Bryce L. Kille

Seqwin identifies microbial signature sequences by analyzing large genome collections, outperforming existing methods in efficiency and quality.

The paper introduces Min-Frame Transformation (MFT) to improve viral genome alignment by enhancing MUM-based seeding, resulting in longer and more contiguous matches with better alignment coverage and SNP recall.

The paper introduces CLASSIC, a platform that maps sequence-to-function relationships in synthetic biology by combining long- and short-read sequencing to analyze gene circuits.

Strainify estimates strain-level abundances from low-coverage short-read metagenomic data, outperforming existing methods in simulated and real datasets.

tMHG-Finder uses Mash guide trees and consensus representative sequences to find maximal homologous groups in bacterial genomes with linear scaling, reaching F-score 0.932 on simulated data.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

The paper establishes a near-tight lower bound on the density of forward sampling schemes and shows existing schemes are closer to optimal than previously thought.

Olivar automates variant-aware primer design for tiled amplicon sequencing of pathogens, improving mapping rates and coverage compared to existing methods.

This paper introduces Lemur and Magnet, lightweight tools for accurate taxonomic profiling of long-read metagenomic datasets, showing they run efficiently on laptops.

Parsnp 2.0 improves scalability and control for multiple genome alignment of microbial datasets, reducing memory and runtime while maintaining accuracy.

The paper introduces minmers, a generalization of minimizers that provide unbiased local Jaccard similarity estimates, improving the accuracy and speed of sequence comparison tools like MashMap.

SeqScreen uses ensemble learning to accurately label pathogenic sequences with functional annotations, achieving high recall and precision for microbial pathogenesis.

Variabel identifies low frequency intra-host variants from Oxford Nanopore sequencing data, outperforming existing tools for this task.