Hiroyuki Kuwahara

Publication Activity (10 Years)

Years Active: 2006-2022
Publications (10 Years): 12

Top Topics

Support Vector Regression

Gene Expression

Top Venues

Briefings Bioinform.

J. Cheminformatics

Publications

Yu Li, Siyuan Chen, Trisevgeni Rapakoulia, Hiroyuki Kuwahara, Kevin Y. Yip, Xin Gao
Deep learning identifies and quantifies recombination hotspot determinants. Bioinform. 38 (10) (2022)
Hiroyuki Kuwahara, Xin Gao
Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach. J. Cheminformatics 13 (1) (2021)
Hiroyuki Kuwahara, Xin Gao
Stable maintenance of hidden switches as a strategy to increase the gene expression stability. Nat. Comput. Sci. 1 (1) (2021)
Meshari Alazmi, Hiroyuki Kuwahara, Othman Soufan, Lizhong Ding, Xin Gao
Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions. Bioinform. 35 (15) (2019)
Ramzan Umarov, Hiroyuki Kuwahara, Yu Li, Xin Gao, Victor V. Solovyev
Promoter analysis and prediction in the human genome using sequence-based deep learning models. Bioinform. 35 (16) (2019)
Ramzan Umarov, Hiroyuki Kuwahara, Yu Li, Xin Gao, Victor V. Solovyev
PromID: human promoter prediction by deep learning. CoRR (2018)
Chisato Fujii, Hiroyuki Kuwahara, Ge Yu, Lili Guo, Xin Gao
Learning gene regulatory networks from gene expression data using weighted consensus. Neurocomputing 220 (2017)
Hanjun Dai, Ramzan Umarov, Hiroyuki Kuwahara, Yu Li, Le Song, Xin Gao
Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape. Bioinform. 33 (22) (2017)
Majed Alzahrani, Hiroyuki Kuwahara, Wei Wang, Xin Gao
Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data. Bioinform. 33 (16) (2017)
Hiroyuki Kuwahara, Meshari Alazmi, Xuefeng Cui, Xin Gao
MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Ming Fan, Hiroyuki Kuwahara, Xiaolei Wang, Suojin Wang, Xin Gao
Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study. Briefings Bioinform. 16 (6) (2015)
Xuefeng Cui, Hiroyuki Kuwahara, Shuai Cheng Li, Xin Gao
Compare local pocket and global protein structure models by small structure patterns. BCB (2015)
Xiaolei Wang, Hiroyuki Kuwahara, Xin Gao
Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels. BMC Syst. Biol. 8 (S-5) (2014)
Hiroyuki Kuwahara, Ming Fan, Suojin Wang, Xin Gao
A framework for scalable parameter estimation of gene circuit models using structural information. Bioinform. 29 (13) (2013)
Hiroyuki Kuwahara, Xin Gao
An efficient parallel stochastic simulation method for analysis of nonviral gene delivery systems. CMSB (2011)
Hiroyuki Kuwahara, Chris J. Myers
Erlang-delayed stochastic chemical kinetic formalism for efficient analysis of biological systems with non-elementary reaction effects. BCB (2011)
Nathan A. Barker, Chris J. Myers, Hiroyuki Kuwahara
Learning Genetic Regulatory Network Connectivity from Time Series Data. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (1) (2011)
Hiroyuki Kuwahara, Chris J. Myers, Michael S. Samoilov
: Quantitative Analysis via Automated Model Abstraction. PLoS Comput. Biol. 6 (3) (2010)
Chris J. Myers, Nathan A. Barker, Kevin R. Jones, Hiroyuki Kuwahara, Curtis Madsen, Nam-Phuong D. Nguyen
iBioSim: a tool for the analysis and design of genetic circuits. Bioinform. 25 (21) (2009)
Chris J. Myers, Nathan A. Barker, Hiroyuki Kuwahara, Kevin R. Jones, Curtis Madsen, Nam-Phuong D. Nguyen
Genetic design automation. ICCAD (2009)
Masayuki Arai, Yoshinori Tanaka, Shigeo Hirose, Hiroyuki Kuwahara, Shingo Tsukui
Development of "Souryu-IV" and "Souryu-V: " Serially connected crawler vehicles for in-rubble searching operations. J. Field Robotics 25 (1-2) (2008)
Hiroyuki Kuwahara, Chris J. Myers
Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions. J. Comput. Biol. 15 (7) (2008)
Nam-Phuong D. Nguyen, Hiroyuki Kuwahara, Chris J. Myers, James P. Keener
The Design of a Genetic Muller C-Element. ASYNC (2007)
Hiroyuki Kuwahara, Chris J. Myers
Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions. RECOMB (2007)
Nathan A. Barker, Chris J. Myers, Hiroyuki Kuwahara
Learning Genetic Regulatory Network Connectivity from Time Series Data. IEA/AIE (2006)
Hiroyuki Kuwahara, Chris J. Myers, Michael S. Samoilov, Nathan A. Barker, Adam P. Arkin
Automated Abstraction Methodology for Genetic Regulatory Networks. Trans. Comp. Sys. Biology 6 (2006)
Hiroyuki Kuwahara, Chris J. Myers, Michael S. Samoilov
Abstracted Stochastic Analysis of Type 1 Pili Expression in E.coli. BIOCOMP (2006)