Christina A. Boucher

alamem and alasight are tools for fast and memory-efficient local alignment and horizontal gene transfer detection in bacterial genomes.

Vir2vec is a genome-wide viral embedding model that outperforms existing models in viral genome understanding tasks and provides explainability for host adaptation mutations.

This paper introduces an algorithmic framework for comparing and sorting RLZ compressed sequences, achieving speedups over character-based sorting.

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

RAmpSim simulates hybridization capture in metagenomic sequencing by modeling thermodynamic binding and fragment generation, improving coverage accuracy over uniform baselines.

RAPID-PFP accelerates Prefix-Free Parsing using GPU parallelism, achieving significant speedups on genomic datasets compared to CPU implementations.

AURA is a scalable machine learning framework for predicting antibiotic resistance in Mycobacterium tuberculosis, identifying novel resistance-associated loci.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

The paper introduces PBML, an algorithm for efficiently detecting long-range shared ancestry tracts in large haplotype panels by filtering short, uninformative matches.

This paper introduces a scalable framework for variant-aware primer design that improves robustness and efficiency in multiplex PCR assays.

The paper introduces RLZ-RePair, a method that combines RLZ parsing with RePair to create efficient grammar-based compression with reduced memory usage and comparable performance to standard RePair.

divider reconstructs haplotypes from long-read sequencing data, achieving higher accuracy than existing methods on synthetic and real datasets.

This paper introduces Re2Pair, a modified RePair algorithm that reduces memory usage and improves speed for compressing large genomic datasets.

This paper develops a machine learning classifier to predict antibiotic resistance in Mycobacterium tuberculosis using genomic data and achieves high accuracy for first-line antibiotics.

OCTOPUS is a metagenomics classifier for portable sequencing data that improves accuracy and reduces false positives on mobile devices.

ONeSAMP 3.0 estimates genetic effective population size (Ne) from SNP data of a single population using Approximate Bayesian Computation and local linear regression, showing robustness and accuracy in simulated and empirical data.

KARGVA identifies antibiotic resistance gene variants from metagenomics data with high accuracy and efficiency, outperforming existing tools in detecting ARGVs.

This paper introduces recursive prefix-free parsing to reduce memory needed for building run-length encoded BWTs, showing effective memory reduction in experiments.

The paper introduces μ-PBWT, a memory-efficient method for haplotype matching, reducing memory usage by up to 25 times and enabling storage of large datasets on a commodity laptop.

The paper introduces a recursive prefix-free parsing method to improve the efficiency of building pangenome alignment indexes, reducing construction time and memory usage.

The paper presents efficient data structures for storing and querying the positional Burrows-Wheeler Transform (PBWT) to improve memory usage for large haplotype datasets.

The paper introduces Syotti, a heuristic method for designing DNA baits that outperforms existing methods in speed and coverage efficiency.

The paper evaluates AMR prediction methods using HTS data from clinical isolates, finding high variance in performance and highlighting issues with sampling bias and uncharacterized AMR genes.

The paper introduces a Gaussian mixture model clustering method to find overlapping Rmaps without quantization, improving precision and efficiency in optical mapping analysis.

MONI is a pangenomics index that efficiently finds maximal exact matches by combining prefix-free parsing with threshold calculation, outperforming existing tools in speed and memory usage.

SPUMONI enables fast and accurate targeted nanopore sequencing using efficient pangenome indexes, outperforming minimap2 in speed and memory usage.

The paper introduces BufBOSS, a compressed dynamic de Bruijn graph that improves update efficiency by buffering changes, outperforming existing tools in time, memory, and deletion speed.

The paper surveys computational methods for indexing and querying large sequencing datasets using k-mer-based data structures.

This paper introduces DynamicBOSS, a succinct dynamic de Bruijn graph representation that supports unlimited additions and deletions of nodes and edges, outperforming existing methods for large-scale datasets.

The paper introduces an efficient method for constructing a complete index for pan-genomics read alignment, improving memory and time efficiency over existing methods.