Abstracted Stochastic Analysis of Type 1 Pili Expression in E.coli. - Hiroyuki Kuwahara; Chris J. Myers; Michael S. Samoilov (BIOCOMP, 2006)

Automated Abstraction Methodology for Genetic Regulatory Networks. - Hiroyuki Kuwahara; Chris J. Myers; Michael S. Samoilov; Nathan A. Barker; Adam P. Arkin (Trans. Comp. Sys. Biology, 2006)

The Design of a Genetic Muller C-Element. - Nam-Phuong D. Nguyen; Hiroyuki Kuwahara; Chris J. Myers; James P. Keener (ASYNC, 2007)

Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions. - Hiroyuki Kuwahara; Chris J. Myers (J. Comput. Biol., 2008)

Development of "Souryu-IV" and "Souryu-V: " Serially connected crawler vehicles for in-rubble searching operations. - Masayuki Arai; Yoshinori Tanaka; Shigeo Hirose; Hiroyuki Kuwahara; Shingo Tsukui (J. Field Robotics, 2008)

Model Abstraction and Temporal Behavior Analysis of Genetic Regulatory Networks. - Hiroyuki Kuwahara (2008)

Genetic design automation. - Chris J. Myers; Nathan A. Barker; Hiroyuki Kuwahara; Kevin R. Jones; Curtis Madsen; Nam-Phuong D. Nguyen (ICCAD, 2009)

iBioSim: a tool for the analysis and design of genetic circuits. - Chris J. Myers; Nathan A. Barker; Kevin R. Jones; Hiroyuki Kuwahara; Curtis Madsen; Nam-Phuong D. Nguyen (Bioinform., 2009)

Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction. - Hiroyuki Kuwahara; Chris J. Myers; Michael S. Samoilov (PLoS Comput. Biol., 2010)

Erlang-delayed stochastic chemical kinetic formalism for efficient analysis of biological systems with non-elementary reaction effects. - Hiroyuki Kuwahara; Chris J. Myers (BCB, 2011)

An efficient parallel stochastic simulation method for analysis of nonviral gene delivery systems. - Hiroyuki Kuwahara; Xin Gao 001 (CMSB, 2011)

Learning Genetic Regulatory Network Connectivity from Time Series Data. - Nathan A. Barker; Chris J. Myers; Hiroyuki Kuwahara (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

A framework for scalable parameter estimation of gene circuit models using structural information. - Hiroyuki Kuwahara; Ming Fan 003; Suojin Wang; Xin Gao 001 (Bioinform., 2013)

Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels. - Xiaolei Wang; Hiroyuki Kuwahara; Xin Gao 001 (BMC Syst. Biol., 2014)

Compare local pocket and global protein structure models by small structure patterns. - Xuefeng Cui; Hiroyuki Kuwahara; Shuai Cheng Li 001; Xin Gao 001 (BCB, 2015)

Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study. - Ming Fan 003; Hiroyuki Kuwahara; Xiaolei Wang; Suojin Wang; Xin Gao 001 (Briefings Bioinform., 2015)

MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind. - Hiroyuki Kuwahara; Meshari Alazmi; Xuefeng Cui; Xin Gao 001 (Nucleic Acids Res., 2016)

Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data. - Majed Alzahrani; Hiroyuki Kuwahara; Wei Wang 012; Xin Gao 001 (Bioinform., 2017)

Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape. - Hanjun Dai; Ramzan Umarov; Hiroyuki Kuwahara; Yu Li 006; Le Song; Xin Gao 001 (Bioinform., 2017)

Learning gene regulatory networks from gene expression data using weighted consensus. - Chisato Fujii; Hiroyuki Kuwahara; Ge Yu; Lili Guo; Xin Gao 001 (Neurocomputing, 2017)

PromID: human promoter prediction by deep learning. - Ramzan Umarov; Hiroyuki Kuwahara; Yu Li 006; Xin Gao 001; Victor V. Solovyev (CoRR, 2018)

Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions. - Meshari Alazmi; Hiroyuki Kuwahara; Othman Soufan; Lizhong Ding 001; Xin Gao 001 (Bioinform., 2019)

Promoter analysis and prediction in the human genome using sequence-based deep learning models. - Ramzan Umarov; Hiroyuki Kuwahara; Yu Li 006; Xin Gao 001; Victor V. Solovyev (Bioinform., 2019)

Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach. - Hiroyuki Kuwahara; Xin Gao 001 (J. Cheminformatics, 2021)

Stable maintenance of hidden switches as a strategy to increase the gene expression stability. - Hiroyuki Kuwahara; Xin Gao 001 (Nat. Comput. Sci., 2021)

Deep learning identifies and quantifies recombination hotspot determinants. - Yu Li 006; Siyuan Chen; Trisevgeni Rapakoulia; Hiroyuki Kuwahara; Kevin Y. Yip; Xin Gao 001 (Bioinform., 2022)