Masaru Tomita (Japanese: 冨田 勝, Hepburn: Tomita Masaru, born December 28, 1957) is a Japanese scientist in the fields of systems biology and computer science, best known as the founder of the E-Cell simulation system^[1] and/or the inventor of GLR parser algorithm.^[2] He served a professor of Keio University, Director of the Institute for Advanced Biosciences, and the founder and board member of various spinout companies, including Human Metabolome Technologies, Inc. and Spiber Inc. He is also the co-founder and on the board of directors of The Metabolomics Society.^[3] His father was the renowned composer and synthesiser pioneer Isao Tomita.

From Oct. 2005 to Sep. 2007, he served as Dean of Faculty of Environment and Information Studies, Keio University.^[4]

He received an M.S. (1983) and a Ph.D. (1985) in computer science from Carnegie Mellon University (CMU) under Jaime Carbonell, and two other doctoral degrees in electronic engineering and molecular biology from Kyoto University (1994) and Keio University (1998).^[5]

At CMU, starting in 1985, Tomita achieved a series of academic promotions from assistant professor to associate professor of computer science and from 1986 he became an associate director of the Center for Machine Translation.^{[citation needed]}

In 1990, he returned to Keio University and served as associate professor, professor, and Dean of the faculty of Environmental Information. At Keio University, he shifted his research emphasis to the studies of molecular biology and systems biology. In 2001, he founded Institute for Advanced Biosciences, Keio University in Tsuruoka City, Yamagata Prefecture, and served as Director of the institute.^[6]

Tomita is a recipient of the Presidential Young Investigator Award from the National Science Foundation of the USA (1988), IBM Japan Science Prize (2002), IBM Shared University Research Award (2003), Minister of Science and Technology Policy Award (2004), The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology (2007), Audi Innovation Award (2016), International Metabolomics Society Lifetime Honorary Fellow (2017), 68th Kahoku Bunka Prize (2019), 5th Bioindustry Award Grand Prize (2021), and 27th Momofuku Ando Award Grand Prize (2023).

Selected papers

• "Building Working Cells 'in Silico'", Science 1999; 284-5411:80 - 81
• "Going for Grand Challenges", Nature 1999; 402:C70
• "E-CELL: Software environment for whole cell simulation", Bioinformatics 1999; 15:72-84
• "Computerized role models: Japan's push to create a virtual cell signals a new approach to research", Nature 2002; 417
• "Multiple high-throughput analyses monitor the response of E. coli to perturbations", Science 2007; 316:593-7