Donald F. Conrad

The paper functionally characterizes human PRDM9 alleles to show that despite sequence diversity, most alleles function similarly, while rare variants show extreme DNA binding effects.

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

The paper analyzes the genetic diversity and population structure of US marmosets, revealing pre-colony population structure and generating a pedigree-based recombination map.

The paper estimates realized relatedness in free-ranging macaques using IBD analysis from low coverage whole genome data, revealing genetic variation within kin classes and cryptic relatives.

This study identifies CCDC112 as essential for sperm mitochondrial sheath formation and epididymal maturation, impacting fertility and motility.

PSAP-genomic-regions improves variant prioritization in whole genome sequencing by incorporating functional genomic regions, enhancing detection of both coding and non-coding pathogenic variants in rare disease diagnosis.

This study shows that deleting a conserved TAD boundary near Dmrtb1 and Lrp8 in mice impairs spermatogenesis but not fertility.

The paper introduces HISTA, an interactive scRNA-seq reference for the human testis, and demonstrates its use in analyzing lncRNA regulation and NANOS gene function in spermatogenesis.

This study identifies a naturally occurring MBD4 variant in rhesus macaques that causes maternal germline hypermutation, leading to increased de novo mutations in offspring.

The paper identifies SMC3 loss-of-function variants associated with variable growth and developmental features, including some unexpected phenotypes like bone marrow failure and leukemia.

This paper introduces a GCN-based method for automating and interpreting scRNA-seq cell type annotation, showing improved accuracy over consensus and neighbor majority approaches.

This study maps postzygotic mutations across tissues and lifespan, showing their functional variation and selection pressures, suggesting multiple dynamic genomes per individual.

This study identifies genetic subforms of non-obstructive azoospermia using exome sequencing and single-cell RNA sequencing, revealing molecular groups of genes involved in spermatogenesis.

SATINN automates testis histology analysis using CNNs to classify cell types and tubule stages in mouse mutants with high accuracy.

The paper identifies de novo mutations as a significant genetic cause of male infertility, finding several candidate genes and an enrichment of loss-of-function and missense mutations in intolerant genes.

The paper evaluates the functional impact of missense variants in human reproductive genes using mouse models and finds that many predicted pathogenic variants do not cause detectable phenotypes.

The paper presents a large ASE resource from GTEx v8 with 431 million SNP-level and 153 million haplotype-level measurements, and extends phASER to estimate cis regulatory variant effect sizes.

The paper uses bulk RNA-seq data to estimate cell type abundances and identifies cell type interaction QTLs that provide finer resolution of tissue specificity than bulk cis-eQTLs.

The paper examines telomere length variation across 6,391 tissue samples from 952 individuals, showing tissue-specific differences, positive correlations between tissues, and associations with age and ancestry.

Integrating expression, allelic expression and splicing across tissues identifies rare variants with relevance to traits.

This study identifies mutations in CFAP57 as a cause of primary ciliary dyskinesia by showing they disrupt asymmetric inner dynein arm assembly in cilia.

The paper identifies biallelic M1AP mutations as a cause of meiotic arrest and male infertility through whole exome sequencing and cohort screening.

The paper develops a framework to analyze single-cell transcriptomes from mouse testes, identifying gene regulatory programs and pathological processes in mutant strains.

This study identifies genetic variants associated with sporadic and recurrent miscarriage through large-scale association analyses and Mendelian randomization.

Arnav identifies RNA sequencing variants using site-specific error models, showing utility with GTEx data.

The paper identifies somatically mutated genes under positive and negative selection and links them to oncogenic processes using transcriptome sequence analysis.

The paper develops S-PrediXcan to compute gene expression associations from GWAS summary data and applies it to 44 GTEx tissues and 100+ phenotypes, finding tissue-specific effects and colocalized associations.

The paper identifies CSMD1 variants linked to gonadal function in both sexes and shows that Csmd1 knockout mice have reproductive defects, implicating the complement system in postnatal development.