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Sema Kachalo, Hammad Naveed, Youfang Cao, Jieling Zhao, Jie Liang. (2015) Mechanical Model of Geometric Cell and Topological Algorithm for Cell Dynamics from Single-Cell to Formation of Monolayered Tissues with Pattern PLoS ONE, 2015 10(5): e012648.
Yingzi Li, Hammad Naveed, Sema Kachalo, Lisa X Xu and Jie Liang. (2014) Mechanisms of Regulating Tissue Elongation in Drosophila Wing: Impact of Oriented Cell Divisions, Oriented Mechanical Forces, and Reduced Cell Size. PLoS ONE, 2014 9(2): e86725.
Jieliang Zhao, Hammad Naveed, Sema Kachalo, Youfang Cao, Wei Tian, and Jie Liang. (2013) Dynamic Mechanical Finite Element Model of Biological Cells for Studying Cellular Pattern Formation. Conf Proc IEEE Eng Med Biol Soc. 2013, 2013:4517–4520.
Yingzi Li, Hammad Naveed, Sema Kachalo, Lisa X. Xu, and Jie Liang. (2012) Mechanisms of Regulating Cell Topology in Proliferating Epithelia: Impact of Division Plane, Mechanical Forces, and Cell Memory. PLoS ONE, 2012 7(8): e43108.
Yingzi Li, Hammad Naveed, Sema Kachalo, Lisa X. Xu, and Jie Liang. (2011) Mechanical Forces Mediate Localized Topological Change in Epithelia. Conf Proc IEEE Eng Med Biol Soc. 2011, 2011:178-81.
Jieling Zhao, Joe Dudnas, Sema Kachalo, Zheng Ouyang, and Jie Liang. (2011) Accuracy of functional surfaces on comparatively modeled protein structures. J Struct Funct Genomics 2011,12(2):97-107.
Hammad Naveed, Yinzi Li, S. Kachalo, Jie Liang. (2010) Geometric order in proliferating epithelia: Impact of rearrangements and cleavage plane orientation. Conf Proc IEEE Eng Med Biol Soc. 2010, 2010:3808-3811.
Sema Kachalo, Ranran Zhang, Eduardo Sontag, Reka Albert and Bhaskar DasGupta. (2008) NET-SYNTHESIS: A software for synthesis, inference and simplification of signal transduction networks. Bioinformatics, 24(2):293-295.
Reka Albert, Bhaskar DasGupta, Riccardo Dondi, Sema Kachalo, Eduardo Sontag, Alexander Zelikovsky and Kelly Westbrooks. (2007) A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence. J Computational Biology, 14(7):927-949.
Sema Kachalo, Hsiao-Mei Lu and Jie Liang. (2006) Protein folding dynamics via quantification of kinematic energy landscape. Physical Review Letters, 2006, 96:058106:1-4.
Sema Kachalo, Hsiao-Mei Lu, and Jie Liang. (2005) Protein folding dynamics in lattice model with physical movement. Conf Proc IEEE Eng Med Biol Soc. 2005, 2005 27:4449-4452.
Sema Kachalo, Zarema Arbieva and Jie Liang. (2003) Assessing effect of cross-hybridization on oligonucleotide microarrays. Methods of microarray data analysis III, 2003, CAMDA' 02:185-198.
Jie Liang and Sema Kachalo. (2002) Computational Analysis of Microarray Gene Expression Profiles Clustering, Classification, and Beyond. Chemometrics and Intelligent Laboratory Systems, 2002, 62:199-216.