Omar E. Cornejo

This paper introduces the Phenotype Shift Score (PSS) to identify highly differentiated primate species pairs and shows it improves comparative-genomic signal detection.

HLA-Resolve improves HLA typing and MHC variant detection using long-read sequencing and hybrid capture, achieving high accuracy across diverse samples.

StrataBionn is a neural network classifier for microbial communities that outperforms traditional methods in vaginal and oral microbiome classification.

The paper evaluates the reliability of phylogenetic inference using primate enamel proteins by simulating sequence fragmentation and comparing results to a reference species tree.

The paper compares the distribution of fitness effects of new amino acid changing mutations between dogs and wolves to assess the impact of domestication on selective pressures.

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

The paper integrates multi-omic data to identify genetic and microbiome factors associated with severe COVID-19, independent of ancestry and social factors.

The paper identifies differentially expressed genes and potential regulatory factors involved in spathe color variation in Anthurium andraeanum using transcriptomic analysis.

The paper investigates how PRDM9 influences competition between meiotic transcription and recombination by relocating recombination hotspots and identifies a potential role for retrotransposons in hotspot direction.

The paper introduces a pipeline using invariant coordinate selection (ICS) to identify outlier loci under selection across multiple genomic scans, showing improved performance over Mahalanobis distance.

The paper examines recombination hotspots in cocoa tree populations, finding higher rates in domesticated and bottlenecked populations, and links them to genetic differentiation and specific genomic features.

The paper uses a modified GBS approach to identify ancestry informative SNPs in Theobroma cacao, finding 7,009 variants useful for ancestry assignment.

The paper sequenced 200 genomes of Theobroma cacao to show that domestication of the Criollo population occurred around 3,600 years ago, with strong selection on genes related to anthocyanin, theobromine metabolism, and disease resistance, and found a negative correlation between Criollo ancestry and bean yield.

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

The paper analyzes the DARC locus in humans to show strong selection on the FY*O allele associated with malaria resistance, with a selection coefficient of 5% and a TMRCA of 42 kya.