Ardalan Naseri

Sum-h2, enabling genetic discovery for deep learning-derived phenotypes through a fast evaluation framework and arena of performance

The paper introduces sum-h2, a fast framework for evaluating genetic discovery from deep learning-derived phenotypes using heritability measures, and establishes a Genetic Discovery Arena for benchmarking.

RLBWT-Based LCP Computation in Compressed Space for Terabase-Scale Pangenome Analysis

The paper introduces algorithms for constructing RLBWT-based compressed full text indexes in compressed space, reducing memory usage for large-scale pangenome analysis.

SLAB: A Sweep Line Algorithm in PBWT for Finding Haplotype Block Cores

This paper introduces SLAB, an algorithm for identifying haplotype block cores using PBWT, and applies it to UK Biobank data to detect selection signals.

HiFiMAP: High-resolution fast identity-by-descent mapping test

HiFiMAP provides high-resolution IBD mapping at SNP level, outperforming window-based methods and detecting novel associations in UK Biobank and brain imaging data.

GWAS for Periodontitis Phenotypes Using Multi-Ancestry All of Us Research Platform

This study conducts a multi-ancestry GWAS on periodontitis using EHR data from the All of Us Research Platform, identifying significant genetic loci associated with periodontitis grade and other phenotypes.

Local Haplotype Classifiers enable Efficient, Flexible, and Secure Genotype Imputation and Downstream Analyses

The paper introduces a privacy-preserving genotype imputation method using haplotype classifiers, improving accuracy and throughput compared to linear models.

Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in UK Biobank

The paper introduces ROH-DICE, a method to identify ROH diplotypes in UK Biobank, finding associations between clustered ROHs and diseases like autoimmune disorders and haemochromatosis.

FastRecomb: Fast inference of genetic recombination rates in biobank scale data

FastRecomb efficiently estimates population-specific genetic maps from large biobank-scale genotyping data, achieving state-of-the-art performance at 10k resolution.

RaPID-Query for Fast Identity by Descent Search and Genealogical Analysis

RaPID-Query enables fast and accurate genealogical search by identifying IBD segments between a query and a large database, achieving low error rates and quick processing times.

Syllable-PBWT for space-efficient haplotype long-match query

The paper introduces Syllable-PBWT, a space-efficient data structure for haplotype long-match queries, reducing memory use by over 100 times compared to existing methods.

mcPBWT: Space-efficient Multi-column PBWT Scanning Algorithm for Composite Haplotype Matching

The paper introduces mcPBWT, an algorithm for efficiently scanning composite haplotype patterns in PBWT data, identifying crossover events and gene-conversion tracts.

Personalized genealogical history inferred from biobank-scale IBD segments

The paper infers genealogical history and social behaviors from IBD segments in UK Biobank data, revealing population-scale genetic connections and regional family preferences.

Simultaneous Epigenetic Perturbation and Genome Imaging Reveal Distinct Roles of H3K9me3 in Chromatin Architecture and Transcription

This study uses EpiGo-KRAB to introduce H3K9me3 at specific loci and shows it forms heterochromatin-like domains without widespread gene repression.

CRISPR-based Live Imaging of Epigenetic Modification-Mediated Genome Reorganization

The paper develops a CRISPR-based system to image epigenetic modification effects on genome organization in living cells and shows it induces genomic relocation and H3K9me3 decoration.

CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome Dynamics

The paper uses CRISPR-Sirius to track chromosomal loci dynamics in living cells and finds cell cycle-dependent changes in DNA contortion and movement.

Ultra-fast Identity by Descent Detection in Biobank-Scale Cohorts using Positional Burrows-Wheeler Transform

RaPID detects identity by descent in large biobank-scale cohorts using a randomized positional BWT approach, achieving linear scaling and high accuracy.