Karen M. Vásquez

HSeeker: an algorithm for systematic H-DNA sequence identification

HSeeker identifies and scores H-DNA-forming sequences using a three-part algorithm, providing genomic coordinates and stability scores for further analysis.

HMGB1 assists in overcoming cisplatin resistance in chemoresistant human ovarian cancer cells

This study shows HMGB1 helps ovarian cancer cells resist cisplatin, and inhibiting HMGB1 makes these cells more sensitive to cisplatin treatment.

Characterization of Z-DNA dynamics across the tree of life

The paper characterizes Z-DNA dynamics across different lineages using ZSeeker, finding lineage-specific enrichment and depletion patterns in cellular and viral genomes.

ZSeekerDB: A database of Z-nucleic acid sequences across organismal genomes

ZSeekerDB catalogs Z-nucleic acid sequences across organismal genomes, enabling cross-species analysis of their distribution and evolutionary significance.

Landscape and mutational dynamics of G-quadruplexes in the complete human genome and in haplotypes of diverse ancestry

The paper maps G-quadruplexes across the human genome and haplotypes, showing their enrichment in repetitive regions and association with genomic instability and PRDM9 binding.

ZSeeker: An optimized algorithm for Z-DNA detection in genomic sequences

ZSeeker detects potential Z-DNA-forming sequences in genomes with improved accuracy and accessibility through a Python package and web interface.

Characterization of hairpin loops and cruciforms across 118,065 genomes spanning the tree of life

The paper analyzes inverted repeats across 118,065 genomes to study their distribution, frequency, and functional roles in genomic instability and evolution.

Quadrupia: Derivation of G-quadruplexes for organismal genomes across the tree of life

Quadrupia identifies and characterizes G-quadruplex sequences across 108,449 genomes, revealing taxonomic patterns and experimentally validating key structures.

MoCoLo: a testing framework for motif co-localization

MoCoLo tests motif co-localization by analyzing reciprocal co-occurrence and accounting for confounders, confirming histone marker co-occurrence and oxidative DNA damage localization.