Publications
2015. RNA-Seq identifies novel myocardial gene expression signatures of heart failure.. Genomics. 105(2):83-9.
2014. Removing batch effects for prediction problems with frozen surrogate variable analysis.. PeerJ. 2:e561.
2012. Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.. Mol Syst Biol. 8:602.
2015. Proteomics-based metabolic modeling reveals that fatty acid oxidation (FAO) controls endothelial cell (EC) permeability.. Mol Cell Proteomics. 14(3):621-34.
2009. Protein quantification across hundreds of experimental conditions. Proceedings of the National Academy of Sciences. 106(37):15544-15548.
2013. Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures. Science. 342(6162):1100-1104.
2009. A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays. Bioinformatics. 25(13):1609-1616.
2012. Plasmodium falciparum merozoite surface protein 1 blocks the proinflammatory protein S100P.. Proc Natl Acad Sci U S A. 109(14):5429-34.
2015. Phenotype-Dependent Coexpression Gene Clusters: Application to Normal and Premature Ageing. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 12(1):30-39.
2005. An outdoor 3-D visual tracking system for the study of spatial navigation and memory in rhesus monkeys.. Behav Res Methods. 37(3):453-63.
2014. Network-level architecture and the evolutionary potential of underground metabolism. Proceedings of the National Academy of Sciences. 111(32):11762-11767.
2015. Moving ahead on harnessing synthetic lethality to fight cancer. Molecular & Cellular Oncology. 2(2):e977150.
2014. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.. Bioinformatics. 30(10):1363-9.
2009. Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. BMC Genomics. 10(1):221.
2005. MCMC-Based Particle Filtering for Tracking a Variable Number of Interacting Targets. IEEE Transactions on Pattern Analysis and Machine Intelligence. 27(11):1805-1918.
2005. MCMC-based particle filtering for tracking a variable number of interacting targets.. IEEE Trans Pattern Anal Mach Intell. 27(11):1805-19.
2006. MCMC data association and sparse factorization updating for real time multitarget tracking with merged and multiple measurements.. IEEE Trans Pattern Anal Mach Intell. 28(12):1960-72.
2014. Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms. PLoS ONE. 9(5):e98372.
2014. Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors.. Genome Med. 6(8):61.
2014. Integrating Transcriptomics with Metabolic Modeling Predicts Biomarkers and Drug Targets for Alzheimer's Disease. PLoS ONE. 9(8):e105383.
2015. Insights from GWAS: emerging landscape of mechanisms underlying complex trait disease.. BMC Genomics. 16 Suppl 8:S4.
2015. Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm.. Front Plant Sci. 6:142.