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Publications

2009

  1. Djikeng A, Spiro D. Advancing full length genome sequencing for human RNA viral pathogens. Future Virol. 2009 Jan;4(1):47-53. [PubMed]
  2. Eppinger M, Guo Z, Sebastian Y, Song Y, Lindler LE, Yang R, Ravel J. Draft genome sequences of Yersinia pestis isolates from natural foci of endemic plague in China. J Bacteriol. 2009 Dec;191(24):7628-9. Epub 2009 Oct 9. [PubMed]
  3. Fricke WF, McDermott PF, Mammel MK, Zhao S, Johnson TJ, Rasko DA, Fedorka-Cray PJ, Pedroso A, Whichard JM, Leclerc JE, White DG, Cebula TA, Ravel J. Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar Kentucky isolates from poultry. Appl Environ Microbiol. 2009 Sep;75(18):5963-71. Epub 2009 Jul 31. [PubMed]
  4. Fricke WF, Welch TJ, McDermott PF, Mammel MK, LeClerc JE, White DG, Cebula TA, Ravel J. Comparative genomics of the IncA/C multidrug resistance plasmid family. J Bacteriol. 2009 Aug;191(15):4750-7. Epub 2009 May 29. [PubMed]
  5. Ghedin E, Fitch A, Boyne A, Griesemer S, Depasse J, Bera J, Zhang X, Halpin RA, Smit M, Jennings L, St George K, Holmes EC, Spiro DJ. (2009) Mixed Infection and the Genesis of Influenza Diversity. J Virol. Epub 2009 Jun 24. [PubMed]
  6. Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC. (2009) The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Virology 2009 Jun 5;388(2):270-8. Epub 2009 Apr 24. [PubMed]
  7. Gilsenan JE, Giles PF, Anderson MJ, Attwood TK, Paton NW, Robson GD, Oliver SG, Denning DW. Aspergillus Genomes and the Aspergillus Cloud. Nucleic Acids Res. 2009: 37:D509-14. [PubMed]
  8. McDonald SM, Matthijnssens J, McAllen JK, Hine E, Overton L, Wang S, Lemey P, Zeller M, Van Ranst M, Spiro DJ, Patton JT. Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations. PLoS Pathog. 2009 Oct;5(10):e1000634. Epub 2009 Oct 23. [PubMed]
  9. Nelson M, Spiro D, Wentworth D, Beck E, Fan J, Ghedin E, Halpin R, Bera J, Hine E, Proudfoot K, Stockwell T, Lin X, Griesemer S, Kumar S, Bose M, Viboud C, Holmes E, Henrickson K. The early diversification of influenza A/H1N1pdm. PLoS Curr Influenza. 2009 Nov 3:RRN1126. [PubMed]
  10. P.A. Beare, N. Unsworth, M. Andoh, D.E. Voth, A. Omsland, S.D. Gilk, K.P. Williams, B.W. Sobral, J.J. Kupko, Porcella,  J.E. Samuel and R.A. Heinzen. Comparative genomics reveal extensive transposon-mediated genomic plasticity and diversity among potential effector proteins within the genus Coxiella. 2009. Infect. Immun. 77:642-656. [PubMed]
  11. Wozniak RA, Fouts DE, Spagnoletti M, Colombo MM, Ceccarelli D, Garriss G, Déry C, Burrus V, Waldor MK. Comparative ICE genomics: insights into the evolution of the SXT/R391 family of ICEs. PLoS Genet. 2009 Dec;5(12):e1000786. Epub 2009 Dec 24. [PubMed]
  12. Wywial E., Haven, J., Singh, S., Casjens, S., Mongodin, E., Fraser, C., Luff, B., Schutzer, S., and Qi, W. Fast, adaptive evolution at a bacterial host-resistance locus: the PFam54 gene array in Borrelia burgdorferi. Gene. 2009 Sep 15;445(1-2):26-37. Epub 2009 Jun 6. [PubMed]

2008

  1. Nelson MI, Edelman L, Spiro DJ, Boyne AR, Bera J, Halpin R, Ghedin E, Miller MA, Simonsen L, Viboud C, Holmes EC. (2008) Molecular epidemiology of A/H3N2 and A/H1N1 influenza virus during a single epidemic season in the United States. PLoS Pathog 2008 Aug 22;4(8):e1000133. [Link]
  2. Dugan VG, Chen R, Spiro DJ, Sengamalay N, Zaborsky J, Ghedin E, Nolting J, Swayne DE, Runstadler JA, Happ GM, Senne DA, Wang R, Slemons RD, Holmes EC, Taubenberger JK. (2008) The Evolutionary Genetics and Emergence of Avian Influenza Viruses in Wild Birds. PLoS Pathog 2008 May 30;4(5):e1000076. [Link]
  3. Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, Tatusova T, Ostell J, Lipman D. (2008) The influenza virus resource at the National Center for Biotechnology Information. J Virol 2008 Jan;82(2):596-601. Epub 2007 Oct 17. [Link]
  4. Boni MF, Zhou Y, Taubenberger JK, Holmes EC. (2008) Homologous Recombination Is Very Rare or Absent in Human Influenza A Virus. J Virol 2008 May;82(10):4807-11. Epub 2008 Mar 19. [Link]
  5. Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, Holmes EC. (2008) The genomic and epidemiological dynamics of human influenza A virus. Nature 2008 May 29;453(7195):615-9. Epub 2008 Apr 16. [PubMed]
  6. Tumapa S, Holden MTG, Vesaratchavest M, Wuthiekanun V, Limmathurotsakul L, Chierakul W, Feil EJ, Currie BJ, Day NP, Nierman WC, Peacock SJ. (2008) Burkholderia pseudomallei genome plasticity: genomic island variation in relation to virulence and origins. PLoS Genetics In press.
  7. Nelson MI, Viboud C, Simonsen L, Bennett RT, Griesemer SB, et al. (2008) Multiple Reassortment Events in the Evolutionary History of H1N1 Influenza A Virus Since 1918. PLoS Pathog 4(2):e1000012. [Link]
  8. Fedorova ND, Harris S, Chen D, Denning D, Cotty PJ, Nierman WC. (2008) Using genomic-level approaches to study intraspecific molecular divergence in two pathogenic molds, A. fumigatus and A. flavus. Medical Mycology Submitted.
  9. Fedorova ND, Joardar V, Crabtreee J, Anderson M, Maiti R, Amedeo P, Wortman JR, Albarraq A, Angiuoli S, Bowyer P, Bussey H, Cyer P, Egan A, Galens A, Haas B, Inman J, Lemieus S, Malavazi I, Orvis J, Roemer T, Ronning C, Silva J, Sundaram J, Whitty B, Youngman P, Fraser CM, Sutton G, Venter JC, White W, Goldman G, Turner G, Jiang B, Denning D, Nierman WC. (2008) Comparison of the genomes of Aspergillus fumigatus and its closest relatives: insights into genome evolution in filamentous fungi. PLoS Genetics In Press.
  10. Fedorova ND, Nierman WC, Turner G, Joardar V, Maiti R, Anderson MJ, Denning DW, Wortman JR. (2008) A comparative view of the genome of Aspergillus fumigatus. The Aspergilli Genomics, Medical Aspects, Biotechnology, and Research Methods eds Goldman, GH and Osmani, SA CRC Press:25-42.
  11. Schutzer SE, Schlater LRK, Ronning CM, DeShazer D, Luft BJ, Dunn JJ, Fraser-Liggett CM, Nierman WC. (2008) Characterization of Clinically-Attenuated Burkholderia mallei by Whole Genome Sequencing: Candidate Strain for Exclusion from Select Agent Lists. PLoS ONE In press.
  12. Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sperandio V, Ravel J. (2008) The pan-genome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol. [Link]

2007

  1. Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC. (2007) Phylogenetic analysis reveals the global migration of seasonal influenza A viruses. PLoS Pathog 2007 Sep 14;3(9):1220-8. [Link]
  2. Rokas A, Payne G, Fedorova ND, Baker SE, Machida M, Bruno KS, Yu J, Georgianna DR, Dean RA, Bhatnagar D, Cleveland TE, Wortman JR, Maiti R, Joardar V, Amedeo P, Denning D, Nierman WC. (2007) What can genomics tell us about species concepts in the genus Aspergillus. Studies in Mycology 59(1):11-17.
  3. Patron NJ, Waller RF, Cozijnsen AJ, Gardiner DM, Nierman WC, Howlett BJ. (2007) Origin and distribution of epipolythiodioxopiperazine (ETP) gene clusters in filamentous ascomycetes. BMC Evolutionary Biology 7:174. [PubMed]
  4. Allan G, Williams A, Rabinowicz P, Chan A, Ravel J and Keim P. (2007) Worldwide genotyping of castor bean germplasm (Ricinus communis L.) using AFLPs and SSRs. Genet Resour Crop Evol In press. [Link]
  5. Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedo P, Arsenburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston SJ, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, Labutti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'leary SB, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Bruce B, Fraser-Liggett CM, Severson DW. (2007) Genome Sequence of Aedes aegypti, a Major Arbovirus Vector. Science 316(5832):1718-1723. [PubMed]
  6. Zhang X, Hasoksuz M, Spiro D, Halpin R, Wang S, Vlasova A, Janies D, Jones LR, Ghedin E, Saif LJ. (2007) Quasispecies of bovine enteric and respiratory coronaviruses based on complete genome sequences and genetic changes after tissue culture adaptation. Virology 363(1):1-10. [PubMed]
  7. Hasoksuz M, Alekseev K, Vlasova A, Zhang X, Spiro D, Halpin R, Wang S, Ghedin E, Saif LJ. (2007) Biologic, antigenic, and full-length genomic characterization of a bovine-like coronavirus isolated from a giraffe. J Virol 81(10):4981-4990. [PubMed]
  8. Salzberg SL, Kingsford C, Cattoli G, Spiro DJ, Janies DA, Aly MM, Brown IH, Couacy-Hymann E, Mario De Mia G, Dung DH, Guercio A, Joannis T, Ali AS, Osmani IP, Saad MD, Savic V, Sengamalay N, Yingst S, Zaborsky J, Zorman-Rojs O, Ghedin E, Capua I. (2007) Genome analysis linking recent European and African influenza (H5N1) viruses. Emerg Infect Dis [serial on the Internet] 13(5). [Link]
  9. Tiyawisutsri R, Holden MTG, Tumapa S, Rengpipat S, Clarke SR, Foster SJ, Nierman WC, Day NPJ, Peacock SJ. (2007) Burkholderia Hep_Hag autotransporter (BuHA) preteins are highly immunogenic during experimental glanders but not melioidosis. BMC Microbiology 7:19. [PubMed]
  10. Welch TJ, Fricke WF, McDermott PF, White DG, Rosso ML, Rasko DA, Mammel MK, Eppinger M, Rosovitz MJ, Wagner D, Rahalison L, Leclerc JE, Hinshaw JM, Lindler LE, Cebula TA, Carniel E, Ravel J. (2007) Multiple antimicrobial resistance in plague: an emerging public health risk. PLoS ONE 2:e309. [PubMed]
  11. Zhang X, Hasoksuz M, Spiro D, Halpin R, Wang S, Stollar S, Janies D, Hadya N, Tang Y, Ghedin E, Saif L. (2007) Complete genomic sequences, a key residue in the spike protein and deletions in nonstructural protein 3b of US strains of the virulent and attenuated coronaviruses, transmissible gastroenteritis virus and porcine respiratory coronavirus. Virology 358(2):424-35. [PubMed]
  12. Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van de Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Muller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu CL, Osoegawa K, de Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik SB, Logsdon JM Jr, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu CH, Lee YS, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-Liggett CM, Johnson PJ. (2007) Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science 315(5809):201-212. [PubMed]

2006

  1. Wolf YI, Viboud C, Holmes EC, Koonin EV, Lipman DJ. (2006) Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol Direct 2006 Oct 26;1:34. [Link]
  2. Nelson MI, Simonsen L, Viboud C, Miller MA, Taylor J, George KS, Griesemer SB, Ghedi E, Sengamalay NA, Spiro DJ, Volkov I, Grenfell BT, Lipman DJ, Taubenberger JK, Holmes EC. (2006) Stochastic Processes Are Key Determinants of Short-Term Evolution in Influenza A Virus. PLoS Pathog 2(12):e125. [PubMed]
  3. Rasko DA, Rosovitz MJ, Okstad OA, Fouts DE, Jiang L, Cer RZ, Kolsto AB, Gill SR, Ravel J. (2006) Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus group plasmids including B. anthracis pXO1. J Bacteriol Epub ahead of print.[PubMed]
  4. Romero CM, DeShazer D, Feldblyum T, Ravel J, Woods D, Kim HS, Yu Y, Ronning CM, Nierman WC.. (2006) Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts. BMC Genomics 7(1):228. [PubMed]
  5. Wortman JR, Fedorova N, Crabtree J, Joardar V, Maiti R, Haas BJ, Amedeo P, Lee E, Angiuoli SV, Jiang B, Anderson MJ, Denning DW, White OR, Nierman WC. (2006) Whole genome comparison of the A. fumigatus family. Med Mycol 44(Suppl):3-7. [PubMed]
  6. Salzberg S, Ghedin E, Spiro D. (2006) Shared data are key to beating threat from flu. Nature 440(7084):605. [PubMed]

2005

  1. Seshadri R, Samuel J. (2005) Genome analysis of Coxiella burnetii species: insights into pathogenesis and evolution and implications for biodefense. Ann N Y Acad Sci 1063:442-450. [PubMed]
  2. Cui L, Fan Q, Hu Y, Karamycheva SA, Quackenbush J, Khuntirat B, Sattabongkot J, Carlton JM. (2005) Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages. Mol Biochem Parasitol 144(1):38961. [PubMed]
  3. Ghedin E, Sengamalay NA, Shumway M, Zaborsky J, Feldblyum T, Subbu V, Spiro DJ, Sitz J, Koo H, Bolotov P, Dernovoy D, Tatusova T, Bao Y, St George K, Taylor J, Lipman DJ, Fraser CM, Taubenberger JK, Salzberg SL. (2005) Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature 437(7062):1162-1166. [PubMed]
  4. Lal K, Field MC, Carlton JM, Warwicker J, Hirt RP. (2005) Identification of a very large Rab GTPase family in the parasitic protozoan Trichomonas vaginalis. Mol Biochem Parasitol 143(2):226-235. [PubMed]
  5. Loftus BJ, Hall N. (2005) Entamoeba: still more to be learned from the genome. Trends Parasitol 21(10):453. [PubMed]
  6. Holmes EC, Ghedin E, Miller N, Taylor J, Bao Y, St George K, Grenfell BT, Salzberg SL, Fraser CM, Lipman DJ, Taubenberger JK. (2005) Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol 3(9):e300. [PubMed]
  7. Wang R, Arevalo-Herrera M, Gardner MJ, Bonelo A, Carlton JM, Gomez A, Vera O, Soto L, Vergara J, Bidwell SL, Domingo A, Fraser CM, Herrera S. (2005) Immune responses to Plasmodium vivax pre-erythrocytic stage antigens in naturally exposed Duffy-negative humans: a potential model for identification of liver-stage antigens. Eur J Immunol 35(6):1859-1868. [PubMed]
  8. Vanacova S, Yan W, Carlton JM, Johnson PJ. (2005) Spliceosomal introns in the deep-branching eukaryote Trichomonas vaginalis. Proc Natl Acad Sci U S A 102(12):4430-4435. [PubMed]
  9. Loftus B, Anderson I, Davies R, Alsmark UC, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, Nozaki T, Suh B, Pop M, Duchene M, Ackers J, Tannich E, Leippe M, Hofer M, Bruchhaus I, Willhoeft U, Bhattacharya A, Chillingworth T, Churcher C, Hance Z, Harris B, Harris D, Jagels K, Moule S, Mungall K, Ormond D, Squares R, Whitehead S, Quail MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillen N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-Ponten T, Weber C, Singh U, Mukherjee C, El-Sayed NM, Petri WA Jr, Clark CG, Embley TM, Barrell B, Fraser CM, Hall N. (2005) The genome of the protist parasite Entamoeba histolytica. Nature 433(7028):865-868. [PubMed]
  10. Silva JC, Bastida F, Bidwell SL, Johnson PJ, Carlton JM. (2005) A potentially functional mariner transposable element in the protist Trichomonas vaginalis. Mol Biol Evol 22(1):126-134. [PubMed]

2004

  1. Lyons EJ, Carlton JM. (2004) Mind the gap: bridging the divide between clinical and molecular studies of the trichomonads. Trends Parasitol 20(5):204-207. [PubMed]

2003

  1. Carlton J. (2003) The Plasmodium vivax genome sequencing project. Trends Parasitol 19(5):227-231. [PubMed]

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