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Items: 11

1.

The Perceptual Proxies of Visual Comparison.

Jardine N, Ondov BD, Elmqvist N, Franconeri S.

IEEE Trans Vis Comput Graph. 2019 Aug 20. doi: 10.1109/TVCG.2019.2934786. [Epub ahead of print]

PMID:
31443016
2.

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.

3.

BLAST-based validation of metagenomic sequence assignments.

Bazinet AL, Ondov BD, Sommer DD, Ratnayake S.

PeerJ. 2018 May 28;6:e4892. doi: 10.7717/peerj.4892. eCollection 2018.

4.

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.

5.
6.

Genome Sequence of the Attenuated Carbosap Vaccine Strain of Bacillus anthracis.

Harrington R, Ondov BD, Radune D, Friss MB, Klubnik J, Diviak L, Hnath J, Cendrowski SR, Blank TE, Karaolis D, Friedlander AM, Burans JP, Rosovitz MJ, Treangen T, Phillippy AM, Bergman NH.

Genome Announc. 2013 Jan;1(1). pii: e00067-12. doi: 10.1128/genomeA.00067-12. Epub 2013 Jan 15.

7.

Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis.

Passalacqua KD, Varadarajan A, Weist C, Ondov BD, Byrd B, Read TD, Bergman NH.

PLoS One. 2012;7(8):e43350. doi: 10.1371/journal.pone.0043350. Epub 2012 Aug 22.

8.

Interactive metagenomic visualization in a Web browser.

Ondov BD, Bergman NH, Phillippy AM.

BMC Bioinformatics. 2011 Sep 30;12:385. doi: 10.1186/1471-2105-12-385.

9.

An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System.

Ondov BD, Cochran C, Landers M, Meredith GD, Dudas M, Bergman NH.

Bioinformatics. 2010 Aug 1;26(15):1901-2. doi: 10.1093/bioinformatics/btq291. Epub 2010 Jun 18.

10.

Structure and complexity of a bacterial transcriptome.

Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, Zwick ME, Bergman NH.

J Bacteriol. 2009 May;191(10):3203-11. doi: 10.1128/JB.00122-09. Epub 2009 Mar 20.

11.

Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications.

Ondov BD, Varadarajan A, Passalacqua KD, Bergman NH.

Bioinformatics. 2008 Dec 1;24(23):2776-7. doi: 10.1093/bioinformatics/btn512. Epub 2008 Oct 7.

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