James C. Mullikin

The paper presents a chromosome-level genome assembly of the Hispid cotton rat, annotating 24,878 protein-coding genes and identifying genetic innovations.

This study characterizes the genome and single-cell transcriptome of Hydractinia, revealing that its stem cells use a conserved gene toolkit shared with all animals.

The paper analyzes genomic data from patients with FPDMM to identify germline RUNX1 variants and somatic mutations linked to clonal hematopoiesis and myeloid malignancies.

The paper uses random forest classifiers trained on simulated data to accurately genotype structural variants in the alpha globin region, outperforming existing software in ancestry-specific allele frequency estimation.

The paper presents a genome catalog of the early-life human skin microbiome, expanding diversity and improving classification rates using metagenomic data from infants and their mothers.

The paper identifies a family of immunoglobulin superfamily genes in the cnidarian Hydractinia symbiolongicarpus, showing they are homologous to vertebrate histocompatibility genes and suggest an ancient origin of V-set domains.

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 paper presents a gapless, telomere-to-telomere assembly of the human X chromosome using ultra-long-read nanopore sequencing and complementary technologies.

The paper identifies gemin3 as a regeneration-essential gene in zebrafish and shows smn1, gemin3, and gemin5 inhibit the ErbB pathway to promote cell proliferation during tissue regeneration.

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

This paper presents a high-quality goldfish genome assembly and analyzes gene evolution after whole genome duplication, identifying gene divergence patterns across tissues.

The paper characterizes the Morpheus gene family, identifying two subfamilies, expression patterns, and potential immune-related functions.