READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation

Rapid identification of non-human sequences in high-throughput sequencing datasets

(2012) Aparna Bhaduri et al.   BIOINFORMATICS

CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes

(2012) Ivan Borozan et al.   BMC BIOINFORMATICS

Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities

(2012) John Martin et al.   PLoS One

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

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

(2011) John R Prensner et al.   NATURE BIOTECHNOLOGY

Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads

(2011) Li C. Xia et al.   PLoS One

Harnessing parallelism in multicore clusters with the All-Pairs, Wavefront, and Makeflow abstractions

(2010) Li Yu et al.   Cluster Computing-The Journal of Networks Software Tools and Applications