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Results: 1 to 20 of 23

1.

Reducing assembly complexity of microbial genomes with single-molecule sequencing.

Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, Mcvey SD, Radune D, Bergman NH, Phillippy AM.

Genome Biol. 2013;14(9):R101.

PMID:
24034426
[PubMed - in process]
Free PMC Article
2.

Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution.

Fang G, Passalacqua KD, Hocking J, Llopis PM, Gerstein M, Bergman NH, Jacobs-Wagner C.

BMC Genomics. 2013 Jul 5;14:450. doi: 10.1186/1471-2164-14-450.

PMID:
23829427
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
23405332
[PubMed - as supplied by publisher]
Free PMC Article
4.

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.

PMID:
22937038
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Molecular epidemiologic investigation of an anthrax outbreak among heroin users, Europe.

Price EP, Seymour ML, Sarovich DS, Latham J, Wolken SR, Mason J, Vincent G, Drees KP, Beckstrom-Sternberg SM, Phillippy AM, Koren S, Okinaka RT, Chung WK, Schupp JM, Wagner DM, Vipond R, Foster JT, Bergman NH, Burans J, Pearson T, Brooks T, Keim P.

Emerg Infect Dis. 2012 Aug;18(8):1307-13. doi: 10.3201/eid1808.111343.

PMID:
22840345
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
21961884
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Genomic fluidity: an integrative view of gene diversity within microbial populations.

Kislyuk AO, Haegeman B, Bergman NH, Weitz JS.

BMC Genomics. 2011 Jan 13;12:32. doi: 10.1186/1471-2164-12-32.

PMID:
21232151
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
20562417
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

A class I ligase ribozyme with reduced Mg2+ dependence: Selection, sequence analysis, and identification of functional tertiary interactions.

Bagby SC, Bergman NH, Shechner DM, Yen C, Bartel DP.

RNA. 2009 Dec;15(12):2129-46. doi: 10.1261/rna.1912509.

PMID:
19946040
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
19304856
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Comparative transcriptional profiling of Bacillus cereus sensu lato strains during growth in CO2-bicarbonate and aerobic atmospheres.

Passalacqua KD, Varadarajan A, Byrd B, Bergman NH.

PLoS One. 2009;4(3):e4904. doi: 10.1371/journal.pone.0004904. Epub 2009 Mar 19.

PMID:
19295911
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Structural and functional analysis of AsbF: origin of the stealth 3,4-dihydroxybenzoic acid subunit for petrobactin biosynthesis.

Pfleger BF, Kim Y, Nusca TD, Maltseva N, Lee JY, Rath CM, Scaglione JB, Janes BK, Anderson EC, Bergman NH, Hanna PC, Joachimiak A, Sherman DH.

Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):17133-8. doi: 10.1073/pnas.0808118105. Epub 2008 Oct 27.

PMID:
18955706
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
18842598
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Transcriptional profiling of Bacillus anthracis during infection of host macrophages.

Bergman NH, Anderson EC, Swenson EE, Janes BK, Fisher N, Niemeyer MM, Miyoshi AD, Hanna PC.

Infect Immun. 2007 Jul;75(7):3434-44. Epub 2007 Apr 30.

PMID:
17470545
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

The global transcriptional responses of Bacillus anthracis Sterne (34F2) and a Delta sodA1 mutant to paraquat reveal metal ion homeostasis imbalances during endogenous superoxide stress.

Passalacqua KD, Bergman NH, Lee JY, Sherman DH, Hanna PC.

J Bacteriol. 2007 Jun;189(11):3996-4013. Epub 2007 Mar 23.

PMID:
17384197
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Biosynthetic analysis of the petrobactin siderophore pathway from Bacillus anthracis.

Lee JY, Janes BK, Passalacqua KD, Pfleger BF, Bergman NH, Liu H, HÃ¥kansson K, Somu RV, Aldrich CC, Cendrowski S, Hanna PC, Sherman DH.

J Bacteriol. 2007 Mar;189(5):1698-710. Epub 2006 Dec 22.

PMID:
17189355
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Operon prediction for sequenced bacterial genomes without experimental information.

Bergman NH, Passalacqua KD, Hanna PC, Qin ZS.

Appl Environ Microbiol. 2007 Feb;73(3):846-54. Epub 2006 Nov 22.

PMID:
17122389
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Transcriptional profiling of the Bacillus anthracis life cycle in vitro and an implied model for regulation of spore formation.

Bergman NH, Anderson EC, Swenson EE, Niemeyer MM, Miyoshi AD, Hanna PC.

J Bacteriol. 2006 Sep;188(17):6092-100.

PMID:
16923876
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

The superoxide dismutases of Bacillus anthracis do not cooperatively protect against endogenous superoxide stress.

Passalacqua KD, Bergman NH, Herring-Palmer A, Hanna P.

J Bacteriol. 2006 Jun;188(11):3837-48.

PMID:
16707676
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Murine macrophage transcriptional responses to Bacillus anthracis infection and intoxication.

Bergman NH, Passalacqua KD, Gaspard R, Shetron-Rama LM, Quackenbush J, Hanna PC.

Infect Immun. 2005 Feb;73(2):1069-80.

PMID:
15664951
[PubMed - indexed for MEDLINE]
Free PMC Article

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