Ali Torkamani

Improved Identification of Large-effect Rare Genetic Variants using Haplotype Aggregated Allele-specific Expression Data

ANEVA-h improves detection of rare regulatory variants by analyzing haplotype-level ASE data, increasing testable genes and reducing false positives in GTEx and clinical cohorts.

Allele Specific Expression Quality Control Fills Critical Gap in Transcriptome Assisted Rare Variant Interpretation

aseQC identifies low-quality samples in transcriptome data by quantifying allele-specific expression variation, improving rare variant interpretation.

AoUPRS: A Cost-Effective and Versatile PRS Calculator for the All of Us Program

AoUPRS provides a cost-effective PRS calculator for the All of Us dataset, offering both dense and sparse approaches with comparable predictive power.

Selphi: Empowering GWAS Discovery through Enhanced Genotype Imputation

Selphi improves genotype imputation accuracy, especially for rare variants, enhancing GWAS discovery and polygenic risk scores.

Large-scale Rare Variant Burden Testing in Parkinson's Disease Identifies Novel Associations with Genes Involved in Neuro-inflammation

Rapid, Reference-Free Human Genotype Imputation with Denoising Autoencoders

This paper introduces a denoising autoencoder for rapid, reference-free human genotype imputation, achieving higher accuracy and faster runtime than standard methods.

Genome-wide analysis of Structural Variants in Parkinson's Disease using Short-Read Sequencing data

This study identifies 3,154 high-confidence structural variants in Parkinson's disease using short-read sequencing and validates some with long-read data, highlighting limitations of short-read methods.

Response to Polygenic Risk: Results of the MyGeneRank Mobile Application-Based Coronary Artery Disease Study

This study evaluates the impact of coronary artery disease polygenic risk scores on lipid-lowering therapy initiation via a mobile application, finding higher therapy rates among high-risk individuals.

Decoding the transcriptome of atherosclerotic plaque at single-cell resolution

The paper analyzes single-cell transcriptomes of atherosclerotic plaques and adjacent tissue to identify gene drivers of cellular transdifferentiation and inflammatory processes.

High throughput Characterization of KCNB1 variants Associated with Developmental and Epileptic Encephalopathy

This study evaluates 17 KCNB1 variants associated with DEE and NDD using high-throughput assays to identify functional defects in Kv2.1 channels.

Identification of essential regulatory elements in the human genome

The paper develops a model to identify essential regulatory elements in the human genome using machine learning and validates it with functional screens.

Moving Beyond Clinical Risk Scores with a Mobile App for the Genomic Risk of Coronary Artery Disease

The paper introduces a mobile app, MyGeneRank, that provides individuals with their genomic risk of coronary artery disease to inform lifestyle and medication decisions.

Assessment of Circulating Copy Number Variant Detection for Cancer Screening

This study assesses the potential of circulating tumor DNA copy number variant detection for cancer screening using in silico methods.

RASLseqTools: open-source methods for designing and analyzing RNA-mediated oligonucleotide Annealing, Selection, and, Ligation sequencing (RASL-seq) experiments

The paper introduces RASLseqTools, an open-source software package for designing and analyzing RASL-seq experiments, and demonstrates normalization methods for improving reproducibility.