Parithi Balachandran

The paper presents a population-scale Y chromosome reference panel with 142 assemblies, revealing structural and epigenetic variation across 180,000 years of evolution.

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

The paper identifies SD-mediated rearrangements in mouse genomes using long-read sequencing and other methods, revealing their impact on gene content and function.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

The paper identifies structural variants in 20 mouse strains using long-read sequencing, revealing transposable elements' role in chromatin remodeling and gene expression in mESCs.

The paper identifies transposable element-mediated rearrangements (TEMRs) in human genomes, showing they are enriched in genic regions and can create risk alleles.

SvAnna predicts pathogenicity of structural variants in long-read sequencing data by integrating transcript and regulatory annotations with clinical phenotype data, achieving high accuracy in prioritizing pathogenic variants.

This paper introduces SNaReSim, a new nanopore read simulator that better captures k-mer error distributions compared to existing tools.

This paper introduces an unsupervised learning method to correct errors in nanopore sequencing data, achieving performance comparable to existing techniques while preserving repeat detection and long sequence analysis.