Preprint

• Ahmed Elhussein and Gamze Gürsoy, A Universal Metric of Dataset Similarity for Cross-silo Federated Learning (arxiv, 2024)

Published

2024

• Jacob Blindenbach*, Jiayi Kang*, Seungwan Hong*#, Caline Karam, Thomas Lehner, and Gamze Gürsoy# , Ultra-secure storage and analysis of genetic data for the advancement of precision medicine (Genome Biology, 2024) accepted.
• Jacob Blindenbach, Jung Hee Cheon, Gamze Gürsoy, Jiayi Kang, On the overflow and p-adic theory applied to homomorphic encryption (The International Symposium on Cyber Security, Cryptology and Machine Learning [CSCML'24], 2024) accepted.
• Conor R. Walker, Xiaoting Li, Manav Chakravarthy, William Lounsbery-Scaife, Yoolim. A. Choi, Ritambhara Singh, Gamze Gürsoy, Private information leakage from single-cell count matrices (Cell, 2024) available online.
• Ahmed Elhussein, Ulugbek Baymuradov, NYGC ALS Consortium, Noémie Elhadad, Karthik Natarajan, Gamze Gürsoy, A framework for sharing of clinical and genetic data for precision medicine applications (Nature Medicine, 2024) available online.
• Seungwan Hong*, Yoolim A. Choi*, Daniel S. Joo, Gamze Gürsoy, Privacy-preserving model evaluation for logistic and linear regression using homomorphically encrypted genotype data (Journal of Biomedical Informatics, 2024) 156:104678.
• Fangyi Chen, Syed Mohtashim Abbas Bokhari, Kenrick Cato, Gamze Gürsoy, Sarah Collins Rosetti, Examining the Generalizability of Pretrained De-identification Transformer Models on Narrative Nursing Notes (Applied Clinical Informatics, 2024) 1:1-198.
• Suchen Zheng*, Nitya Thakkar*, Hannah L Harris, Megan Zhang, Susanna Liu, Mark Gerstein, Erez Lieberman Aiden, Jordan Rowley, William S Noble, Gamze Gürsoy#, Ritambhara Singh#, Predicting A/B compartments from histone
  modifications using deep learning (iScience, 2024) accepted.

2023

• Ahmed Elhussein, Murad Megjhani, Daniel Nametz, Miriam Weiss, Jude Savarraj, Soon Bin Kwon, David J. Roh, Saachin Agarwal, Sander Connolly, Angela Velazquez, Jan Claassen, Huimahn Choi, Gerrit Schubert, Soojin Park#, Gamze Gürsoy#, A generalizable physiological model for detection of delayed cerebral ischemia using federated learning (IEEE Bioinformatics and Biomedicine, 2023)
• Prashant Emani, Maya Geradi, Gamze Gürsoy, Monica Grasty, Andrew Miranker, and Mark Gerstein, Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases (Genome Research, 2023) 33:2156-2173.
• Ahmed Elhussein and Gamze Gürsoy, Privacy-preserving patient clustering for personalized federated learning (Proceedings of Machine Learning Research, 2023) Machine Learning for Healthcare Conference.
• Joel Rozowsky*, Jiahao Gao*, Beatrice Borsari*, Yucheng T Yang*, Timur Galeev*, Gamze Gürsoy*, Charles Epstein*, Kun Xiong*, Jinrui Xu*, Tianxiao Li*, Jason Liu* et al., The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models (Cell, 2023) 186(7):1493-1511.
• Rockwell J. Weiner, Chirag Lakhani, David A. Knowles, Gamze Gürsoy, LDmat: Efficiently Queryable Compression of Linkage Disequilibrium Matrices (Bioinformatics, 2023) 39(2): btad092.
• Esha Sarkar, Eduardo Chielle, Gamze Gürsoy, Leo Chen, Mark Gerstein, Michail Maniatakos, Privacy-preserving cancer type prediction with homomorphic encryption (Scientific Reports, 2023) 13:1661.

2022

• Graham S. Erwin*, Gamze Gürsoy*, Rashid Al-Abri, Ashwini Suriyaprakash, EgorDolzhenko, Kevin Zhu, Christian R. Hoerner, Shannon M. White, Lucia Ramirez, AnanyaVadlakonda, Alekhya Vadlakonda, Konor von Kraut, Julia Park, Charlotte M. Brannon,Daniel A. Sumano, Raushun A. Kirtikar, Alicia A. Erwin, Thomas J. Metzner, Ryan K. C.Yuen, Alice C. Fan, John T. Leppert, Michael A. Eberle, Mark Gerstein#, Michael P. Snyder#, A genome-wide atlas of recurrent repeat expansions in human cancer (Nature, 2022)
• Amol Khanna, Vincent Schaffer, Gamze Gürsoy#, Mark Gerstein#, Privacy-preserving model training for disease prediction using federated learning with differential privacy (44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society, 2022) pp. 1358-1361.
• Gamze Gursoy*, Charlotte Brannon*, Sarah Wagner, and Mark Gerstein, Storing and analyzing a genome on a blockchain (Genome Biology, 2022) accepted.
• Gamze Gürsoy, Genome privacy and trust (Annual Reviews of Biomedical Data Science, 2022) Vol 5.
• Gamze Gürsoy, Tianxiao Li, Susanna Liu, Eric Ni, Mark Gerstein, Functional genomics data: privacy risk assessment and technological mitigation. (Nature Reviews Genetics, 2022) 23, 245–258 (2022).
• Gamze Gürsoy*, Eduardo Chielle*, Charlotte Brannon, Michail Maniatakos#, Mark Gerstein#, Privacy-preserving genotype imputation with fully homomorphic encryption (Cell Systems, 2022) 13(2): 173-182.

2021

• Gamze Gursoy, Nancy Lu, Sarah Wagner, and Mark Gerstein, Recovering genotypes and phenotypes using allele-specific genes (Genome Biology, 2021) 22:263.
• Esha Sarkar, Eduardo Chielle, Gamze Gursoy, Oleg Mazonka, Mark Gerstein, Mihalis Maniatakos, Fast and Scalable Private Genotype Imputation Using Machine Learning and Partially Homomorphic Encryption (IEEE Access, 2021) vol. 9, pp. 93097-93110.

2020

• Gamze Gürsoy, Prashant Emani, Charlotte M Brannon, Otto A Jolanki, Arif Harmanci, J Seth Strattan, J Michael Cherry, Andrew D Miranker, and Mark Gerstein, Data Sanitization to Reduce Private Information Leakage from Functional Genomics (Cell, 2020) 183(4): 903-917.
• Gamze Gürsoy, Charlotte M Brannon, Fabio CP Navarro, Mark Gerstein, FANCY: fast estimation of privacy risk in functional genomics data (Bioinformatics, 2020) 36(21): 5145-5150.
• Gamze Gürsoy, Robert Bjornson, Molly E Green, Mark Gerstein, Using blockchain to log genome dataset access: efficient storage and query (BMC Medical Genomics, 2020) 13(7): 1-9.
• Jing Zhang, Jason Liu, Donghoon Lee, Shaoke Lou, Zhanlin Chen, Gamze Gürsoy, and Mark Gerstein , DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring (BMC Bioinformatics, 2020) 21:281.
• Gamze Gursoy*, Charlotte Brannon*, and Mark Gerstein, Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts (BMC Medical Genomics, 2020) 13:74.
• Jing Zhang, Donghoon Lee, Vineet Dhiman, Peng Jiang, Jie Xu, Patrick McGillivray, Hongbo Yang, Jason Liu, William Meyerson, Declan Clarke, Mengting Gu, Shantao Li, Shaoke Lou, Jinrui Xu, Lucas Lochovsky, Matthew Ung, Lijia Ma, Shan Yu, Qin Cao, Arif Harmanci, Koon-Kiu Yan, Anurag Sethi, Gamze Gürsoy, Michael Rutenberg Schoenberg, Joel Rozowsky, Jonathan Warrell, Prashant Emani, Yucheng T Yang, Timur Galeev, Xiangmeng Kong, Shuang Liu, Xiaotong Li, Jayanth Krishnan, Yanlin Feng, Juan Carlos Rivera-Mulia, Jessica Adrian, James R Broach, Michael Bolt, Jennifer Moran, Dominic Fitzgerald, Vishnu Dileep, Tingting Liu, Shenglin Mei, Takayo Sasaki, Claudia Trevilla-Garcia, Su Wang, Yanli Wang, Chongzhi Zang, Daifeng Wang, Robert J Klein, Michael Snyder, David M Gilbert, Kevin Yip, Chao Cheng, Feng Yue, X Shirley Liu, Kevin P White, Mark Gerstein, An integrative ENCODE resource for cancer genomics (Nature communications, 2020) 11(1): 1-11.

2017

• Gamze Gursoy, Jie Liang, Three-dimensional chromosome structures from energy landscape (Proceedings of the National Academy of Sciences, 2017) 113(43): 11991-11993.
• Gamze Gursoy, Yun Xu, Jie Liang, 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, 2017) 13(7): e1005658.
• Game Gursoy*, Yun Xu*, Amy Kenter, Jie Liang, Computational construction of 3D chromatin ensembles and prediction of functional interactions of alpha-globin locus from 5C data (Nucleic Acids Research, 2017) 45(20): 11547-11558.

2016

• Gamze Gursoy, Anna Terebus, Youfang Cao, 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.

2014

• Gamze Gursoy*, Yun Xu*, Amy Kenter, Jie Liang, Spatial confinement is a major determinant of the folding landscape of human chromosomes (Nucleic Acids Research, 2014) 42(13): 8223-8230.