Secure and scalable gene expression quantification with pQuant.

Next generation sequencing reads from RNA-seq studies expose private genotypes of individuals during computation. Here, we introduce pQuant, an algorithm that employs homomorphic encryption to ensure privacy-preserving quantification of gene expression from RNA-seq data across public and cloud servers. pQuant performs computations on encrypted data, allowing researchers to handle sensitive information without exposing it.

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

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.

Secure and federated quantitative trait loci mapping with privateQTL.

Understanding the relationship between genotypes and phenotypes is crucial for advancing personalized medicine. Expression quantitative trait loci (eQTL) mapping plays a significant role by correlating genetic variants to gene expression levels. Despite the progress made by large-scale projects, eQTL mapping still faces challenges in statistical power and privacy concerns.

SQUiD: ultra-secure storage and analysis of genetic data for the advancement of precision medicine.

Cloud computing allows storing the ever-growing genotype-phenotype datasets crucial for precision medicine. Due to the sensitive nature of this data and varied laws and regulations, additional security measures are needed to ensure data privacy. We develop SQUiD, a secure queryable database for storing and analyzing genotype-phenotype data.

Paired CRISPR screens to map gene regulation in and .

Recent massively-parallel approaches to decipher gene regulatory circuits have focused on the discovery of either -regulatory elements (CREs) or -acting factors. Here, we develop a scalable approach that pairs - and -regulatory CRISPR screens to systematically dissect how the key immune checkpoint is regulated. In human pancreatic ductal adenocarcinoma (PDAC) cells, we tile the locus using ∼25,000 CRISPR perturbations in constitutive and IFNγ-stimulated conditions.