Publications

“The joy of discovery is certainly the liveliest that the mind of man can ever feel”
– Claude Bernard –

  • Gamze Gursoy, Yun Xu, Amy Kenter and Jie Liang. “Identifying functional chromatin interactions from chromosome conformation capture data using large 3D ensembles of n-Constrained Self-Avoiding Chromatin chains”, Nucleic Acids Research, Accepted, 2017
  • Gamze Gursoy, Yun Xu, and Jie Liang. “Spatial organization of budding yeast genome from landmark constraints and predicting biological chromatin interactions from Chromosome Conformation Capture Data”, PLOS Comp. Bio., 2017:13(7):e1005658
  • Gamze Gursoy and Jie Liang. “3D Chromosome Structures from Energy Landscape”, PNAS, 2016, 113, (43), 11991-11993
  • Gamze Gursoy, Anna Terebus, Youfang Cao and Jie Liang. “Mechanisms of Stochastic Focusing and Defocusing in Biological Reaction Networks: Insight from Accurate Chemical Master Equation (ACME) Solutions”, Conf Proc IEEE Eng Med Biol Soc., 2016:1480-1483, doi: 10.1109/EMBC.2016.7590989
  • Jie Liang, Youfang Cao, Gamze Gursoy, Hammad Naveed, Anna Terebus, and Jieling Zhao. “Multiscale modeling of cellular epigenetic states and tissue patterning: stochasticity in molecular network chromatin folding in cell nucleus, and cell-cell interactions in tissue patterning”, Critical Reviews in Biomedical Engineering , 2016, Accepted.
  • Sara M. Camp, Ermelinda Ceco, Carrie L. Evenoski, Sergei M. Danilov, Tong Zhou, Eddie T. Chiang, Liliana Moreno-Vinasco, Brandon Mapes, Jieling Zhao, Gamze Gursoy, Mary E. Brown, Djanybek M. Adyshev, Shahid S. Siddiqui, Hector Quijada, Saad Sammani, Eleftheria Letsiou, Laleh Saadat, Mohammed Yousef, Ting Wang, Jie Liang, and Joe G. N. Garcia. “Unique Toll-Like Receptor 4 Activation by NAMPT/PBEF Induces NF?B Signaling and Inflammatory Lung Injury”, Scientific Reports, 2015, 14(5), 13135
  • Gamze Gursoy, Yun Xu and Jie Liang. “Computational predictions of structures of multichromosomes of budding yeast”, Conf Proc IEEE Eng Med Biol Soc., 2014
  • Gamze Gursoy, Yun Xu, Amy Kenter and Jie Liang. “Spatial confinement is a major determinant of folding landscape of human genome”, Nucleic Acids Research, 2014, 42 (13), 8223-8230
  • Reka Albert, Bhaskar DasGupta, Rashmi Hedge, Gowri Sangeetha Sivanathan, Anthony Gitter, Gamze Gursoy, Pradyut Paul, Eduardo Sontag. “Computationally efficient measure of topological redundancy of biological and social networks”, Physical Review E, 2011, 84, 036117
  • Georgi Z. Genchev, Morten Kallberg, Gamze Gursoy, Anuradha Mittal, Lalit Dubey, Ognjen Perisic, Gang Feng, and Hui Lu. “Mechanical signaling on the single protein level studies using steered molecular dynamics”, Cell Biochemistry and Biophysics, 2009, 55:141-152, (2009)
  • Mariam N. Ismail, Naftali D. Fraiman, Dennis M. Callahan Jr., Gamze Gursoy, Edward Viveiros, Onnaz Ozkanat, Zhaoxia Ji, Ronald J. Willey, Juliusz Warzywoda and Albert Sacco Jr. “First unseeded hydrothermal synthesis of microporous vanadosilicate AM-6”, Microporous and Mesoporous Materials, 2009, 120: 454-459