Publications
2006. Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region.. BMC Genomics. 7:60.
2011. Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC bioinformaticsBMC Bioinformatics. 12
2009. Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples. PLoS Comput BiologyPLoS Comput BiolPLoS Comput BiologyPLoS Comput Biol. 5
2010. Alignment and clustering of phylogenetic markers - implications for microbial diversity studies. BMC BioinformaticsBMC Bioinformatics. 11
2008. Figaro: A Novel Statistical Method for Vector Sequence Removal. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 24
2010. Identification of Pathogenic Vibrio Species by Multilocus PCR-Electrospray Ionization Mass Spectrometry and Its Application to Aquatic Environments of the Former Soviet Republic of Georgia. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 76
2010. Intensity normalization improves color calling in SOLiD sequencing. Nat MethNat MethNat MethNat Meth. 7
2011. Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1. BMC Evolutionary BiologyBMC Evolutionary Biology. 11
2007. Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex. Genome BiolGenome Biol. 8
2014. BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution.. Bioinformatics. 30(9):1214-9.
2014. A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration.. Mol Syst Biol. 10:744.
2014. A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness. PLoS Computational Biology. 10(7):e1003726.
2014. Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms. PLoS ONE. 9(5):e98372.
2007. GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo. DevelopmentDevelopment. 134
2009. Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development.. Plant Physiol. 150(3):1450-8.
2015. Fumarate induces redox-dependent senescence by modifying glutathione metabolism.. Nat Commun. 6:6001.
2014. A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology direct. 9:20.
2008. Covariability of Vibrio Cholerae Microdiversity and Environmental Parameters. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 74
2008. A simple binomial test for estimating sequencing errors in public repository 16S rRNA sequences. Journal of Microbiological MethodsJournal of Microbiological Methods. 72
2002. Genomic profiles of clinical and environmental isolates of Vibrio cholerae O1 in cholera-endemic areas of Bangladesh. Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences. 99
2009. Diversity and Seasonality of Bioluminescent Vibrio Cholerae Populations in Chesapeake Bay. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 75