Publications

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Journal Article
Lin H, Doddapaneni H, Bai X, Yao J, Zhao X, Civerolo EL. Acquisition of uncharacterized sequences from Candidatus liberibacter, an unculturable bacterium, using an improved genomic walking method. Mol Cell Probes. 2008 ;22(1):30-7.
Xu Y, Singh KV, Qin X, Murray BE, Weinstock GM. Analysis of a gene cluster of Enterococcus faecalis involved in polysaccharide biosynthesis. Infect Immun. 2000 ;68(2):815-23.
Doddapaneni H, Yao J, Lin H, M Walker A, Civerolo EL. Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa. BMC Genomics. 2006 ;7:225.
Nasser W, Santhanam B, Miranda ERoshan, Parikh A, Juneja K, Rot G, Dinh C, Chen R, Zupan B, Shaulsky G, Kuspa A. Bacterial discrimination by dictyostelid amoebae reveals the complexity of ancient interspecies interactions. Curr Biol. 2013 ;23(10):862-72.
Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HHuot, Wortman JRusso, 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 MGwinn, 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. A catalog of reference genomes from the human microbiome. Science. 2010 ;328(5981):994-9.
Seshadri R, Myers GSA, Tettelin H, Eisen JA, Heidelberg JF, Dodson RJ, Davidsen TM, DeBoy RT, Fouts DE, Haft DH, Selengut J, Ren Q, Brinkac LM, Madupu R, Kolonay J, Durkin SA, Daugherty SC, Shetty J, Shvartsbeyn A, Gebregeorgis E, Geer K, Tsegaye G, Malek J, Ayodeji B, Shatsman S, McLeod MP, Smajs D, Howell JK, Pal S, Amin A, Vashisth P, McNeill TZ, Xiang Q, Sodergren E, Baca E, Weinstock GM, Norris SJ, Fraser CM, Paulsen IT. Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proc Natl Acad Sci U S A. 2004 ;101(15):5646-51.
Durfee T, Nelson R, Baldwin S, Plunkett G, Burland V, Mau B, Petrosino JF, Qin X, Muzny DM, Ayele M, Gibbs RA, Csörgo B, Pósfai G, Weinstock GM, Blattner FR. The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol. 2008 ;190(7):2597-606.
McLeod MP, Qin X, Karpathy SE, Gioia J, Highlander SK, Fox GE, McNeill TZ, Jiang H, Muzny DM, Jacob LS, Hawes AC, Sodergren E, Gill R, Hume J, Morgan M, Fan G, Amin AG, Gibbs RA, Hong C, Yu X-J, Walker DH, Weinstock GM. Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae. J Bacteriol. 2004 ;186(17):5842-55.
Price DC, Chan CXin, Yoon HSu, Yang EChan, Qiu H, Weber APM, Schwacke R, Gross J, Blouin NA, Lane C, Reyes-Prieto A, Durnford DG, Neilson JAD, B Lang F, Burger G, Steiner JM, Löffelhardt W, Meuser JE, Posewitz MC, Ball S, Arias MCecilia, Henrissat B, Coutinho PM, Rensing SA, Symeonidi A, Doddapaneni H, Green BR, Rajah VD, Boore J, Bhattacharya D. Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science. 2012 ;335(6070):843-7.
Mamun AAmar MAl, Marians KJ, M Humayun Z. DNA polymerase III from Escherichia coli cells expressing mutA mistranslator tRNA is error-prone. J Biol Chem. 2002 ;277(48):46319-27.
Qin X, Singh KV, Weinstock GM, Murray BE. Effects of Enterococcus faecalis fsr genes on production of gelatinase and a serine protease and virulence. Infect Immun. 2000 ;68(5):2579-86.
Mamun AAmar MAl. Elevated expression of DNA polymerase II increases spontaneous mutagenesis in Escherichia coli. Mutat Res. 2007 ;625(1-2):29-39.
Mylonakis E, Engelbert M, Qin X, Sifri CD, Murray BE, Ausubel FM, Gilmore MS, Calderwood SB. The Enterococcus faecalis fsrB gene, a key component of the fsr quorum-sensing system, is associated with virulence in the rabbit endophthalmitis model. Infect Immun. 2002 ;70(8):4678-81.
Teng F, Kawalec M, Weinstock GM, Hryniewicz W, Murray BE. An Enterococcus faecium secreted antigen, SagA, exhibits broad-spectrum binding to extracellular matrix proteins and appears essential for E. faecium growth. Infect Immun. 2003 ;71(9):5033-41.
Mamun AA al, Rahman MS, Humayun MZ. Escherichia coli cells bearing mutA, a mutant glyV tRNA gene, express a recA-dependent error-prone DNA replication activity. Mol Microbiol. 1999 ;33(4):732-40.
Arias CA, Panesso D, McGrath DM, Qin X, Mojica MF, Miller C, Diaz L, Tran TT, Rincon S, E Barbu M, Reyes J, Roh JH, Lobos E, Sodergren E, Pasqualini R, Arap W, Quinn JP, Shamoo Y, Murray BE, Weinstock GM. Genetic basis for in vivo daptomycin resistance in enterococci. N Engl J Med. 2011 ;365(10):892-900.
Yerrapragada S, Siefert JL, Fox GE. Horizontal gene transfer in cyanobacterial signature genes. Methods Mol Biol. 2009 ;532:339-66.
Sillanpaa J, Nallapareddy SR, Prakash VP, Qin X, Höök M, Weinstock GM, Murray BE. Identification and phenotypic characterization of a second collagen adhesin, Scm, and genome-based identification and analysis of 13 other predicted MSCRAMMs, including four distinct pilus loci, in Enterococcus faecium. Microbiology. 2008 ;154(Pt 10):3199-211.
Nur-E-Kamal MS, Mamun AA al, Ahmed ZU. Molecular cloning of the wild-type and mutant thyA gene from Shigella flexneri Y. Microbiol Immunol. 1994 ;38(4):309-12.
Yao J, Lin H, Doddapaneni H, Civerolo EL. nWayComp: a genome-wide sequence comparison tool for multiple strains/species of phylogenetically related microorganisms. In Silico Biol. 2007 ;7(2):195-200.
Gioia J, Yerrapragada S, Qin X, Jiang H, Igboeli OC, Muzny DM, Dugan-Rocha S, Ding Y, Hawes A, Liu W, Perez L, Kovar C, Dinh H, Lee S, Nazareth L, Blyth P, Holder M, Buhay C, Tirumalai MR, Liu Y, Dasgupta I, Bokhetache L, Fujita M, Karouia F, Moorthy PEswara, Siefert J, Uzman A, Buzumbo P, Verma A, Zwiya H, McWilliams BD, Olowu A, Clinkenbeard KD, Newcombe D, Golebiewski L, Petrosino JF, Nicholson WL, Fox GE, Venkateswaran K, Highlander SK, Weinstock GM. Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS One. 2007 ;2(9):e928.
Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W. PipMaker--a web server for aligning two genomic DNA sequences. Genome Res. 2000 ;10(4):577-86.
Ren L, Mamun AA al, Humayun MZ. Requirement for homologous recombination functions for expression of the mutA mistranslator tRNA-induced mutator phenotype in Escherichia coli. J Bacteriol. 2000 ;182(5):1427-31.
Okinaka RT, Cloud K, Hampton OA, Hoffmaster AR, Hill KK, Keim P, Koehler TM, Lamke G, Kumano S, Mahillon J, Manter D, Martinez Y, Ricke D, Svensson R, Jackson PJ. Sequence and organization of pXO1, the large Bacillus anthracis plasmid harboring the anthrax toxin genes. J Bacteriol. 1999 ;181(20):6509-15.
Okinaka R, Cloud K, Hampton OA, Hoffmaster A, Hill K, Keim P, Koehler T, Lamke G, Kumano S, Manter D, Martinez Y, Ricke D, Svensson R, Jackson P. Sequence, assembly and analysis of pX01 and pX02. J Appl Microbiol. 1999 ;87(2):261-2.