© 2000 - 2012 Virginia Bioinformatics Institute
Wednesday, 16 May 2012
Gillespie, Joseph , PhD
Faculty - Publications - Gillespie, Joseph

Senior Computational Biologist

Phone: (540) 231-4869
Email:jgille@vbi.vt.edu
Fax:

Personal_Page | Computational Biology and Bioinformatics | Cyberinfrastructure Division



Publications:

2011


Gillespie JJ, Wattam AR, Cammer SA, et al. PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species. Infect Immun. 2011;79:4286–4298.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21896772

2010


Dreher-Lesnick SM, Ceraul SM, Lesnick SC, et al. Analysis of Rickettsia typhi-infected and uninfected cat flea (Ctenocephalides felis) midgut cDNA libraries: deciphering molecular pathways involved in host response to R. typhi infection. Insect Mol Biol. 2010;19:229–241.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20017753

Gillespie JJ, Brayton KA, Williams KP, et al. Phylogenomics reveals a diverse Rickettsiales type IV secretion system. Infect Immun. 2010;78:1809–1823.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20176788

Sutten EL, Norimine J, Beare PA, et al. Anaplasma marginale type IV secretion system proteins VirB2, VirB7, VirB11, and VirD4 are immunogenic components of a protective bacterial membrane vaccine. Infect Immun. 2010;78:1314–1325.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20065028

Williams KP, Gillespie JJ, Sobral BW, et al. Phylogeny of gammaproteobacteria. J Bacteriol. 2010;192:2305–2314.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20207755

2009


Ammerman NC, Gillespie JJ, Neuwald AF, Sobral BW, Azad AF. A typhus group-specific protease defies reductive evolution in rickettsiae. J Bacteriol. 2009;191:7609–7613.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19820087

Gillespie JJ, Ammerman NC, Beier-Sexton M, Sobral BS, Azad AF. Louse- and flea-borne rickettsioses: biological and genomic analyses. Vet Res. 2009;40:12.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19036234

Gillespie JJ, Ammerman NC, Dreher-Lesnick SM, et al. An anomalous type IV secretion system in Rickettsia is evolutionarily conserved. PLoS ONE. 2009;4:e4833.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19279686

Kjer KM, Roshan U, Gillespie JJ. Structural and evolutionary considerations for multiple sequence alignment of RNA, and the challenges for algorithms that ignore them. In: Rosenberg MS, ed. Sequence Alignment: Methods, Models, Concepts, and Strategies. University of California Press; 2009:105–149.  

Kjos SA, Gillespie JJ, Olson JK, Snowden KF. Detection of Blastocrithidia spp. (Kinetoplastida: Trypanosomatidae) in Chagas disease vectors from Texas, USA. Vector Borne Zoonotic Dis. 2009;9:213–216.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18803501

Marvaldi AE, Duckett CN, Kjer KM, Gillespie JJ. Structural alignment of 18S and 28S rDNA sequences provides insights into the phylogeny of Phytophaga and related beetles (Coleoptera: Cucujiformia). Zoologica Scripta. 2009;38:63–77.  

2008


Azad A, Beier MS, Gillespie JJ. The Rickettsiaceae. In: Goldman LG and E, ed. Practical Handbook of Microbiology. CRC Press; 2008:439–450.  

Gillespie JJ, Tallamy DW, Riley EG, Cognato AI. Molecular phylogeny of rootworms and related galerucine beetles (Coleoptera: Chrysomelidae). Zoologica Scripta. 2008;37:195–222.  

Gillespie JJ, Williams K, Shukla M, et al. Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life. PLoS ONE. 2008;3:e2018.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19194535

Jordal B, Gillespie JJ, Cognato AI. Secondary structure alignment and direct optimization of 28S rDNA sequences provide limited phylogenetic resolution in bark and ambrosia beetles (Curculionidae: Scolytinae). Zoologica Scripta. 2008;37:43–56.  

2007


Ceraul SM, Dreher-Lesnick SM, Gillespie JJ, Rahman MS, Azad AF. New tick defensin isoform and antimicrobial gene expression in response to Rickettsia montanensis challenge. Infect Immun. 2007;75:1973–1983.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17261604

Gillespie JJ, Beier MS, Rahman MS, et al. Plasmids and rickettsial evolution: insight from Rickettsia felis. PLoS ONE. 2007;2:e266.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17342200

Hines HM, Hunt JH, O'Connor TK, Gillespie JJ, Cameron SA. Multigene phylogeny reveals eusociality evolved twice in vespid wasps. Proc Natl Acad Sci U S A. 2007;104:3295–3299.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17360641

Kathirithamby J, Gillespie JJ, Cognato AI, Johnston JS. Cordelia. Zootaxa. 2007;1636:59–68.  

Kjer KM, Gillespie JJ, Ober KA. Opinions on multiple sequence alignment, and an empirical comparison of repeatability and accuracy between POY and structural alignment. Syst Biol. 2007;56:133–146.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17366144

Snyder EE, Kampanya N, Lu J, et al. PATRIC: the VBI PathoSystems Resource Integration Center. Nucleic Acids Res. 2007;35:D401–6.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17142235

2006


Consortium HBGS. Insights into social insects from the genome of the honeybee Apis mellifera. Nature. 2006;443:931–949.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17073008

Deans AR, Gillespie JJ, Yoder MJ. An evaluation of ensign wasp classification (Hymenoptera: Evaniidae) based on molecular data and insights from ribosomal RNA secondary structure. Systematic Entomology. 2006;31:517–528.  

Gillespie JJ, Johnston JS, Cannone JJ, Gutell RR. Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements. Insect Mol Biol. 2006;15:657–686.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17069639

Kjer KM, Gillespie JJ, Ober KA. Structural homology in ribosomal RNA, and a deliberation on POY. Arthropod Systematics & Phylogenetics. 2006;64:159–164.  

Wharton RA, Yoder MJ, Gillespie JJ, Patton JC, Honeycutt RL. Relationships of Exodontiella, a non-alysiine, exodont member of the family Braconidae (Insecta, Hymenoptera). Zoologica Scripta. 2006;35:323–340.  

2005


Gillespie JJ, McKenna CH, Yoder MJ, et al. Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted-wing parasites (Insecta: Strepsiptera). Insect Mol Biol. 2005;14:625–643.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16313563

Gillespie JJ, Munro JB, Heraty JM, Yoder MJ, Owen AK, Carmichael AE. A secondary structural model of the 28S rRNA expansion segments D2 and D3 for Chalcidoid wasps (Hymenoptera: Chalcidoidea). Mol Biol Evol. 2005;22:1593–1608.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15843598

Gillespie JJ, Yoder MJ, Wharton RA. Predicted secondary structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): impact on sequence alignment and phylogeny estimation. J Mol Evol. 2005;61:114–137.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16059751

Tallamy DW, Hibbard BE, Clark TL, Gillespie JJ. Western corn rootworm, cucurbits, and cucurbitacins. In: S.Vidal, Kuhlmann U, Edwards R, eds. Ecology and Management of Western Corn Rootworm (Diabrotica virgifera virgifera LeConte). Wallingford, United Kingdom: CABI publishers; 2005:67–93.  

2004


Duckett CN, Gillespie JJ, Kjer KM. Reanalysis of Chrysomelidae data (18S) based on homology assessments. In: Jolivet PH, Santiago-Blay JA, Schmitt M, eds. New Developments on The Biology of Chrysomelidae. Boston, MA.: Kluwer Academic; 2004:3–18.  

Gillespie J, Cannone J, Gutell R, Cognato A. A secondary structural model of the 28S rRNA expansion segments D2 and D3 from rootworms and related leaf beetles (Coleoptera: Chrysomelidae; Galerucinae). Insect Mol Biol. 2004;13:495–518.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15373807

Gillespie JJ. Characterizing regions of ambiguous alignment caused by the expansion and contraction of hairpin-stem loops in ribosomal RNA molecules. Mol Phylogenet Evol. 2004;33:936–943.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15522814

Gillespie JJ, Kjer KM, Riley EG, Tallamy DW. The evolution of cucurbitacin pharmacophagy in rootworms: Insight from Luperini paraphyly. In: Jolivet PH, Santiago-Blay JA, Schmitt M, eds. New Developments on The Biology of Chrysomelidae. Boston, MA.: Kluwer Academic; 2004:37–58.  

2003


Gillespie JJ, Kjer KM, Duckett CN, Tallamy DW. Convergent evolution of cucurbitacin feeding in spatially isolated rootworm taxa (Coleoptera: Chrysomelidae; Galerucinae, Luperini). Mol Phylogenet Evol. 2003;29:161–175.  http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12967617

2001


Gillespie JJ, Duckett CN, Kjer KM. Identification of a gene region that gives good phylogenetic signal for determining high level divergences within alticine and galerucine chrysomelids. Chrysomela. 2001;40/41:10–11.