Publications

Book chapters:

• Gamze Gursoy. “Criticality of data sharing in genomic research and public views of genomic” in the book Responsible Genomic Data Sharing: Challenges and Approaches

Opinion & Commentary:

• Gamze Gursoy and Mark Gerstein. “As coronavirus testing expands, new personal privacy issues arise” in Hartford Courant.
• Gamze Gursoy, Megan Doerr, John Wilbanks, Jennifer K Wagner, Haixu Tang, Steven E Brenner. “Navigating ethical quandaries with the privacy dilemma of biomedical datasets“, Pacific Symposium on Biocomputing, 2020
• Gamze Gursoy, Arif Harmanci, Haixu Tang, Erman Ayday, Steven E Brenner. “When Biology Gets Personal: Hidden Challenges of Privacy and Ethics in Biological Big Data“,  Pacific Symposium on Biocomputing, 2019
• Gamze Gursoy and Jie Liang. “3D Chromosome Structures from Energy Landscape“, PNAS, 2016, 113, (43), 11991-11993

First author pre-prints & peer reviewed publications:

• Gamze Gursoy*, Eduardo Chielle*, Charlotte Brannon, Mihalis Maniatakos, Mark Gerstein. “Privacy-preserving genotype imputation with fully homomorphic encryption“,Biorxiv
• Gamze Gursoy*, Charlotte Brannon*, Sarah Wagner, Mark Gerstein. “Storing and analyzing a genome on a blockchain“, Biorxiv
• Gamze Gursoy, Prashant Emani, Otto A Jolanki, Charlotte Brannon, Arif Harmanci, J. Seth Strattan, Andrew Miranker, Mark Gerstein. “Private information leakage from functional genomics data: Quantification with calibration experiments and reduction via data sanitization protocols“, Biorxiv
• Gamze Gursoy, Charlotte Brannon, Fabio Navarro, Mark Gerstein. “FANCY: Fast Estimation of Privacy Risk in Functional Genomics Data“, Bioinformatics, accepted
• Gamze Gursoy, Rob Bjornson, Molly E. Green, Mark Gerstein. “Using blockchain to log genome dataset access: Efficient storage and query”, BMC Med Genomics, 13(Suppl 7):78, 2020.
• Gamze Gursoy*, Charlotte Brannon*, Mark Gerstein. “Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts“, BMC Med Genomics 13, 74, 2020
• Gamze Gursoy*, Yun Xu*, Amy Kenter and Jie Liang. “Computational construction of 3D chromatin ensembles and prediction of functional interactions of alpha-globin locus from 5C data“, Nucleic Acids Research, 45(20):11547-11558, 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, 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
• 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

Contributed publications & pre-prints:

• J Zhang*, D Lee*, V Dhiman*, P Jiang*, J Xu*, P McGillivray*, H Yang*, …, Gamze Gursoy, … , M Gerstein. “An integrative ENCODE resource for cancer genomics”, Nature Communications, accepted.
• Wang et al., … ,PsychENCODE Consortium including Gamze Gursoy, …, Gerstein. “Comprehensive functional genomic resource and integrative model for the human brain”, Science, 2018:362(6420):eaat8464
• Gandal et al., … ,PsychENCODE Consortium including Gamze Gursoy. “Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder”, Science, 2018:362(6420):eaat8127
• Amiri et al., … ,PsychENCODE Consortium including Gamze Gursoy, …, Vaccarino. “Transcriptome and epigenome landscape of human cortical development modeled in organoids”, Science, 2018:362(6420):eaat6720
• Li et al., … ,PsychENCODE Consortium including Gamze Gursoy, …, Sestan. “Integrative functional genomic analysis of human brain development and neuropsychiatric risks”, Science, 2018:362(6420):eaat7615
• 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
• 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