{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:13:00Z","timestamp":1760145180314,"version":"build-2065373602"},"reference-count":109,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2024,6,27]],"date-time":"2024-06-27T00:00:00Z","timestamp":1719446400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The Consejo Nacional de Ciencia, Humanidades y Tecnolog\u00eda (CONAHCYT)","award":["319,732 (2021)","486528","CFINN0177 (2016)"],"award-info":[{"award-number":["319,732 (2021)","486528","CFINN0177 (2016)"]}]},{"name":"CONAHCYT Ph.D. fellowship","award":["319,732 (2021)","486528","CFINN0177 (2016)"],"award-info":[{"award-number":["319,732 (2021)","486528","CFINN0177 (2016)"]}]},{"name":"IDEA Guanajuato project","award":["319,732 (2021)","486528","CFINN0177 (2016)"],"award-info":[{"award-number":["319,732 (2021)","486528","CFINN0177 (2016)"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Algorithms"],"abstract":"<jats:p>L-tryptophan is an essential amino acid widely used in the pharmaceutical and feed industries. Enhancing its production in microorganisms necessitates activating and inactivating specific genes to direct more resources toward its synthesis. In this study, we developed a classification model based on Qualitative Perturbation Analysis and Machine Learning (QPAML). The model uses pFBA to obtain optimal reactions for tryptophan production and FSEOF to introduce perturbations on fluxes of the optima reactions while registering all changes over the iML1515a Genome-Scale Metabolic Network model. The altered reaction fluxes and their relationship with tryptophan and biomass production are translated to qualitative variables classified with GBDT. In the end, groups of enzymatic reactions are predicted to be deleted, overexpressed, or attenuated for tryptophan and 30 other metabolites in E. coli with a 92.34% F1-Score. The QPAML model can integrate diverse data types, promising improved predictions and the discovery of complex patterns in microbial metabolic engineering. It has broad potential applications and offers valuable insights for optimizing microbial production in biotechnology.<\/jats:p>","DOI":"10.3390\/a17070282","type":"journal-article","created":{"date-parts":[[2024,6,27]],"date-time":"2024-06-27T13:26:43Z","timestamp":1719494803000},"page":"282","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Qualitative Perturbation Analysis and Machine Learning: Elucidating Bacterial Optimization of Tryptophan Production"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0165-8408","authenticated-orcid":false,"given":"Miguel Angel","family":"Ramos-Valdovinos","sequence":"first","affiliation":[{"name":"Laboratorio de Ingenier\u00eda Biol\u00f3gica, Departamento de Ingenier\u00eda Gen\u00e9tica, Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional (CINVESTAV-Unidad Irapuato), Km 9.6 Carr. Irapuato-Le\u00f3n, Irapuato 36824, Guanajuato, Mexico"}]},{"given":"Prisciluis Caheri","family":"Salas-Navarrete","sequence":"additional","affiliation":[{"name":"Data Science Manager Analytics and Data Governance, Nacional de Drogas Av. Vasco de Quiroga No. 3100 Col. Centro de Ciudad Santa Fe, \u00c1lvaro Obreg\u00f3n, Mexico City 01210, Mexico"}]},{"given":"Gerardo R.","family":"Amores","sequence":"additional","affiliation":[{"name":"Laboratorio de Ingenier\u00eda Biol\u00f3gica, Departamento de Ingenier\u00eda Gen\u00e9tica, Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional (CINVESTAV-Unidad Irapuato), Km 9.6 Carr. Irapuato-Le\u00f3n, Irapuato 36824, Guanajuato, Mexico"}]},{"given":"Ana Lilia","family":"Hern\u00e1ndez-Orihuela","sequence":"additional","affiliation":[{"name":"Biofab M\u00e9xico, 5 de Mayo No. 517, Irapuato 36500, Guanajuato, Mexico"}]},{"given":"Agustino","family":"Mart\u00ednez-Antonio","sequence":"additional","affiliation":[{"name":"Laboratorio de Ingenier\u00eda Biol\u00f3gica, Departamento de Ingenier\u00eda Gen\u00e9tica, Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional (CINVESTAV-Unidad Irapuato), Km 9.6 Carr. Irapuato-Le\u00f3n, Irapuato 36824, Guanajuato, Mexico"}]}],"member":"1968","published-online":{"date-parts":[[2024,6,27]]},"reference":[{"doi-asserted-by":"crossref","unstructured":"Gang, S., Sharma, S., Saraf, M., Buck, M., and Schumacher, J. (2019). Analysis of Indole-3-Acetic Acid (IAA) Production in Klebsiella by LC-MS\/MS and the Salkowski Method. 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