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Items: 25

1.

Traumatic Brain Injury in Mice Induces Acute Bacterial Dysbiosis Within the Fecal Microbiome.

Treangen TJ, Wagner J, Burns MP, Villapol S.

Front Immunol. 2018 Nov 27;9:2757. doi: 10.3389/fimmu.2018.02757. eCollection 2018.

2.

You can't always sequence your way out of a tight spot: Next-generation sequencing holds great promise for pathogen detection, but the devil is in the details.

Treangen TJ, Pop M.

EMBO Rep. 2018 Dec;19(12). pii: e47036. doi: 10.15252/embr.201847036. Epub 2018 Nov 21. No abstract available.

PMID:
30467235
3.

Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.

Meisel JS, Nasko DJ, Brubach B, Cepeda-Espinoza V, Chopyk J, Corrada-Bravo H, Fedarko M, Ghurye J, Javkar K, Olson ND, Shah N, Allard SM, Bazinet AL, Bergman NH, Brown A, Caporaso JG, Conlan S, DiRuggiero J, Forry SP, Hasan NA, Kralj J, Luethy PM, Milton DK, Ondov BD, Preheim S, Ratnayake S, Rogers SM, Rosovitz MJ, Sakowski EG, Schliebs NO, Sommer DD, Ternus KL, Uritskiy G, Zhang SX, Pop M, Treangen TJ.

Microbiome. 2018 Nov 5;6(1):197. doi: 10.1186/s40168-018-0582-5.

4.

RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification.

Nasko DJ, Koren S, Phillippy AM, Treangen TJ.

Genome Biol. 2018 Oct 30;19(1):165. doi: 10.1186/s13059-018-1554-6.

5.

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.

Olson ND, Treangen TJ, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, Pop M.

Brief Bioinform. 2017 Aug 7. doi: 10.1093/bib/bbx098. [Epub ahead of print]

PMID:
28968737
6.

Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station.

Venkateswaran K, Checinska Sielaff A, Ratnayake S, Pope RK, Blank TE, Stepanov VG, Fox GE, van Tongeren SP, Torres C, Allen J, Jaing C, Pierson D, Perry J, Koren S, Phillippy A, Klubnik J, Treangen TJ, Rosovitz MJ, Bergman NH.

Genome Announc. 2017 Aug 10;5(32). pii: e00680-17. doi: 10.1128/genomeA.00680-17.

7.

Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.

Davison M, Treangen TJ, Koren S, Pop M, Bhaya D.

PLoS One. 2016 Sep 9;11(9):e0160574. doi: 10.1371/journal.pone.0160574. eCollection 2016.

8.

Mash: fast genome and metagenome distance estimation using MinHash.

Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM.

Genome Biol. 2016 Jun 20;17(1):132. doi: 10.1186/s13059-016-0997-x.

9.

Identification and Genomic Analysis of a Novel Group C Orthobunyavirus Isolated from a Mosquito Captured near Iquitos, Peru.

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

PLoS Negl Trop Dis. 2016 Apr 13;10(4):e0004440. doi: 10.1371/journal.pntd.0004440. eCollection 2016 Apr.

10.
11.

Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923.

Treangen TJ, Maybank RA, Enke S, Friss MB, Diviak LF, Karaolis DK, Koren S, Ondov B, Phillippy AM, Bergman NH, Rosovitz MJ.

Genome Announc. 2014 Nov 6;2(6). pii: e01110-14. doi: 10.1128/genomeA.01110-14.

12.

Automated ensemble assembly and validation of microbial genomes.

Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM.

BMC Bioinformatics. 2014 May 3;15:126. doi: 10.1186/1471-2105-15-126.

13.

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.

Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M.

Genome Biol. 2013 Jan 15;14(1):R2. doi: 10.1186/gb-2013-14-1-r2.

14.

Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone.

Treangen TJ, Phillippy AM.

Genome Biol. 2012 Dec 27;13(12):181. doi: 10.1186/gb-2012-13-12-181.

15.

Deep sequencing of the oral microbiome reveals signatures of periodontal disease.

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.

PLoS One. 2012;7(6):e37919. doi: 10.1371/journal.pone.0037919. Epub 2012 Jun 4.

16.

GAGE: A critical evaluation of genome assemblies and assembly algorithms.

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.

Genome Res. 2012 Mar;22(3):557-67. doi: 10.1101/gr.131383.111. Epub 2012 Jan 6. Erratum in: Genome Res. 2012 Jun;22(6):1196.

17.

Repetitive DNA and next-generation sequencing: computational challenges and solutions.

Treangen TJ, Salzberg SL.

Nat Rev Genet. 2011 Nov 29;13(1):36-46. doi: 10.1038/nrg3117. Review. Erratum in: Nat Rev Genet. 2012 Feb;13(2):146.

18.

Bambus 2: scaffolding metagenomes.

Koren S, Treangen TJ, Pop M.

Bioinformatics. 2011 Nov 1;27(21):2964-71. doi: 10.1093/bioinformatics/btr520. Epub 2011 Sep 16.

19.

Next generation sequence assembly with AMOS.

Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M.

Curr Protoc Bioinformatics. 2011 Mar;Chapter 11:Unit 11.8. doi: 10.1002/0471250953.bi1108s33.

20.

Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes.

Treangen TJ, Rocha EP.

PLoS Genet. 2011 Jan 27;7(1):e1001284. doi: 10.1371/journal.pgen.1001284.

21.

A novel heuristic for local multiple alignment of interspersed DNA repeats.

Treangen TJ, Darling AE, Achaz G, Ragan MA, Messeguer X, Rocha EP.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):180-9. doi: 10.1109/TCBB.2009.9.

PMID:
19407343
22.

Genesis, effects and fates of repeats in prokaryotic genomes.

Treangen TJ, Abraham AL, Touchon M, Rocha EP.

FEMS Microbiol Rev. 2009 May;33(3):539-71. Review.

23.

The impact of the neisserial DNA uptake sequences on genome evolution and stability.

Treangen TJ, Ambur OH, Tonjum T, Rocha EP.

Genome Biol. 2008;9(3):R60. doi: 10.1186/gb-2008-9-3-r60. Epub 2008 Mar 26.

24.

Analyzing patterns of microbial evolution using the mauve genome alignment system.

Darling AE, Treangen TJ, Messeguer X, Perna NT.

Methods Mol Biol. 2007;396:135-52.

PMID:
18025691

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