Travis Gagie

SIFT selects reference haplotypes for genome patching using compressed indexing and pseudo-MEM queries to improve T2T imputation efficiency.

Sarand extracts AMR gene contexts from metagenomic assembly graphs, improving precision and sensitivity over existing methods.

Movi 2 improves pangenome indexing by reducing memory footprint and enabling space-time tradeoffs for efficient querying.

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

Columba is a high-performance lossless aligner for Illumina sequencing data that outperforms existing tools in speed and memory efficiency, particularly for large datasets.

This paper introduces a run-length compressed metagenomic read classification method that outperforms existing tools in accuracy and runtime while maintaining efficient memory usage.

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.

Movi is a fast pangenome index that enables efficient querying of nanopore sequencing reads using move structures, achieving faster speeds than existing methods.

The paper introduces b-move, a bidirectional extension of the move structure for run-length compressed indices, achieving faster character extensions than existing methods while maintaining memory efficiency.

SPUMONI 2 improves pangenome classification by using a compressed index of minimizer digests, achieving faster speed, lower memory use, and better performance for short and long reads.

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 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 k-MEMs and extends the MONI index to efficiently find them for pangenome-to-pangenome comparison.

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

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

The paper introduces a preprocessing algorithm called prefix-free parsing to efficiently build compressed Burrows-Wheeler Transform indexes for large genomic datasets.

The paper compares finite-state machines and position weight matrices for modeling sequence motifs, finding FSMs provide better discrimination of positive and negative sequences.

The paper introduces a data structure that efficiently represents colored de Bruijn graphs, reducing memory usage for genetic variant detection and genotyping in population-level data.

This paper surveys the history of using reference genomes and differential regions for genomic database search and indexing, relating it to kernelization in parameterized complexity.