Jeffrey Rogers

Pseudo-observations of longevity improve detection of resilience-associated genes in the Radiation Late Effects Cohort of rhesus macaques.

The paper uses pseudo-observations of longevity to identify resilience-associated genes in rhesus macaques exposed to radiation and aging challenges.

MosaicSim: A Novel Mosaic Variant Simulator Reveals Diminishing Returns of Ultra-High Coverage for Mosaic Variant Detection

MosaicSim simulates mosaic variants in sequencing data to evaluate detection methods, showing that higher coverage improves detection rates without false positives.

A phylogenetic protein-coding genome-phenome map of complex traits across 224 primate species.

Cross-species genome-phenome mapping in primates reveals thousands of protein-coding variants linked to the evolution of complex traits.

Drift and isolation drive genomic erosion and island speciation in a lineage of macaques

The paper shows that island isolation and genetic drift rapidly drive speciation in macaques, leading to genomic divergence, loss of diversity, and adaptive mutations.

Low mutation rate but high male-bias in the germline of a short-lived opossum

This study reports the lowest germline mutation rate in mammals and a typical male mutation bias in the gray short-tailed opossum, suggesting alternative mechanisms to cell division drive sex-specific mutation rates.

Unprecedented female mutation bias in aye-ayes

This study finds a female mutation bias in aye-ayes, contrasting the typical male mutation bias in mammals, and identifies potential genetic causes.

Genomic signatures of island colonization in highly diverse primates

The paper compares genomic diversity, inbreeding, and genetic load between insular and mainland populations of three West African primates, finding lower diversity and higher inbreeding in island populations but no evidence of increased deleterious variation.

Complete genomic assembly of Mauritian cynomolgus macaque killer immunoglobulin-like receptor and natural killer group 2 haplotypes

The paper assembles KIR and NKG2 genomic haplotypes in Mauritian cynomolgus macaques using long-read sequencing and develops a strategy for genotyping using short-read data.

The landscape of tolerated genetic variation in humans and primates

The paper uses primate genetic data to predict human variant pathogenicity with a deep learning classifier trained on 4.3 million common missense variants.

A global catalog of whole-genome diversity from 233 primate species

This study presents whole-genome data from 233 primate species, revealing patterns of genetic diversity, mutation rates, and recurrent missense mutations across primate clades.

Rare penetrant mutations confer severe risk of common diseases

The paper identifies rare variant polygenic risk scores as more effective than common variant polygenic risk scores in identifying individuals with outlier phenotypes in common human diseases and complex traits.

Comparison of Mitogenomic and Mitochondrial Markers for the Phylogenetic and Evolutionary Study of Marmosets, with special focus on captive Callithrix jacchus

This study compares mitogenome and mtDNA control region markers to determine the ancestry and diversity of captive Callithrix jacchus marmosets, finding mitogenomes provide better resolved phylogenies.

Loci on chromosome 12q13.2 encompassing ERBB3, PA2G4 and RAB5B are associated with polycystic ovary syndrome

The paper identifies 15 SNPs associated with androgen production in theca cells and a haplotype on chromosome 12q13.2 linked to PCOS and AMH levels.

High-altitude adaptation and incipient speciation in geladas

This study identifies genomic and karyotypic changes in geladas that may contribute to high-altitude adaptation and speciation.

Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus

The paper presents an improved chromosome-scale genome assembly for the Syrian hamster using long-read sequencing, resulting in higher continuity and gene annotation accuracy.

Age-Related Changes in the Rhesus Macaque Eye

This study examines age-related changes in rhesus macaque eyes and compares them to human age-related eye diseases, finding similarities in intraocular pressure, retinal structure, and macular lesions.

Infant Inhibited Temperament in Primates Predicts Adult Behavior, is Heritable, and is Associated with Anxiety Relevant Genetic Variation

The paper shows infant inhibited temperament in monkeys predicts adult behavior, is heritable, and links to anxiety-related genetic variants.

SVhound: Detection of future Structural Variation hotspots

SVhound predicts regions likely to contain novel structural variations by analyzing population-level SV datasets, showing high correlation with full datasets and applicability across species.

Variation in predicted COVID-19 risk among lemurs and lorises

The paper analyzes ACE2 gene sequences in strepsirrhine primates to assess their susceptibility to SARS-CoV-2, finding high variability and potential risk in some species.

Evolution of DNA methylation in Papio baboons

The paper profiles DNA methylation in Papio baboons to study evolutionary changes and finds that methylation divergence mirrors genetic structure and is influenced by selection in functionally relevant regions.

Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques

The paper improves KIR allele discovery in Mauritian cynomolgus macaques using high-throughput sequencing and develops a new target capture reagent, finding nine novel alleles.