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Gamze Gursoy - Publications

Affiliations: 
Yale University, New Haven, CT 
Area:
Computational Biology and Bioinformatics
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39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Zheng S, Thakkar N, Harris HL, Liu S, Zhang M, Gerstein M, Aiden EL, Rowley MJ, Noble WS, Gürsoy G, Singh R. Predicting A/B compartments from histone modifications using deep learning. Iscience. 27: 109570. PMID 38646172 DOI: 10.1016/j.isci.2024.109570  0.458
2023 Emani PS, Geradi MN, Gürsoy G, Grasty MR, Miranker A, Gerstein MB. Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases. Genome Research. 33: 2156-73. PMID 38097386 DOI: 10.1101/gr.278322.123  0.398
2023 Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, et al. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell. 186: 1493-1511.e40. PMID 37001506 DOI: 10.1016/j.cell.2023.02.018  0.682
2023 Sarkar E, Chielle E, Gursoy G, Chen L, Gerstein M, Maniatakos M. Privacy-preserving cancer type prediction with homomorphic encryption. Scientific Reports. 13: 1661. PMID 36717667 DOI: 10.1038/s41598-023-28481-8  0.415
2022 Erwin GS, Gürsoy G, Al-Abri R, Suriyaprakash A, Dolzhenko E, Zhu K, Hoerner CR, White SM, Ramirez L, Vadlakonda A, Vadlakonda A, von Kraut K, Park J, Brannon CM, Sumano DA, et al. Recurrent repeat expansions in human cancer genomes. Nature. 613: 96-102. PMID 36517591 DOI: 10.1038/s41586-022-05515-1  0.422
2022 Khanna A, Schaffer V, Gursoy G, Gerstein M. Privacy-preserving Model Training for Disease Prediction Using Federated Learning with Differential Privacy. Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual International Conference. 2022: 1358-1361. PMID 36086138 DOI: 10.1109/EMBC48229.2022.9871742  0.382
2022 Gürsoy G, Brannon CM, Ni E, Wagner S, Khanna A, Gerstein M. Storing and analyzing a genome on a blockchain. Genome Biology. 23: 134. PMID 35765079 DOI: 10.1186/s13059-022-02699-7  0.46
2021 Gürsoy G, Li T, Liu S, Ni E, Brannon CM, Gerstein MB. Author Correction: Functional genomics data: privacy risk assessment and technological mitigation. Nature Reviews. Genetics. PMID 34811555 DOI: 10.1038/s41576-021-00440-x  0.391
2021 Gürsoy G, Li T, Liu S, Ni E, Brannon CM, Gerstein MB. Functional genomics data: privacy risk assessment and technological mitigation. Nature Reviews. Genetics. PMID 34759381 DOI: 10.1038/s41576-021-00428-7  0.454
2021 Gürsoy G, Chielle E, Brannon CM, Maniatakos M, Gerstein M. Privacy-preserving genotype imputation with fully homomorphic encryption. Cell Systems. PMID 34758288 DOI: 10.1016/j.cels.2021.10.003  0.41
2021 Gürsoy G, Lu N, Wagner S, Gerstein M. Recovering genotypes and phenotypes using allele-specific genes. Genome Biology. 22: 263. PMID 34493313 DOI: 10.1186/s13059-021-02477-x  0.394
2021 Sarkar E, Chielle E, Gürsoy G, Mazonka O, Gerstein M, Maniatakos M. Fast and Scalable Private Genotype Imputation Using Machine Learning and Partially Homomorphic Encryption. Ieee Access : Practical Innovations, Open Solutions. 9: 93097-93110. PMID 34476144 DOI: 10.1109/access.2021.3093005  0.445
2021 Ash GI, Stults-Kolehmainen M, Busa MA, Gaffey AE, Angeloudis K, Muniz-Pardos B, Gregory R, Huggins RA, Redeker NS, Weinzimer SA, Grieco LA, Lyden K, Megally E, Vogiatzis I, Scher L, ... ... Gursoy G, et al. Establishing a Global Standard for Wearable Devices in Sport and Exercise Medicine: Perspectives from Academic and Industry Stakeholders. Sports Medicine (Auckland, N.Z.). PMID 34468950 DOI: 10.1007/s40279-021-01543-5  0.531
2020 Gürsoy G, Emani P, Brannon CM, Jolanki OA, Harmanci A, Strattan JS, Cherry JM, Miranker AD, Gerstein M. Data Sanitization to Reduce Private Information Leakage from Functional Genomics. Cell. 183: 905-917.e16. PMID 33186529 DOI: 10.1016/j.cell.2020.09.036  0.491
2020 Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, et al. An integrative ENCODE resource for cancer genomics. Nature Communications. 11: 3696. PMID 32728046 DOI: 10.1038/S41467-020-14743-W  0.691
2020 Gürsoy G, Brannon CM, Navarro FCP, Gerstein M. FANCY: Fast Estimation of Privacy Risk in Functional Genomics Data. Bioinformatics (Oxford, England). PMID 32726397 DOI: 10.1093/Bioinformatics/Btaa661  0.485
2020 Gürsoy G, Bjornson R, Green ME, Gerstein M. Using blockchain to log genome dataset access: efficient storage and query. Bmc Medical Genomics. 13: 78. PMID 32693796 DOI: 10.1186/S12920-020-0716-Z  0.503
2020 Zhang J, Liu J, Lee D, Lou S, Chen Z, Gürsoy G, Gerstein M. DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring. Bmc Bioinformatics. 21: 281. PMID 32615918 DOI: 10.1186/S12859-020-03605-3  0.576
2020 Gürsoy G, Brannon CM, Gerstein M. Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts. Bmc Medical Genomics. 13: 74. PMID 32487214 DOI: 10.1186/S12920-020-00732-X  0.468
2020 Mali S, Perez-Rathke A, Sun Q, Gürsoy G, Liang J. Chromatin Folding under Different Nuclear Confinement Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.587  0.399
2019 Mali S, Perez-Rathke A, Sun Q, Gursoy G, Liang J. Roles of Nuclear Confinement, Excluded Volume, and Persistence on TAD Formations, Chromosome Territories, and Chromatin-Nuclear Envelope Interactions Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.3018  0.421
2017 Gürsoy G, Xu Y, Kenter AL, Liang J. Computational construction of 3D chromatin ensembles and prediction of functional interactions of alpha-globin locus from 5C data. Nucleic Acids Research. PMID 28981716 DOI: 10.1093/Nar/Gkx784  0.46
2017 Gürsoy G, Xu Y, Liang J. Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model. Plos Computational Biology. 13: e1005658. PMID 28704374 DOI: 10.1371/Journal.Pcbi.1005658  0.522
2016 Giirsoy G, Terebus A, Cao Y, Liang J, Gursoy G, Terebus A, Youfang Cao, Jie Liang, Gursoy G, Cao Y, Terebus A, Liang J. Mechanisms of stochastic focusing and defocusing in biological reaction networks: insight from accurate chemical master equation (ACME) solutions. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2016: 1480-1483. PMID 28226785 DOI: 10.1109/EMBC.2016.7590989  0.332
2016 Gürsoy G, Liang J. Three-dimensional chromosome structures from energy landscape. Proceedings of the National Academy of Sciences of the United States of America. 113: 11991-11993. PMID 27790979 DOI: 10.1073/Pnas.1614535113  0.507
2016 Gürsoy G, Xu Y, Liang J. The NC-SAC: Computational Pipeline for Predicting Structures of 3D Chromatin Chains from Experimental Data: Origin of Scaling Properties, Emergence of Chromosome Territories and Discovery of Novel Loci Interactions Associated with Differential Gene Expression Biophysical Journal. 110. DOI: 10.1016/J.Bpj.2015.11.423  0.515
2016 Gürsoy G, Terebus A, Cao Y, Liang J. Stochastic Focusing and Defocusing in Biological Reaction Networks: Lessons Learned from Accurate Chemical Master Equation (ACME) Solutions Biophysical Journal. 110. DOI: 10.1016/J.Bpj.2015.11.1695  0.407
2015 Liang J, Cao Y, Gursoy G, Naveed H, Terebus A, Zhao J. Multiscale Modeling of Cellular Epigenetic States: Stochasticity in Molecular Networks, Chromatin Folding in Cell Nuclei, and Tissue Pattern Formation of Cells. Critical Reviews in Biomedical Engineering. 43: 323-46. PMID 27480462 DOI: 10.1615/Critrevbiomedeng.2016016559  0.678
2015 Camp SM, Ceco E, Evenoski CL, Danilov SM, Zhou T, Chiang ET, Moreno-Vinasco L, Mapes B, Zhao J, Gursoy G, Brown ME, Adyshev DM, Siddiqui SS, Quijada H, Sammani S, et al. Unique Toll-Like Receptor 4 Activation by NAMPT/PBEF Induces NFκB Signaling and Inflammatory Lung Injury. Scientific Reports. 5: 13135. PMID 26272519 DOI: 10.1038/Srep13135  0.382
2015 Gürsoy G, Xu Y, Liang J. Effect of Architecture of Cell Nucleus on the Folding Principles of 3D Genome of Budding Yeast Biophysical Journal. 108: 538. DOI: 10.1016/J.Bpj.2014.11.2953  0.516
2014 Gürsoy G, Xu Y, Liang J. Computational predictions of structures of multichromosomes of budding yeast. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2014: 3945-8. PMID 25570855 DOI: 10.1109/EMBC.2014.6944487  0.465
2014 Gürsoy G, Xu Y, Kenter AL, Liang J. Spatial confinement is a major determinant of the folding landscape of human chromosomes. Nucleic Acids Research. 42: 8223-30. PMID 24990374 DOI: 10.1093/Nar/Gku462  0.456
2014 Gürsoy G, Xu Y, Kenter A, Liang J. Population Properties and Complex Folding Behavior of Chromosome Arise from Spatial Confinement of Self-Avoiding Chromatin Chains Biophysical Journal. 106: 78a. DOI: 10.1016/J.Bpj.2013.11.506  0.467
2014 Gürsoy G, Xu Y, Kenter A, Liang J. Three-Dimensional Chromatin Model of α-Globin Gene Locus in Differentially Activated States Biophysical Journal. 106: 78a. DOI: 10.1016/J.Bpj.2013.11.505  0.492
2013 Gursoy G, Xu Y, Kenter A, Liang J. Population Properties of Self-Avoiding Polymer Chain Models of Chromosomes in a Confined Space of Nucleus Biophysical Journal. 104: 581a. DOI: 10.1016/J.Bpj.2012.11.3229  0.476
2012 Gursoy G, Adamian L, Lu H, Liang J. Predicting Allosteric Pathways for Activation of K+ Channels by Perturbation Based Markovian Transmission Model Biophysical Journal. 102: 686a. DOI: 10.1016/J.Bpj.2011.11.3729  0.58
2011 Gursoy G, Adamian L, Lu H, Liang J. Effects of Electric Field on Channel Proteins Through Dipole Perturbation and Network of Signal Transmission Biophysical Journal. 100: 567a. DOI: 10.1016/J.Bpj.2010.12.3287  0.578
2011 Gursoy G, Lu H, Liang J. Predicting Sequence of Events upon Ligand Binding Using PMT Model: A Case Study of Adenylate Kinase Biophysical Journal. 100: 537a. DOI: 10.1016/J.Bpj.2010.12.3134  0.594
2009 Källberg M, Genchev GZ, Gürsoy G, Lu H. Deciphering Protein Mechanical Stability By Comparing Different Folds Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.3097  0.305
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