Christopher Pockrandt

CHESS 3 improves upon previous versions by using better algorithms and filtering to create a more accurate catalog of human genes and transcripts.

KrakenUniq improves metagenomic classification on low-memory systems by processing databases in chunks without sacrificing accuracy.

PhyloCSF++ provides a fast, parallelized implementation of PhyloCSF for genome-wide coding/non-coding region prediction and includes annotation tools.

This paper introduces Bolotie, a method to detect recombination in SARS-CoV-2 genomes, identifying hundreds of recombinant isolates and showing some persist in the population.

GenMap computes genome mappability exactly and efficiently, outperforming existing methods and enabling marker gene identification in bacterial strains.

This paper introduces a mixed integer program to find optimal search schemes for approximate string matching using bidirectional FM-index, significantly improving speed over previous methods.