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Items: 1 to 20 of 35

1.

Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens.

Loreille O, Ratnayake S, Bazinet AL, Stockwell TB, Sommer DD, Rohland N, Mallick S, Johnson PLF, Skoglund P, Onorato AJ, Bergman NH, Reich D, Irwin JA.

Genes (Basel). 2018 Mar 1;9(3). pii: E135. doi: 10.3390/genes9030135.

2.

Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation.

Miller JR, Koren S, Dilley KA, Puri V, Brown DM, Harkins DM, Thibaud-Nissen F, Rosen B, Chen XG, Tu Z, Sharakhov IV, Sharakhova MV, Sebra R, Stockwell TB, Bergman NH, Sutton GG, Phillippy AM, Piermarini PM, Shabman RS.

Gigascience. 2018 Mar 1;7(3):1-13. doi: 10.1093/gigascience/gix135.

3.

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.

4.

Non-Toxin-Producing Bacillus cereus Strains Belonging to the B. anthracis Clade Isolated from the International Space Station.

Venkateswaran K, Singh NK, Checinska Sielaff A, Pope RK, Bergman NH, van Tongeren SP, Patel NB, Lawson PA, Satomi M, Williamson CHD, Sahl JW, Keim P, Pierson D, Perry J.

mSystems. 2017 Jun 27;2(3). pii: e00021-17. doi: 10.1128/mSystems.00021-17. eCollection 2017 May-Jun.

5.

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.

Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM.

Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116. Epub 2017 Mar 15.

6.

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.

7.

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.

8.

Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes.

Hall AB, Papathanos PA, Sharma A, Cheng C, Akbari OS, Assour L, Bergman NH, Cagnetti A, Crisanti A, Dottorini T, Fiorentini E, Galizi R, Hnath J, Jiang X, Koren S, Nolan T, Radune D, Sharakhova MV, Steele A, Timoshevskiy VA, Windbichler N, Zhang S, Hahn MW, Phillippy AM, Emrich SJ, Sharakhov IV, Tu ZJ, Besansky NJ.

Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):E2114-23. doi: 10.1073/pnas.1525164113. Epub 2016 Mar 29.

9.

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.

10.

Filovirus RefSeq entries: evaluation and selection of filovirus type variants, type sequences, and names.

Kuhn JH, Andersen KG, Bào Y, Bavari S, Becker S, Bennett RS, Bergman NH, Blinkova O, Bradfute S, Brister JR, Bukreyev A, Chandran K, Chepurnov AA, Davey RA, Dietzgen RG, Doggett NA, Dolnik O, Dye JM, Enterlein S, Fenimore PW, Formenty P, Freiberg AN, Garry RF, Garza NL, Gire SK, Gonzalez JP, Griffiths A, Happi CT, Hensley LE, Herbert AS, Hevey MC, Hoenen T, Honko AN, Ignatyev GM, Jahrling PB, Johnson JC, Johnson KM, Kindrachuk J, Klenk HD, Kobinger G, Kochel TJ, Lackemeyer MG, Lackner DF, Leroy EM, Lever MS, Mühlberger E, Netesov SV, Olinger GG, Omilabu SA, Palacios G, Panchal RG, Park DJ, Patterson JL, Paweska JT, Peters CJ, Pettitt J, Pitt L, Radoshitzky SR, Ryabchikova EI, Saphire EO, Sabeti PC, Sealfon R, Shestopalov AM, Smither SJ, Sullivan NJ, Swanepoel R, Takada A, Towner JS, van der Groen G, Volchkov VE, Volchkova VA, Wahl-Jensen V, Warren TK, Warfield KL, Weidmann M, Nichol ST.

Viruses. 2014 Sep 26;6(9):3663-82. doi: 10.3390/v6093663.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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