Hiroyuki Kuwahara

Research Scientists


​Hiro got his PhD in Computer Science from University of Utah in 2008. He was then a junior reseacrcher at Microsoft Research - Trento during 2007 and 2009. During 2009 and 2012, he was a Ray and Stephanie Lane Fellow at School of Computer Science at Carnegie Mellon University. Since 2012, he joined the SFB group as a research scientist.

Research Interests

Synthetic biology.

Selected Publications

​1. H. Kuwahara, X. Cui, R. Umarov, R. Grunberg, C. Myers, and X. Gao, "BOLme: a repository of SBOL parts for metabolic engineering," ACS Synthetic Biology, 2017 (doi: 10.1021/acssynbio.6b00278).
2. H. Kuwahara, R. Umarov, I. Almasri, and X. Gao, "ACRE: absolute concentration robustness explorationin module-based combinatorial networks," Synthetic Biology, Oxford University Press, 2017 (doi: 10.1093/synbio/ysx001).
3. H. Kuwahara, M. Alazmi, X. Cui, and X. Gao, "MRE: a web tool to suggest foreign enzymes for thebiosynthesis pathway design with competing endogenous reactions in mind," Nucleic Acids Research, 2016 (doi:10.1093/nar/gkw342).
4. C. Fujii, H. Kuwahara, G. Yu, L. Guo, and X. Gao "Learning gene interaction networks from gene expression data using weighted concensus," Neurocomputing, 2017 (doi: 10.1016/j.neucom.2016.02.087). equal contribution.
5. H. Kuwahara, S Arold, and X. Gao, "Beyond initiation-limited translational bursting: the e ects of burst size distributions on the stability of gene expression," Integrative Biology, 2015 (doi: 10.1039/C5IB00107B). In the top 25% of all research outputs scored by Altmetric.
6. M. Fan, H. Kuwahara, X. Wang, S. Wang, and X. Gao, "Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study," Brie ngs in Bioinformatics, 2015 (doi:10.1093/bib/bbv015). equal contribution.
7. X. Wang, H. Kuwahara, and X. Gao, "Modeling DNA anity landscape through two-round support vector regression with weighted degree kernels," BMC Systems Biology, 8(Suppl 5):S5, 2014.
8. H. Kuwahara and X. Gao, "Stochastic e ects as a force to increase the complexity of signaling networks," Scienti c Reports, 3, 2013. In the top 25% of all research outputs scored by Altmetric.
9. H. Kuwahara, M. Fan, S. Wang, and X. Gao, "A framework for scalable parameter estimation of gene circuit models using structural information," Bioinformatics, 29(13), 2013. Highlighted in Nature Middle East, July 2013.
10. P. Chen, J. Li, L. Wong, H. Kuwahara, J. Huang, and X. Gao, "Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences," Proteins, 81(8), 2013.
11. H. Kuwahara and R. Schwartz, "Stochastic steady state gain in a gene expression process with mRNA degradation control," Journal of the Royal Society Interface, 2012 (doi: 10.1098/rsif.2011.0757).
12. H. Kuwahara and O. Soyer, "Bistability in feedback circuits as a byproduct of evolution of evolvability," Molecular Systems Biology, 8, 2012. F1000Prime recommended.
13. H. Kuwahara, C. Myers, and M. Samoilov, "Temperature control of mbriation circuit switch in uropathogenic Escherichia coli : quantitative analysis via automated model abstraction," PLoS Computational Biology, 6(3): e1000723, 2010.