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Articles by Gamze Gürsoy
African green monkeys respond to synthetic Aβ oligomers with persistent Alzheimer’s-like activation
Abstract African green monkeys (AGMs) provide a promising alternative to congenic rodent models because of their closer evolutionary relationship to humans and natural genetic variation. They share key physiological and biochemical traits with humans, including neuroanatomy, vascular structure, inflammatory responses, and lifespan. Unlike rodents, AGMs naturally develop Alzheimer’s-like amyloid-β (Aβ) plaques and tau pathology with age.
Privacy-preserving pangenome graphs - Nature Communications
Abstract The human pangenome reference, often represented as a graph, promises to capture genetic diversity across populations, but open release of individual haplotypes raises significant privacy concerns, including risks of re-identification and inference of sensitive traits. To address these challenges, we introduce PanMixer, a framework for privacy-preserving pangenome graph releases that selectively obfuscates an individual’s haplotypes while retaining the utility of the reference graph.
Long-Term Endocrine Effects of Hematopoietic Stem Cell Transplantation in Children: A Reappraisal
BMD bone mineral density fT4 free thyroxine GvHD graft-versus-host disease HSCT hematopoietic stem cell transplantation SDS standard deviation score T4 total thyroxine TBI total body irradiation TSH thyroid-stimulating hormone 1 Introduction Hematopoietic stem cell transplantation (HSCT) cures a range of malignant and non-malignant hematologic diseases, immunodeficiencies, and certain inherited metabolic diseases in children [1].
Estimating the size of long tandem repeat expansions from short reads with ScatTR
1,2,3 1Department of Biomedical Informatics, Columbia University, New York, New York 10032, USA; 2New York Genome Center, New York, New York 10013, USA; 3Department of Computer Science, Columbia University, New York, New York 10027, USA Corresponding author: gamze.gursoy{at}columbia.edu Footnotes [Supplemental material is available for this article.] Article published online before print.
ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads
Abstract Tandem repeats (TRs) are sequences of DNA where two or more base pairs are repeated back-to-back at specific locations in the genome. The expansions of TRs are implicated in over 50 conditions, including Friedreich's ataxia, autism, and cancer. However, accurately measuring the copy number of TRs is challenging, especially when their expansions are larger than the fragment sizes used in standard short-read genome sequencing.
SQUiD: ultra-secure storage and analysis of genetic data for the advancement of precision medicine - Genome Biology
Our conceptual framework is focused on solving real-world security challenges encountered in the storage and querying large-scale genotype-phenotype datasets. These challenges involve safeguarding the confidential information contained within such data from third party cloud providers and outside adversaries. Our framework is based on a scenario that involves three parties: the data owner, the researcher(s), and the public cloud.
Private information leakage from single-cell count matrices
Keywords genome privacy single-cell gene expression linking attack Introduction Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to study gene expression variability at the cellular level within tissues, shedding light on complex biological processes, including human health.1,2,3 Once costly and limited to small numbers of cells, scRNA-seq data now routinely include thousands of cells, enabling researchers to decipher cellular dynamics across a range of human...
Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases
1,2,3,4 1Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA; 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA; 3Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA; 4Department of Statistics and Data Science, Yale University, New Haven, Connecticut 06520, USA Corresponding author: mark{at}gersteinlab.org Footnotes [Supplemental material is available for...
[2307.08847] Privacy-preserving patient clustering for personalized federated learning
arXiv:2307.08847 (cs) Download a PDF of the paper titled Privacy-preserving patient clustering for personalized federated learning, by Ahmed Elhussein and Gamze Gursoy Download PDF Submission history From: Gamze Gursoy [ view email] [v1] Mon, 17 Jul 2023 21:19:08 UTC (1,165 KB) Bibliographic Tools Bibliographic Explorer Toggle Bibliographic Explorer () Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Links to Code...
Recurrent repeat expansions in human cancer genomes - Nature
Data curation We obtained white-listed data from the ICGC and TCGA PCAWG dataset. The term ‘white-listed’ refers to samples that passed quality control by the PCAWG consortium24. Data were accessed through the Cancer Genome Collaboratory. We used aligned reads (BAM files), which were aligned to GRCh37 as described previously24. These data are available through the PCAWG data portal (https://docs.icgc.org/pcawg). A list of samples included in the analysis is available in Supplementary Table 2.
A genome-wide atlas of recurrent repeat expansions in human cancer
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Genome Privacy and Trust
Visualization of Biomedical Data Seán I. O'Donoghue, Benedetta Frida Baldi, Susan J. Clark, Aaron E. Darling, James M. Hogan, Sandeep Kaur, Lena Maier-Hein, Davis J. McCarthy, William J. Moore, Esther Stenau, Jason R. Swedlow, Jenny Vuong, James B. Procter Vol. 1, 2018 Abstract - FiguresPreview Abstract The rapid increase in volume and complexity of biomedical data requires changes in research, communication, and clinical practices.
Do antimicrobial stewardship programs improve the quality of care in ICU patients diagnosed with infectious diseases following consultation? Experience in a tertiary care hospital
HIGHLIGHTS • The growing problem of antibiotic resistance is a major public health concern. • An antimicrobial stewardship study was conducted in intensive care units. • There was a significant increase in total quality-of-care scores. ABSTRACT Background One of the most important public health concerns is the ever-growing problem of antibiotic resistance. Importantly, the rate of introduction of new molecules into clinical practice has slowed down considerably.
Recovering genotypes and phenotypes using allele-specific genes - Genome Biology
Genome Biology volume 22, Article number: 263 (2021) Cite this article Abstract With the recent increase in RNA sequencing efforts using large cohorts of individuals, surveying allele-specific gene expression is becoming increasingly frequent. Here, we report that, despite not containing explicit variant information, a list of genes known to be allele-specific in an individual is enough to recover key variants and link the individuals back to their genotypes and phenotypes.
PLIGHT: A tool to assess privacy risk by inferring identifying characteristics from sparse, noisy genotypes
Abstract The leakage of identifying information in genetic and omics data has been established in many studies, with single nucleotide polymorphisms (SNPs) shown to carry a strong risk of reidentification for individuals and their genetic relatives.
Data Sanitization to Reduce Private Information Leakage from Functional Genomics
Highlights • Surging functional genomics data necessitates improved data-sharing modes • Quantification of private information in these data is done via linkage attacks • A data sanitization protocol grounded in privacy and utility is developed • The sanitized format is compatible with existing file formats and pipelines Summary The generation of functional genomics datasets is surging, because they provide insight into gene regulation and organismal phenotypes (e.g., genes upregulated in...
Data Sanitization to Reduce Private Information Leakage from Functional Genomics
Highlights • Surging functional genomics data necessitates improved data-sharing modes • Quantification of private information in these data is done via linkage attacks • A data sanitization protocol grounded in privacy and utility is developed • The sanitized format is compatible with existing file formats and pipelines Summary The generation of functional genomics datasets is surging, because they provide insight into gene regulation and organismal phenotypes (e.g., genes upregulated in...
Sensitive information leakage from functional genomics data: Theoretical quantifications & practical file formats for privacy preservation
Abstract Functional genomics experiments on human subjects present a privacy conundrum. On one hand, many of the conclusions we infer from these experiments are not tied to the identity of individuals but represent universal statements about biology and disease. On the other hand, by virtue of the experimental procedure, the sequencing reads are tagged with small bits of patients' variant information, which presents privacy challenges in terms of data sharing.
Spatial confinement is a major determinant of the folding landscape of human chromosomes
The global architecture of the cell nucleus and the spatial organization of chromatin play important roles in gene expression and nuclear function. Single-cell imaging and chromosome conformation capture-based techniques provide a wealth of information on the spatial organization of chromosomes. However, a mechanistic model that can account for all observed scaling behaviors governing long-range chromatin interactions is missing.
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