Publications
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2011. Next Generation Sequence Assembly with AMOS. Current Protocols in BioinformaticsCurrent Protocols in Bioinformatics. 11
2009. A novel heuristic for local multiple alignment of interspersed DNA repeats. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB). 6:180–189.
2009. Genesis, effects and fates of repeats in prokaryotic genomes. FEMS microbiology reviews. 33:539–571.
2014. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome biology. 15:524.
2006. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC bioinformatics. 7:433.
2009. Novel computational methods for large scale genome comparison. 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008).
2013. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome BiolGenome Biol. 14
2009. A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 6(2):180-189.
2011. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature Reviews Genetics.
2016. Identification and genomic analysis of a novel group C orthobunyavirus isolated from a mosquito captured near Iquitos, Peru. PLoS Negl Trop Dis. 10:e0004440.
2011. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet. 7:e1001284.
2010. Hopx and Hdac2 Interact to Modulate Gata4 Acetylation and Embryonic Cardiac Myocyte Proliferation. Developmental CellDevelopmental Cell. 19
2016. Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease. Nature Communications. 7:8994.
2015. The effects of telomere shortening on cancer cells: a network model of proteomic and microRNA analysis.. Genomics. 105(1):5-16.
2016. The fruRBA Operon Is Necessary for Group A Streptococcal Growth in Fructose and for Resistance to Neutrophil Killing during Growth in Whole Human Blood. Infection and Immunity. 84(4):1016-1031.
2016. The fruRBA operon is necessary for Group A Streptococcal growth in fructose and for resistance to neutrophil killing during growth in whole human blood.. Infect Immun.
2007. Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acids ResearchNucleic Acids Research. 35
2017. Draft Genome Sequences from a Novel Clade of Bacillus cereus sensu lato Strains Isolated from the International Space Station. Genome Announcements. 1:1.
2002. Sequencing the human genome. Proceedings of the sixth annual international conference on Computational biology.
2008. Dual role colonization factors connecting Vibrio cholerae's lifestyles in human and aquatic environments open new perspectives for combating infectious diseases. Current Opinion in BiotechnologyCurrent Opinion in Biotechnology. 19
2010. Environmental reservoirs of Vibrio cholerae and their role in cholera. Environmental Microbiology ReportsEnvironmental Microbiology Reports. 2
2011. Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios. The ISME JournalThe ISME journal. 6
2010. Young Proteins Experience More Variable Selection Pressures Than Old Proteins. Genome ResearchGenome Res.Genome ResearchGenome Res.. 20
2011. Genome-Wide Survey of Natural Selection on Functional, Structural, and Network Properties of Polymorphic Sites in Saccharomyces Paradoxus. Molecular Biology and EvolutionMol Biol EvolMolecular Biology and EvolutionMol Biol Evol. 28
1992. copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USAProc Natl Acad Sci USA. 89