Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae. - Patrick H. Bradley; Matthew J. Brauer; Joshua D. Rabinowitz; Olga G. Troyanskaya (PLoS Comput. Biol., 2009)

GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality. - Thomas D. Wu; Jens Reeder; Michael Lawrence; Gabe Becker; Matthew J. Brauer (Statistical Genomics, 2016)

In silico tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales. - Jieming Chen; Shravan Madireddi; Deepti Nagarkar; Maciej Migdal; Jason A. Vander Heiden; Diana Chang; Kiran Mukhyala; Suresh Selvaraj; Edward E. Kadel; Matthew J. Brauer; Sanjeev Mariathasan; Julie Hunkapiller; et al. (Briefings Bioinform., 2021)