Material Related to Digital Privacy, esp. Genomic Privacy

Op-eds

http://info.gersteinlab.org/Hartford_Courant_OpEd_from_Other_Papers_for_M_Gerstein

http://info.gersteinlab.org/SF_Chron_OpEd_from_Other_Papers_for_M_Gerstein

http://info.gersteinlab.org/Hartford_Courant_OpEd2_from_Other_Papers_for_M_Gerstein

http://info.gersteinlab.org/USA_Today_Oped_from_Other_Papers_for_M_Gerstein

http://info.gersteinlab.org/SF_Chron_Oped_on_GINA_from_Other_Papers_for_M_Gerstein

Letters to the Editor

http://blog.gerstein.info/2011/11/sharing-too-much-online-letter-re-at.html

http://blog.gerstein.info/2011/07/benefits-of-snooping-letter-re-how-to.html

http://blog.gerstein.info/2010/10/concern-for-privacy-letter-re-dna.html

http://blog.gerstein.info/2010/10/thrills-and-traps-lurking-on-web-letter.html

http://textstream.blogspot.com/2009/11/let-to-ed-re-your-genome-isnt-that.html

http://textstream.blogspot.com/2008/02/let-to-ed-23andmashup-re-23andme-will.html

http://textstream.blogspot.com/2007/09/let-to-ed-re-moms-genes-or-dads-map-can.html

Panel Discussion

http://info.gersteinlab.org/Commonwealth_Club_of_California_from_Other_Papers_for_M_Gerstein

Scientific Writings

Homomorphic Encryption: An Application to Polygenic Risk Scores
Israel Yolou, Jiaqi Li, Can Kockan, Matthew Jensen, Mark Gerstein (2024). bioRxiv.

Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases.
PS Emani, MN Geradi, G Gursoy, MR Grasty, A Miranker, MB Gerstein (2023). Genome Res 33: 2156-2173.

Privacy-preserving cancer type prediction with homomorphic encryption
E Sarkar, E Chielle, G Gursoy, L Chen, M Gerstein, M Maniatakos (2023). Sci Rep 13: 1661.

Genomic research data and the justice system.
D Greenbaum, M Gerstein (2022). Science 377: 826-827.

GATTACA is still pertinent 25 years later
D Greenbaum, M Gerstein (2022). Nat Genet 54: 1758-1760.

Genomic Privacy: Advocating for the Convergence of Legal and Technical Solutions
C Kockan, D Greenbaum, D Lee, M Gerstein (2022). Georgetown Journal of International Affairs 23.2 (2022): 246-253..

Privacy-preserving Model Training for Disease Prediction Using Federated Learning with Differential Privacy.
A Khanna, V Schaffer, G Gursoy, M Gerstein (2022). Annu Int Conf IEEE Eng Med Biol Soc 2022: 1358-1361.

Storing and analyzing a genome on a blockchain.
G Gursoy, CM Brannon, E Ni, S Wagner, A Khanna, M Gerstein (2022). Genome Biol 23: 134.

Functional genomics data: privacy risk assessment and technological mitigation.
G Gursoy, T Li, S Liu, E Ni, CM Brannon, MB Gerstein (2021). Nat Rev Genet 23: 245-258.

Privacy-preserving genotype imputation with fully homomorphic encryption.
G Gursoy, E Chielle, CM Brannon, M Maniatakos, M Gerstein (2021). Cell Syst 13: 173-182e3.

Recovering genotypes and phenotypes using allele-specific genes.
G Gursoy, N Lu, S Wagner, M Gerstein (2021). Genome Biol 22: 263.

Data Sanitization to Reduce Private Information Leakage from Functional Genomics.
G Gursoy, P Emani, CM Brannon, OA Jolanki, A Harmanci, JS Strattan, JM Cherry, AD Miranker, M Gerstein (2020). Cell 183: 905-917e16.

FANCY: fast estimation of privacy risk in functional genomics data.
G Gursoy, CM Brannon, FCP Navarro, M Gerstein (2020). Bioinformatics 36: 5145-5150.

Using blockchain to log genome dataset access: efficient storage and query.
G Gursoy, R Bjornson, ME Green, M Gerstein (2020). BMC Med Genomics 13: 78.

Origins and characterization of variants shared between databases of somatic and germline human mutations.
W Meyerson, J Leisman, FCP Navarro, M Gerstein (2020). BMC Bioinformatics 21: 227.

Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts.
G Gursoy, CM Brannon, M Gerstein (2020). BMC Med Genomics 13: 74.

Analysis of sensitive information leakage in functional genomics signal profiles through genomic deletions.
A Harmanci, M Gerstein (2018). Nat Commun 9: 2453.

Quantification of private information leakage from phenotype-genotype data: linking attacks
A Harmanci, M Gerstein (2016). Nat Methods 13: 251-6.

Proposed social and technological solutions to issues of data privacy in personal genomics
D Greenbaum, A Harmanci, M Gerstein (2014). IEEE IEEE International Symposium on Ethics in Science, Technology and Engineering.

Proceed with Caution
D Greenbaum, M Gerstein (2013). The Scientist 27:26 (1 Oct.)

Genomics and Privacy: Implications of the New Reality of Closed Data for the Field
D Greenbaum, A Sboner, XJ Mu, M Gerstein (2011). PLoS Comput Biol 7: e1002278.

The role of cloud computing in managing the deluge of potentially private genetic data
D Greenbaum, M Gerstein (2011). Am J Bioeth 11: 39-41.

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.
L Habegger, A Sboner, TA Gianoulis, J Rozowsky, A Agarwal, M Snyder, M Gerstein (2011). Bioinformatics 27: 281-3.

Reproducible Research: Addressing the need for data and code sharing in computational science
Yale Law School Roundtable on Data and Code Sharing (2010). Computing in Science & Engineering 12(5): 8-13 (Sept/Oct).

Social networking and personal genomics: suggestions for optimizing the interaction.
D Greenbaum, M Gerstein (2009). Am J Bioeth 9: 15-9.

Genomic anonymity: have we already lost it?
D Greenbaum, J Du, M Gerstein (2008). Am J Bioeth 8: 71-4.

Network security and data integrity in academia: an assessment and a proposal for large-scale archiving.
A Smith, D Greenbaum, SM Douglas, M Long, M Gerstein (2005). Genome Biol 6: 119.

Impediments to database interoperation: legal issues and security concerns
D Greenbaum, A Smith, M Gerstein (2005). Nucleic Acids Res 33: D3-4.

Computer security in academia-a potential roadblock to distributed annotation of the human genome
D Greenbaum, SM Douglas, A Smith, J Lim, M Fischer, M Schultz, M Gerstein (2004). Nat Biotechnol 22: 771-2.

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