Publications

Peer-reviewed journal articles

  1. Dunning, J. C., Y. Ma, and R. E. Marquis. (1998) “Anaerobic Killing of Oral Streptococci by Reduced, Transitional Metal Cations.” Appl. Environ. Microbiol. 64(1): 27-33. PubMed
  2. Dunning Hotopp, J. C. and R. P. Hausinger. (2001) “Alternative Substrates of 2,4-Dichlorophenoxyacetate/alpha-ketoglutarate Dioxygenase.” J. Molec. Catalysis B: Enzymatic 15(4-6): 155-162.
  3. Elkins, J. M., M. J. Ryle, I. J. Clifton, J. C. Dunning Hotopp, J. S. Lloyd, N. I. Burzlaff, J. E. Baldwin, R. P. Hausinger, and P. L. Roach. (2002) “X-Ray Crystal Structure of Escherichia coli Taurine/alpha-ketoglutarate Dioxygenase Complexed to Ferrous Iron and Substrates.” Biochemistry 41(16):5185-92.
  4. Dunning Hotopp, J. C. and R. P. Hausinger. (2002) “Probing the 2,4-Dichlorophenoxyacetate/ alpha-ketoglutarate Dioxygenase Substrate-binding Site by Site-directed Mutagenesis and Mechanism-based Inactivation.” Biochemistry 41(31):9787-94.
  5. Dunning Hotopp, J. C., T. A. Auchtung, D. A. Hogan, and R. P. Hausinger. (2003) “Intrinsic Tryptophan Fluorescence as a Probe of Metal and alpha-Ketoglutarate Binding to TfdA, a Mononuclear Non-heme Iron Dioxygenase.” J. Inorg. Biochem. 93(1-2):66-70.
  6. Salzberg, S. L., Dunning Hotopp, J. C., Delcher, A. L., Pop M., Smith, D. R., Eisen, M. B., and W. C. Nelson. (2005) “Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.” Genome Biology 6:R23.
  7. Dunning Hotopp, J. C., M. Lin, R. Madupu, J. Crabtree, S. V. Angiuoli, J. Eisen, R. Seshadri, Q. Ren, M. Wu, T. R. Utterback, S. Smith, M. Lewis, H. Khouri, C. Zhang, N. Hua, Q. Lin, N. Ohashi, N. Zhi, W. Nelson, L. M. Brinkac, R. J. Dodson, M. J. Rosovitz, J. Sundaram, S. C. Daugherty, T. Davidsen, A. Durkin, M. Gwinn, D. H. Haft, J. D. Selengut, S. A. Sullivan, N. Zafar, L. Zhou, F. Benahmed, H. Forberger, R. Halpin, S. Mulligan, J. Robinson, Y. Rikihisa, and H. Tettelin. (2006) “Comparative Genomics of Emerging Human Ehrlichiosis Agents.” PLoS Genet. 2(2):e21.
  8. Baldo, L., J. C. Dunning Hotopp, K. A. Jolley, S. R. Bordenstein, S. A. Biber, R. R. Choudhury, C. Hayashi, M. C. J. Maiden, H. Tettelin, and J. H. Werren. (2006) “A Multilocus Sequence Typing System for the endosymbiont Wolbachia.” Appl. Environ. Microbiol. 72(11):7098-110.
  9. Dunning Hotopp, J. C., R. Grifantini, N. Kumar, Y. L. Tzeng, D. Fouts, E. Frigimelica, M. Draghi, M. M. Giuliani, R. Rappuoli, D. S. Stephens, G. Grandi, and H. Tettelin. (2006) “Comparative Genomics of Neisseria meningitidis: Core Genome, Islands of Horizontal Transfer and Pathogen Specific Genes.” Microbiology 152(12):3733-49.
  10. Ioannidis, P., J. C. Dunning Hotopp, P. Sapountzis, S. Siozios, G. Tsiamis, S. R. Bordenstein, L. Baldo, J. H. Werren, and K. Bourtzis. (2007) “New Criteria for Selecting the Origin of DNA Replication in Wolbachia and Closely Related Bacteria.” BMC Genomics 8:182.
  11. Dunning Hotopp, J. C., M. E. Clark, D. C. S. G. Oliveira, J. M. Foster, P. Fischer, M. C. Muñoz Torres, J. D. Giebel, N. Kumar, N. Ishmael, S. Wang, J. Ingram, R. V. Nene, J. Shepard, J. Tomkins, S. Richards, D. J. Spiro, E. Ghedin, B. E. Slatko, H. Tettelin, and  J. H. Werren. (2007) “Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes.” Science 317(5845):1753-6. *J. C. Dunning Hotopp and M. E. Clark are co-first authors.
  12. Jiang, S. M., N. Ishmael, J. C. Dunning Hotopp, M. Puliti, L. Tissi, N. Kumar, M. J. Cieslewicz, H. Tettelin, and M. R. Wessels (2008) “Variation in the group B Streptococcus CsrRS regulon and effects on pathogenicity.” J Bacteriol 190(6):1956-65.
  13. Bordenstein, S.R., C. Paraskevopoulos, J. C. Dunning Hotopp, P. Sapountzis, N. Lo, C. Bandi, H. Tettelin, J. Werren, and K. Bourtzis. (2009) “Parasitism and mutualism in Wolbachia: what the phylogenomic trees can and cannot say,” Mol Biol Evol 26(1):231-41.
  14. Ishmael, N., J. C. Dunning Hotopp, P. Ioannidis, S. Biber, J. Sakamoto, S. Siozios, V. Nene, J. H. Werren, K. Bourtzis, S. R. Bordenstein, and H. Tettelin. (2009). “Extensive genomic diversity of closely related Wolbachia strains.” Microbiology 155:2211-2222. *N. Ishmael and J. C. Dunning Hotopp are co-first authors.
  15. McNulty, S. N., J. Foster, M. Mitreva, J. C. Dunning Hotopp, J. Martin, K. Fischer, B. Wu, P. J. David, S. Kumar, N. W. Brattig, B. E. Slatko, G. J. Weil, and P. U. Fischer. (2010) “Endosymbiont DNA in endobacteria-free filarial nematodes indicates past symbiosis and ancient horizontal genetic transfer.” PLoS ONE 5(6): e11029.
  16. Donati, C., N. L. Hiller, H. Tettelin, A. Muzzi, N. J. Croucher, S. V. Angiuoli, M. Oggioni, J. C. Dunning Hotopp, F. Z. Hu, D. R. Riley, A. Covacci, T. J. Mitchell, S. D. Bentley, M. Kilian, G. D. Ehrlich, R. Rappuoli, E. R. Moxon, and V. Masignani. (2010) “Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species.” Genome Biol. 11:R107.
  17. Budroni, S., E. Siena, J. C. Dunning Hotopp, K. Sieb, D. Serruto, C. Nofroni, M. Comanducci, D. Riley, S. Daugherty, S. Angiuoli, A. Covacci, M. G. Pizza, R. Rappuoli, R. Moxon, H. Tettelin, and D. Medini. (2011) “Neisseria meningitidis population is structure in phylogenetic clades, associated with restriction-modification systems that modulate the effect of homologous recombination.” Proc Natl Acad Sci U S A 108(11):4494-9.
  18. Dunning Hotopp, J. C. (2011) “Horizontal Gene Transfer Between Bacteria and Animals” Trends in Genetics, 27(4):157-63.
  19. Angiuoli, S. V., J. C. Dunning Hotopp, S. L. Salzberg, and H. Tettelin. (2011) “Improving pan-genome annotation using whole genome multiple alignment.” BMC Bioinformatics, 12:272.
  20. Bessen, D. E, N. Kumar, G. S. Hall, D. R. Riley, F. Luo, S. Lizano, C. N. Ford, W. M. McShan, S. V. Nguyen, J. C. Dunning Hotopp, and H. Tettelin. (2011) “Whole-genome association study on tissue tropism phenotypes in group A Streptococcus.” J. Bacteriol. 192(23): 6651-63.
  21. Sanchez C. J., N. Kumar, A. Lizcano, P. Shivshankar, J. C. Dunning Hotopp, J. H. Jorgensen, H. Tettelin, and C. J. Orihuela. (2011) “Streptococcus pneumoniae in Biofilms Are Unable to Cause Invasive Disease Due to Altered Virulence Determinant Production.” PLoS One 6(12):e28738.
  22. Riley D. R., S. V. Angiuoli, J. Crabtree, J. C. Dunning Hotopp, and H. Tettelin. (2012) “Using Sybil for interactive comparative genomics of microbes on the web.” Bioinformatics 28(2):160-6.
  23. de Filippis, I, A. P. de Lemos, J. B. Hostetler, K. Wollenberg, C. T. Sacchi, J. C. Dunning Hotopp, L. H. Harrison, M. C. Bash, and D. R. Prevots. (2012) “Molecular epidemiology of Neisseria meningitidis serogroup B in Brazil.” PLoS One 7(3):e33016.
  24. Krauland, M. G., J. C. Dunning Hotopp, D. R. Riley, S. C. Daugherty, J. W. Marsh, N. E. Messonnier, L. W. Mayer, H. Tettelin, and L. H. Harrison. (2012) “Whole genome sequencing to investigate the emergence of clonal complex 23 Neisseria meningitidis serogroup Y disease in the United States.” PLoS One 7(4):e35699.
  25. Kumar, N., T. Creasy, Y. Sun, M. Flowers, L. J. Tallon, and J. C. Dunning Hotopp. (2012) “Efficient subtraction of insect rRNA prior to transcriptome analysis of Wolbachia-Drosophila lateral gene transfer.” BMC Res Note 5(1):230.
  26. Desjardins, C. A., G. C. Cerqueira, J. M. Goldberg, J. C. Dunning Hotopp, B. J. Haas, J. Zucker, J. M. Ribeiro, S. Saif, J. Z. Levin, L. Fan, Q. Zeng, C. Russ, J. R. Wortman, D. L. Fink, B. W. Birren, T. B. Nutman. (2013) “Genomics of Loa loa, a Wolbachia-free filarial parasite of humans.” Nat Genet 45(5):495-500.
  27. Kimaro Mlacha, S. Z., S. Romero-Steiner, J. C. Dunning Hotopp, N. Kumar, N. Ishmael, D. R. Riley, U. Farooq, T. H. Creasy, L. J. Tallon, X. Liu, C. S. Goldsmith, J. Sampson, G. M. Carlone, S. K. Hollingshead, J. A. G. Scott, H. Tettelin. (2013) “Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells.” BMC Genomics, 14:383.
  28. Kimaro Mlacha, S. Z., T. C. T. Peret, N. Kumar, S. Romero-Steiner, J. C. Dunning Hotopp, N. Ishmael, V. Grinblat-Huse, D. R. Riley, D. D. Erdman, G. M. Carlone, J. Sampson, J. A. G. Scott, H. Tettelin. (2013) “Transcriptional adaptation of pneumococci and human pharyngeal cells in the presence of a virus infection.” BMC Genomics, 14:378.
  29. Riley, D. R., K. B. Sieber, K. M. Robinson, J. R. White, A. Ganesan, S. Nourbakhsh, and J. C. Dunning Hotopp. 2013. Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples. PLoS Comput Bio, 9(6): e1003107. Facebook-IFLS
  30. Klinzing, D. C., N. Ishmael, J. C. Dunning Hotopp, H. Tettelin, K. R. Shields, L. C. Madoff, K. M. Puopolo. (2013) “The two-component response regulator LiaR regulates cell wall stress responses, pili expression and virulence in group B Streptococcus.” Microbiology, 159:1521-34.
  31. Ioannidis, P, K. L. Johnston, D. R. Riley, N. Kumar, J. R. White, K. T. Olarte, S. Ott, L. J. Tallon, J. M. Foster, M. J. Taylor, and J. C. Dunning Hotopp*. (2013) “Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi.” BMC Genomics 14:639.
  32. Estes, A. M., D. J. Hearn, E. C. Snell-Rood, M. Feindler, K. Feeser, T. Abebe, J. C. Dunning Hotopp* and Armin P. Moczek*. (2013) “Brood ball-mediated transmission of microbiome members in the dung beetle, Onthophagus taurus (Coleoptera: Scarabaeidae).” PLoSOne 8(11):e79061. *These authors contributed equally to this work.
  33. Robinson, K. M., K. B. Sieber, and J. C. Dunning Hotopp. (2013) A review of bacteria-animal lateral gene transfer may inform our understanding of diseases like cancer. PLoS Genet 9:e1003877.
  34. Dugan V. G. , S. J. Emrich, G. I. Giraldo-Calderón, O. S. Harb, R. M. Newman, B. E. Pickett, L. M. Schriml, T. B. Stockwell, C. J. Stoeckert, D. E. Sullivan, I. Singh, D. V. Ward, A. Yao, J. Zheng, T. Barrett, B. Birren, L. Brinkac, V. M. Bruno, E. Caler, S. Chapman, F. H. Collins, C. A. Cuomo, V. Di Francesco, S. Durkin, M. Eppinger, M. Feldgarden, C. Fraser, W. F. Fricke, M. Giovanni, M. R. Henn, E. Hine, J. Dunning Hotopp, I. Karsch-Mizrachi, J. C. Kissinger, E. M. Lee, P. Mathur, E. F. Mongodin, C. I. Murphy, G. Myers, D. E. Neafsey, K. E. Nelson, W. C. Nierman, J. Puzak, D. Rasko, D. S. Roos, L. Sadzewicz, J. C. Silva, B. Sobral, R. B. Squires, R. L. Stevens, L. Tallon, H. Tettelin, D. Wentworth, O. White, R. Will, J. Wortman, Y. Zhang, R. H. Scheuermann. (2014) “Standardized Metadata for Human Pathogen/Vector Genomic Sequences.” PLoSOne 9(6):e99979.
  35. Tallon, L. J., X. Liu, S. Bennuru, M. C. Chibucos, A. Godinez, S. Ott, X. Zhao, L. Sadzewicz, C. M. Fraser, T. B. Nutman, and J.  C. Dunning Hotopp. (2014.) “Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis.” BMC Genomics 15:788.
  36. Ioannidis, P., Y. Lu, N. Kumar, T. Creasy, S. Daugherty, M. C. Chibucos, J. Orvis, A. Shetty, S. Ott, M. Flowers, N. Sengamalay, L. J. Tallon, L. Pick and J.  C. Dunning Hotopp. (2014) “Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys.” BMC Genomics 15:738.
  37. Klasson, L., N. Kumar, R. Bromley, K. Sieber, M. Flowers, S. H. Ott, L. J. Tallon, S. G. Andersson, and J.  C. Dunning Hotopp. (2014) “Extensive duplication of the Wolbachia DNA in chromosome four of Drosophila ananassae.” BMC Genomics 15:1097.
  38. Robinson, K. M., and J.  C. Dunning Hotopp. (2014) “Mobile elements and viral integrations prompt considerations for bacterial DNA integration as a novel carcinogen.” Cancer Lett 352:137-44.
  39. Dunning Hotopp, J. C., A. M. Estes (2014) “Biology wars: the eukaryotes strike back.” Cell Host Microbe 16:701-3.
  40. Mustapha, M. M., J. W. Marsh, M. G. Krauland, J. O. Fernandez, A. P. de Lemos, J. C. Dunning Hotopp, X. Wang, L. W. Mayer, J. G. Lawrence, N. L. Hiller, L. H. Harrison (2015) “Genomic Epidemiology of Hypervirulent Serogroup W, ST-11 Neisseria meningitidis.” EBioMedicine 2(10):1447-55.
  41. Sieber, K. B., P. Gajer, and J.  C. Dunning Hotopp. (2016) “Modeling the integration of bacterial rRNA fragments into the human cancer genome.” BMC Bioinformatics 17:134.
  42. Mustapha, M. M., J. W. Marsh, M. G. Krauland, J. O. Fernandez, A. P. de Lemos, J. C. Dunning Hotopp, X. Wang, L. W. Mayer, J. G. Lawrence, N. L. Hiller, L. H. Harrison (2016) “Genomic Investigation Reveals Highly Conserved, Mosaic, Recombination Events Associated with Capsular Switching among Invasive Neisseria meningitidis Serogroup W Sequence Type (ST)-11 Strains,” Genome Biol Evol 8(6):2065-75.
  43. Kumar N., M. Lin, X. Zhao, S. Ott, I. Santana-Cruz, S. Daugherty, Y. Rikihisa, L. Sadzewicz, L. J. Tallon, C. M. Fraser, J.  C. Dunning Hotopp (2016) “Efficient Enrichment of Bacterial mRNA from Host-Bacteria Total RNA Samples,” Sci Rep 6:34850.
  44. Ghedin E., J. Cotton, S. Bennuru, A. Grote, B. Harsha, A. Tracey, R. Beech, S. Doyle, M. Dunn, J.  C. Dunning Hotopp, N. Holroyd, T. Kikuchi, O. Lambert, A. Mhashilkar, P. Mutowo, N. Nursimulu, J. Ribeiro, M. Rogers, E. Stanley, L. Swapna, I. Tsai, T. Unnasch, D. Voronin, J. Parkinson, T. Nutman, M. Berriman, and S. Lustigman (2016) “The genome of Onchocerca volvulus, agent of river blindness” Nature Microbiology 2:16216.
  45. Robinson, K. M., J. Crabtree, J. S. Mattick, K. E. Anderson, and J. C. Dunning Hotopp. (2017) “Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data,” Microbiome 5(1):9.
  46. Dunning Hotopp, J. C., B. E. Slatko, and J. M. Foster. (2017) “Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers” Sci Rep, under revision.
  47. Lin, M, K. Bachman, Z. Cheng, S. C. Daugherty, S. Nagaraj, N. Sengamalay, S. Ott, Z. Godinez, L. J. Tallon, L. Sadzewicz, C. Fraser, J.  C. Dunning Hotopp, and Y. Rikihisa. (2017) “ Analaysis of complete genome sequence and major surface antigens of Neorickettsia helminthoeca, causative agent of salmon poisoning disease.” Microb. Biotechnol. 10(4):933-57.
  48. Robinson, K. M., A. S. Hawkins, I. Santana-Cruz, R. S. Adkins, A. C. Shetty, S. Nagaraj, L. Sadzewicz, L. J. Tallon, D. A. Rasko, C. M. Fraser, A. Mahurkar, Joana C. Silva, and J. C. Dunning Hotopp. (2017) “Aligner Optimization Increases Accuracy and Decreases Compute Times in Multi-Species Sequence Data,” Microbial Genomics 3(9):e000122.
  49. Chung, M., S. T. Small, D. Serre, P. A. Zimmerman, and J. C. Dunning Hotopp. (2017) “Draft Genome Sequence of the Wolbachia Endosymbiont of Wuchereria bancrofti wWb,” 75(9).
  50. Dunning Hotopp, J. C. and L. Klasson. (2018) “The Complexities and Nuances of Analyzing the Genome of Drosophila ananassae and Its Wolbachia Endosymbiont” G3 (Bethesda) 8(1):373-4.
  51. Watkins, T. N., H. Liu, M. Chung, T. H. Hazen, J. C. Dunning Hotopp, S. G. Filler, and V. M. Bruno. (2018) “Comparative transcriptomics of Aspergillus fumigatus strains upon exposure to human airway epithelial cells.” Microbial Genomics. DOI 10.1099/mgen.0.000154
  52. Vincent, L. R, S. R. Kerr, Y. Tan, J. Tomberg, E. L. Raterman, J. C. Dunning Hotopp, M. Unemo, R. A. Nicholas, and A. E. Jerse. (2018) “In Vivo-Selected Compensatory Mutations Restore the Fitness Cost of Mosaic penA Alleles That Confer Ceftriaxone Resistance in Neisseria gonorrhoeae.” MBio 9(2): e01905-17.
  53. Dunning Hotopp J. C. (2018) “Grafting or pruning in the animal tree: lateral gene transfer and gene loss?” BMC Genomics 19(1):470.
  54. Izzard L, M. Chung, J. Dunning Hotopp, G. Vincent, D. Paris, S. Graves, and J. Stenos. (2018) “Isolation of a divergent strain of Rickettsia japonica from Dew’s Australian bat Argasid ticks (Argas (Carios) dewae) in Victoria, Australia.” Ticks Tick Borne Dis. https://doi.org/10.1016/j.ttbdis.2018.07.007.
  55. Chung, M., L. Teigen, H. Liu, S. Libro, A. Shetty, N. Kumar, X. Zhao, R. E. Bromley, L. J. Tallon, L. Sadzewicz, C. M. Fraser, D. A. Rasko, S. G. Filler, J. M. Foster, M. L. Michalski, V. M. Bruno, and J. C. Dunning Hotopp. (2018) “Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses” Scientific Reports 8:13377.
  56. Estes A. M., D. J. Hearn, S. Agrawal, E. A. Pierson, and J. C. Dunning Hotopp. (2018) “Comparative genomics of the Erwinia and Enterobacter olive fly endosymbionts” Scientific Reports 8:15936.
  57. Estes A. M., D. J. Hearn, S. Nadendla, E. A. Pierson, and J. C. Dunning Hotopp. (2018) “Draft Genome Sequence of Enterobacter sp. Strain OLF, a Colonizer of Olive Flies.” Microbiol Resour Announc. 7(9).
  58. Estes A. M., D. J. Hearn, S. Nadendla, E. A. Pierson, and J. C. Dunning Hotopp. (2018) “Draft Genome Sequence of Erwinia dacicola, a Dominant Endosymbiont of Olive Flies.” Microbiol Resour Announc. 7(10).
  59. Chung M, L. Teigen, S. Libro, R. E. Bromley, N. Kumar, L. Sadzewicz, L. J. Tallon, J. M. Foster, M. L. Michalski, J. C. Dunning Hotopp. (2018) “Multispecies Transcriptomics Data Set of Brugia malayi, Its Wolbachia Endosymbiont wBm, and Aedes aegypti across the B. malayi Life Cycle.” Microbiol Resour Announc. 7(18).
  60. Chung M., J. B. Munro, H. Tettelin, and J. C. Dunning Hotopp. (2018) “Using Core Genome Alignments To Assign Bacterial Species.” mSystems 3(6).
  61. Kessler M. D., N. W. Bateman, T. P. Conrads, G. L. Maxwell, J. C. Dunning Hotopp, and T. D. O’Connor. (2019) “Ancestral characterization of 1018 cancer cell lines highlights disparities and reveals gene expression and mutational differences.” Cancer 125(12):2076-2088.

Book Chapters

  1. Dunning Hotopp, J. C. “Lateral gene transfer in multicellular organisms” in “Lateral Gene Transfer in Evolution, edited by U. Gophna, anticipated 2013.

Non-Peer-Reviewed Journal Articles

  1. Dunning Hotopp, J. C. and J. L. Rasgon. 2008. “Bacterial sequences in an invertebrate genome.” Microbiology Today. Nov: 176-179.
  2. Robinson, K. and J. C. Dunning Hotopp. 2016. “Bacteria and humans have been swapping DNA for millennia.” The Scientist. Oct: 46-51.
  3. Sieber, K. B., R. E. Bromley and J. C. Dunning Hotopp, (2017) “Lateral gene transfer between prokaryotes and eukaryotes”, Experimental Cell Research, http://dx.doi.org/10.1016/j.yexcr.2017.02.009.

Other Brief Communications

  1. Salzberg, S. L., Dunning Hotopp, J. C., Delcher, A. L., Pop M., Smith, D. R., Eisen, M. B. and W. C. Nelson. (2005) “Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.” Genome Biology 6:R23.
  2. Dunning Hotopp, J. C., Nelson, W. C., and S. L. Salzberg. (2005) A response to “New names for old strains? Wolbachia wSim is actually wRi.” Genome Biology 6:401.