BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets

(2014) Guorong Xu et al.   PLoS One

The landscape of viral expression and host gene fusion and adaptation in human cancer

(2013) Ka-Wei Tang et al.   Nature Communications

Lightweight Data Indexing and Compression in External Memory

(2011) Paolo Ferragina et al.   ALGORITHMICA

Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma

(2011) M. Castellarin et al.   GENOME RESEARCH

PathSeq: software to identify or discover microbes by deep sequencing of human tissue

(2011) Aleksandar D Kostic et al.   NATURE BIOTECHNOLOGY

Classification of DNA sequences using Bloom filters

(2010) Henrik Stranneheim et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS