Peer-reviewed journal articles

  1. Watson KJ, Bromley RE, Sparklin BC, Gasser MT, Bhattacharya T, Lebov JF, Tyson T, Dai N, Teigen LE, Graf KT, Foster JM, Michalski M, Bruno VM, Lindsey AR, Corrêa IR Jr, Hardy RW, Newton IL, Dunning Hotopp JC. (2023) Life Sci Alliance 7(2):e202302201. Open Access PMID: 38030223
  2. Tvedte, ES, Gasser M, Zhao X, Tallon LJ, Sadzewicz L, Bromley RE, Chung M, Mattick J, Sparklin BJ, Dunning Hotopp JC. (2022) “Accumulation of endosymbiont genomes in an insect autosome followed by endosymbiont replacement” Curr Biol 32(12):2786-2795. Open Access PMID: 35671755
  3. Chung M, Adkins RS, Mattick JSA, Bradwell KR, Shetty AC, Sadzewicz L, Tallon LJ, Fraser CM, Rasko DA, Mahurkar A, Dunning Hotopp JC. (2021) “FADU: a Quantification Tool for Prokaryotic Transcriptomic Analyses.” mSystems. 6(1):e00917-20. OPEN ACCESS PMID: 33436511
  4. Soliman SSM, Baldin C, Gu Y, Singh S,Gebremariam T, Swidergall M, Alqarihi A, Youssef EG, Alkhazraji S, Pikoulas A, Perske C, Venkataramani V, Rich A, Bruno VM, Dunning Hotopp J, Mantis NJ, Edwards JE, Filler SG, Chamilos G, Vitetta ES, Ibrahim AS. (2021) “Mucroricin is a ricin-like toxin that is critical for pathogeneiss of mucormycosis” Nat Microbiol. 6(3):313-326. PMID: 33462434
  5. Lin M, Xiong Q, Chung M, Daugherty SC, Nagaraj S, Sengamalay N, Ott S, Godinez A, Tallon LJ, Sadzewicz L, Fraser C, Dunning Hotopp JC, Rikihisa Y. (2021) “Comparative Analysis of Genome of Ehrlichia sp. HF, a Model Bacterium to Study Fatal Human Ehrlichiosis.” BMC Genomics. 22(1):11. OPEN ACCESS PMID
  6. Mattick J, Libro S, Bromley R, Chaicumpa W, Chung M, Cook D, Khan MB, Kumar N, Lau YL, Misra-Bhattacharya S, Rao R, Sadzewicz L, Saeung A, Shahab M, Sparklin BC, Steven A, Turner JD, Tallon LJ, Taylor MJ, Moorhead AR, Michalski M, Foster JM, Dunning Hotopp JC. (2021) “X-treme loss of sequence diversity linked to neo-X chromosomes in filarial nematodes” PLoS Negl Trop Dis 15(10):e0009838. Open Access PMID: 34705823
  7. Tvedte ES, Michalski J, Cheng S, Patkus RS, Tallon LJ, Sadzewicz L, Bruno VM, Silva JC, Rasko DA, Dunning Hotopp JC. (2021) “Evaluation of a high-throughput, cost-effective Illumina library preparation kit” Sci Rep. 11(1):15925. Open Access PMID: 34354114
  8. Chung M, Bruno VM, Rasko DA, Cuomo CA, Muñoz JF, Livny J, Shetty AC, Mahurkar A, Dunning Hotopp JC. (2021) “Best practices on the differential expression analysis of multi-species RNA-Seq” Genome Biol 22(1):121. Open Access PMID: 33926528
  9. Scarpa M, Kapoor S, Tvedte ES, Doshi KA, Zou YS, Singh P, Lee JK, Chatterjee A, Mustafa Ali MK, Bromley RE, Dunning Hotopp JC, Rassool FV, Baer MR. (2021) “Pim kinase inhibitor co-treatment decreases alternative non-homologous end-joining DNA repair and genomic instability induced by topoisomerase 2 inhibitors in cells with FLT3 internal tandem duplication” Oncotarget 12(18)1763-1779. Open Access PMID: 34504649
  10. Tvedte ES, Gasser M, Sparklin BC, Michalski J, Hjelmen CE, Johnston JS, Zhao X, Bromley R, Tallon LJ, Sadzewicz L, Rasko DA, Dunning Hotopp JC. (2021) “Comparison of long read sequencing technologies in interrogating bacteria and fly genomes” G3(Bethesda) 11(6):jkab083. Open Access PMID: 33768248
  11. Moser K. A., E. F. Drábek, A. Dwivedi, E. M. Stucke, J. Crabtree, A. Dara, Z. Shah, M. Adams, T. Li, P. T. Rodrigues, S. Koren, A. M. Phillippy, J. B. Munro, A. Ouattara, B. C. Sparklin, J. C. Dunning Hotopp, K. E. Lyke, L. Sadzewicz, L. J. Tallon, M. D. Spring, K. Jongsakul, C. Lon, D. L. Saunders, M. U. Ferreira, M. M. Nyunt, M. K. Laufer, M. A. Travassos, R. W. Sauerwein, S. Takala-Harrison, C. M. Fraser, B. K. L. Sim, S. L. Hoffman, C. V. Plowe, J. C. Silva. (2020) “Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential.” Genome Med. 12(1):6. OPEN ACCESS PMID:31915075
  12. Shetty A. C., J. Mattick, M. Chung, C. McCracken, A. Mahurkar, S. G. Filler, C. M. Fraser, D. A. Rasko, V. M. Bruno, J. C. Dunning Hotopp. (2020) “Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics.” Microb Genom. 6(1). OPEN ACCESS PMID: 31851607
  13. Foster J. M., Grote A., Mattick J., Tracey A., Tsai Y. C., Chung M., Cotton J. A., Clark T. A., Geber A., Holroyd N., Korlach J., Li Y., Libro S., Lustigman S., Michalski M. L., Paulini M., Rogers M. B., Teigen L., Twaddle A., Welch L., Berriman M., Dunning Hotopp J. C., Ghedin E. (2020) “Sex chromosome evolution in parasitic nematodes of humans.” Nature Communications. 2020;11(1):1964. Epub 2020/04/25. doi: 10.1038/s41467-020-15654-6. OPEN ACCESS PMID: 32327641; PMCID: PMC7181701.
  14. Tracey A., Foster J. M., Paulini M., Grote A., Mattick J., Tsai Y. C., Chung M., Cotton J. A., Clark T. A., Geber A., Holroyd N., Korlach J., Libro S., Lustigman S., Michalski M. L., Rogers M. B., Twaddle A., Dunning Hotopp J. C., Berriman M., Ghedin E. (2020) “Nearly Complete Genome Sequence of Brugia malayi Strain FR3.” Microbiol Resour Announc. 2020;9(24). Epub 2020/06/13. doi: 10.1128/MRA.00154-20. OPEN ACCESS PMID: 32527783; PMCID: PMC7291094.
  15. Lebov J. F., Mattick J., Libro S., Sparklin B. C., Chung M., Bromley R. E., Nadendla S., Zhao X., Ott S., Sadzewicz L., Tallon L. J., Michalski M. L., Foster J. M., Dunning Hotopp J. C. (2020) “Complete Genome Sequence of wBp, the Wolbachia Endosymbiont of Brugia pahangi FR3.” Microbiol Resour Announc. 2020;9(27). Epub 2020/07/04. doi: 10.1128/MRA.00480-20. OPEN ACCESS PMID: 32616636; PMCID: PMC7330238.
  16. Mattick J., Libro S., Sparklin B. C., Chung M., Bromley R. E., Nadendla S., Zhao X., Ott S., Sadzewicz L., Tallon L. J., Michalski M. L., Foster J. M., Dunning Hotopp J. C. (2020) Nearly Complete Genome Sequence of Brugia pahangi FR3. Microbiol Resour Announc. 2020;9(27). Epub 2020/07/04. doi: 10.1128/MRA.00479-20. OPEN ACCESS PMID: 32616635; PMCID: PMC7330237.
  17. Chung M, Aluvathingal J, Bromley RE, Nadendla S, Fombad FF, Kien CA, Gandjui NVT, Njouendou AJ, Ritter M, Sadzewicz L, Tallon LJ, Wanji S, Hoerauf A, Pfarr K, Dunning Hotopp JC. (2020) “Complete Mitochondrial Genome Sequence of Mansonella perstans” Microbiol Resour Announc. 2020 Jul 23;9(30):e00490-20. OPEN ACCESS PMID: 32703831
  18. Dunning Hotopp JC, Baltrus DA, Bruno VM, Dennehy JJ, Gill SR, Maresca JA, Matthijnssens J, Newton ILG, Putonti C, Rasko DA, Rokas A, Roux S, Stajich JE, Stedman KM, Stewart FJ, Thrash JC. (2020) “Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements” Microbiol Resour Announc. 9(36):e00763-20. OPEN ACCESS PMID: 32883786
  19. Chung M, Basting PJ, Patkus RS, Grote A, Luck AN, Ghedin E, Slatko BE, Michalski M, Foster J, Bergman CM, Dunning Hotopp JC. (2020) “A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts.” G3 27:g3.401534.2020; OPEN ACCESS PMID: 32718933
  20. 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. OPEN ACCESS PMID: 30865299
  21. Chung M., Teigen L. E., Libro S., Bromley R. E., Olley D., Kumar N., Sadzewicz L., Tallon L. J., Mahurkar A., Foster J. M., Michalski M. L., and J. C. Dunning Hotopp. (2019) “Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics.” mSystems. 2019 Dec 3;4(6). OPEN ACCESS PMID: 31796568
  22. Gasser M. T., Chung M., Bromley R. E., Nadendla S., and J. C. Dunning Hotopp. (2019) “Complete Genome Sequence of wAna, the Wolbachia Endosymbiont of Drosophila ananassae.” Microbiol Resour Announc. 8(43). OPEN ACCESS PMID: 31649084
  23. Baltrus D. A., Cuomo C. A., Dennehy J. J., Dunning Hotopp, J. C., Maresca J. A., Newton I. L. G., Rasko D. A., Rokas A., Roux S., Stajich J. E. (2019) “Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity.” Microbiol Resour Announc. 8(36). OPEN ACCESS PMID: 31488541
  24. Dunning Hotopp, J. C., Matsumura J, Bromley R. E., Riley D. R., Agrawal S., Sparklin B., Mattick J., Crabtree J., Mahurkar A. (2019) “TwinBLAST: When Two Is Better than One.” Microbiol Resour Announc. 8(35). OPEN ACCESS PMID: 31467106
  25. 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. OPEN ACCESS PMCID: 29301977
  26. 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 OPEN ACCESS PMID: 29345613
  27. 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. OPEN ACCESS PMID: 29615507
  28. Dunning Hotopp J. C. (2018) “Grafting or pruning in the animal tree: lateral gene transfer and gene loss?” BMC Genomics 19(1):470. OPEN ACCESS PMID: 29914363
  29. 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. PMID: 30025798
  30. 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. OPEN ACCESS PMID: 30190541
  31. Chung, M, J. B. Munro, H. Tettelin, and J. C. Dunning Hotopp. (2018) “Using core genome alignments to assign bacterial species.” mSystems. 3(6): e00236-18. OPEN ACCESS PMID: 30534598
  32. 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): e01068-18. OPEN ACCESS PMID: 30533936
  33. Chung M, L. Teigen, S. Libro, R. E. Bromley, N. Kumar, L. Sadzewicz, L. J. Tallon, J. M. Foster, M. L. Michalski, and 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): e01306-18. OPEN ACCESS PMID: 30533772
  34. 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): e01067-18. OPEN ACCESS PMID: 30533624
  35. 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.” Sci Rep. 8(1):15936. OPEN ACCESS PMID: 30374192
  36. 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.
  37. 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, 7(1):857.
  38. 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) “Analysis of complete genome sequence and major surface antigens of Neorickettsia helminthoeca, causative agent of salmon poisoning disease.” Microb. Biotechnol. 10(4):933-57.
  39. 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.
  40. 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,” Pathog Dis 75(9).
  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. Cotton J.A., S. Bennuru, A. Grote, B. Harsha, A. Tracey, R. Beech, S. R. Doyle, M. Dunn, J. C. Dunning Hotopp, N. Holroyd, T. Kikuchi, O. Lambert, A. Mhashilkar, P. Mutowo, N. Nursimulu, J. M. Ribeiro, M. B. Rogers, E. Stanley, L. S. Swapna, I. J. Tsai, T. R. Unnasch, D. Voronin, J. Parkinson, T. B. Nutman, E. Ghedin, M. Berriman, S. Lustigman. (2016) “The genome of Onchocerca volvulus, agent of river blindness” Nature Microbiology 2:16216.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  51. Dunning Hotopp, J. C., A. M. Estes (2014) “Biology wars: the eukaryotes strike back.” Cell Host Microbe 16:701-3.
  52. 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.
  53. 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.
  54. 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.
  55. 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.
  56. 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.
  57. 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.
  58. 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.
  59. 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 Genetics 9(10):e1003877.
  60. 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.
  61. 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.
  62. 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.
  63. 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.
  64. 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.
  65. Dunning Hotopp, J. C. (2011) “Horizontal Gene Transfer Between Bacteria and Animals” Trends in Genetics, 27(4):157-63.
  66. Angiuoli, S., J. C. Dunning Hotopp, S. L. Salzberg, and H. Tettelin. (2011) “Improving pan-genome annotation using whole genome multiple alignment.” BMC Bioinformatics, 12:272.
  67. 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.
  68. 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.
  69. 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.
  70. 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.
  71. 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.
  72. 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.
  73. 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.
  74. 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 H. Werren. (2007) “Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes.” Science 317(5845):1753-6.
  75. 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.
  76. 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.
  77. 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.
  78. 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.
  79. 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” Genome Biology 6:R23.
  80. 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.
  81. 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/α-ketoglutarate Dioxygenase Complexed to Ferrous Iron and Substrates.” Biochemistry 41(16):5185-92.
  82. 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.
  83. 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.
  84. 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.

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

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.