Rajiv C. McCoy

The paper measures recombination rates between inversion haplotypes at 17q21.31, finds gene flux occurs despite suppression, and shows its impact on fertility and genetic diversity.

The paper investigates the relationship between mtDNA copy number and gene expression, finding they are largely decoupled and that mtDNA accessibility, not copy number, better explains expression variation.

The paper assembles unmapped reads from South Asian genomes to reveal hidden genetic variation not captured by traditional reference-based methods.

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

The paper estimates rates of meiotic and mitotic errors in human embryos using simulation and approximate Bayesian computation, finding high levels of chromosomal mosaicism.

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

This study reveals chromosomal instability as an inherent feature of trophoblast lineage, showing high prevalence of aneuploidy in human placentas and TSCs despite maintaining proliferative capacity.

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 genetic variants in meiosis genes associated with recombination phenotypes and aneuploidy risk using preimplantation genetic testing data.

This study shows that using a T2T-CHM13 recombination map and haplotype panel improves phasing and imputation accuracy compared to GRCh38.

This study remaps Neanderthal and Denisovan genomes onto new and old references, finds improved mapping with T2T-CHM13, and identifies new introgressed sequences and population-specific archaic ancestry.

The paper analyzes gene expression and splicing variation across diverse human populations, identifying population-specific and shared genetic regulatory elements.

This study identifies conserved and species-specific cis-regulatory elements in human and mouse blood cells using integrative epigenomic analysis and clustering.

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 infers sex-specific meiotic recombination landscapes from low-coverage embryo sequencing data, revealing chromosome-specific patterns linked to aneuploidies.

The paper identifies novel transcripts, eQTLs, and caQTLs in African populations and fine-maps GWAS signals for complex diseases.

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

The paper uses ulc-WGS data from PGT-A to identify a genetic locus associated with maternal meiotic aneuploidy risk and validates its function in mouse oocytes.

The paper identifies and categorizes large-scale genomic differences between the T2T-CHM13 and GRCh38 human genome assemblies, highlighting their implications for disease and evolution.

The paper analyzes human sperm genomes to test for transmission distortion, finding no evidence of weak TD and introducing a new method for low-coverage data.

This study analyzes aneuploidy in arrested IVF embryos and finds that meiotic and mitotic aneuploidies are strongly associated with developmental arrest.

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.

The T2T-CHM13 reference genome improves read mapping and variant calling across diverse samples, reducing false positives and enabling novel variant discovery.

This paper introduces a statistical method to distinguish meiotic and mitotic aneuploidies using low-coverage whole-genome sequencing data from IVF embryos, improving the accuracy of preimplantation genetic testing.

SVCollector selects an optimal subset of individuals for long-read sequencing to maximize genetic diversity representation across subpopulations.

The paper investigates the spatiotemporal development of M and L cones in the human retina, finding that retinoic acid signaling promotes M cone fate early in development.

The paper analyzes single-cell RNA sequencing data from human embryos to quantify aneuploidy and mosaicism, finding widespread mosaic aneuploidies in 80% of embryos.

The paper assesses STR variation across 96 Arabidopsis thaliana strains, finding high polymorphism and functional consequences, including novel STR-phenotype associations.

The paper identifies tripolar mitosis as a mechanism causing aneuploidy in human embryos and links it to maternal PLK4 genetic variants.