Richard A. Goldstein

The paper compares the distribution of young de novo proteins, old canonical proteins, and randomized sequences in sequence space using k-mer-based distances, finding distinct patterns and potential pathways between classes.

HerpesDRG provides a database and tools for drug resistance mutation analysis in human herpesviruses using genotype-phenotype literature.

AYUKA is a fast, reliable viral genotyping tool using whole genome sequencing that requires no pre-processing and provides quality control metrics and genotype identification.

The paper introduces a sequence-weighting method for linkage disequilibrium calculations to reduce sampling bias by giving more weight to underrepresented sequences.

The paper shows that HIV-positive mothers have compartmentalized CMV genotypes, with three infants transmitting a single closely related maternal cervix strain, and identifies gene similarities linked to tissue-tropism and immunomodulation.

This paper introduces HaROLD, a method for haplotype reconstruction from longitudinal viral sequencing data using co-varying variant frequencies, showing high accuracy with synthetic datasets.