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Hiroyuki Kuwahara
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2020 – today
- 2022
- [j18]Yu Li
, Siyuan Chen
, Trisevgeni Rapakoulia, Hiroyuki Kuwahara, Kevin Y. Yip
, Xin Gao
:
Deep learning identifies and quantifies recombination hotspot determinants. Bioinform. 38(10): 2683-2691 (2022) - 2021
- [j17]Hiroyuki Kuwahara, Xin Gao
:
Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach. J. Cheminformatics 13(1): 27 (2021) - [j16]Hiroyuki Kuwahara
, Xin Gao
:
Stable maintenance of hidden switches as a strategy to increase the gene expression stability. Nat. Comput. Sci. 1(1): 62-70 (2021)
2010 – 2019
- 2019
- [j15]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): 2634-2643 (2019) - [j14]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): 2730-2737 (2019) - 2018
- [i1]Ramzan Umarov, Hiroyuki Kuwahara, Yu Li, Xin Gao, Victor V. Solovyev:
PromID: human promoter prediction by deep learning. CoRR abs/1810.01414 (2018) - 2017
- [j13]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): 2523-2531 (2017) - [j12]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): 3575-3583 (2017) - [j11]Chisato Fujii
, Hiroyuki Kuwahara, Ge Yu, Lili Guo, Xin Gao
:
Learning gene regulatory networks from gene expression data using weighted consensus. Neurocomputing 220: 23-33 (2017) - 2016
- [j10]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): W217-W225 (2016) - 2015
- [j9]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): 987-999 (2015) - [c8]Xuefeng Cui, Hiroyuki Kuwahara, Shuai Cheng Li
, Xin Gao
:
Compare local pocket and global protein structure models by small structure patterns. BCB 2015: 355-365 - 2014
- [j8]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): S5 (2014) - 2013
- [j7]Hiroyuki Kuwahara, Ming Fan, Suojin Wang, Xin Gao
:
A framework for scalable parameter estimation of gene circuit models using structural information. Bioinform. 29(13): 98-107 (2013) - 2011
- [j6]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): 152-165 (2011) - [c7]Hiroyuki Kuwahara, Chris J. Myers
:
Erlang-delayed stochastic chemical kinetic formalism for efficient analysis of biological systems with non-elementary reaction effects. BCB 2011: 425-429 - [c6]Hiroyuki Kuwahara, Xin Gao
:
An efficient parallel stochastic simulation method for analysis of nonviral gene delivery systems. CMSB 2011: 83-93 - 2010
- [j5]Hiroyuki Kuwahara, Chris J. Myers
, Michael S. Samoilov
:
Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction. PLoS Comput. Biol. 6(3) (2010)
2000 – 2009
- 2009
- [j4]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): 2848-2849 (2009) - [c5]Chris J. Myers, Nathan A. Barker, Hiroyuki Kuwahara, Kevin R. Jones, Curtis Madsen, Nam-Phuong D. Nguyen:
Genetic design automation. ICCAD 2009: 713-716 - 2008
- [b1]Hiroyuki Kuwahara:
Model Abstraction and Temporal Behavior Analysis of Genetic Regulatory Networks. University of Utah, USA, 2008 - [j3]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): 779-792 (2008) - [j2]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): 31-65 (2008) - 2007
- [c4]Nam-Phuong D. Nguyen, Hiroyuki Kuwahara, Chris J. Myers, James P. Keener:
The Design of a Genetic Muller C-Element. ASYNC 2007: 95-104 - [c3]Hiroyuki Kuwahara, Chris J. Myers:
Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions. RECOMB 2007: 166-180 - 2006
- [j1]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: 150-175 (2006) - [c2]Hiroyuki Kuwahara, Chris J. Myers, Michael S. Samoilov:
Abstracted Stochastic Analysis of Type 1 Pili Expression in E.coli. BIOCOMP 2006: 125-134 - [c1]Nathan A. Barker, Chris J. Myers, Hiroyuki Kuwahara:
Learning Genetic Regulatory Network Connectivity from Time Series Data. IEA/AIE 2006: 962-971
Coauthor Index
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