Computational Systems Biology | Publication Areas

G.M. Gyori, G. Venkatachalam, P.S. Thiagarajan, D. Hsu, and M.V. Clement. OpenComet: An automated tool for comet assay image analysis. Redox Biology, 2(2):457–465, 2014.
BibTeX PDF

@article{GyoVen14,
	Author = {G.M. Gyori and G. Venkatachalam and P.S. Thiagarajan and D. Hsu and M.V. Clement},
	Bib2Html_Dl_Pdf = {http://dx.doi.org/10.1016/j.redox.2013.12.020},
	Bib2Html_Pubtype = {Journal},
	Bib2Html_Rescat = {Computational Systems Biology},
	Journal = {Redox Biology},
	Note = {doi:10.1016/j.redox.2013.12.020},
	Number = {2},
	Pages = {457--465},
	Title = {{OpenComet}: An Automated Tool for Comet Assay Image Analysis},
	Volume = {2},
	Year = {2014}}

S.K. Palaniappan, B.M. Gyori, B. Liu, D. Hsu, and P.S. Thiagarajan. Statistical model checking based calibration and analysis of bio-pathway models. In Proc. Conf. on Computational Methods in Systems Biology, 2013.
BibTeX PDF

@inproceedings{PalGyo13,
	Author = {S.K. Palaniappan and B.M. Gyori and B. Liu and D. Hsu and P.S. Thiagarajan},
	Bib2Html_Pubtype = {Refereed Conference and Workshop},
	Bib2Html_Rescat = {Computational Systems Biology},
	Booktitle = {Proc. Conf. on Computational Methods in Systems Biology},
	Title = {Statistical model checking based calibration and analysis of bio-pathway models},
	Year = {2013}}

B. Liu, J. Zhang, P.Y. Tan, D. Hsu, A.M. Blom, B. Leong, S. Sethi, B. Ho, J.L. Ding, and P.S. Thiagarajan. A computational and experimental study of the regulatory mechanisms of the complement system. PloS Computational Biology, 7(1), 2011.
BibTeX PDF

@Article{LiuZha11,
 author = {B. Liu and J. Zhang and P.Y. Tan and D. Hsu and A.M. Blom and B. Leong and S. Sethi and  B. Ho and  J.L. Ding and P.S. Thiagarajan},
 title = {A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System},
 journal = {PloS Computational Biology},
 year = {2011},
 volume = {7},
 number = {1},
 Bib2Html_Dl_Pdf = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001059},
 Bib2Html_Pubtype = {Journal},
 Bib2Html_Rescat = {Computational Systems Biology},
 note = {doi: 10.1371/journal.pcbi.1001059},
}

B. Liu, D. Hsu, and P. S. Thiagarajan. Probabilistic approximations of ODEs-based bio-pathway dynamics. Theoretical Computer Science, 412(21):2188-2206, 2011.
BibTeX PDF

@Article{LiuHsu11,
 author = {B. Liu and D. Hsu and P.S. Thiagarajan},
 title = {Probabilistic Approximations of {ODEs}-based Bio-Pathway Dynamics},
 journal = {Theoretical Computer Science},
 volume = {412},
 number = {21},
 pages = {2188--2206},
 year = {2011},
 Bib2Html_Dl_Pdf = {http://dx.doi.org/10.1016/j.tcs.2011.01.021},
 Bib2Html_Pubtype = {Journal},
 Bib2Html_Rescat = {Computational Systems Biology},
 note = {doi: 10.1016/j.tcs.2011.01.021},
}

G. Koh, D. Hsu, and P. S. Thiagarajan. Component-based construction of bio-pathway models: The parameter estimation problem. Theoretical Computer Science, 412(26):2840–2853, 2011.
BibTeX PDF

@Article{KohHsu11,
 author = {G. Koh and D. Hsu and P.S. Thiagarajan},
 title     = {Component-based construction of bio-pathway models: The parameter estimation problem},
 journal = {Theoretical Computer Science},
 volume = {412},
 number = {26},
 pages = {2840-2853},
 year   = {2011},
 Bib2Html_Dl_Pdf = {http://dx.doi.org/10.1016/j.tcs.2011.02.013},
 Bib2Html_Pubtype = {Journal},
 Bib2Html_Rescat = {Computational Systems Biology},
 note = {doi:10.1016/j.tcs.2011.02.013},
}

G. Koh, D. Hsu, and P.S. Thiagarajan. Incremental signaling pathway modeling by data integration. In Proc. ACM Int. Conf. on Computational Biology (RECOMB), 2010.
BibTeX PDF

@InProceedings{KohHsu10,
   author = {G. Koh and  D. Hsu and P.S. Thiagarajan},
   title = {Incremental Signaling Pathway Modeling by Data Integration},
   booktitle = 'Proc. ACM Int. Conf. on Computational Biology (RECOMB)',
   year = {2010},
   Bib2Html_Dl_Pdf = {http://adacomp.org/papers/rec10.pdf},
   Bib2Html_Pubtype = {Refereed Conference and Workshop},
   Bib2Html_Rescat = {Computational Systems Biology},
}

B. Liu, P.S. Thiagarajan, and D. Hsu . Probabilistic approximations of signaling pathway dynamics. In Proc. Conf. on Computational Methods in Systems Biology, 2009.
BibTeX PDF

@InProceedings{LiuThi09,
   author = {B. Liu and  P.S. Thiagarajan and D. Hsu },
   title = {Probabilistic approximations of signaling pathway dynamics},
   booktitle = {Proc. Conf. on Computational Methods in Systems Biology},
   year = {2009},
   Bib2Html_Dl_Pdf = {http://adacomp.org/papers/cmsb09.pdf},
   Bib2Html_Pubtype = {Refereed Conference and Workshop},
   Bib2Html_Rescat = {Computational Systems Biology},
}

B. Liu, P.S. Thiagarajan, and D. Hsu. Probabilistic approximations of bio-pathway dynamics. In ACM Int. Conf. on Computational Biology (RECOMB) Poster Book, 2009.
BibTeX PDF

@InProceedings{LiuHsu09,
   author = {B. Liu and  P.S. Thiagarajan and D. Hsu},
   title = {Probabilistic approximations of bio-pathway dynamics},
   booktitle = {ACM Int. Conf. on Computational Biology (RECOMB) Poster Book},
   year = {2009},
   Bib2Html_Dl_Pdf = {http://adacomp.org/papers/recomb09.pdf},
   Bib2Html_Pubtype = {Refereed Conference and Workshop},
   Bib2Html_Rescat = {Computational Systems Biology},
}

G. Koh, D. Hsu, and P.S. Thiagarajan. Composition of signaling pathway models and its application to parameter estimation. In ACM Int. Conf. on Computational Biology (RECOMB) Poster Book, 2008.
BibTeX PDF

@InProceedings{KohHsu08,
   author = {G. Koh and  D. Hsu and P.S. Thiagarajan},
   title = {Composition of signaling pathway models and its application to parameter estimation},
   booktitle = {ACM Int. Conf. on Computational Biology (RECOMB) Poster Book},
   year = {2008},
   Bib2Html_Dl_Pdf = {http://adacomp.org/papers/recomb08.pdf},
   Bib2Html_Pubtype = {Refereed Conference and Workshop},
   Bib2Html_Rescat = {Computational Systems Biology},
}

G. Koh, L. Tucker-Kellogg, D. Hsu, and P.S. Thiagarajan. Globally consistent pathway parameter estimates through belief propagation. In Proc. Workshop on Algorithms in Bioinformatics (WABI), 2007.
BibTeX PDF

@InProceedings{KohTuc07,
   author = {G. Koh and L. Tucker-Kellogg and D. Hsu and P.S. Thiagarajan},
   title = {Globally consistent pathway parameter estimates through belief propagation},
   booktitle = 'Proc. Workshop on Algorithms in Bioinformatics (WABI)',
   year = {2007},
   Bib2Html_Dl_Pdf = {http://adacomp.org/papers/wabi07.pdf},
   Bib2Html_Pubtype = {Refereed Conference and Workshop},
   Bib2Html_Rescat = {Computational Systems Biology},
}

G. Koh, H.F.C. Teong, M.-V. Clément, D. Hsu, and P.S. Thiagarajan. A decompositional approach to parameter estimation in pathway modeling: A case study of the Akt and MAPK pathways and their crosstalk. Bioinformatics, 22(14):271–280, 2006. Special issue on Int. Conf. on Intelligent Systems for Molecular Biology (ISMB) 2006.
BibTeX PDF

@article{KohTeo06,
   Author = {G. Koh and H.F.C. Teong and M.-V. Cl'{e}ment and D. Hsu and P.S. Thiagarajan},
   Journal = {Bioinformatics},
   Note = {Special issue on Int. Conf. on Intelligent Systems for Molecular Biology (ISMB) 2006.},
   Title = {A decompositional approach to parameter estimation in pathway modeling: A case study of the {Akt} and {MAPK} pathways and their crosstalk},
   Year = {2006},
   Volume = {22},
   Number = {14},
   Pages = {271--280},
   Bib2Html_Dl_Pdf = {http://adacomp.org/papers/ismb06.pdf},
   Bib2Html_Pubtype = {Journal},
   Bib2Html_Rescat = {Computational Systems Biology},
}

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