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Comparative genomics of the Erwinia and Enterobacter olive fly endosymbionts.

Estes AM, Hearn DJ, Agrawal S, Pierson EA, Dunning Hotopp JC.

Sci Rep. 2018 Oct 29;8(1):15936. doi: 10.1038/s41598-018-33809-w.


Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses.

Chung M, Teigen L, Liu H, Libro S, Shetty A, Kumar N, Zhao X, Bromley RE, Tallon LJ, Sadzewicz L, Fraser CM, Rasko DA, Filler SG, Foster JM, Michalski ML, Bruno VM, Dunning Hotopp JC.

Sci Rep. 2018 Sep 6;8(1):13377. doi: 10.1038/s41598-018-31420-7.


Grafting or pruning in the animal tree: lateral gene transfer and gene loss?

Dunning Hotopp JC.

BMC Genomics. 2018 Jun 18;19(1):470. doi: 10.1186/s12864-018-4832-5.


In Vivo-Selected Compensatory Mutations Restore the Fitness Cost of Mosaic penA Alleles That Confer Ceftriaxone Resistance in Neisseria gonorrhoeae.

Vincent LR, Kerr SR, Tan Y, Tomberg J, Raterman EL, Dunning Hotopp JC, Unemo M, Nicholas RA, Jerse AE.

MBio. 2018 Apr 3;9(2). pii: e01905-17. doi: 10.1128/mBio.01905-17.


Comparative transcriptomics of Aspergillus fumigatus strains upon exposure to human airway epithelial cells.

Watkins TN, Liu H, Chung M, Hazen TH, Dunning Hotopp JC, Filler SG, Bruno VM.

Microb Genom. 2018 Jan 18. doi: 10.1099/mgen.0.000154. [Epub ahead of print]


The Complexities and Nuances of Analyzing the Genome of Drosophila ananassae and Its Wolbachia Endosymbiont.

Dunning Hotopp JC, Klasson L.

G3 (Bethesda). 2018 Jan 4;8(1):373-374. doi: 10.1534/g3.117.300164.


Aligner optimization increases accuracy and decreases compute times in multi-species sequence data.

Robinson KM, Hawkins AS, Santana-Cruz I, Adkins RS, Shetty AC, Nagaraj S, Sadzewicz L, Tallon LJ, Rasko DA, Fraser CM, Mahurkar A, Silva JC, Dunning Hotopp JC.

Microb Genom. 2017 Jul 8;3(9):e000122. doi: 10.1099/mgen.0.000122. eCollection 2017 Sep.


Draft genome sequence of the Wolbachia endosymbiont of Wuchereria bancrofti wWb.

Chung M, Small ST, Serre D, Zimmerman PA, Dunning Hotopp JC.

Pathog Dis. 2017 Dec 29;75(9). doi: 10.1093/femspd/ftx115.


Analysis of complete genome sequence and major surface antigens of Neorickettsia helminthoeca, causative agent of salmon poisoning disease.

Lin M, Bachman K, Cheng Z, Daugherty SC, Nagaraj S, Sengamalay N, Ott S, Godinez A, Tallon LJ, Sadzewicz L, Fraser C, Dunning Hotopp JC, Rikihisa Y.

Microb Biotechnol. 2017 Jul;10(4):933-957. doi: 10.1111/1751-7915.12731. Epub 2017 Jun 6.


Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers.

Dunning Hotopp JC, Slatko BE, Foster JM.

Sci Rep. 2017 Apr 12;7(1):857. doi: 10.1038/s41598-017-00814-4.


Lateral gene transfer between prokaryotes and eukaryotes.

Sieber KB, Bromley RE, Dunning Hotopp JC.

Exp Cell Res. 2017 Sep 15;358(2):421-426. doi: 10.1016/j.yexcr.2017.02.009. Epub 2017 Feb 9. Review.


Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data.

Robinson KM, Crabtree J, Mattick JS, Anderson KE, Dunning Hotopp JC.

Microbiome. 2017 Jan 25;5(1):9. doi: 10.1186/s40168-016-0224-8.


Efficient Enrichment of Bacterial mRNA from Host-Bacteria Total RNA Samples.

Kumar N, Lin M, Zhao X, Ott S, Santana-Cruz I, Daugherty S, Rikihisa Y, Sadzewicz L, Tallon LJ, Fraser CM, Dunning Hotopp JC.

Sci Rep. 2016 Oct 7;6:34850. doi: 10.1038/srep34850.


Genomic Investigation Reveals Highly Conserved, Mosaic, Recombination Events Associated with Capsular Switching among Invasive Neisseria meningitidis Serogroup W Sequence Type (ST)-11 Strains.

Mustapha MM, Marsh JW, Krauland MG, Fernandez JO, de Lemos AP, Dunning Hotopp JC, Wang X, Mayer LW, Lawrence JG, Hiller NL, Harrison LH.

Genome Biol Evol. 2016 Jul 3;8(6):2065-75. doi: 10.1093/gbe/evw122.


Modeling the integration of bacterial rRNA fragments into the human cancer genome.

Sieber KB, Gajer P, Dunning Hotopp JC.

BMC Bioinformatics. 2016 Mar 21;17:134. doi: 10.1186/s12859-016-0982-0.


Genomic Epidemiology of Hypervirulent Serogroup W, ST-11 Neisseria meningitidis.

Mustapha MM, Marsh JW, Krauland MG, Fernandez JO, de Lemos AP, Dunning Hotopp JC, Wang X, Mayer LW, Lawrence JG, Hiller NL, Harrison LH.

EBioMedicine. 2015 Sep 8;2(10):1447-55. doi: 10.1016/j.ebiom.2015.09.007. eCollection 2015 Oct.


Biology wars: the eukaryotes strike back.

Dunning Hotopp JC, Estes AM.

Cell Host Microbe. 2014 Dec 10;16(6):701-3. doi: 10.1016/j.chom.2014.11.014.


Extensive duplication of the Wolbachia DNA in chromosome four of Drosophila ananassae.

Klasson L, Kumar N, Bromley R, Sieber K, Flowers M, Ott SH, Tallon LJ, Andersson SG, Dunning Hotopp JC.

BMC Genomics. 2014 Dec 12;15:1097. doi: 10.1186/1471-2164-15-1097.


Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis.

Tallon LJ, Liu X, Bennuru S, Chibucos MC, Godinez A, Ott S, Zhao X, Sadzewicz L, Fraser CM, Nutman TB, Dunning Hotopp JC.

BMC Genomics. 2014 Sep 12;15:788. doi: 10.1186/1471-2164-15-788.


Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys.

Ioannidis P, Lu Y, Kumar N, Creasy T, Daugherty S, Chibucos MC, Orvis J, Shetty A, Ott S, Flowers M, Sengamalay N, Tallon LJ, Pick L, Dunning Hotopp JC.

BMC Genomics. 2014 Aug 29;15:738. doi: 10.1186/1471-2164-15-738.


Mobile elements and viral integrations prompt considerations for bacterial DNA integration as a novel carcinogen.

Robinson KM, Dunning Hotopp JC.

Cancer Lett. 2014 Oct 1;352(2):137-44. doi: 10.1016/j.canlet.2014.05.021. Epub 2014 Jun 21. Review.


Brood ball-mediated transmission of microbiome members in the dung beetle, Onthophagus taurus (Coleoptera: Scarabaeidae).

Estes AM, Hearn DJ, Snell-Rood EC, Feindler M, Feeser K, Abebe T, Dunning Hotopp JC, Moczek AP.

PLoS One. 2013 Nov 1;8(11):e79061. doi: 10.1371/journal.pone.0079061. eCollection 2013.


A review of bacteria-animal lateral gene transfer may inform our understanding of diseases like cancer.

Robinson KM, Sieber KB, Dunning Hotopp JC.

PLoS Genet. 2013;9(10):e1003877. doi: 10.1371/journal.pgen.1003877. Epub 2013 Oct 17. Review.


Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi.

Ioannidis P, Johnston KL, Riley DR, Kumar N, White JR, Olarte KT, Ott S, Tallon LJ, Foster JM, Taylor MJ, Dunning Hotopp JC.

BMC Genomics. 2013 Sep 22;14:639. doi: 10.1186/1471-2164-14-639.


Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples.

Riley DR, Sieber KB, Robinson KM, White JR, Ganesan A, Nourbakhsh S, Dunning Hotopp JC.

PLoS Comput Biol. 2013;9(6):e1003107. doi: 10.1371/journal.pcbi.1003107. Epub 2013 Jun 20.


Transcriptional adaptation of pneumococci and human pharyngeal cells in the presence of a virus infection.

Kimaro Mlacha SZ, Peret TC, Kumar N, Romero-Steiner S, Dunning Hotopp JC, Ishmael N, Grinblat-Huse V, Riley DR, Erdman DD, Carlone GM, Sampson J, Scott JA, Tettelin H.

BMC Genomics. 2013 Jun 7;14:378. doi: 10.1186/1471-2164-14-378.


The two-component response regulator LiaR regulates cell wall stress responses, pili expression and virulence in group B Streptococcus.

Klinzing DC, Ishmael N, Dunning Hotopp JC, Tettelin H, Shields KR, Madoff LC, Puopolo KM.

Microbiology. 2013 Jul;159(Pt 7):1521-34. doi: 10.1099/mic.0.064444-0. Epub 2013 May 23.


Genomics of Loa loa, a Wolbachia-free filarial parasite of humans.

Desjardins CA, Cerqueira GC, Goldberg JM, Dunning Hotopp JC, Haas BJ, Zucker J, Ribeiro JM, Saif S, Levin JZ, Fan L, Zeng Q, Russ C, Wortman JR, Fink DL, Birren BW, Nutman TB.

Nat Genet. 2013 May;45(5):495-500. doi: 10.1038/ng.2585. Epub 2013 Mar 24.


Efficient subtraction of insect rRNA prior to transcriptome analysis of Wolbachia-Drosophila lateral gene transfer.

Kumar N, Creasy T, Sun Y, Flowers M, Tallon LJ, Dunning Hotopp JC.

BMC Res Notes. 2012 May 14;5:230. doi: 10.1186/1756-0500-5-230.


Whole genome sequencing to investigate the emergence of clonal complex 23 Neisseria meningitidis serogroup Y disease in the United States.

Krauland MG, Dunning Hotopp JC, Riley DR, Daugherty SC, Marsh JW, Messonnier NE, Mayer LW, Tettelin H, Harrison LH.

PLoS One. 2012;7(4):e35699. doi: 10.1371/journal.pone.0035699. Epub 2012 Apr 27.


Molecular epidemiology of Neisseria meningitidis serogroup B in Brazil.

de Filippis I, de Lemos AP, Hostetler JB, Wollenberg K, Sacchi CT, Dunning Hotopp JC, Harrison LH, Bash MC, Prevots DR.

PLoS One. 2012;7(3):e33016. doi: 10.1371/journal.pone.0033016. Epub 2012 Mar 14. Erratum in: PLoS One. 2012;7(7): doi/10.1371/annotation/6318254d-3f13-4cca-8bbe-08d0ff29aa64. Dunning Hotopp, Julie C [added].


Streptococcus pneumoniae in biofilms are unable to cause invasive disease due to altered virulence determinant production.

Sanchez CJ, Kumar N, Lizcano A, Shivshankar P, Dunning Hotopp JC, Jorgensen JH, Tettelin H, Orihuela CJ.

PLoS One. 2011;6(12):e28738. doi: 10.1371/journal.pone.0028738. Epub 2011 Dec 8.


Using Sybil for interactive comparative genomics of microbes on the web.

Riley DR, Angiuoli SV, Crabtree J, Dunning Hotopp JC, Tettelin H.

Bioinformatics. 2012 Jan 15;28(2):160-6. doi: 10.1093/bioinformatics/btr652. Epub 2011 Nov 24.


Whole-genome association study on tissue tropism phenotypes in group A Streptococcus.

Bessen DE, Kumar N, Hall GS, Riley DR, Luo F, Lizano S, Ford CN, McShan WM, Nguyen SV, Dunning Hotopp JC, Tettelin H.

J Bacteriol. 2011 Dec;193(23):6651-63. doi: 10.1128/JB.05263-11. Epub 2011 Sep 23.


Improving pan-genome annotation using whole genome multiple alignment.

Angiuoli SV, Dunning Hotopp JC, Salzberg SL, Tettelin H.

BMC Bioinformatics. 2011 Jun 30;12:272. doi: 10.1186/1471-2105-12-272.


Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination.

Budroni S, Siena E, Dunning Hotopp JC, Seib KL, Serruto D, Nofroni C, Comanducci M, Riley DR, Daugherty SC, Angiuoli SV, Covacci A, Pizza M, Rappuoli R, Moxon ER, Tettelin H, Medini D.

Proc Natl Acad Sci U S A. 2011 Mar 15;108(11):4494-9. doi: 10.1073/pnas.1019751108. Epub 2011 Feb 28.


Horizontal gene transfer between bacteria and animals.

Dunning Hotopp JC.

Trends Genet. 2011 Apr;27(4):157-63. doi: 10.1016/j.tig.2011.01.005. Epub 2011 Feb 18. Review.


Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species.

Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, Oggioni M, Dunning Hotopp JC, Hu FZ, Riley DR, Covacci A, Mitchell TJ, Bentley SD, Kilian M, Ehrlich GD, Rappuoli R, Moxon ER, Masignani V.

Genome Biol. 2010;11(10):R107. doi: 10.1186/gb-2010-11-10-r107. Epub 2010 Oct 29. Erratum in: Genome Biol. 2011;12(10):140.


Endosymbiont DNA in endobacteria-free filarial nematodes indicates ancient horizontal genetic transfer.

McNulty SN, Foster JM, Mitreva M, Dunning Hotopp JC, Martin J, Fischer K, Wu B, Davis PJ, Kumar S, Brattig NW, Slatko BE, Weil GJ, Fischer PU.

PLoS One. 2010 Jun 9;5(6):e11029. doi: 10.1371/journal.pone.0011029.


Extensive genomic diversity of closely related Wolbachia strains.

Ishmael N, Dunning Hotopp JC, Ioannidis P, Biber S, Sakamoto J, Siozios S, Nene V, Werren J, Bourtzis K, Bordenstein SR, Tettelin H.

Microbiology. 2009 Jul;155(Pt 7):2211-22. doi: 10.1099/mic.0.027581-0. Epub 2009 Apr 23.


Parasitism and mutualism in Wolbachia: what the phylogenomic trees can and cannot say.

Bordenstein SR, Paraskevopoulos C, Dunning Hotopp JC, Sapountzis P, Lo N, Bandi C, Tettelin H, Werren JH, Bourtzis K.

Mol Biol Evol. 2009 Jan;26(1):231-41. doi: 10.1093/molbev/msn243. Epub 2008 Oct 28.


Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes.

Dunning Hotopp JC, Clark ME, Oliveira DC, Foster JM, Fischer P, Muñoz Torres MC, Giebel JD, Kumar N, Ishmael N, Wang S, Ingram J, Nene RV, Shepard J, Tomkins J, Richards S, Spiro DJ, Ghedin E, Slatko BE, Tettelin H, Werren JH.

Science. 2007 Sep 21;317(5845):1753-6. Epub 2007 Aug 30.


New criteria for selecting the origin of DNA replication in Wolbachia and closely related bacteria.

Ioannidis P, Dunning Hotopp JC, Sapountzis P, Siozios S, Tsiamis G, Bordenstein SR, Baldo L, Werren JH, Bourtzis K.

BMC Genomics. 2007 Jun 20;8:182.


Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes.

Dunning Hotopp JC, Grifantini R, Kumar N, Tzeng YL, Fouts D, Frigimelica E, Draghi M, Giuliani MM, Rappuoli R, Stephens DS, Grandi G, Tettelin H.

Microbiology. 2006 Dec;152(Pt 12):3733-49.


Multilocus sequence typing system for the endosymbiont Wolbachia pipientis.

Baldo L, Dunning Hotopp JC, Jolley KA, Bordenstein SR, Biber SA, Choudhury RR, Hayashi C, Maiden MC, Tettelin H, Werren JH.

Appl Environ Microbiol. 2006 Nov;72(11):7098-110. Epub 2006 Aug 25.


Comparative genomics of emerging human ehrlichiosis agents.

Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, Niu H, Lin Q, Ohashi N, Zhi N, Nelson W, Brinkac LM, Dodson RJ, Rosovitz MJ, Sundaram J, Daugherty SC, Davidsen T, Durkin AS, Gwinn M, Haft DH, Selengut JD, Sullivan SA, Zafar N, Zhou L, Benahmed F, Forberger H, Halpin R, Mulligan S, Robinson J, White O, Rikihisa Y, Tettelin H.

PLoS Genet. 2006 Feb;2(2):e21. Epub 2006 Feb 17. Erratum in: PLoS Genet. 2006 Dec;2(12):e213. Eisen, Jonathan [corrected to Eisen, Jonathan A].


Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.

Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB, Nelson WC.

Genome Biol. 2005;6(7):402. Epub 2005 Jun 24.


Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.

Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB, Nelson WC.

Genome Biol. 2005;6(3):R23. Epub 2005 Feb 22. Erratum in: Genome Biol. 2005;6(7):402.


Intrinsic tryptophan fluorescence as a probe of metal and alpha-ketoglutarate binding to TfdA, a mononuclear non-heme iron dioxygenase.

Dunning Hotopp JC, Auchtung TA, Hogan DA, Hausinger RP.

J Inorg Biochem. 2003 Jan 1;93(1-2):66-70.


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