Sollier, J., Basler, M., Broz, P., Dittrich, P. S., Drescher, K., Egli, A., Harms, A., Hierlemann, A., Hiller, S., King, C. G., McKinney, J. D., Moran-Gilad, J., Neher, R. A., Page, M. G. P., Panke, S., Persat, A., Picotti, P., Rentsch, K. M., Rivera-Fuentes, P., … Dehio, C. (2024). Revitalizing antibiotic discovery and development through in vitro modelling of in-patient conditions. Nature Microbiology, 9(1), 1–3.


Gomez Solsona, B., Horn, H., Schmitt, A., Xu, W., Bucher, P., Heinrich, A., Kalmbach, S., Kreienkamp, N., Franke, M., Wimmers, F., Schuhknecht, L., Rosenwald, A., Zampieri, M., Ott, G., Lenz, G., Schulze-Osthoff, K., & Hailfinger, S. (2023). Inhibition of glutaminase-1 in DLBCL potentiates venetoclax-induced antitumor activity by promoting oxidative stress. Blood Advances, 7(24), 7433–7444.
Schmitt, A., Grimm, M., Kreienkamp, N., Junge, H., Labisch, J., Schuhknecht, L., Schönfeld, C., Görsch, E., Tibello, A., Menck, K., Bleckmann, A., Lengerke, C., Rosenbauer, F., Grau, M., Zampieri, M., Schulze-Osthoff, K., Klener, P., Dolnikova, A., Lenz, G., & Hailfinger, S. (2023). BRD4 inhibition sensitizes diffuse large B-cell lymphoma cells to ferroptosis. Blood, 142(13), 1143–1155.


Ortmayr, K., & Zampieri, M. (2022). Sorting‐free metabolic profiling uncovers the vulnerability of fatty acid β‐oxidation in in vitro quiescence models. Molecular Systems Biology, 18(9), e10716.
Ortmayr, K., De La Cruz Moreno, R., & Zampieri, M. (2022). Expanding the search for small-molecule antibacterials by multidimensional profiling. Nature Chemical Biology, 18(6), 584–595.
Anglada-Girotto, M., Handschin, G., Ortmayr, K., Campos, A. I., Gillet, L., Manfredi, P., Mulholland, C. V., Berney, M., Jenal, U., Picotti, P., & Zampieri, M. (2022). Combining CRISPRi and metabolomics for functional annotation of compound libraries. Nature Chemical Biology, 18(5), 482–491.


Zampieri, M. (2021). The genetic underground of antibiotic resistance. Science, 371(6531), 783–784.
Fuentes, D. A. F., Manfredi, P., Jenal, U., & Zampieri, M. (2021). Pareto optimality between growth-rate and lag-time couples metabolic noise to phenotypic heterogeneity in Escherichia coli. Nature Communications, 12(1), 3204.
Trauner, A., Banaei-Esfahani, A., Gygli, S. M., Warmer, P., Feldmann, J., Zampieri, M., Borrell, S., Collins, B. C., Beisel, C., Aebersold, R., & Gagneux, S. (2021). Expression Dysregulation as a Mediator of Fitness Costs in Antibiotic Resistance. Antimicrobial Agents and Chemotherapy, 65(9), e00504-21.


Øyås, O., Borrell, S., Trauner, A., Zimmermann, M., Feldmann, J., Liphardt, T., Gagneux, S., Stelling, J., Sauer, U., & Zampieri, M. (2020). Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences, 117(15), 8494–8502.


Ortmayr, K., Dubuis, S., & Zampieri, M. (2019). Metabolic profiling of cancer cells reveals genome-wide crosstalk between transcriptional regulators and metabolism. Nature Communications, 10(1), 1841.
Campos, A. I., & Zampieri, M. (2019). Metabolomics-Driven Exploration of the Chemical Drug Space to Predict Combination Antimicrobial Therapies. Molecular Cell, 74(6), 1291-1303.e6.
Zampieri, M., Hörl, M., Hotz, F., Müller, N. F., & Sauer, U. (2019). Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli. Nature Communications, 10(1), 3354.


Zampieri, M., Szappanos, B., Buchieri, M. V., Trauner, A., Piazza, I., Picotti, P., Gagneux, S., Borrell, S., Gicquel, B., Lelievre, J., Papp, B., & Sauer, U. (2018). High-throughput metabolomic analysis predicts mode of action of uncharacterized antimicrobial compounds. Science Translational Medicine, 10(429), eaal3973.
Zampieri, M. (2018). From the metabolic profiling of drug response to drug mode of action. Current Opinion in Systems Biology, 10, 26–33.
Dubuis, S., Ortmayr, K., & Zampieri, M. (2018). A framework for large-scale metabolome drug profiling links coenzyme A metabolism to the toxicity of anti-cancer drug dichloroacetate. Communications Biology, 1(1), 101.


Fuhrer, T., Zampieri, M., Sévin, D. C., Sauer, U., & Zamboni, N. (2017). Genomewide landscape of gene–metabolome associations in Escherichia coli. Molecular Systems Biology, 13(1), 907.
Gonçalves, E., Raguz Nakic, Z., Zampieri, M., Wagih, O., Ochoa, D., Sauer, U., Beltrao, P., & Saez-Rodriguez, J. (2017). Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. PLOS Computational Biology, 13(1), e1005297.
Zampieri, M., Sekar, K., Zamboni, N., & Sauer, U. (2017). Frontiers of high-throughput metabolomics. Current Opinion in Chemical Biology, 36, 15–23.
Zampieri, M., Enke, T., Chubukov, V., Ricci, V., Piddock, L., & Sauer, U. (2017). Metabolic constraints on the evolution of antibiotic resistance. Molecular Systems Biology, 13(3), 917.
Zampieri, M., Zimmermann, M., Claassen, M., & Sauer, U. (2017). Nontargeted Metabolomics Reveals the Multilevel Response to Antibiotic Perturbations. Cell Reports, 19(6), 1214–1228.
Zampieri, M., & Sauer, U. (2017). Metabolomics-driven understanding of genotype-phenotype relations in model organisms. Current Opinion in Systems Biology, 6, 28–36.


Zampieri, M., & Sauer, U. (2016). Model-based media selection to minimize the cost of metabolic cooperation in microbial ecosystems. Bioinformatics, 32(11), 1733–1739.


Oliveira, A. P., Ludwig, C., Zampieri, M., Weisser, H., Aebersold, R., & Sauer, U. (2015). Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis. Science Signaling, 8(374).


Schulz, J. C., Zampieri, M., Wanka, S., Von Mering, C., & Sauer, U. (2014). Large-scale functional analysis of the roles of phosphorylation in yeast metabolic pathways. Science Signaling, 7(353).


Schuetz, R., Zamboni, N., Zampieri, M., Heinemann, M., & Sauer, U. (2012). Multidimensional Optimality of Microbial Metabolism. Science, 336(6081), 601–604.
Beg, Q. K., Zampieri, M., Klitgord, N., Collins, S. B., Altafini, C., Serres, M. H., & Segrè, D. (2012). Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis. Nucleic Acids Research, 40(15), 7132–7149.
Facchetti, G., Zampieri, M., & Altafini, C. (2012). Predicting and characterizing selective multiple drug treatments for metabolicdiseases and cancer. BMC Systems Biology, 6(1), 115.


Zampieri, M., Altafini, C., Eduati, F., Di Camillo, B., Toffolo, G., & De Palo, G. (2011). Adaptation as a genome-wide autoregulatory principle in the stress response of yeast. IET Systems Biology, 5(4), 269–279.
Zampieri, M., Legname, G., Segrè, D., & Altafini, C. (2011). A system-level approach for deciphering the transcriptional response to prion infection. Bioinformatics, 27(24), 3407–3414.


Benetti, F., Gasperini, L., Zampieri, M., & Legname, G. (2010). Gene expression profiling to identify druggable targets in prion diseases. Expert Opinion on Drug Discovery, 5(2), 177–202.


Zampieri, M., Legname, G., & Altafini, C. (2009). Investigating the Conformational Stability of Prion Strains through a Kinetic Replication Model. PLoS Computational Biology, 5(7), e1000420.
Bicciato, S., Spinelli, R., Zampieri, M., Mangano, E., Ferrari, F., Beltrame, L., Cifola, I., Peano, C., Solari, A., & Battaglia, C. (2009). A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets †. Nucleic Acids Research, 37(15), 5057–5070.
Soranzo, N., Zampieri, M., Farina, L., & Altafini, C. (2009). mRNA stability and the unfolding of gene expression in the long-period yeast metabolic cycle. BMC Systems Biology, 3(1), 18.


Zampieri, M., Soranzo, N., & Altafini, C. (2008). Discerning static and causal interactions in genome-wide reverse engineering problems. Bioinformatics, 24(13), 1510–1515.
Zampieri, M., Soranzo, N., Bianchini, D., & Altafini, C. (2008). Origin of Co-Expression Patterns in E.coli and S.cerevisiae Emerging from Reverse Engineering Algorithms. PLoS ONE, 3(8), e2981.