About me

I am a Research Scientist at the Joint Genome Institute, Lawrence Berkeley National Laboratory. I study plant–microbial interactions using synthetic biology and functional genomics, with a focus on developing platform technologies to uncover gene function and regulation in rhizobacteria. I aim to translate these insights into strategies for engineering rhizosphere environments that enhance plant productivity.

I conducted my doctoral research at University of California, San Diego in the laboratory of Terence Hwa, where I studied E. coli adaptation and chemotaxis, revealing simple quantitative principles of bacterial behavior.

Before coming to the United States, I received my bachelor’s degree in Bioengineering from Osaka University. As an undergraduate researcher in the laboratory of Tetsuya Yomo, I studied the evolutionary dynamics of E. coli.

Publications

Tomoya Honda§, Sora Yu, Dung Mai, Leo Baumgart, Emory Chan, Gyorgy Babnigg, Yasuo Yoshikuni§

"CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization"

Nature Communications  2026 (§corresponding author) 

Tomoya Honda*, Jonas Cremer*, Leonardo Mancini, Zhongge Zhang, Teuta Pilizota, Terence Hwa

"Coordination of gene expression with cell size enables Esherichia coli to efficiently maintain motility across conditions"

Proceedings of the National Academy of Sciences  2022 (*equal contribution) 

Markus Basan*, Tomoya Honda*, Dimitris Christodoulou, Manuel Hörl, Yu-Fang Chang, Emanuele Leoncini, Avik Mukherjee, Hiroyuki Okano, Brian R. Taylor, Josh M. Silverman, Carlos Sanchez, James R. Williamson, Johan Paulsson, Terence Hwa, Uwe Sauer

"A universal trade-off between growth and lag in fluctuating environments"

Nature  2020 (*equal contribution) 

 Jonas Cremer*, Tomoya Honda*, Jerome Wong Ng, Ying Tang, Massimo Vergassola, Terence Hwa

"Chemotaxis as a navigation strategy to boost range expansion"

Nature  2019 (*equal contribution) 

[News & Views, Nature] [Research highlight, Nature Reviews Microbiology]

Bei-wen Ying, Tomoya Honda, Saburo Tsuru, Shigeto Seno, Hideo Matsuda, Yasuaki Kazuta, Tetsuya Yomo

"Evolutionary consequence of a trade-off between growth and maintenance along with ribosomal damages"

PLoS ONE  2015

Pre-print

Hiroya Oka, Dung Mai, Sora Yu, Nicolas Grosjean, Zong-Yen Wu, Nam Pham, David Robinson, Yasuo Yoshikuni, Nigel Mouncey, Tomoya Honda§ 

"A pooled screening approach reveals bacterial chemoreceptors for short-chain carboxylic acids"

bioRxiv  2026 (§corresponding author)