Pille Hallast

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.

The paper identifies a Denisovan-derived Alu insertion in OCA2 associated with increased pigmentation in Melanesians and demonstrates its functional impact in melanocytes.

The paper develops a minimally invasive workflow to recover biological signatures from Renaissance-era artifacts, revealing microbial biomes and Y-chromosome markers linked to historical handling and conservation.

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 uses a four-generation family to systematically assess de novo mutations and recombination, finding high mutation rates and paternal bias, along with a detailed recombination map.

The paper analyzes segmental duplications in human genomes using long-read sequencing, identifying structurally polymorphic events and novel genes associated with copy number variation.

The paper identifies 56 recent functional variants in modern humans, 24 linked to brain functions and skull morphology, which did not introgress into Neanderthals.

The paper presents whole-genome sequences from 16 Himalayan populations to study population structure, adaptation, and genetic history, revealing early population divergence, shared adaptive haplotypes, and recent gene flow.

The paper resolves the amylase locus at nucleotide resolution in modern and ancient humans, showing AMY1 copy number variation predated agriculture and was driven by recombination.

The paper introduces NAHRwhals, a method to detect serial structural variations in long-read genomes, identifies 37 sSV loci in humans, and shows their relevance to disease.

The paper produces gapless assemblies of ape sex chromosomes for five great apes and a lesser ape, revealing divergence in Y chromosomes and evolutionary dynamics.

The paper presents long-read assemblies of 43 diverse human Y chromosomes, revealing extensive structural complexity and variation across 180,000 years of evolution.

The paper investigates the 3q29 genomic region, identifying novel haplotypes and breakpoint segments associated with deletion and duplication syndromes, and categorizes cases into distinct classes.

This paper develops an automated workflow to place ancient DNA sequences into reference phylogenies, using a parsimony and likelihood-based approach, and applies it to Y-chromosomal data.

The paper identifies recurrent inversions in human genomes and links them to genomic disorders through mutational recurrence and structural diversity.

This study analyzes 137 Middle Eastern genomes to reveal population history, ancestry, and selection patterns, showing no out-of-Africa expansions but elevated Basal Eurasian ancestry in Arabians.

The paper identifies a 1.6 Mb Y-chromosomal inversion in the AZFc region as a high-penetrant risk factor for male infertility, increasing the risk of spermatogenic failure by 8.6-fold.

This study presents 929 high-coverage human genome sequences from 54 populations, revealing new insights into genetic variation and population history.

The paper uses Y-chromosome phylogenetic and phylogeographic analyses to show that non-African male lineages originated in East/South-east Asia 50,000-55,000 years ago, replacing earlier lineages.