H. Kuwahara, C. Madsen, I. Mura, C. Myers, A. Tejeda, and C. Winstead. Efficient Stochastic Simulation to Analyze Targeted Properties of Biological Systems (2010) In Stochastic Control, Editor: Chris Myers. Publisher: Sciyo. [link]
H. Kuwahara and C. Myers. Abstraction Methods for Analysis of Gene Regulatory Networks (2010). In Computational Methods in Gene Regulatory Networks. Editors: Sanjoy Das, Doina Caragea, Stephen Welch, William Hsu. Publisher: IGI Global.
H. Kuwahara, F. Alkuraya, and X. Gao. An RNA-seq quantification method for analysis of transcriptional aberrations, 2019 [BIORXIV/2019/766121]
H. Kuwahara, and X. Gao. Stable maintenance of a hidden switch as a way to increase the gene expression stability, 2019 [BIORXIV/2019/615500]
H. E. Shamseldin, L. Al-Abdi, S. Maddirevula, H. Alsaif, F. Alzahrani, N. Ewida, M. Hashem, F. Abdulwahab, O. Abuyousef, H. Kuwahara, X. Gao, Molecular Autopsy Consortium, F. S. Alkuraya. Lethal variants in humans: Lessons learned from a large molecular autopsy cohort. Genome Medicine, 2021 (doi: 10.1186/s13073-021-00973-0). [link]
H. Kuwahara and X. Gao. Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach. Journal of Cheminformatics, 2021 (doi: 10.1186/s13321-021-00506-2). [link]
H. Kuwahara and X. Gao. Stable maintenance of hidden switches as a strategy to increase the gene expression stability. Nature Computational Science, 2021 (doi: 10.1038/s43588-020-00001-y). [link]
F. Alzahrani1, H. Kuwahara1, Y. Long, M. Al-Owain, M. Tohary, M. AlSayed, M. Mahnashi, L. Fathi, M. Alnemer, M. H Al-Hamed, G. Lemire, K. M. Boycott, M. Hashem, W. Han, A. Al-Maawali, F. Al Mahriz, K. Al-Thihli, X. Gao, and F. S. Alkuraya. Recessive deleterious variants in SMG8 expand the role of nonsense-mediated decay in developmental disorders in humans. The American Journal of Human Genetics, 2020 (doi: 10.1016/j.ajhg.2020.11.007). [link] (1joint first authors.)
S. Maddirevula1, H. Kuwahara1, N. Ewida, H. E. Shamseldin, N. Patel, F. Alzahrani, T. AlSheddi, E. AlObeid, M. Alenazi, H. S. Alsaif, M. Alqahtani, M. AlAli, H. Al Ali, R. Helaby, N. Ibrahim, F. Abdulwahab, M. Hashem, N. Hanna, D. Monies, N. Derar, A. Alsagheir, A. Alhashem, B. Alsaleem, H. Alhebbi, S. Wali, R. Umarov, X. Gao, and F. S. Alkuraya. Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics. Genome Biology, 2020 (doi: 10.1186/s13059-020-02053-9). [link] (1joint first authors.)
R. Umarov, H. Kuwahara, Y. Li, X. Gao, and V. Solovyev. Promoter analysis and prediction in the human genome using sequence-based deep learning models. Bioinformatics, 2019 (doi: 10.1093/bioinformatics/bty1068). [link]
M. Alazmi1, H. Kuwahara1,*, O. Soufan, L. Ding, and X. Gao*. Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions. Bioinformatics, 2018 (doi: 10.1093/bioinformatics/bty1035). [link] (1joint first authors, *joint corresponding authors.)
H. Dai, R. Umarov, H. Kuwahara, Y. Li, L. Song, and X. Gao. Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape. Bioinformatics, 2017 (doi: 10.1093/bioinformatics/btx480). [link]
C. Myers, J. Beal, T. Gorochowski, H. Kuwahara, C. Madsen, J. McLaughlin, G. Misirli, T. Nguyen, E. Oberortner, M. Samineni, A. Wipat, M. Zhang, and Z. Zundel. A standard-enabled workflow for synthetic biology. Biochemical Society Transactions, 2017 (doi: 10.1042/BST20160347). [link]
M. Alzahrani, H. Kuwahara, W. Wang, X. Gao. Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data. Bioinformatics, 2017 (doi: 10.1093/bioinformatics/btx199). [link]
H. Kuwahara, X. Cui, R. Umarov, R. Grünberg, C. Myers, and X. Gao. SBOLme: a repository of SBOL parts for metabolic engineering. ACS Synthetic Biology, 2017 (doi: 10.1021/acssynbio.6b00278). [link]
H. Kuwahara, R. Umarov, I. Almasri, and X. Gao. ACRE: absolute concentration robustness exploration in module-based combinatorial networks. Synthetic Biology, Oxford University Press, 2017. (doi: 10.1093/synbio/ysx001). [link]
H. Kuwahara, M. Alazmi, X. Cui, and X. Gao. MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind. Nucleic Acids Research, 2016. (doi: 10.1093/nar/gkw342). [link]
C. Fujii*, H. Kuwahara*, G. Yu, L. Guo, and X. Gao. Learning gene interaction networks from gene expression data using weighted consensus. Neurocomputing, 2017. (*equal contribution) (doi: 10.1016/j.neucom.2016.02.087). [link]
H. Kuwahara, S Arold, and X. Gao. Beyond initiation-limited translational bursting: the effects of burst size distributions on the stability of gene expression. Integrative Biology, 2015. (doi: 10.1039/C5IB00107B). [link]
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. Briefings in Bioinformatics, 2015. (*equal contribution) [link]
X. Wang, H. Kuwahara, and X. Gao. Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels. BMC Systems Biology, 2014. [link]
H. Kuwahara and X. Gao. Stochastic effects as a force to increase the complexity of signaling networks. Scientific Reports, 2013. [link]
H. Kuwahara*, M. Fan*, S. Wang, and X. Gao. A framework for scalable parameter estimation of gene circuit models using structural information. Bioinformatics, 2013. (*equal contribution) [link]
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, 2013. [link]
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. [link]
H. Kuwahara and O. Soyer. Bistability in feedback circuits as a byproduct of evolution of evolvability. Molecular Systems Biology, 2012. [link]
H. Kuwahara, C. Myers, and M. Samoilov. Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction. PLoS Comput Biol, 6(3): e1000723. doi:10.1371/journal.pcbi.1000723. [link]
N. Nguyen, C. Myers, H. Kuwahara, C. Winstead, and J. Keener. Design and analysis of a robust genetic Muller C-element. To appear in Journal of Theoretical Biology. doi:10.1016/j.jtbi.2009.10.026. [link]
C. Myers, N. Barker, K. Jones, H. Kuwahara, C. Madsen, and N. Nguyen. iBioSim: a tool for the analysis and design of genetic circuits. To appear in Bioinformatics. [link]
N. Barker, C. Myers, and H. Kuwahara. Learning genetic regulatory network connectivity from time series data. To appear in IEEE Transactions on Computational Biology and Bioinformatics. [link]
O. S. Soyer, H. Kuwahara, and A. Csikász-Nagy. Regulating the total level of a signaling protein can vary its dynamics. FEBS Journal, 2009, 276(12): 3290-3298, doi: 10.1111/j.1742-4658.2009.07054.x. [link]
H. Kuwahara and I. Mura. An efficient and exact stochastic simulation method to analyze rare events in biochemical systems. Journal of Chemical Physics, October 22, 2008, Volume 129, Issue 16, doi:10.1063/1.2987701. [.pdf]
Copyright (2008) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. This article appeared in H. Kuwahara and I. Mura, J. Chem. Phys. 129, 165101 (2008) and may be found at Kuwahara & Mura, J. Chem. Phys. 129, 165101 (2008)
H. Kuwahara and C. Myers. Production-passage-time approximation: A new approximation method to accelerate the simulation process of enzymatic reactions. Journal of Computational Biology, September 1, 2008, 15(7): 779-792. doi:10.1089/cmb.2007.0135. [.pdf]
H. Kuwahara, C. Myers, M. Samoilov, and N. Barker, and A. Arkin. Automated abstraction methodology for genetic regulatory networks. Trans. on Comput. Syst. Biol. VI, pages 150-175, 2006. Invited. [ .pdf ]
X. Cui, H. Kuwahara, S. Li, and X. Gao. Compare local pocket and global protein structure models by small structure patterns. ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2015 (ACM-BCB2015), 2015.
X. Wang, H. Kuwahara, and X. Gao. Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels. The 25th International Conference on Genome Informatics (GIW/ISCB-Asia 2014), 2014. [link]
H. Kuwahara, M. Fan, S. Wang, and X. Gao. A framework for scalable parameter estimation of gene circuit models using structural information. The 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2013), 2013. [link]
H. Kuwahara and X. Gao. An efficient parallel stochastic simulation method for analysis of nonviral gene delivery systems. In 9th International Conference on Computational Methods in Systems Biology, 2011. [ .pdf]
H. Kuwahara and C. Myers. Erlang-delayed stochastic chemical kinetic formalism for efficient analysis of biological systems with non-elementary reaction effects. In ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2011. [ .pdf]
C. Myers, N. Barker, H. Kuwahara, K. Jones, C. Madsen, and N. Nguyen, Genetic design automation. In 2009 International Conference on Computer-Aided Design, 2009. [ link]
N. Nguyen, N. Barker, H. Kuwahara, C. Madsen, and C. Myers. Synthesis of genetic circuits from graphical specifications. In 2008 Int. Workshop on Logic Synthesis, 2008 (invited). [ .pdf]
H. Kuwahara and C. Myers. Production-passage-time approximation: A new approximation method to accelerate the simulation process of enzymatic reactions. Iin Eleventh Annual International Conference on Research in Computational Molecular Biology, 2007 (RECOMB 2007). [ .pdf ]
N. Nguyen, H. Kuwahara, C. Myers, and J. Keener. The design of a genetic muller C-element. In The 13th IEEE International Symposium on Asynchronous Circuits and Systems, 2007 (ASYNC 07) Best Paper Award.
H. Kuwahara, C. Myers, and M. Samoilov. Abstracted stochastic analysis of type 1 pili expression in E. coli. In The 2006 International Conference on Bioinformatics and Computational Biology, 2006. [ .pdf ]
N. Barker, C. Myers, and H. Kuwahara. Learning genetic regulatory network connectivity from time series data. In The 19th International Conference on Industrial, Engineering, and Other Applications of Applied Intelligent Systems, 2006. [ .pdf ]
H. Kuwahara, C. Myers, N. Barker, M. Samoilov, and A. Arkin. Asynchronous abstraction methodology for genetic regulatory networks. In The Third International Workshop on Computational Methods in Systems Biology, 2005. [ .pdf ]
K. Slind, S. Barrus, S. Choe, C. Condrat, J. Duan, S. Gopalakrishnan, A. Knoll, H. Kuwahara, G. Li, S. Little, L. Liu, S. Moor, R. Palmer, C. Tuttle, S. Walton, Y. Yang, and J. Zhang. Teaching a HOL course: experience report. In International Conference on Theorem Proving in Higher Order Logics (TPHOLS), 2005.