Publications

Selected Research Publications

† Equal contributions; * Corresponding Author; For full list of publications, please visit our PI's Google Scholar profile

Preprints

1. Giusto, P.D., Choi, D.-H., Antonakoudis, A., Duraikannan, V.G., Craveur, P., Cowie, N.L., Ganapathy, T., Ramesh, K., Benavidez-Lopez, S., Orellana, C.A., Jimnez, N.E., Dworkin, L.A., Morrissey, J., de Mas, I.G., Strain, B., Valdez-Cruz, N.A., Trujillo-Roldan, M.A., Marzluf, J., Martinez, V.S., Zhetener, L., Altamirano, C., Vega-Letter, A.M., Priem, B., Cao, H.C., Hold, M., Ma, J., Hong, Y.F., Gopalakrihnan, S., Enuh, B.M., Tarzi, C., Pang, K.T., Angione, C., Zanghellini, J., Kontravdi, C., Hefzi, H., Betenbaugh, M.J., Nielsen, L.K., Lakshmanan, M.*, Lee, D.-Y.*, Richelle, A.*, Lewis, N.E.* (2025) “A community-consensus genome-scale metabolic reconstruction of the Chinese Hamster enables structural systems biology analyses to decipher metabolic rewiring in lactate-free CHO cells”, biorxiv DOI: 10.1101/2025.04.10.647063

Published Journal Articles

2. Kai, S.O. J., Myint, M., Tan, C.F., Hong, Y.F., Lakshmanan, M., Ho, Y.S., Wheeler, T.T., Bi, X., Walsh, I., Chia, S., Pang K.T. (2025) "Is green algae polysaccharide a ‘green path’ to health?", Algal Research 91, 104268.

3. Lee, Y.Q., Choi, Y.-M., Park, S.-Y., Kim, S.-K., Lee, M., Kim, D., Koduru, L., Lakshmanan, M., Jung, S., Kim, M.J., Choe, Y.H., Lee, D.-Y. (2025) "Genome-scale metabolic model-guided systematic framework for designing customized live biotherapeutic products", npj Systems Biology and Applications, 11, 73. DOI:10.1038/s41540-025-00555-5

4. Kang, D.E., Senthilkumar, D., Jeon, J.H., You, W.-K., Ganapathy, T., Lakshmanan, M.*, Hong, J.-K.* (2025) "Differential polyamine metabolism in CHO cell lines: Insights into cell growth and antibody quality”, New Biotechnology 88, 100-113. DOI:10.1016/j.nbt.2025.04.007

5. Pang, K.T., Hong, Y.F., Shozui, F., Furomitsu, S., Myint, M., Ho, Y.S., Silberberg, Y.R., Walsh, I.*, Lakshmanan, M.* (2024) "Genome-Scale Modeling of CHO Cells Unravel the Critical Role of Asparagine in Cell Culture Feed Media", Biotechnology Journal, 19(11), e202400072. DOI:10.1002/biot.202400072

6. Lakshmanan, M., Chia, S., Pang, K.T., Sim, L.C., Teo, G., Mak, S.Y., Chen, S., Lim, H.S., Lee, A.P., Mahfut, F.B., Ng, S.K., Yang, Y., Soh, A., Tan, A.H.-M., Choo, A., Ho, Y.S., Ngyuyen-Khuong, T., Walsh, I. (2024) "Antibody glycan quality predicted from CHO cell culture media markers and machine learning", Computational and Structural Biotechnology Journal, 23:2497-2506. DOI: 10.1016/j.csbj.2024.05.046

7. Park, S.-Y., Choi, D.-H., Song, J., Lakshmanan, M., Richelle, A., Yoon, S., Kontoravdi, C., Lewis, N.E., Lee, D.-Y. (2024) "Driving towards digital biomanufacturing by CHO genome-scale models", Trends in Biotechnology, In Press. DOI: 10.1016/j.tibtech.2024.03.001

8. Choi, Y., Long, S., Ang, K.S., Lewis, N.E., Lakshmanan, M.*, Lee, D.-Y*. (2023) “Mitigating biomass composition uncertainties in flux balance analysis using ensemble representations”, Computational and Structural Biotechnology Journal, 21: 3736-3745. DOI: 10.1016/j.csbj.2023.07.025

9. Koduru, L.†, Lakshmanan, M.†, Yu, L.P., Banu, M., Ow, D. S.-K., Lee, D.-Y. (2022) “Systematic evaluation of genome-wide metabolic landscapes in lactic acid bacteria reveals diet-induced and strain-specific probiotic idiosyncrasies”, Cell Reports, 41(10): 111735; DOI: 10.1016/j.celrep.2022.111735

10. Walsh, I.*, Myint, M., Nguyen-Khuong, T., Ho, Y.S., Ng, S.K., Lakshmanan, M.* (2022) “Harnessing the potential of machine learning for advancing “Quality by Design” in biomanufacturing”, mAbs, 6(6): e00599-21. DOI: 10.1080/19420862.2021.2013593

11. Lee A.P.†, Kok, Y.J.†, Lakshmanan, M.† et al. (2021) “Multi-omics profiling of a CHO cell culture system unravels the effect of culture pH on cell growth, antibody titer and product quality”, Biotechnology & Bioengineering 118(11):4305-4316. DOI: 10.1002/bit.27899.

12. Yeo, H.C., Hong, J.K., Lakshmanan, M.*, Lee, D.-Y.* (2020) “Enzyme capacity–based genome-scale modelling of CHO cells”, Metabolic Engineering, 60:138–147. DOI: 10.1016/j.ymben.2020.04.005.

13. Lieven, C. , Beber, M.E., Olivier, B.G. , Bergmann, F.T., Babaei, P., Bartell, J.A., Blank, L.M., Chauhan, S., Correia, K., Diener, C., Dräger, A., Ebert, B.E., Edirisinghe, J.N., Fleming, R.M.T., García-Jiménez, B., van Helvoirt, W., Henry, C.S., Hermjakob, H., Herrgård, M.J., Kim, H.U., King, Z., Koehorst, J.J., Klamt, S., Klipp, E., Lakshmanan, M., Le Novère, N., Lee, D.-Y., Lee, S.Y., Lee, S., Lewis, N.E., Ma, H., Machado, M., Mahadevan, R., Maia, P., Mardinoglu, A., Medlock, G.L., Monk, J.M., Nielsen, J., Nielsen, L.K., Nogales, J., Nookaew, I., Resendis-Antonio, O., Palsson, B.O., Papin, J.A., Patil, K.R., Price, N.D., Richelle, A., Rocha, I., Schaap, P.J., Sheriff, R.S.M., Shoaie, S., Sonnenschein, N., Teusink, B., Vilaça, P., Vik, J.O., Wodke, J.A., Xavier, J.C., Yuan, Q., Zakhartsev, M., Zhang. C. (2020) “Memote: A community driven effort towards a standardized genome-scale metabolic model test suite”, Nature Biotechnology, 38:272–276. DOI: 10.1038/s41587-020-0446-y.

14. Lakshmanan, M., Kok, Y.J., Lee, A.P., Kyriakopoulos, S., Lim, H.L., Teo, G., Poh, S.L., Tang, W.Q., Hong, J., Tan, A.H.-M., Bi, X., Ho, Y.S., Zhang, P., Ng, S.K., Lee, D.-Y. (2019) “Multi-omics profiling of CHO parental hosts reveals cell line-specific variations in bioprocessing traits”, Biotechnology & Bioengineering, 116(9):2117-2129; DOI: 10.1002/bit.27014.

15. Hong, J.K.†, Lakshmanan, M.†, Lee, D.-Y. (2018) “Towards next generation CHO cell line development and engineering by systems approaches”, Current Opinion in Chemical Engineering, 22:1-10. DOI: 10.1016/j.coche.2018.08.002.

16. Kyriakopoulos, S., Ang, K.S., Lakshmanan, M., Huang, Z., Yoon, S., Gunawan, R., Lee, D.-Y. (2018) “Kinetic modeling of mammalian cell culture bioprocessing: the quest to advance biomanufacturing”, Biotechnology Journal, 13(3):e1700229. DOI: 10.1002/biot.201700229. 

17. Koduru, L., Kim, Y., Bang, J., Lakshmanan, M., Han, N.S., Lee, D.-Y. (2017) “Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria”, Scientific Reports, 7: 15721. DOI: 10.1038/s41598-017-16026-9.

18. Yusufi, F.N.K.†, Lakshmanan, M.†, Ho, Y.S.*, Loo, B.L.W., Yeo, H.C., Ariyaratne, P., Lee, T.S., Yang, Y.S., Ng, S.K., Tan, T.R.M., Lim, H.S.,  Ng, S.W., Hiu, A.P.,  Chow, C.P., Wan, C., Teo, G., Song, G., Chin, J.X., Ruan, X., Sung, K.W.K., Hu, W.-S., Yap, M.G.S., Bardor, M., Nagarajan, N., Lee, D.-Y. (2017) “Mammalian systems biotechnology reveals global cellular adaptations in a recombinant CHO cell line”, Cell Systems, 4(5):530-542. DOI: 10.1016/j.cels.2017.04.009

19. Hefzi, H., Ang, K.S., Hanscho, M., Bordbar, A., Ruckerbauer, D., Lakshmanan, M., Orellana, C.A., Baycin-Hizal, D., Huang, Y., Ley, D., Martinez, V.S., Kyriakopoulos, S., Jiménez, N.E., Zielinski, D.C., Quek, L.-E., Wulff, T., Arnsdorf, J., Li, S., Lee, J.S., Paglia, G., Loira, N., Spahn, P.N., Pedersen, L.E., Gutierrez, J.M., Lund, A.M., Nagarajan, H., Thomas, A., Abdel-Haleem, A.M., Zanghellini, J., Kildegaard, H.F., Voldborg, B.G., Gerdtzen, Z.P., Betenbaugh, M.J.,  Palsson, B.O., Andersen, M.R., Nielsen, L.K., Borth, N., Lee, D.-Y., Lewis, N.E. (2016) “A consensus genome-scale reconstruction of CHO cell metabolism for improved biotherapeutic protein production”, Cell Systems, 3(5):434-443. DOI: 10.1016/j.cels.2016.10.020.

20. Swainston, N., Smallbone, K., Hefzi, H., Dobson, P.D., Brewer, J., Gardiner, N.J., Zielinski, D.C., Ang, K.S., Gutierrez, J.M., Hanscho, M., Kyriakopoulos, S., Lakshmanan, M., Li, S., Liu, J.K., Martinez, V.S., Orellana, C.A., Quek, L.-E., Thomas, A., Borth, N., Lee, D.-Y., Nielsen, L.K., Kell, D.B., Mendes, P. (2016) “Recon 2.2: from reconstruction to model of human metabolism”, Metabolomics, 12:109. DOI: 10.1007/s11306-016-1051-4.

21. Lakshmanan, M., Koh, G., Chung, B.K.S., Lee, D.-Y. (2014) “Software applications for flux balance analysis”, Briefings in Bioinformatics, 15(1):108-22. DOI:10.1093/bib/bbs069. One of the top 5 highly cited paper in Briefings in Bioinformatics (2014).

Book Chapters

1. Ang K.S., Hong, J.K., Lakshmanan, M., Lee, D.-Y. (2019) “Towards integrated multi-omics analysis for improving CHO cell bioprocessing”, In G. M. Lee and H. F. Kidegaard (Ed.), Advanced Biotechnology, Wiley, DOI: 10.1002/9783527811410.ch7.

2. Lakshmanan, M., Koduru, L., Lee, D.-Y. (2017) “Software applications for phenotype analysis and strain design of cellular systems”, In H. N. Chang, S.-Y. Lee, J. B. Nielsen and G. Stephanopolous (Ed.), Emerging Areas in Bioengineering, Wiley, DOI:10.1002/9783527803293.ch44