Publications
2012. Speeding Up Particle Trajectory Simulations under Moving Force Fields using GPUs. Journal of Computing and Information Science in EngineeringJournal of Computing and Information Science in Engineering.
2011. Social Snapshot: A System for Temporally Coupled Social Photography. Computer Graphics and Applications, IEEEComputer Graphics and Applications, IEEE. 31
2014. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.. Nat Biotechnol. 32(5):462-4.
2015. Proteomics-based metabolic modeling reveals that fatty acid oxidation (FAO) controls endothelial cell (EC) permeability.. Mol Cell Proteomics. 14(3):621-34.
2005. Data sharing in ecology and evolution. Trends in Ecology & EvolutionTrends in Ecology & Evolution. 20
2014. Removing batch effects for prediction problems with frozen surrogate variable analysis.. PeerJ. 2:e561.
2014. Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals. BMC Genomics. 15(1):526.
2015. Insights from GWAS: emerging landscape of mechanisms underlying complex trait disease.. BMC Genomics. 16 Suppl 8:S4.
1983. Splicing of messenger RNA precursors is inhibited by antisera to small nuclear ribonucleoprotein.. Cell. 35(1):101-7.
2005. Promoter architecture and response to a positive regulator of archaeal transcription. Molecular MicrobiologyMolecular Microbiology. 56
1996. Inferring phylogenies from DNA sequence data: The effects of sampling. New Uses for New PhylogeniesNew Uses for New Phylogenies.
2016. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biology. (1Suppl 19)
2015. Shape analysis of high-throughput transcriptomics experiment data.. Biostatistics. 16(4):627-40.
2016. Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli.. PLoS Comput Biol. 12(1):e1004705.
2015. Harnessing the landscape of microbial culture media to predict new organism-media pairings.. Nat Commun. 6:8493.
2014. Network-level architecture and the evolutionary potential of underground metabolism. Proceedings of the National Academy of Sciences. 111(32):11762-11767.
2011. Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis. Genome Biology. 12(9):R93.
2013. Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold. Bioinformatics (Oxford, England)Bioinformatics (Oxford, England). 29
2004. Structural flexibility in the Burkholderia mallei genome. Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America. 101
2013. Somatic alterations contributing to metastasis of a castration-resistant prostate cancer. Human mutationHuman mutation. 34
2016. A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity. npj Biofilms and Microbiomes. 2:16004.
2012. Drosophila Src regulates anisotropic apical surface growth to control epithelial tube size. Nature Cell Biology. 14(5):518-525.
2012. Drosophila Src regulates anisotropic apical surface growth to control epithelial tube size.. Nat Cell Biol. 14(5):518-25.
2004. Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic acids researchNucleic Acids Research. 32