User:Jbadger
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Jonathan Badger
I'm a staff scientist in the microbial genomics department of the Institute for Genomic Research (TIGR). My work focuses on phylogenetic analysis and how genomics can help our understanding of evolution and vice-versa.
my publications in PubMed
- 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, and Ward NL. Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus. J Bacteriol. 2006 Oct;188(19):6841-50. DOI:10.1128/JB.00111-06 |
- Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK Jr, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, and Orias E. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol. 2006 Sep;4(9):e286. DOI:10.1371/journal.pbio.0040286 |
- Fedorova ND, Badger JH, Robson GD, Wortman JR, and Nierman WC. Comparative analysis of programmed cell death pathways in filamentous fungi. BMC Genomics. 2005 Dec 8;6:177. DOI:10.1186/1471-2164-6-177 |
- El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran AN, Wortman JR, Alsmark UC, Angiuoli S, Anupama A, Badger J, Bringaud F, Cadag E, Carlton JM, Cerqueira GC, Creasy T, Delcher AL, Djikeng A, Embley TM, Hauser C, Ivens AC, Kummerfeld SK, Pereira-Leal JB, Nilsson D, Peterson J, Salzberg SL, Shallom J, Silva JC, Sundaram J, Westenberger S, White O, Melville SE, Donelson JE, Andersson B, Stuart KD, and Hall N. Comparative genomics of trypanosomatid parasitic protozoa. Science. 2005 Jul 15;309(5733):404-9. DOI:10.1126/science.1112181 |
- Badger JH, Eisen JA, and Ward NL. Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales. Int J Syst Evol Microbiol. 2005 May;55(Pt 3):1021-1026. DOI:10.1099/ijs.0.63510-0 |
- 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, and Nelson KE. Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biol. 2005 Jan;3(1):e15. DOI:10.1371/journal.pbio.0030015 |
- Wang HC, Badger J, Kearney P, and Li M. Analysis of codon usage patterns of bacterial genomes using the self-organizing map. Mol Biol Evol. 2001 May;18(5):792-800. DOI:10.1093/oxfordjournals.molbev.a003861 |
- Li M, Badger JH, Chen X, Kwong S, Kearney P, and Zhang H. An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics. 2001 Feb;17(2):149-54. DOI:10.1093/bioinformatics/17.2.149 |
- Badger JH and Olsen GJ. CRITICA: coding region identification tool invoking comparative analysis. Mol Biol Evol. 1999 Apr;16(4):512-24. DOI:10.1093/oxfordjournals.molbev.a026133 |
- Haney PJ, Badger JH, Buldak GL, Reich CI, Woese CR, and Olsen GJ. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3578-83. DOI:10.1073/pnas.96.7.3578 |
- Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, McKenney K, Adams MD, Loftus B, Peterson S, Reich CI, McNeil LK, Badger JH, Glodek A, Zhou L, Overbeek R, Gocayne JD, Weidman JF, McDonald L, Utterback T, Cotton MD, Spriggs T, Artiach P, Kaine BP, Sykes SM, Sadow PW, D'Andrea KP, Bowman C, Fujii C, Garland SA, Mason TM, Olsen GJ, Fraser CM, Smith HO, Woese CR, and Venter JC. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature. 1997 Nov 27;390(6658):364-70. DOI:10.1038/37052 |
