Conflict of interest
The authors declare no financial or commercial conflict of interest.
References :
[1] Choi, K. R., Jang, W. D., Yang, D., Cho, J. S., et al. ,Trends Biotechnol 2019, 37 , 817.
[2] Singh, V., Haque, S., Niwas, R., Srivastava, A., et al. ,Front Microbiol 2017, 7 , 2087.
[3] Kim, G. B., Kim, W. J., Kim, H. U., Lee, S. Y., Curr Opin Biotechnol 2020, 64 , 1.
[4] Galbraith, S. C., Bhatia, H., Liu, H., Yoon, S., Curr Opin Chem Eng 2018, 22 , 42.
[5] Shih, W., Chai, S., Academy of Management Proceedings , Academy of Management Briarcliff Manor, NY 10510 2016, p. 14843.
[6] Hyduke, D. R., Lewis, N. E., Palsson, B. Ø., Mol Biosyst2013, 9 , 167.
[7] Presnell, K. V., Alper, H. S., Biotechnol J 2019,14 , 1800416.
[8] Çalik, P., Ileri, N., Chem Eng Sci 2007, 62 , 5206.
[9] Nielsen, J., Annu Rev Biochem 2017, 86 , 245.
[10] Bordbar, A., Monk, J. M., King, Z. A., Palsson, B. O.,Nat Rev Genet 2014, pp. 107.
[11] Orth, J. D., Thiele, I., Palsson, B. Ø., Nat Biotechnol2010, 28 , 245.
[12] Thiele, I., Palsson, B. Ø., Nat Protoc 2010, 5 , 93.
[13] Reed, J. L., The Chemistry of Microbiomes: Proceedings of a Seminar Series , National Academies Press (US) 2017.
[14] Chowdhury, S., Fong, S. S., Curr Opin Biotechnol 2020, pp. 267.
[15] Gu, C., Kim, G. B., Kim, W. J., Kim, H. U., Lee, S. Y.,Genome Biol 2019, 20 , 121.
[16] Zhang, J., Petersen, S. D., Radivojevic, T., Ramirez, A., et al. , Nat Commun 2020, 11 , 4880.
[17] Rana, P., Berry, C., Ghosh, P., Fong, S. S., Curr Opin Biotechnol 2020, 64 , 85.
[18] Tarca, A. L., Carey, V. J., Chen, X.-w., Romero, R., Drăghici, S., PLoS Comput Biol 2007, 3 , e116.
[19] Helmy, M., Smith, D., Selvarajoo, K., Metab Eng Commun2020, 11 , e00149.
[20] Chen, F., Li, H., Xu, Z., Hou, S., Yang, D., Electron J Biotechnol 2015, 18 , 273.
[21] Suryawanshi, N., Sahu, J., Moda, Y., Eswari, J. S., Prep Biochem Biotechnol 2020, 50 , 1031.
[22] Antonakoudis, A., Barbosa, R., Kotidis, P., Kontoravdi, C.,Comput Struct Biotechnol J 2020.
[23] Kim, Y., Kim, G. B., Lee, S. Y., Curr Opin Syst Biol2021, 25 , 42.
[24] Lawson, C. E., Martí, J. M., Radivojevic, T., Jonnalagadda, S. V. R., et al. , Metab Eng 2021, 63 , 34.
[25] Oyetunde, T., Bao, F. S., Chen, J.-W., Martin, H. G., Tang, Y. J., Biotechnol Adv 2018, 36 , 1308.
[26] Zampieri, G., Vijayakumar, S., Yaneske, E., Angione, C.,PLoS Comput Biol 2019, 15 , e1007084.
[27] Yasemi, M., Jolicoeur, M., Processes 2021, 9 , 322.
[28] Kim, O. D., Rocha, M., Maia, P., Front Microbiol 2018,9 , 1690.
[29] Traustason, B., Cheeks, M., Dikicioglu, D., Int J Mol Sci 2019, 20 , 5464.
[30] Srinivasan, S., Cluett, W. R., Mahadevan, R., Biotechnol J 2015, 10 , 1345.
[31] Volkova, S., Matos, M. R. A., Mattanovich, M., Marín de Mas, I., Metabolites 2020, 10 , 303.
[32] King, Z. A., Lloyd, C. J., Feist, A. M., Palsson, B. O.,Curr Opin Biotechnol 2015, 35 , 23.
[33] Maia, P., Rocha, M., Rocha, I., Microbiol Mol Biol Rev2016, 80 , 45.
[34] Li, S., Richelle, A., Lewis, N. E., in: Lee, G. M., Faustrup Kildegaard, H., Lee, S. Y., Nielsen, J., Stephanopoulos, G. (Eds.),Cell Culture Engineering , Wiley 2019, pp. 73.
[35] Reed, J. L., Palsson, B. Ø., Genome Res 2004, 14 , 1797.
[36] Rau, M. H., Zeidan, A. A., Biochem Soc Trans 2018,46 , 249.
[37] Huang, Z., Lee, D.-Y., Yoon, S., Biotechnol Bioeng 2017,114 , 2717.
[38] O’Brien, E. J., Monk, J. M., Palsson, B. O., Cell 2015,161 , 971.
[39] Reed, J. L., PLoS Comput Biol 2012, 8 , e1002662.
[40] Suthers, P. F., Maranas, C. D., AlChE J 2020, 66 .
[41] Anand, S., Mukherjee, K., Padmanabhan, P., Biotechnol Genet Eng Rev 2020, pp. 1.
[42] Antoniewicz, M. R., Curr Opin Biotechnol 2013, pp. 973.
[43] Long, M. R., Ong, W. K., Reed, J. L., Curr Opin Biotechnol 2015, 34 , 135.
[44] Motamedian, E., Sarmadi, M., Derakhshan, E., Process Biochem 2019, 87 , 10.
[45] Ebrahim, A., Lerman, J. A., Palsson, B. O., Hyduke, D. R.,BMC Syst Biol 2013, 7 , 74.
[46] Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S. N., et al. , Nat Protoc 2019, 14 , 639.
[47] Fouladiha, H., Marashi, S.-A., J Biomed Inform 2017,68 , 35.
[48] Rai, A., Saito, K., Curr Opin Biotechnol 2016,37 , 127.
[49] Ramon, C., Gollub, M. G., Stelling, J., Essays Biochem2018, 62 , 563.
[50] Reinhart, D., Damjanovic, L., Kaisermayer, C., Kunert, R.,Appl Microbiol Biotechnol 2015, 99 , 4645.
[51] Ritacco, F. V., Wu, Y., Khetan, A., Biotechnol Progr2018, 34 , 1407.
[52] Maghsoudi, A., Hosseini, S., Shojaosadati, S. A., Vasheghani-Farahani, E., et al. , Biotechnol Bioprocess Eng2012, 17 , 76.
[53] Kishishita, S., Nishikawa, T., Shinoda, Y., Nagashima, H., et al. , J Biosci Bioeng 2015, 119 , 700.
[54] Calmels, C., McCann, A., Malphettes, L., Andersen, M. R.,Metab Eng 2019, 51 , 9.
[55] Emenike, V. N., Schenkendorf, R., Krewer, U., Comput Chem Eng 2018, 118 , 1.
[56] Huang, Z., Xu, J., Yongky, A., Morris, C. S., et al. ,Biochem Eng J 2020, 160 , 107638.
[57] Irani, Z. A., Maghsoudi, A., Shojaosadati, S. A., Motamedian, E., Biochem Eng J 2015, 98 , 1.
[58] Meadows, A. L., Karnik, R., Lam, H., Forestell, S., Snedecor, B., Metab Eng 2010, 12 , 150.
[59] Bideaux, C., Montheard, J., Cameleyre, X., Molina-Jouve, C., Alfenore, S., Appl Microbiol Biotechnol 2016, 100 , 1489.
[60] Pham, N., Reijnders, M., Suarez-Diez, M., Nijsse, B., et al. , Biotechnol Biofuels 2021, 14 , 1.
[61] Zhao, X., Kasbi, M., Chen, J., Peres, S., Jolicoeur, M.,Biotechnol Bioeng 2017, 114 , 2907.
[62] Boyle, N. R., Morgan, J. A., BMC Syst Biol 2009,3 , 1.
[63] Parichehreh, R., Gheshlaghi, R., Mahdavi, M. A., Elkamel, A.,Biochem Eng J 2019, 141 , 131.
[64] Aminian-Dehkordi, J., Mousavi, S. M., Marashi, S. A., Jafari, A., Mijakovic, I., Front Bioeng Biotechnol 2020, 8 , 528.
[65] Fan, S., Zhang, Z., Zou, W., Huang, Z., et al. , J Biotechnol 2014, 169 , 15.
[66] Lee, K., Park, J., Kim, T., Yun, H., Lee, S., Microb Cell Fact 2010, 9 , 94.
[67] Swayambhu, G., Moscatello, N., Atilla-Gokcumen, G. E., Pfeifer, B. A., iScience 2020, 23 , 101016.
[68] Fouladiha, H., Marashi, S.-A., Torkashvand, F., Mahboudi, F., et al. , Bioprocess Biosystems Eng 2020, 43 , 1381.
[69] Yegane‑Sarkandy, S., Farnoud, A. M., Shojaosadati, S. A., Khalilzadeh, R., et al. , Biotechnol Appl Biochem 2009,54 , 31.
[70] Savizi, I. S. P., Soudi, T., Shojaosadati, S. A., Appl Microbiol Biotechnol 2019, 103 , 8315.
[71] Kaushal, M., Chary, K. V. N., Ahlawat, S., Palabhanvi, B., et al. , Bioresour Technol 2018, 249 , 767.
[72] Ivarsson, M., Noh, H., Morbidelli, M., Soos, M.,Biotechnol Progr 2015, 31 , 347.
[73] Sou, S. N., Sellick, C., Lee, K., Mason, A., et al. ,Biotechnol Bioeng 2015, 112 , 1165.
[74] Gupta, M. K., Misra, K., Netw Model Anal Health Inform Bioinform 2016, 5 , 4.
[75] Cioffi, R., Travaglioni, M., Piscitelli, G., Petrillo, A., De Felice, F., Sustainability 2020, 12 , 492.
[76] Venkatasubramanian, V., AlChE J 2019, 65 , 466.
[77] Müller, A. C., Guido, S., 2016.
[78] Erl, T., Khattak, W., Buhler, P., Prentice Hall Boston 2016.
[79] Volk, M. J., Lourentzou, I., Mishra, S., Vo, L. T., et al. , ACS Synth Biol 2020, 9 , 1514.
[80] Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., et al. , J Mach Learn Res 2011, 12 , 2825.
[81] Cielen, D., Meysman, A., Ali, M., 2016.
[82] Kumari, B., Swarnkar, T., Advanced Computing and Intelligent Engineering , Springer 2020, pp. 309.
[83] Jolliffe, I. T., Cadima, J., Philos T R Soc A 2016,374 , 20150202.
[84] Bolón-Canedo, V., Sánchez-Maroño, N., Alonso-Betanzos, A.,Progress in Artificial Intelligence 2016, 5 , 65.
[85] Ardabili, S., Mosavi, A., Várkonyi-Kóczy, A. R., Lecture Notes in Networks and Systems 2020.
[86] Breiman, L., Machine Learning 2001, 45 .
[87] Vabalas, A., Gowen, E., Poliakoff, E., Casson, A. J.,PLoS One 2019, 14 , e0224365.
[88] Zhang, D., Del Rio‐Chanona, E. A., Petsagkourakis, P., Wagner, J., Biotechnol Bioeng 2019, 116 , 2919.
[89] Caglar, M. U., Hockenberry, A. J., Wilke, C. O., PLoS One 2018, 13 , e0206634.
[90] Tokuyama, K., Shimodaira, Y., Terawaki, T., Kusunose, Y., et al. , J Biosci Bioeng 2020, 130 , 409.
[91] Danjuma, K. J., arXiv preprint arXiv:1504.04646 2015.
[92] Saito, T., Rehmsmeier, M., Bioinformatics 2017,33 , 145.
[93] Huang, S., Chaudhary, K., Garmire, L. X., Front genet2017, 8 , 84.
[94] Gilpin, W., Huang, Y., Forger, D. B., Curr Opin Syst Biol 2020, 22 , 1.
[95] Camacho, D. M., Collins, K. M., Powers, R. K., Costello, J. C., Collins, J. J., Cell 2018, pp. 1581.
[96] Smiatek, J., Jung, A., Bluhmki, E., Trends Biotechnol2020.
[97] Cuperlovic-Culf, M., Metabolites 2018, 8 , 4.
[98] Kim, M., Rai, N., Zorraquino, V., Tagkopoulos, I., Nat Commun 2016, 7 , 13090.
[99] Nelofer, R., Ramanan, R. N., Rahman, R. N. Z. R. A., Basri, M., Ariff, A. B., J Ind Microbiol Biotechnol 2012, 39 , 243.
[100] Wang, Y., Yang, G., Sage, V., Xu, J., et al. ,Environ Prog Sustain Energy 2021, 40 .
[101] Unni, S., Prabhu, A. A., Pandey, R., Hande, R., Veeranki, V. D., Can J Chem Eng 2019, 97 , 843.
[102] Tavasoli, T., Arjmand, S., Ranaei Siadat, S. O., Shojaosadati, S. A., Sahebghadam Lotfi, A., Biochem Eng J 2019, 144 , 18.
[103] Zhang, L., Chao, B., Zhang, X., Bioresour Technol 2020,301 , 122781.
[104] Dong, C., Chen, J., Bioresour Technol 2019, 271 , 174.
[105] Kennedy, M. J., Spooner, N. R., Biotechnol Tech 1996,10 , 47.
[106] Melcher, M., Scharl, T., Spangl, B., Luchner, M., et al. , Biotechnol J 2015, 10 , 1770.
[107] Masampally, V. S., Pareek, A., Runkana, V., 2018 IEEE Symposium Series on Computational Intelligence (SSCI) , IEEE 2018, pp. 128.
[108] Patel, G., Patil, M. D., Tangadpalliwar, S., Nile, S. H., et al. , Ultrasound Med Biol 2021, 47 , 777.
[109] Misra, B. B., Langefeld, C., Olivier, M., Cox, L. A., J Mol Endocrinol 2019, 62 , R21.
[110] Noor, E., Cherkaoui, S., Sauer, U., Curr Opin Syst Biol2019, 15 , 39.
[111] Xu, C., Jackson, S. A., Genome Biol 2019, 20 , 76.
[112] Horgan, R. P., Kenny, L. C., Obstet Gynecol 2011,13 , 189.
[113] Krömer, J., Quek, L.-E., Nielsen, L., Aust Biochem2009, 40 , 17.
[114] Sridhara, V., Meyer, A. G., Rai, P., Barrick, J. E., et al. , PLoS One 2014, 9 , e114608.
[115] Oyetunde, T., Liu, D., Martin, H. G., Tang, Y. J., PLoS One 2019, 14 , e0210558.
[116] Wu, S. G., Wang, Y., Jiang, W., Oyetunde, T., et al. ,PLoS Comput Biol 2016, 12 , e1004838.
[117] Schinn, S. M., Morrison, C., Wei, W., Zhang, L., et al. , 2021, 118 , 2118.
[118] Larrimore, K. E., Rancati, G., Curr Opin Genet Dev2019, 58-59 , 55.
[119] Nandi, S., Subramanian, A., Sarkar, R. R., Mol Biosyst2017, 13 , 1584.
[120] Zampieri, G., Coggins, M., Valle, G., Angione, C., The 2nd International Electronic Conference on Metabolomics , MDPI 2017, p. 4993.
[121] Vijayakumar, S., Rahman, P. K. S. M., Angione, C.,iScience 2020, 23 , 101818.
[122] Culley, C., Vijayakumar, S., Zampieri, G., Angione, C.,PNAS 2020, 117 , 18869.
[123] Almquist, J., Cvijovic, M., Hatzimanikatis, V., Nielsen, J., Jirstrand, M., Metab Eng 2014, pp. 38.
[124] Subramanian, I., Verma, S., Kumar, S., Jere, A., Anamika, K.,Bioinform Biol Insights 2020, 14 , 1177932219899051.
[125] Blazier, A. S., Papin, J. A., Front Physiol 2012.
[126] Richelle, A., Chiang, A. W. T., Kuo, C.-C., Lewis, N. E.,PLoS Comput Biol 2019, 15 , e1006867.
Table 1. Overview of constraint-based modeling applications for analysis and optimization of fermentation parameters demonstrated in this review.