Publications

CBMI members (highlighted) have participated in the following publications.

  1. Irit Messika, Mario Garrido, Hadar Kedem, Victor China, Yoni Gavish, Qunfeng Dong, Clay Fuqua, Keith Clay, and Hadas Hawlena (2017) From endosymbionts to host communities: factors determining the reproductive success of arthropod vectors.  Oecologia (2017): 1-13.
  2. A Bayesian Taxonomic Classification Method for 16S rRNA Gene Sequences with Improved Species-level Accuracy. Xiang Gao; Huaiying Lin; Kashi Revanna; Qunfeng Dong BMC Bioinformatics 2017 May 10;18(1):247.
  3. Plichta J, Gao X, Lin H, Dong Q, Toh E, Nelson D, Grice E, Radek, K. Cutaneous Burn Injury Promotes Shifts in the Bacterial Microbiome in Autologous Donor Skin: Implications for Skin Grafting Outcomes. Shock: Injury, Inflammation, and Sepsis: Laboratory and Clinical Approaches. surgery, 138(2), 127-32.
  4. Plichta J, Holmes C, Nienhouse V, Puszynski M, Gao X, Dong Q, Lin H, Sinacore J, Zilliox M, Toh E, Nelson D, Gamelli R, Radek K. Cutaneous burn injury modulates urinary antimicrobial peptide responses and the urinary microbiome. Critical care medicine 45, no. 6 (2017): e543-e551.
  5. Rylance J, Kankwatira A ,Nelson D, Toh E, Day R, Lin H, Gao X, Dong Q, Sodergren E, Weinstock G, Heyderman R, Twigg H, Gordon Y (2016) Household air pollution and the lung microbiome of healthy adults in Malawi: a cross-sectional study. BMC microbiology, 16(1), 182.
  6. Twigg H, Knox K, Zhou J, Crothers K, Nelson D, Toh E, Day R, Lin H, Gao X, Dong Q, Mi D, Katz B, Sodergren R, Weinstock G (2016) Effect of advanced HIV infection on the respiratory microbiome. American Journal of Respiratory and Critical Care Medicine 10.1164/rccm.201509-1875OC 2016.
  7. Dong Q (2015) Mobilizing Undergraduate Students to Develop Practical Bioinformatics Databases and Analysis Tools for Biologists. Next Generat Sequenc & Applic 2: 121. doi:10.4172/jngsa.1000121
  8. Van Rensburg J, Lin H, Gao X, Toh E, Fortney K, Ellinger S, Zwickl B, Janowicz D, Katz B, Nelson D, Dong Q, Spinola S (2015) The human skin microbiome associates with the outcome of and is influenced by bacterial infection. mBio 6(5):e01315-15. doi:10.1128/mBio.01315-15.
  9. Vilo C, Galetovic A, Araya JE, Gómez-Silva B, Dong Q (2015) Draft genome sequence of a Bacillus bacterium from the Atacama Desert wetlands metagenome. Genome Announc. 3(4):e00955-15. doi:10.1128/genomeA.00955-15.
  10. Cohen C, Toh E, Munro D, Dong Q, Hawlena H (2015) Similarities and seasonal variations in bacterial communities from the blood of rodents and from their flea vectors. ISME J. 2015 Jan 9. doi: 10.1038/ismej.2014.255.
  11. Nienhouse V, Gao X, Dong Q, Nelson DE, Toh E, McKinley K, Schreckenberger P, Shibata N, Fok SC, Mueller ER, Brubaker L, Wolfe AJ, Radek KA (2014) Interplay between Bladder Microbiota and Urinary Antimicrobial Peptides: Mechanisms for Human Urinary Tract Risk Symptom Severity. PLoS ONE 9(12): e114185. doi: 10.1371/journal.pone.0114185.
  12. Gavish Y, Kedem H, Messika I, Cohen C, Toh E, Munro D, Dong Q, Fuqua C, Clay K, Hawlena H (2014) Association of Host and Microbial Species Diversity across Spatial Scales in Desert Rodent Communities. PLoS ONE 9(10): e109677. doi: 10.1371/journal.pone.0109677.
  13. Vilo C, Benedik M, Ilori M, Dong Q (2014) Draft genome sequence of Cupriavidus sp. strain SK-3, a 4-chlorobiphenyl and 4-clorobenzoic acid degrading bacterium. Genome Announc. 2:(4)e00664-14. doi:10.1128/genomeA.00664-14.
  14. Vilo C, Benedik M, Ilori M, Dong Q (2014) Draft genome sequence of Cupriavidus sp. strain SK-4, a di-ortho-substituted biphenyl-utilizing bacterium isolated from polychlorinated biphenyl-contaminated sludge. Genome Announc. 2(3):e00474-14. doi:10.1128/genomeA.00474-14.
  15. Jones AM, Xuan Y, Xu M, Wang RS, Ho CH, Lalonde S, You CH, Sardi MI, Parsa SA, Smith-Valle E, Su T, Frazer KA, Pilot G, Pratelli R, Grossmann G, Acharya BR, Hu HC, Engineer C, Villiers F, Ju C, Takeda K, Su Z, Dong Q, Assmann SM, Chen J, Kwak JM, Schroeder J, Albert R, Rhee SY, Frommer WB (2014) Border control—a membrane-linked interactome of Arabidopsis. Science, 344(6185), 711-716.
  16. Kedem H, Gavish Y, Messika I, Cohen C, Toh E, Munro D, Dong Q, Fuqua C, Clay K, Hawlena H (2014) Association of host and microbial species diversity across spatial scales in desert rodent communities. PLoS ONE 9(10): e109677. doi:10.1371/journal.pone.0109677.
  17. Twigg HL, Nelson DE, Day RB, Gregory RL, Dong Q, Rong R, Knox K, Crothers K, Sodergren E, Weinstock G (2014) Comparison of whole and acellular bronchoalveolar lavage to oral wash microbiomes: should acellular bronchoalveolar lavage be the standard? AST Journal, Ann Am Thorac Soc. 2014 Jan;11 Suppl 1:S72-3. doi: 10.1513/AnnalsATS.201306-162MG.0061959.
  18. Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q, Dong Q (2013) Investigation of the effect of type 2 diabetes on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing. PLoS One 8(4): e61516. doi:10.1371/journal.pone.0061516.
  19. Kuehn J, Gorden P, Munro D, Rong R, Dong Q, Plummer P, Wang C, Phillips J (2013) Bacterial community profiling of milk samples as a means to understand culture-negative bovine clinical mastitis.PLoS One 8(4): e61959. doi:10.1371/journal.pone.0061959.
  20. Vilo C, Benedik M, Kunz D, Dong Q (2012) Draft genome sequence of the cyanide-utilizing bacterium Pseudomonas fluorescens strain NCIMB 11764. Journal of Bacteriology 194(23):6618-9.
  21. Revanna K, Munro D, Gao A, Chiu C, Pathak A, Dong Q (2012) A web-based multi-genome synteny viewer for customized data. BMC Bioinformatics 13:190. doi:10.1186/1471-2105-13-190.
  22. Vilo C, Dong Q (2012) Evaluation of the RDP Classifier accuracy using 16S rRNA gene variable regions. Metagenomics. doi:10.4303/mg/235551.
  23. Hawlena H, Rynkiewicz E, Toh E, Alfred A, Durden LA, Hastriter MW, Nelson DE, Rong R, Munro D, Dong Q, Fuqua C, Clay K (2012) The arthropod, but not the vertebrate host or its environment, dictates bacterial community composition of fleas and ticks. The ISME Journal 28 June 2012; doi: 10.1038/ismej.2012.71.
  24. Nelson DE, Dong Q, Van Der Pol B, Fan B, Toh E, Katz BP, Mi D, Rong R, Weinstock GM, Sodergren E, Fortenberry JD (2012) Bacterial communities of the coronal sulcus and distal urethra of adolescent males. PLoS ONE 7(5): e36298. doi:10.1371/journal.pone.0036298.
  25. Meckfessel MH, Blancaflor EB, Plunkett M, Dong Q, Dickstein R (2012) Multiple domains in MtENOD8 protein including the signal peptide target it to the symbiosome. Plant Physiol, 2012 May;159(1):299-310.
  26. Wolfe A, Toh E, Shibata N, Rong R, Kenton K, Fitzgerald MP, Mueller ER, Schreckenberger P, Dong Q, Nelson D, Brubaker L (2012) Evidence of uncultivated bacteria in the adult female bladder. J Clin Microbiol. 50(4):1376-1383.
  27. Hughes A, Ruan Y, Ekanayake S, Bae S-H, Dong Q, Rho M, Qiu J, Fox G (2012) Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets. BMC Bioinformatics 2012, 13(Suppl 2):S9 doi:10.1186/1471-2105-13-S2-S9.
  28. Revanna K, Chiu CC, Bierschank E, Dong Q (2011) GSV: A web-based genome synteny viewer for customized data. BMC Bioinformatics 12(1):316. Ranked as “highly accessed” paper by the journal.
  29. Dong Q, Nelson DE, Toh E, Diao L, Gao X, Fortenberry J, Van Der Pol B (2011) The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens. PLOS ONE 6(5): e19709. doi:10.1371/journal.pone.0019709.
  30. Dong Q, Brulc JM, Iovieno A, Bates B, Garoutte A, Miller D, Revanna K, Gao X, Antonopoulos DA, Slepak VZ, Shestopalov VI (2011) Diversity of bacteria at healthy human conjunctiva. Investigative Ophthalmology and Visual Science. 52(8):5408-13.
  31. Nelson DE, Van Der Pol B, Dong Q, Revanna K, Fan B, Easwaran S, Sodergren E, Weinstock GM, Diao L, Fortenberry JD (2010) Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection. PLOS ONE 5(11): e14116. doi:10.1371/journal.pone.0014116.
  32. Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Caceres CE, Carmel L, Casola C, Choi J, Detter JC, Dong Q, Dusheyko S, Eads BD, Frohlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kultz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL (2011) The ecoresponsive genome of Daphnia pulex. Science vol. 331 pp. 555-561. DOI:10.1126/science.1197761.
  33. Podicheti R, Dong Q (2011) Administering GBrowse sites with WebGBrowse. Current Protocols in Bioinformatics 2011 Mar;Chapter 9:Unit 9.14. Baxevan A, Petsko G, Stein L, Stormo G (ed.), John Wiley & Sons, Inc. NJ, U.S.A.
  34. Fortenberry D, Nelson DE, Dong Q (2010) The urethral microbiome of adolescent males. Nature Precedings.
  35. Podicheti R, Revanna K, Dong Q (2010) WebGBrowse 2.0 - A web server supporting multiple versions of the Generic Genome Browser for customizable genome annotation display. F. Columbus (ed.), Web Servers: Types, Software and Applications, Nova Science Publishers, Inc. Hauppauge, NY, U.S.A.
  36. Rho M, Schaack S, Gao X, Kim S, Lynch M, Tang H. LTR retroelements in the genome of Daphnia pulex. BMC Genomics. 2010 Jul 9;11:425.
  37. Hemmerich C, Buchlein A, Podicheti R, Revanna K, Dong Q (2010) An Ergatis-based prokaryotic genome annotation web server. Bioinformatics 26: 1122-1124.
  38. Podicheti R, Dong Q (2010) Using WebGBrowse to visualize genome annotation on GBrowse. Cold Spring Harbor Protocols (invited submission) 2010(3):pdb.prot5392. doi:10.1101.
  39. Gao X, Lynch M (2009) Ubiquitous internal gene duplication and intron creation. PNAS. 106:20818-20823 (co-corresponding author). Selected for Faculty of 1000 Biology and highlighted in Nature Reviews Genetics.
  40. Catania F, Gao X, Scofield D (2009) Endogenous mechanisms for the origins of spliceosomal introns. Journal of Heredity, 100(5):591-6. Review.
  41. Podicheti R, Gollapudi R, Dong Q (2009) WebGBrowse - a web server for customized GBrowse. Bioinformatics 25(12):1550-1.
  42. Rho M, Zhou M, Gao X, Kim S, Tang H, Lynch M (2009) Independent mammalian genome contractions following the KT boundary. Genome Biology and Evolution 2009:2-12.
  43. Revanna K, Krishnakumar V, Dong Q (2009) A web-based software system for dynamic gene cluster comparison across multiple genomes. Bioinformatics 25(7):956-7.
  44. Tang Z, Choi JH, Hemmerich C, Sarangi A, Colbourne JK, Dong Q (2009) ESTPiper--a web-based analysis pipeline for expressed sequence tags. BMC Genomics, 10:174.
  45. Durden C, Dong Q (2009) RICHEST - a web server for richness estimation in biological data. Bioinformation, 3(7), 296-298.
  46. Pallickara S, Pierce M, Dong Q, Kong C (2009) Enabling large scale scientific computations for expressed sequence tag sequencing over grid and cloud computing clusters. 8th International Conference on Parallel Processing and Applied Mathematics, Wroclaw, Poland.
  47. Gollapudi R, Revanna K, Hemmerich C, Schaack S, Dong Q (2008) BOV--A web-based BLAST output visualization tool. BMC Genomics 9, 414.
  48. Gao X, Hou Y, Hirotaka E, Levin HL, Voytas DF (2008) Chromodomains direct integration of retrotransposons to heterochromatin. Genome Res. 18(3):359-69. (Cover paper and selected for Podcast.)
  49. Lushbough CM, Duvick J, Dong Q, Jennewein D, Reynoldson J, Brendel V (2008) TableMaker: an ad hoc query tool for relational databases. In H.R. Arabnia, M.Q. Yang, and J.Y. Yang (eds.), Proceedings of the International Conference on Bioinformatics & Computational Biology (BIOCOMP'08).
  50. Dong Q, Wilkerson MD, Brendel V (2007) Tracembler--software for in-silico chromosome walking in unassembled genomes. BMC Bioinformatics 8, 151.
  51. Schlueter SD, Wilkerson MD, Dong Q, Brendel V (2006) xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features. Genome Biol. 7, R111.
  52. Dong Q, Lawrence CJ, Schlueter SD, Wilkerson MD, Kurtz S, Lushbough C, Brendel V (2005) Comparative plant genomics resources at PlantGDB. Plant Physiol. 139, 610-618.
  53. Havecker EH, Gao X, Voytas DF (2005) The Sireviruses, a plant-specific lineage of the Ty1/copia retrotransposons, interact with a family of proteins related to dynein light chain 8. Plant Physiol. 139(2):857-68.
  54. Dong Q, Brendel V (2005) Computational identification of related proteins: BLAST, PSI-BLAST, and other tools. In J.M. Walker (ed.),The Proteomics Protocols Handbook, Humana Press, U.S.A, pp. 555-570.
  55. Gao X, Vender Valden K, Voytas DF, Gu X (2005) SplitTester: software to identify domains responsible for functional divergence in protein family. BMC Bioinformatics. 6(1):137.
  56. Dong Q, Kroiss L, Oakley FD, Wang B, Brendel V (2005) Comparative EST analyses in plant systems. In Molecular Evolution: Producing the Biochemical Data, E.A. Zimmer and E.H. Roalson (eds.), Methods Enzymol, 395, 400-418.
  57. Havecker ER, Gao X, Voytas DF (2004) The diversity of LTR retrotransposons. Genome Biol. 5(6):225. (Review.)
  58. Gao X, Voytas DF (2005) A eukaryotic gene family related to retroelement integrases. Trends Genet. 21(3):133-7. (Research paper.)
  59. Dong Q, Schlueter SD, Brendel V (2004) PlantGDB, plant genome database and analysis tools. Nucl. Acids Res. 32, D354-D359.
  60. Fernandes JF, Dong Q*, Schneider B, Morrow DJ, Nan GL, Brendel V, Walbot V (2004) Genome-wide mutagenesis of Zea mays L. using RescueMu transposons. Genome Biol. 5, R82. (*Co-first author.)
  61. Lawrence CJ, Dong Q, Polacco ML, Seigfried TE, Brendel V (2004) MaizeGDB, the community database for maize genetics and genomics. Nucl. Acids Res. 32, D393-D397.
  62. Gao X, Havecker ER, Baranov PV, Atkins JF, Voytas DF (2003) Translational recoding signals between gag and pol in diverse LTR retrotransposons. RNA. (12):1422-30.
  63. Dong Q, Roy L, Freeling M, Walbot V, Brendel V (2003) ZmDB, an integrated database for maize genome research. Nucl. Acids Res. 31, 244-247.
  64. Schlueter SD, Dong Q, Brendel V (2003) GeneSeqer@PlantGDB: gene structure prediction in plant genomes. Nucl. Acids Res. 31, 3597-3600.
  65. Dong Q, Wu Z (2003) A geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data. J. Global Optimization 26, 321-333.
  66. Gao X, Rowley D, Gai X, Voytas DF (2002) Ty5 gag Mutations Increase Retrotransposition and Suggest a Role for Hydrogen Bonding in the Function of the Nucleocapsid Zinc Finger. J Virol. 76(7): 3240-7.
  67. Dong Q, Wu Z (2002) A linear-time algorithm for solving the molecular distance geometry problem with exact inter-atomic distances. J. Global Optimization 22, 365-375.
  68. Ke N, Gao X, Keeney JB, Broeke JD, Voytas DF (1999) The yeast retrotransposon Ty5 uses the anticodon stem-loop of the initiator methionine tRNA as a primer for reverse transcription. RNA. 5: 929-38.

Jennifer K. Plichta, Casey J. Holmes, Vanessa Nienhouse, Michelle Puszynski, Xiang Gao, Qunfeng Dong, Huaiying Lin, James Sinacore, Michael Zilliox, Evelyn Toh, David E. Nelson, Richard L. Gamelli and Katherine A. Radek. Cutaneous burn injury modulates urinary antimicrobial peptide responses and the urinary microbiome. Critical Care Medicine. Accepted, September 25, 2016.