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Items: 1 to 50 of 60

1.

A Zoonotic Adenoviral Human Pathogen Emerged through Genomic Recombination among Human and Nonhuman Simian Hosts.

Dehghan S, Seto J, Liu EB, Ismail AM, Madupu R, Heim A, Jones MS, Dyer DW, Chodosh J, Seto D.

J Virol. 2019 Aug 28;93(18). pii: e00564-19. doi: 10.1128/JVI.00564-19. Print 2019 Sep 15.

PMID:
31243128
2.

Author Correction: Genomic analysis of a large set of currently-and historically-important human adenovirus pathogens.

Ismail AM, Cui T, Dommaraju K, Singh G, Dehghan S, Seto J, Shrivastava S, Fedorova NB, Gupta N, Stockwell TB, Halpin R, Madupu R, Heim A, Kajon AE, Romanowski EG, Kowalski RP, Malathi J, Therese KL, Madhavan HN, Zhang Q, Ferreyra LJ, Jones MS, Rajaiya J, Dyer DW, Chodosh J, Seto D.

Emerg Microbes Infect. 2018 Dec 8;7(1):208. doi: 10.1038/s41426-018-0200-4.

3.

Co-occurrence of Anaerobes in Human Chronic Wounds.

Choi Y, Banerjee A, McNish S, Couch KS, Torralba MG, Lucas S, Tovchigrechko A, Madupu R, Yooseph S, Nelson KE, Shanmugam VK, Chan AP.

Microb Ecol. 2019 Apr;77(3):808-820. doi: 10.1007/s00248-018-1231-z. Epub 2018 Aug 23.

PMID:
30141127
4.

Genomic analysis of a large set of currently-and historically-important human adenovirus pathogens.

Ismail AM, Cui T, Dommaraju K, Singh G, Dehghan S, Seto J, Shrivastava S, Fedorova NB, Gupta N, Stockwell TB, Halpin R, Madupu R, Heim A, Kajon AE, Romanowski EG, Kowalski RP, Malathi J, Therese KL, Madhavan HN, Zhang Q, Ferreyra LJ, Jones MS, Rajaiya J, Dyer DW, Chodosh J, Seto D.

Emerg Microbes Infect. 2018 Feb 7;7(1):10. doi: 10.1038/s41426-017-0004-y. Erratum in: Emerg Microbes Infect. 2018 Dec 8;7(1):208.

5.

Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function.

Singh H, Yu Y, Suh MJ, Torralba MG, Stenzel RD, Tovchigrechko A, Thovarai V, Harkins DM, Rajagopala SV, Osborne W, Cogen FR, Kaplowitz PB, Nelson KE, Madupu R, Pieper R.

Theranostics. 2017 Jul 7;7(10):2704-2717. doi: 10.7150/thno.19679. eCollection 2017.

6.

Quantitative Differences in the Urinary Proteome of Siblings Discordant for Type 1 Diabetes Include Lysosomal Enzymes.

Suh MJ, Tovchigrechko A, Thovarai V, Rolfe MA, Torralba MG, Wang J, Adkins JN, Webb-Robertson BJ, Osborne W, Cogen FR, Kaplowitz PB, Metz TO, Nelson KE, Madupu R, Pieper R.

J Proteome Res. 2015 Aug 7;14(8):3123-35. doi: 10.1021/acs.jproteome.5b00052. Epub 2015 Jul 22.

PMID:
26143644
7.

Genome Sequence of a Sulfate-Reducing Thermophilic Bacterium, Thermodesulfobacterium commune DSM 2178T (Phylum Thermodesulfobacteria).

Bhatnagar S, Badger JH, Madupu R, Khouri HM, O'Connor EM, Robb FT, Ward NL, Eisen JA.

Genome Announc. 2015 Jan 29;3(1). pii: e01490-14. doi: 10.1128/genomeA.01490-14.

8.

Genome Sequence of the Sulfate-Reducing Thermophilic Bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347T (Phylum Nitrospirae).

Bhatnagar S, Badger JH, Madupu R, Khouri HM, O'Connor EM, Robb FT, Ward NL, Eisen JA.

Genome Announc. 2015 Jan 29;3(1). pii: e01489-14. doi: 10.1128/genomeA.01489-14.

9.

A Statistical Analysis of the Effects of Urease Pre-treatment on the Measurement of the Urinary Metabolome by Gas Chromatography-Mass Spectrometry.

Webb-Robertson BJ, Kim YM, Zink EM, Hallaian KA, Zhang Q, Madupu R, Waters KM, Metz TO.

Metabolomics. 2014 Oct 1;10(5):897-908.

10.

Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12.

Coil DA, Badger JH, Forberger HC, Riggs F, Madupu R, Fedorova N, Ward N, Robb FT, Eisen JA.

Genome Announc. 2014 Feb 20;2(1). pii: e00109-14. doi: 10.1128/genomeA.00109-14.

11.

Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets.

Ma Y, Madupu R, Karaoz U, Nossa CW, Yang L, Yooseph S, Yachimski PS, Brodie EL, Nelson KE, Pei Z.

J Virol. 2014 May;88(9):4786-97. doi: 10.1128/JVI.00093-14. Epub 2014 Feb 12.

12.

Evidence for horizontal gene transfer between Chlamydophila pneumoniae and Chlamydia phage.

Rosenwald AG, Murray B, Toth T, Madupu R, Kyrillos A, Arora G.

Bacteriophage. 2014 Dec 15;4(4):e965076. eCollection 2014.

13.

The COMBREX project: design, methodology, and initial results.

Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.

PLoS Biol. 2013;11(8):e1001638. doi: 10.1371/journal.pbio.1001638. Epub 2013 Aug 27. No abstract available.

14.

Microbiome in human health and disease.

Madupu R, Szpakowski S, Nelson KE.

Sci Prog. 2013;96(Pt 2):153-70.

PMID:
23901633
15.

Complete genome sequences of Mycoplasma leachii strain PG50T and the pathogenic Mycoplasma mycoides subsp. mycoides small colony biotype strain Gladysdale.

Wise KS, Calcutt MJ, Foecking MF, Madupu R, DeBoy RT, Röske K, Hvinden ML, Martin TR, Durkin AS, Glass JI, Methé BA.

J Bacteriol. 2012 Aug;194(16):4448-9. doi: 10.1128/JB.00761-12.

16.

CharProtDB: a database of experimentally characterized protein annotations.

Madupu R, Richter A, Dodson RJ, Brinkac L, Harkins D, Durkin S, Shrivastava S, Sutton G, Haft D.

Nucleic Acids Res. 2012 Jan;40(Database issue):D237-41. doi: 10.1093/nar/gkr1133. Epub 2011 Dec 2.

17.

Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop.

Brister JR, Bao Y, Kuiken C, Lefkowitz EJ, Le Mercier P, Leplae R, Madupu R, Scheuermann RH, Schobel S, Seto D, Shrivastava S, Sterk P, Zeng Q, Klimke W, Tatusova T.

Viruses. 2010 Oct;2(10):2258-68. doi: 10.3390/v2102258. Epub 2010 Oct 13.

18.

Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.

Bogdanove AJ, Koebnik R, Lu H, Furutani A, Angiuoli SV, Patil PB, Van Sluys MA, Ryan RP, Meyer DF, Han SW, Aparna G, Rajaram M, Delcher AL, Phillippy AM, Puiu D, Schatz MC, Shumway M, Sommer DD, Trapnell C, Benahmed F, Dimitrov G, Madupu R, Radune D, Sullivan S, Jha G, Ishihara H, Lee SW, Pandey A, Sharma V, Sriariyanun M, Szurek B, Vera-Cruz CM, Dorman KS, Ronald PC, Verdier V, Dow JM, Sonti RV, Tsuge S, Brendel VP, Rabinowicz PD, Leach JE, White FF, Salzberg SL.

J Bacteriol. 2011 Oct;193(19):5450-64. doi: 10.1128/JB.05262-11. Epub 2011 Jul 22.

19.

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9.

Davidsen T, Madupu R, Sterk P, Field D, Garrity G, Gilbert J, Glöckner FO, Hirschman L, Kolker E, Kottmann R, Kyrpides N, Meyer F, Morrison N, Schriml L, Tatusova T, Wooley J.

Stand Genomic Sci. 2010 Dec 4;3(3):216-24. doi: 10.4056/sigs.1353455.

20.

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data.

Tanenbaum DM, Goll J, Murphy S, Kumar P, Zafar N, Thiagarajan M, Madupu R, Davidsen T, Kagan L, Kravitz S, Rusch DB, Yooseph S.

Stand Genomic Sci. 2010 Mar 30;2(2):229-37. doi: 10.4056/sigs.651139.

21.

Complete genome sequence of Mycoplasma bovis type strain PG45 (ATCC 25523).

Wise KS, Calcutt MJ, Foecking MF, Röske K, Madupu R, Methé BA.

Infect Immun. 2011 Feb;79(2):982-3. doi: 10.1128/IAI.00726-10. Epub 2010 Dec 6.

22.

A catalog of reference genomes from the human microbiome.

Human Microbiome Jumpstart Reference Strains Consortium, Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D.

Science. 2010 May 21;328(5981):994-9. doi: 10.1126/science.1183605.

23.

Meeting report: a workshop on Best Practices in Genome Annotation.

Madupu R, Brinkac LM, Harrow J, Wilming LG, Böhme U, Lamesch P, Hannick LI.

Database (Oxford). 2010;2010:baq001. Epub 2010 Feb 18.

24.

The complete genome sequence of Haloferax volcanii DS2, a model archaeon.

Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T, Eisen JA.

PLoS One. 2010 Mar 19;5(3):e9605. doi: 10.1371/journal.pone.0009605.

25.

The comprehensive microbial resource.

Davidsen T, Beck E, Ganapathy A, Montgomery R, Zafar N, Yang Q, Madupu R, Goetz P, Galinsky K, White O, Sutton G.

Nucleic Acids Res. 2010 Jan;38(Database issue):D340-5. doi: 10.1093/nar/gkp912. Epub 2009 Nov 5.

26.

Pathema: a clade-specific bioinformatics resource center for pathogen research.

Brinkac LM, Davidsen T, Beck E, Ganapathy A, Caler E, Dodson RJ, Durkin AS, Harkins DM, Lorenzi H, Madupu R, Sebastian Y, Shrivastava S, Thiagarajan M, Orvis J, Sundaram JP, Crabtree J, Galens K, Zhao Y, Inman JM, Montgomery R, Schobel S, Galinsky K, Tanenbaum DM, Resnick A, Zafar N, White O, Sutton G.

Nucleic Acids Res. 2010 Jan;38(Database issue):D408-14. doi: 10.1093/nar/gkp850. Epub 2009 Oct 20.

27.

The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms).

Yang JC, Madupu R, Durkin AS, Ekborg NA, Pedamallu CS, Hostetler JB, Radune D, Toms BS, Henrissat B, Coutinho PM, Schwarz S, Field L, Trindade-Silva AE, Soares CA, Elshahawi S, Hanora A, Schmidt EW, Haygood MG, Posfai J, Benner J, Madinger C, Nove J, Anton B, Chaudhary K, Foster J, Holman A, Kumar S, Lessard PA, Luyten YA, Slatko B, Wood N, Wu B, Teplitski M, Mougous JD, Ward N, Eisen JA, Badger JH, Distel DL.

PLoS One. 2009 Jul 1;4(7):e6085. doi: 10.1371/journal.pone.0006085.

28.

Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.

Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, Barabote RD, Bradley B, Brettin TS, Brinkac LM, Bruce D, Creasy T, Daugherty SC, Davidsen TM, DeBoy RT, Detter JC, Dodson RJ, Durkin AS, Ganapathy A, Gwinn-Giglio M, Han CS, Khouri H, Kiss H, Kothari SP, Madupu R, Nelson KE, Nelson WC, Paulsen I, Penn K, Ren Q, Rosovitz MJ, Selengut JD, Shrivastava S, Sullivan SA, Tapia R, Thompson LS, Watkins KL, Yang Q, Yu C, Zafar N, Zhou L, Kuske CR.

Appl Environ Microbiol. 2009 Apr;75(7):2046-56. doi: 10.1128/AEM.02294-08. Epub 2009 Feb 5.

29.

Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum.

Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA.

PLoS One. 2009;4(1):e4207. doi: 10.1371/journal.pone.0004207. Epub 2009 Jan 16.

30.

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.

Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S, Furutani A, Ochiai H, Delcher AL, Kelley D, Madupu R, Puiu D, Radune D, Shumway M, Trapnell C, Aparna G, Jha G, Pandey A, Patil PB, Ishihara H, Meyer DF, Szurek B, Verdier V, Koebnik R, Dow JM, Ryan RP, Hirata H, Tsuyumu S, Won Lee S, Seo YS, Sriariyanum M, Ronald PC, Sonti RV, Van Sluys MA, Leach JE, White FF, Bogdanove AJ.

BMC Genomics. 2008 May 1;9:204. doi: 10.1186/1471-2164-9-204. Erratum in: BMC Genomics. 2008;9:534.. Seo, Young-Su [added]; Sriariyanum, Malinee [added].

31.

Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation.

Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O.

OMICS. 2008 Jun;12(2):137-41. doi: 10.1089/omi.2008.0017.

32.

Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus.

Myers GS, Parker D, Al-Hasani K, Kennan RM, Seemann T, Ren Q, Badger JH, Selengut JD, Deboy RT, Tettelin H, Boyce JD, McCarl VP, Han X, Nelson WC, Madupu R, Mohamoud Y, Holley T, Fedorova N, Khouri H, Bottomley SP, Whittington RJ, Adler B, Songer JG, Rood JI, Paulsen IT.

Nat Biotechnol. 2007 May;25(5):569-75. Epub 2007 Apr 29.

PMID:
17468768
33.

Evolution of sensory complexity recorded in a myxobacterial genome.

Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA, Ronning CM, Barbazuk WB, Blanchard M, Field C, Halling C, Hinkle G, Iartchuk O, Kim HS, Mackenzie C, Madupu R, Miller N, Shvartsbeyn A, Sullivan SA, Vaudin M, Wiegand R, Kaplan HB.

Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15200-5. Epub 2006 Oct 2. Erratum in: Proc Natl Acad Sci U S A. 2006 Dec 19;103(51):19605. Eisen, J [corrected to Eisen, J A].

34.

Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus.

Badger JH, Hoover TR, Brun YV, Weiner RM, Laub MT, Alexandre G, Mrázek J, Ren Q, Paulsen IT, Nelson KE, Khouri HM, Radune D, Sosa J, Dodson RJ, Sullivan SA, Rosovitz MJ, Madupu R, Brinkac LM, Durkin AS, Daugherty SC, Kothari SP, Giglio MG, Zhou L, Haft DH, Selengut JD, Davidsen TM, Yang Q, Zafar N, Ward NL.

J Bacteriol. 2006 Oct;188(19):6841-50.

35.

Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades.

Seshadri R, Joseph SW, Chopra AK, Sha J, Shaw J, Graf J, Haft D, Wu M, Ren Q, Rosovitz MJ, Madupu R, Tallon L, Kim M, Jin S, Vuong H, Stine OC, Ali A, Horneman AJ, Heidelberg JF.

J Bacteriol. 2006 Dec;188(23):8272-82. Epub 2006 Sep 15.

36.

Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment.

Palenik B, Ren Q, Dupont CL, Myers GS, Heidelberg JF, Badger JH, Madupu R, Nelson WC, Brinkac LM, Dodson RJ, Durkin AS, Daugherty SC, Sullivan SA, Khouri H, Mohamoud Y, Halpin R, Paulsen IT.

Proc Natl Acad Sci U S A. 2006 Sep 5;103(36):13555-9. Epub 2006 Aug 25.

37.

Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens.

Myers GS, Rasko DA, Cheung JK, Ravel J, Seshadri R, DeBoy RT, Ren Q, Varga J, Awad MM, Brinkac LM, Daugherty SC, Haft DH, Dodson RJ, Madupu R, Nelson WC, Rosovitz MJ, Sullivan SA, Khouri H, Dimitrov GI, Watkins KL, Mulligan S, Benton J, Radune D, Fisher DJ, Atkins HS, Hiscox T, Jost BH, Billington SJ, Songer JG, McClane BA, Titball RW, Rood JI, Melville SB, Paulsen IT.

Genome Res. 2006 Aug;16(8):1031-40. Epub 2006 Jul 6.

38.

Comparative genomics of emerging human ehrlichiosis agents.

Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, Niu H, Lin Q, Ohashi N, Zhi N, Nelson W, Brinkac LM, Dodson RJ, Rosovitz MJ, Sundaram J, Daugherty SC, Davidsen T, Durkin AS, Gwinn M, Haft DH, Selengut JD, Sullivan SA, Zafar N, Zhou L, Benahmed F, Forberger H, Halpin R, Mulligan S, Robinson J, White O, Rikihisa Y, Tettelin H.

PLoS Genet. 2006 Feb;2(2):e21. Epub 2006 Feb 17. Erratum in: PLoS Genet. 2006 Dec;2(12):e213. Eisen, Jonathan [corrected to Eisen, Jonathan A].

39.

Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901.

Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Haft DH, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, Eisen JA.

PLoS Genet. 2005 Nov;1(5):e65. Epub 2005 Nov 25. Erratum in: PLoS Genet. 2006 Apr;2(4):e60. Haft, Daniel H [added].

40.

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome".

Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O'Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM.

Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13950-5. Epub 2005 Sep 19. Erratum in: Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16530.

41.

Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition.

Joardar V, Lindeberg M, Jackson RW, Selengut J, Dodson R, Brinkac LM, Daugherty SC, Deboy R, Durkin AS, Giglio MG, Madupu R, Nelson WC, Rosovitz MJ, Sullivan S, Crabtree J, Creasy T, Davidsen T, Haft DH, Zafar N, Zhou L, Halpin R, Holley T, Khouri H, Feldblyum T, White O, Fraser CM, Chatterjee AK, Cartinhour S, Schneider DJ, Mansfield J, Collmer A, Buell CR.

J Bacteriol. 2005 Sep;187(18):6488-98.

42.

The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses.

Methé BA, Nelson KE, Deming JW, Momen B, Melamud E, Zhang X, Moult J, Madupu R, Nelson WC, Dodson RJ, Brinkac LM, Daugherty SC, Durkin AS, DeBoy RT, Kolonay JF, Sullivan SA, Zhou L, Davidsen TM, Wu M, Huston AL, Lewis M, Weaver B, Weidman JF, Khouri H, Utterback TR, Feldblyum TV, Fraser CM.

Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):10913-8. Epub 2005 Jul 25.

43.

Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5.

Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GS, Mavrodi DV, DeBoy RT, Seshadri R, Ren Q, Madupu R, Dodson RJ, Durkin AS, Brinkac LM, Daugherty SC, Sullivan SA, Rosovitz MJ, Gwinn ML, Zhou L, Schneider DJ, Cartinhour SW, Nelson WC, Weidman J, Watkins K, Tran K, Khouri H, Pierson EA, Pierson LS 3rd, Thomashow LS, Loper JE.

Nat Biotechnol. 2005 Jul;23(7):873-8. Epub 2005 Jun 26. Erratum in: Nat Biotechnol. 2006 Apr;24(4):466.

PMID:
15980861
44.

Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain.

Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty SC, Madupu R, Angiuoli SV, Durkin AS, Haft DH, Vamathevan J, Khouri H, Utterback T, Lee C, Dimitrov G, Jiang L, Qin H, Weidman J, Tran K, Kang K, Hance IR, Nelson KE, Fraser CM.

J Bacteriol. 2005 Apr;187(7):2426-38.

45.

Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species.

Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, DeBoy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Sullivan SA, Shetty JU, Ayodeji MA, Shvartsbeyn A, Schatz MC, Badger JH, Fraser CM, Nelson KE.

PLoS Biol. 2005 Jan;3(1):e15. Epub 2005 Jan 4.

46.

Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes.

Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF.

Science. 2005 Jan 7;307(5706):105-8.

47.

Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment.

Moran MA, Buchan A, González JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen JA, Rahe E, Sheldon WM, Ye W, Miller TR, Carlton J, Rasko DA, Paulsen IT, Ren Q, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Rosovitz MJ, Haft DH, Selengut J, Ward N.

Nature. 2004 Dec 16;432(7019):910-3.

PMID:
15602564
48.

Structural flexibility in the Burkholderia mallei genome.

Nierman WC, DeShazer D, Kim HS, Tettelin H, Nelson KE, Feldblyum T, Ulrich RL, Ronning CM, Brinkac LM, Daugherty SC, Davidsen TD, Deboy RT, Dimitrov G, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Khouri H, Kolonay JF, Madupu R, Mohammoud Y, Nelson WC, Radune D, Romero CM, Sarria S, Selengut J, Shamblin C, Sullivan SA, White O, Yu Y, Zafar N, Zhou L, Fraser CM.

Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):14246-51. Epub 2004 Sep 17.

49.

Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species.

Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT, Peterson J, White O, Nelson WC, Nierman W, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Haft DH, Selengut J, Van Aken S, Khouri H, Fedorova N, Forberger H, Tran B, Kathariou S, Wonderling LD, Uhlich GA, Bayles DO, Luchansky JB, Fraser CM.

Nucleic Acids Res. 2004 Apr 28;32(8):2386-95. Print 2004.

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The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou L, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM.

Nat Biotechnol. 2004 May;22(5):554-9. Epub 2004 Apr 11.

PMID:
15077118

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