Publications

Google Scholar (with citation indices) - Most complete list

Publication list on Web of Science (with citation metrics)

Research and review papers, books chapters

1. Sakai, R., Zhao, Y. and Robert, M. LOTUS: A low-cost time-lapse automated imaging system for spatio-temporal analysis of microbial colony or biofilm development. PLOS ONE 21, e0339652 (2026).

2. Robert, M. Integrating Freshman STEM Education into a Big-History Course in Japan. Journal of Big History 6, 73–78 (2023). 

3. Robert, M. Complexity and Possible Emerging Intelligence in Bacterial Collectives. Journal of Cognitive Science 19, 283–284 (2018). (PDF)

4. Iuchi H., Tomita M. and Robert M. (2015) Amino acid acetylation by orphan enzyme YhhY in Escherichia coli. Keio SFC Journal, 15, 1, 402-413 (in Japanese) (PDF)

5. Cheng K.K., Lee B-S., Masuda T., Fujikura J., Ito T., Ikeda K., Deng L., Dong J., Shimizu K., Soga T., Tomita M., Palsson B., and Robert M. (2014) Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol. Nat. Commun. 5:3233

6. Robert M. (2013) A broader perspective on organization and coherence in biological systems.   In Proceedings of the European Conference on Complex Systems 2012. Edited by Gilbert T, Kirkilionis M, Nicolis G. Springer International Publishing, 503–510. [Springer Proceedings in Complexity] Pre-print arXiv:1212.0334

7. Robert M., Murray, D., Honma M., Nakahigashi K., Soga T., and Tomita M. (2012) Extracellular metabolite dynamics and temporal organization of metabolic function in E.  coli. Proceedings of IEEE/ICME International Conference on Complex Medical Engineering (CME 2012), 197-202. Accepted version (PDF), or final version on IEEEXplore

8. Sugimoto M., Kawakami M., Robert M., Soga T., Tomita M. (2012) Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis, Current Bioinformatics, 7, 96-108

9. Saito, N. & Robert, M. (2011) Metabolomics approach for enzyme discovery. Seikagaku 83, 1039-1043. (PDF) (Review in Japanese)

10. Sugimoto M., Hirayama A., Robert M., Abe S., Soga T., and Tomita M. (2010) Prediction of metabolite identity from accurate mass, migration time prediction, and isotopic pattern information in CE-TOF-MS data. Electrophoresis, 31, 2311-2318.

11. Sugimoto M., Hirayama A., Ishikawa T., Robert M., Baran R., Uehara K., Kawai K., Soga T., and Tomita M. (2010). Differential Metabolomics Software for Capillary Electrophoresis-Mass Spectrometry Data Analysis. Metabolomics 6, 27-41

12. Saito, N., Robert, M., Kochi, H., Matsuo, G., Kakazu, Y., Soga, T., and Tomita, M. (2009) Metabolite profiling reveals YihU as a novel hydroxybutyrate dehydrogenase for alternative succinic semialdehyde metabolism in Escherichia coli. J. Biol. Chem. 284, 24, 16442–16451

13. Ishii, N., Nakahigashi, K., Baba, T., Robert, M*., Soga, T., Kanai, A., Hirasawa, T., et al. (2007). Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations. Science 316, 593-597. (*Equivalent contribution of first 7 authors)

14. Robert, M., Soga, T., and Tomita, M. (2007) E. coli metabolomics: capturing the complexity of a “simple” model.  In: Metabolomics, A Powerful Tool in Systems Biology. Topics in Current Genetics. Eds. Nielsen J. Jewett M. pp 189-234, Springer Berlin/Heidelberg

    1. Author final version (PDF) or original version at Springer on-line.

15. Baran R., Robert M*., Suematsu M., Soga T. and Tomita M.  (2007) Visualization of three-way comparisons of omics data. BMC Bioinformatics 8, 72. *as corresponding author.  This manuscript is flagged as “Highly accessed” by BMC Bioinformatics.

16. Baran R., Kochi H., Saito N., Soga T., Nishioka T., Robert M*., and Tomita M. (2006) MathDAMP: a package for differential analysis of metabolite profiles.  BMC Bioinformatics 7, 530 *as corresponding author.  This manuscript is flagged as “Highly accessed” by BMC Bioinformatics.  Fourth most accessed article during the 1st month following publication.

17. Shinoda, K., Sugimoto, M., Yachie, N., Sugiyama, N., Masuda, T., Robert, M., Soga, T., Tomita, M. (2006) Prediction of liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome using artificial neural networks. Journal of Proteome Research, 5, 3312-3317

18. Saito, N., Robert, M., Kitamura, S., Baran, R., Soga, T., Mori, H., Nishioka, T., and Tomita, M. (2006). Metabolomics approach for enzyme discovery. Journal of Proteome Research 5, 1979-1987. In Top 20 Most Accessed Articles in the Journal of Proteome Research for the period of July-September 2006

19. Soga T., Baran R., Suematsu M., Ueno Y., Ikeda S., Sakurakawa T., Kakazu Y., Ishikawa T., Robert M., Nishioka T., and Tomita M. (2006) Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumption.  Journal of Biological Chemistry, 281, 16768-76

20. Arita M., Robert M., and Tomita M. (2005). All systems go: Launching cell simulation fueled by integrated experimental biology data.  Current Opinion in Biotechnology, 16, 344-349.

21. Ishii N., Robert M., Nakayama Y., Kanai A., and Tomita M. (2004). Toward large-scale modeling of the microbial cell for computer simulation. Journal of Biotechnology 113, 281-294.

22. Soga T., Kakazu Y., Robert M., Tomita M., and Nishioka T. (2004). Qualitative and quantitative analysis of amino acids by capillary electrophoresis electrospray ionization tandem mass spectrometry.  Electrophoresis 25, 1964-72

23. Robert M. and Gagnon C. (1999). Semenogelin I: a coagulum forming, multifunctional seminal-vesicle protein.  Cellular and Molecular Life Sciences 55, 944-960.

24. Wadhwa R., Takano S., Robert M., Yoshida A., Nomura H., Reddel R. R., Mitsui Y., and Kaul S. C. (1998). Inactivation of tumor suppressor p53 by mot-2, a hsp70 family member. Journal of Biological Chemistry 273, 29586-91.

25. Robert M., Gibbs B. F., Jacobson E., and Gagnon C. (1997). Characterization of prostate-specific antigen proteolytic activity on its major physiological substrate, the sperm motility inhibitor precursor/semenogelin I. Biochemistry 36, 3811-3819.

26. Robert M., and Gagnon C. (1996). Purification and characterization of the active precursor of a human sperm motility inhibitor secreted by the seminal vesicles: identity with semenogelin. Biology of Reproduction 55, 813-821.

27. Robert M., and Gagnon C. (1995). Sperm motility inhibitor from human seminal plasma: association with semen coagulum. Human Reproduction 10, 2192-2197.

28. Robert M., and Gagnon C. (1994). Sperm motility inhibitor from human seminal plasma: presence of a precursor molecule in seminal vesicle fluid and its molecular processing after ejaculation. International Journal of Andrology 17, 232-240.

29. Gagnon C., Souaid V. and Robert M. (1992). A sperm motility inhibitor in seminal plasma: origin, purification, molecular processing and mode of action. In:  Comparative Spermatology, 20 Years After.   B. Baccetti, ed., pp 1033-1038, Serono Symposia Publications, Raven Press, New York.

Other publications

1. Selvarajoo K. and Robert M. (2013) Open Access and Individual Merits in Scientific Publishing, Advances in Systems Biology, 2, 1, 4-5.

2. Invitation to Metabolomics 2011. Metabolomics 7, 147-148 (2011).

3. Robert M. (2007) Bioinformatics Education at Keio University. Asia Pacific Biotech News, "Bioinformatics in Japan" Special Issue, 11, 15.