The quantitative impact of read mapping to non-native reference genomes in comparative RNA-Seq studies

Integrated genome browser: visual analytics platform for genomics

(2016) Nowlan H. Freese et al.   BIOINFORMATICS

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification

(2014) Marius Vital et al.   ISME Journal

Transcriptome Sequencing Reveals the Virulence and Environmental Genetic Programs of Vibrio vulnificus Exposed to Host and Estuarine Conditions

(2014) Tiffany C. Williams et al.   PLoS One

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Gene expression profiling of resistant and susceptible Bombyx mori strains reveals nucleopolyhedrovirus-associated variations in host gene transcript levels

(2009) Yan-Yuan Bao et al.   GENOMICS