Ivan A. Alexandrov

Pangenome alignment reveals global diversity and evolution of human centromeric regions

The paper introduces Centrolign, a tool for aligning centromeric regions, revealing mutation dynamics and enabling variant calling in human centromeres.

A Complete Genome for the Common Marmoset

The paper presents the first telomere-to-telomere genome for the common marmoset, revealing genomic features and a pangenome resource for biomedical research.

A global view of human centromere variation and evolution

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

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

Haplotype-resolved centromeric chromatin organization from a complete diploid human genome

The paper uses a complete diploid human genome to study centromeric chromatin organization, revealing that DNA methylation regulates centromere structure and plasticity.

Pangenome discovery of missing autism variants

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance

The paper presents T2T reference genomes from a multi-generational pedigree to study genetic and epigenetic inheritance across the complete genome.

Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon

The paper identifies centromeric transposable elements and epigenetic features in the eastern hoolock gibbon that contribute to karyotypic variation and chromosomal instability.

Comparative genomics of macaques and integrated insights into genetic variation and population history

This study presents genome assemblies and analyses of macaques to explore genetic variation, population history, and evolutionary differences between species and humans.

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

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 variation and evolution of complete human centromeres

A second complete human centromere set (CHM1) plus 31 nonhuman primate centromeres reveals extensive α-satellite higher-order repeat variation, kinetochore repositioning, and saltatory emergence of new repeats.

The complete sequence of a human Y chromosome

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

HORmon: automated annotation of human centromeres

HORmon automates human centromere annotation by integrating monomer and HOR inference, producing results consistent with prior semi-manual studies.

The complete sequence of a human genome

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

Complete genomic and epigenetic maps of human centromeres

The paper presents a comprehensive analysis of fully assembled human centromeres, revealing their architecture, variation, and evolutionary dynamics at high resolution.

Classification and monomer-by-monomer annotation of suprachromosomal family 1 alpha satellite higher-order repeats in hg38 human genome assembly

The paper annotates and classifies suprachromosomal family 1 alpha satellite higher-order repeats in the hg38 human genome, discovering new divergent HORs and introducing a naming system for their classification.