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Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential.

Moser KA, Drábek EF, Dwivedi A, Stucke EM, Crabtree J, Dara A, Shah Z, Adams M, Li T, Rodrigues PT, Koren S, Phillippy AM, Munro JB, Ouattara A, Sparklin BC, Dunning Hotopp JC, Lyke KE, Sadzewicz L, Tallon LJ, Spring MD, Jongsakul K, Lon C, Saunders DL, Ferreira MU, Nyunt MM, Laufer MK, Travassos MA, Sauerwein RW, Takala-Harrison S, Fraser CM, Sim BKL, Hoffman SL, Plowe CV, Silva JC.

Genome Med. 2020 Jan 8;12(1):6. doi: 10.1186/s13073-019-0708-9.


Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics.

Shetty AC, Mattick J, Chung M, McCracken C, Mahurkar A, Filler SG, Fraser CM, Rasko DA, Bruno VM, Dunning Hotopp JC.

Microb Genom. 2020 Jan;6(1). doi: 10.1099/mgen.0.000320.


Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics.

Chung M, Teigen LE, Libro S, Bromley RE, Olley D, Kumar N, Sadzewicz L, Tallon LJ, Mahurkar A, Foster JM, Michalski ML, Dunning Hotopp JC.

mSystems. 2019 Dec 3;4(6). pii: e00596-19. doi: 10.1128/mSystems.00596-19.


Complete Genome Sequence of wAna, the Wolbachia Endosymbiont of Drosophila ananassae.

Gasser MT, Chung M, Bromley RE, Nadendla S, Dunning Hotopp JC.

Microbiol Resour Announc. 2019 Oct 24;8(43). pii: e01136-19. doi: 10.1128/MRA.01136-19.


Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity.

Baltrus DA, Cuomo CA, Dennehy JJ, Dunning Hotopp JC, Maresca JA, Newton ILG, Rasko DA, Rokas A, Roux S, Stajich JE.

Microbiol Resour Announc. 2019 Sep 5;8(36). pii: e00954-19. doi: 10.1128/MRA.00954-19.


TwinBLAST: When Two Is Better than One.

Dunning Hotopp JC, Matsumura J, Bromley RE, Riley DR, Agrawal S, Sparklin B, Mattick J, Crabtree J, Mahurkar A.

Microbiol Resour Announc. 2019 Aug 29;8(35). pii: e00842-19. doi: 10.1128/MRA.00842-19.


Ancestral characterization of 1018 cancer cell lines highlights disparities and reveals gene expression and mutational differences.

Kessler MD, Bateman NW, Conrads TP, Maxwell GL, Dunning Hotopp JC, O'Connor TD.

Cancer. 2019 Jun 15;125(12):2076-2088. doi: 10.1002/cncr.32020. Epub 2019 Mar 13.


Using Core Genome Alignments To Assign Bacterial Species.

Chung M, Munro JB, Tettelin H, Dunning Hotopp JC.

mSystems. 2018 Dec 4;3(6). pii: e00236-18. doi: 10.1128/mSystems.00236-18. eCollection 2018 Nov-Dec.


Draft Genome Sequence of Enterobacter sp. Strain OLF, a Colonizer of Olive Flies.

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

Microbiol Resour Announc. 2018 Sep 6;7(9). pii: e01068-18. doi: 10.1128/MRA.01068-18. eCollection 2018 Sep.


Multispecies Transcriptomics Data Set of Brugia malayi, Its Wolbachia Endosymbiont wBm, and Aedes aegypti across the B. malayi Life Cycle.

Chung M, Teigen L, Libro S, Bromley RE, Kumar N, Sadzewicz L, Tallon LJ, Foster JM, Michalski ML, Dunning Hotopp JC.

Microbiol Resour Announc. 2018 Nov 8;7(18). pii: e01306-18. doi: 10.1128/MRA.01306-18. eCollection 2018 Nov.


Draft Genome Sequence of Erwinia dacicola, a Dominant Endosymbiont of Olive Flies.

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

Microbiol Resour Announc. 2018 Sep 13;7(10). pii: e01067-18. doi: 10.1128/MRA.01067-18. eCollection 2018 Sep.


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 Feb;4(2). doi: 10.1099/mgen.0.000154. Epub 2018 Jan 18.


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.


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.


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.

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