Publications

Journal papers (sorted by publication date)

  1. Treangen, TJ., Schoeler, G., Phillippy, A. M., Bergman, N. H., & Turell, M. J. (2016). Identification and Genomic Analysis of a Novel Group C Orthobunyavirus Isolated from a Mosquito Captured near Iquitos, Peru. PLoS Negl Trop Dis, 10(4).
  2. Davison, M., Treangen, TJ., Koren, S., Pop, M., & Bhaya, D. (2016). Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers. PloS one, 11(9)
  3. Ondov BD, Treangen TJ, Koren S, Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash, Genome Biology, 2015.
  4. Treangen TJ, Ondov B, Phillippy AM. Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes. 2014
  5. Zimin A, et al, Treangen TJ, Salzberg SL, Norgren R. A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology Direct, 2014.
  6. Treangen, TJ, et al. “Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. Aureus ATCC 25923”. Genome announcements , 2014.
  7. Koren, S, Treangen, TJ, et al “Automated ensemble assembly and validation of microbial genomes.”. BMC Bioinformatics, 2014.
  8. Treangen, TJ., et al. "MetAMOS: a modular and open source metagenomic assembly and analysis pipeline." Genome biology 14.1 (2013): R2.
  9. Harrington R, Ondov B, Radune D, Friss M, Klubnik J, Diviak L, Hnath J, Cendrowski S, Blank T, Karaolis D, Friedlander A, Burans J, Rosovitz MJ, Treangen TJ, Phillippy AM, Bergman NH. "Genome sequence of the attenuated Carbosap vaccine strain of Bacillus anthracis." Genome announcements 1.1 (2013).
  10. Treangen, TJ, and Adam M. Phillippy. "Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone." Genome biology 2012.13 (2012): 181.
  11. Human Microbiome Project Consortium (Methé BA, Nelson KE, Pop M, et al.). A framework for human microbiome research. Nature. 2012 Jun 13;486(7402):215-21.
  12. Human Microbiome Project Consortium (Huttenhower C, Gevers D, Knight R, et al.). Structure, function and diversity of the healthy human microbiome. Nature. 2012 Jun 13;486(7402):207-14.
  13. Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S. Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One. 2012;7(6):e37919.
  14. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res. 2012 Mar;22(3):557-67.
  15. Treangen TJ and Salzberg SL. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet. 2011 Nov 29;13(1):36-46.
  16. Koren S, Treangen TJ, Pop M. Bambus2: Scaffolding Polymorphic Genomes and Metagenomes. Bioinformatics. 2011 Sep 16. PMID: 21926123.
  17. Enk J, Debruyne R, Devalut A, King CE, Treangen TJ, O’Rourke D, Salzberg SL, Fisher D, MacPhee R, Poinar H. Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths. Genome Biol. 2011 May 31;12(5):R51.
  18. Liu B, Gibbons T, Ghodsi M, Treangen TJ, Pop M. Accurate and Fast Estimation of Taxonomic Profiles from Metagenomic Shotgun Sequences. BMC Genomics. 2011;12:S2.
  19. Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M. Next Generation Sequence Assembly with AMOS. Curr Protoc Bioinformatics. 2011 Mar;Chapter 11:Unit11.8. PubMed PMID: 21400694.
  20. Treangen TJ, Rocha EP. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet. 2011 Jan 27;7(1):e1001284. PubMed PMID: 21298028; PubMed Central PMCID: PMC3029252. **Evaluated by Faculty of 1000.
  21. Treangen TJ, Darling AE, Achaz G, Ragan MA, Messeguer X, Rocha EP. A novel heuristic for local multiple alignment of interspersed DNA repeats. IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):180-9. PubMed PMID: 19407343.
  22. Treangen TJ, Abraham AL, Touchon M, Rocha EP. Genesis, effects and fates of repeats in prokaryotic genomes. FEMS Microbiol Rev. 2009 May;33(3):539-71. Review. PubMed PMID: 19396957.
  23. Treangen TJ, Ambur OH, Tonjum T, Rocha EP. The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome Biol. 2008;9(3):R60. Epub 2008 Mar 26. PubMed PMID: 18366792; PubMed Central PMCID: PMC2397512.
  24. Darling AE, Treangen TJ, Messeguer X, Perna NT. Analyzing patterns of microbial evolution using the mauve genome alignment system. Methods Mol Biol. 2007;396:135-52. PubMed PMID: 18025691.
  25. Treangen TJ, Messeguer X. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC Bioinformatics. 2006 Oct 5;7:433. PubMed PMID: 17022809; PubMed Central PMCID: PMC1629028.

Conference Papers

  1. Darling AE, Treangen TJ, Zhang L, Kuiken C, Messeguer X, Perna NT. Procrastination leads to efficient filtration for local multiple alignment. WABI 2006. Lecture Notes in Bioinformatics 4175, Springer-Verlag 2006.
  2. Treangen TJ, Modi N, and Messeguer X. Optimized search for common unique substrings, on both forward and reverse strands, in multiple DNA sequences. Conference proceedings of the 1st International Conference on Bioinformatics Research and Development (BIRD'07).
  3. Treangen TJ, Darling AE, Achaz G, Ragan MA, Messeguer X. Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats. Lecture Notes in Bioinformatics 4983. pp. 74–86, 2008. c Springer-Verlag Berlin Heidelberg 2008.
  4. Hill CM, Astrovskaya I, Huang H, Koren S, Memon A, Treangen TJ, Pop M. De novo likelihood-based measures for comparing metagenomic assemblies. BIBM 2013.

Book Chapters

  1. Darling AE, Treangen TJ, Messeguer X, Perna NT. Analyzing patterns of microbial evolution using the mauve genome alignment system. Methods Mol Biol. 2007;396:135-52. PubMed PMID: 18025691.