Gamze Gürsoy

Integrating CSF and EV Proteomes Enhances Biomarker Discovery by Capturing Shared Variation Across Compartments

The paper integrates CSF and EV proteomes to enhance biomarker discovery by capturing shared variation across compartments, improving biological concordance and identifying more candidates in a smaller cohort.

Privacy-Preserving Pangenome Graphs

PanMixer reduces re-identification risks in pangenome graphs while preserving utility for downstream genomic analyses.

African Green Monkey Cerebrospinal Fluid miRNome Captures Conserved miRNAs Relevant to Human Neurodegenerative Disease

The paper characterizes the miRNome of African green monkey cerebrospinal fluid, identifying conserved miRNAs relevant to human neurodegenerative diseases and highlighting species-specific variations.

Private Information Leakage from Polygenic Risk Scores

This paper shows that polygenic risk scores can be used to infer genotypes and de-anonymize individuals, and proposes a framework to assess and mitigate privacy risks when sharing PRS values.

The SEA-AD DREAM Challenge: Community benchmarking human and AI agent solutions for Alzheimer's disease neuropathology prediction from single-nucleus transcriptomics

The paper presents a benchmarking challenge to predict Alzheimer's disease neuropathology from single-nucleus transcriptomics using human and AI models, finding that top methods achieve near-perfect categorical staging predictions.

ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads

ScatTR estimates the size of long tandem repeat expansions from short-read sequencing data, outperforming existing methods in simulated and real datasets.

African Green Monkeys Respond to Synthetic AB Oligomers with Persistent Alzheimers-like Activation

This study shows that African green monkeys exposed to synthetic Aβ oligomers exhibit persistent Alzheimer's-like proteomic changes without cognitive decline.

Paired CRISPR screens to map gene regulation in cis and trans

The paper uses paired CRISPR screens to identify cis- and trans-regulatory elements controlling PD-L1 expression in PDAC cells and links them to clinical outcomes.

Ultra-secure storage and analysis of genetic data for the advancement of precision medicine

The paper introduces SQUiD, a secure database for storing and analyzing genotype-phenotype data in the cloud, enabling privacy-preserving queries and analyses.

Predicting A/B compartments from histone modifications using deep learning

This paper introduces a deep learning model to predict A/B compartments from histone modifications, achieving high accuracy across cell types and showing the importance of specific histone marks.

Assessing and mitigating privacy risk of sparse, noisy genotypes by local alignment to haplotype databases

PLIGHT quantifies privacy risks from sparse, noisy genotypes by aligning them to haplotype databases and provides sanitization tools to mitigate reidentification.

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

A genome-wide atlas of recurrent repeat expansions in human cancer

The paper identifies recurrent repeat expansions in cancer genomes, showing their association with gene regulation and demonstrating their therapeutic targeting potential.

Privacy-preserving genotype imputation with fully homomorphic encryption

This paper develops a privacy-preserving genotype imputation algorithm using homomorphic encryption, achieving performance comparable to plaintext methods.

Recovering genomes and phenotypes using allele-specific gene expression

The paper shows that allele-specific gene names can be used to infer key genetic variants and link individuals to their genome or phenotype, raising privacy concerns.

Private information leakage from functional genomics data: Quantification with calibration experiments and reduction via data sanitization protocols

The paper quantifies privacy leakage in functional genomics data and proposes a data-sanitization protocol to reduce it while preserving utility.

An integrative ENCODE resource for cancer genomics

The paper develops a custom ENCODE annotation for cancer genomics, highlighting TF-RBP interactions and network rewiring during oncogenesis, and validates findings using experimental assays.

FANCY: Fast Estimation of Privacy Risk in Functional Genomics Data

FANCY estimates privacy risk in functional genomics data by predicting leaking variants from sequencing reads without explicit genotyping.

DiNeR: a Differential Graphical Model for analysis of co-regulation Network Rewiring

DiNeR identifies significant changes in transcription factor co-regulation networks by analyzing ChIP-seq data from disease and normal samples, revealing key disease-associated regulators.

Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts

This paper develops smart contracts on Ethereum blockchain to store and query pharmacogenomics data, achieving efficient performance for gene-drug interaction data.

Storing and analyzing a genome on a blockchain

This paper develops a method to store and analyze genomic data on a blockchain, addressing security and integrity issues through on-chain reference-aligned reads and tools for variant calling.