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Venkateswaran K, Checinska-Sielaff A, Klubnik J, Treangen T, Rosovitz M.J., Bergman NH. 2017. Draft Genome Sequences from a Novel Clade of Bacillus cereus sensu lato Strains Isolated from the International Space Station. Genome Announcements. 1:1.

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Treangen T, Schoeler G, Phillippy AM, Bergman NH, Turell MJ. 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.

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Treangen TJ, Maybank RA, Enke S, Friss MBeth, Diviak LF, Karaolis DKR, Koren S, Ondov B, Phillippy AM, Bergman NH. 2014. Complete genome sequence of the quality control strain Staphylococcus aureus subsp. aureus ATCC 25923. Genome announcements. 2:e01110–14.

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Treangen T, Ondov BD, Koren S, Phillippy AM. 2014. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome biology. 15:524.

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Zimin AV, Cornish AS, Maudhoo MD, Gibbs RM, Zhang X, Pandey S, Meehan DT, Wipfler K, Bosinger SE, Johnson ZP et al.. 2014. A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology direct. 9:20.

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Harrington R, Ondov BD, Radune D, Friss MBeth, Klubnik J, Diviak L, Hnath J, Cendrowski SR, Blank TE, Karaolis D et al.. 2013. Genome sequence of the attenuated Carbosap vaccine strain of Bacillus anthracis. Genome announcements. 1:e00067–12.

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Consortium HMicrobiome, Treangen T. 2012. A framework for human microbiome research. Nature. 486:215–221.

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Phillippy A, Treangen T. 2012. Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone. Genome Biology. 13

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Consortium HMicrobiome, Treangen T. 2012. Structure, function and diversity of the healthy human microbiome. Nature. 486:207–214.

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Enk J, Devault A, Debruyne R, King CE, Treangen T, O'Rourke D, Salzberg SL, Fisher D, MacPhee R, Poinar H. 2011. Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths. Genome biology. 12:R51.

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Treangen T, Rocha E. 2011. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet. 7:e1001284.

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Treangen T, Salzberg SL. 2011. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature Reviews Genetics.

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Treangen T, Abraham A-L, Touchon M, Rocha EPC. 2009. Genesis, effects and fates of repeats in prokaryotic genomes. FEMS microbiology reviews. 33:539–571.

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Treangen T, Messeguer X. 2009. Novel computational methods for large scale genome comparison. 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008).

Treangen T, Darling AE, Achaz G, Ragan MA, Messeguer X, Rocha EPC. 2009. A novel heuristic for local multiple alignment of interspersed DNA repeats. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB). 6:180–189.

Treangen T, Darling A.E., Achaz G., Ragan M.A., Messeguer X., Rocha E.P.C.. 2009. A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 6(2):180-189.

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Treangen T, Ambur OHerman, Tonjum T, Rocha EPC. 2008. The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome biology. 9:R60.

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Treangen T, Darling AE, Ragan MA, Messeguer X. 2008. Lecture Notes in Computer ScienceBioinformatics Research and ApplicationsGapped Extension for Local Multiple Alignment of Interspersed DNA Repeats. 4983:74-86.

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Darling AE, Treangen T, Messeguer X, Perna NT. 2007. Analyzing patterns of microbial evolution using the mauve genome alignment system. Comparative Genomics. :135–152.

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Darling AE, Treangen T, Messeguer X, Perna NT. 2007. Methods in Molecular BiologyComparative GenomicsAnalyzing Patterns of Microbial Evolution Using the Mauve Genome Alignment System. 396:135-152.

Treangen T, Messeguer X. 2006. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC bioinformatics. 7:433.

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Darling AE, Treangen T, Zhang L, Kuiken C, Messeguer X, Perna NT. 2006. Procrastination leads to efficient filtration for local multiple alignment. International Workshop on Algorithms in Bioinformatics.

Darling AE, Treangen T, Zhang L, Kuiken C, Messeguer X, Perna NT. 2006. Procrastination Leads to Efficient Filtration for Local Multiple Alignment. 4175:126-137.