, D.; Gutjahr, C.: Role of phytohormones in arbuscular mycorrhiza development. In: The Model Legume Medicago truncatula, S. 7.1.2 (Hg. de Bruijn, F.). Wiley (2019)

Llorente, C.; Jimenez, R.; Brotman, Y.; Fernie, A. R.; Sreenivasulu, N.; Jackie: Rice Grain Quality Benchmarking Through Profiling of Volatiles and Metabolites in Grains Using Gas Chromatography Mass Spectrometry. In: Rice Grain Quality: Methods and Protocols, Bd. 1892, S. 187 - 199 (Hg. Sreenivasulu, N.). Springer New York, New York, NY (2019)

Rochange, S.; Goormachtig, S.; Lopez-Raez, J. A.; Gutjahr, C.: The Role of Strigolactones in Plant–Microbe Interactions. In: Strigolactones - Biology and Applications, S. 121 - 142 (Hg. Koltai, H.; Prandi, C.). Springer, Cham (2019)

Wang, Y.; Kulshreshtha, R.; Sampathkumar, A.: Insights into the Cell Wall and Cytoskeletal Regulation by Mechanical Forces in Plants. In: The Cytoskeleton: Diverse Roles in a Plant's Life, S. 23 - 36 (Hg. Sahi, V. P.; Baluška, F.). Springer International Publishing, Cham (2019)

Alseekh, S.; Wu, S.; Brotman, Y.; Fernie, A. R.: Guidelines for Sample Normalization to Minimize Batch Variation for Large-Scale Metabolic Profiling of Plant Natural Genetic Variance. In: Methods in Molecular Biology, Bd. 1778, S. 33 - 46 (Hg. António, C.). Humana Press, Clifton, N.J. (2018)

de Abreu e Lima, F.; Leifels, L.; Nikoloski, Z.: Regression-Based Modeling of Complex Plant Traits Based on Metabolomics Data. In: Plant Metabolomics: Methods and Protocols, S. 321 - 327 (Hg. António, C.). Humana Press, New York (2018)

de Souza, L. P.; Fernie, A. R.; Tohge, T.: Carbon Atomic Survey for Identification of Selected Metabolic Fluxes. In: Methods in Molecular Biology, Bd. 1778, S. 59 - 70 (Hg. António, C.). Humana Press, Clifton, N.J. (2018)

Feil, R.; Lunn, J. E.: Quantification of Soluble Sugars and Sugar Alcohols by LC-MS/MS. In: Methods in Molecular Biology, Bd. 1778, S. 87 - 100 (Hg. Walker, J. M.). Humana Press, Clifton, N.J. (2018)

Hoffmam, Z. B.; da Silva, V. C. H.; Martins, M. C. M.; Caldana, C.: Applications of Mass Spectrometry in Synthetic Biology. In: Mass Spectrometry in Chemical Biology: Evolving Applications, S. 159 - 172. Royal Society of Chemistry, Cambridge (2018)

Martins, M. C. M.; Caldana, C.; Wolf, L. D.; de Abreu, L. G. F.: The Importance of Experimental Design, Quality Assurance, and Control in Plant Metabolomics Experiments. In: Methods in Molecular Biology, Bd. 1778, S. 3 - 18 (Hg. António, C.). Humana Press, Clifton, N.J. (2018)

Salem, M.A.; Giavalisco, P.: Semi-targeted Lipidomics of Plant Acyl Lipids Using UPLC-HR-MS in Combination with a Data-Independent Acquisition Mode. In: Methods in Molecular Biology, Bd. 1778, S. 137 - 156 (Hg. Walker, J. M.). Humana Press, Clifton, N.J. (2018)

Stuchfield, D.; France, A. P.; Migas, L. G.; Thalhammer, A.; Bremer, A.; Bellina, B.; Barran, P. E.: The Use of Mass Spectrometry to Examine IDPs: Unique Insights and Caveats. In: INTRINSICALLY DISORDERED PROTEINS, S. 459 - 502 (Hg. Rhoades, E.). Academic Press, Cambridge, MA (2018)

Takahashi, D.; Uemura, M.; Kawamura, Y.: Freezing tolerance of plant cells: From the aspect of plasma membrane and microdomain. In: Advances in Experimental Medicine and Biology, Bd. 1081, S. 61 - 79 (Hg. Cohen, I. R.; Lajtha, A.; Lambris, J. D.; Paoletti, R.; Rezaei, N.). Springer Nature, Singapore (2018)

Vallarino, J. G.; Erban, A.; Fehrle, I.; Fernie, A. R.; Kopka, J.; Osorio, S.: Acquisition of Volatile Compounds by Gas Chromatography–Mass Spectrometry (GC-MS). In: Methods in Molecular Biology, Bd. 1778, S. 225 - 240 (Hg. António, C.). Humana Press, Clifton, N.J. (2018)

Watanabe, M.; Tohge, T.; Balazadeh, S.; Erban, A.; Giavalisco, P.; Kopka, J.; Mueller-Roeber, B.; Fernie, A. R.; Hoefgen, R.: Comprehensive Metabolomics Studies of Plant Developmental Senescence. In: Plant Senescence: Methods and Protocols, S. 339 - 358 (Hg. Guo, Y.). Springer New York, New York, NY (2018)