Jessica Kissinger
Associate Professor, Department of Genetics
Ph.D. (1995) Indiana University

Phone: 706-542-6562
Fax: 706-542-3582
E-mail: jkissing@uga.edu

See Also:
Plasmodium genome database
Franklin Cronicle Story - Fall 2003

Kissinger Lab Website
Kissinger at UGA Genetics

Research Interest
I am interested in parasite genomics and the biology of genome evolution. How do genomes evolve? Can we trace gene order, identify and determine the fate of horizontally transferred genes (as well as any existing endogenous orthologs) and identify genes that are phylogenetically restricted? The answers to these questions are important because of the insight they provide into parasite biology and the identification of potential drug targets. My research focuses on, but is not limited to, Apicomplexan parasites. The Apicomplexa are ideal for phylogenomic studies for several reasons:

  • All of the estimated 5000 species of Apicomplexa are believed to be parasitic
  • The Apicomplexa have a rich evolutionary history that includes endosymbiotic events and extensive gene transfer
  • There are currently 14 genome sequencing projects underway (2 are complete) and numerous EST and GSS projects for prominent members of this phylum including numerous Plasmodium species (the causative agent of malaria), Theileria, Babesia, Eimeria, Toxoplasma and Cryptosporidium.

Our approach is to apply molecular, computational and phylogenetic tools to the analysis of parasite genomes. Projects include the development of tools for data mining, comparative genomics and assessing the phylogenetic distribution of genes. We utilize standard molecular biology techniques as well as powerful multi-processor Linux clusters on the computational side. I welcome students interested in working on the bench, at the computer, or both.

Grant Support
  • Genome sequencing and comparative analysis of coronaviruses, NIH CSREES/USDA 0624492 (Co-investigator)
  • Informatics analysis of Cryptosporidium gene expression, NIH R01-AI065246 (Co-investigator)
  • Building a Trypanosoma cruzi genome resource: Integrating diverse genomic data sets to facilitate basic research, AHA, 0330338N  
  • Pattern finding and phylogenetic restriction in Trypanosoma cruzi, PhRMA Foundation
  • Perkinsus marinus EST project, NOAA – MD Sea Grant SA7528068-I (Co-investigator)
  • PlasmoDB – The Plasmodium Genome Resource, NIH R01 AI058515-01 (Co-investigator)
  • Integrated databases for Apicomplexan Pathogens, NIH (Co-investigator)
  • Informatics training for Brazilian vector and parasitic diseases, NIH D43 TW007012-01
  • Integrated databases for Apicomplexan Pathogens NIH Contract HHSN26600400037C D43 TW007012-01 (Co-investigator)

Database and Software Projects

  • TcruziDB.org - Trypanosoma genome resource
  • CryptoDB.org - Cryptosporidium genome resource
  • PlasmoDB.org - Plasmodium genome resource
  • ToxoDB.org - Toxoplasma genome resource
  • ApiDB.org - Apicomplexan genome resource spanning CryptoDB, PlasmoDB, and ToxoDB
  • ToxoMap - Toxoplasma gondii apicoplast genome resource
  • YourDB.org - Tools for creating Your own genome resource
  • TATFIND v1.0 - Program detects proteins secretedvia the twin arginine pathway (Provisional patent filed)


Recent Publications (links to PDFs available on Lab website)

Book Chapters

Kissinger, J.C., and Chih-Horng Kuo (2007) Evolution and comparative genomics of Toxoplasma gondii In: The Biology of Toxoplasma gondii Eds. J. Ajioka and D. Soldati. In Press, Horizon Press

Agüero.F., G.C. Oliveira, D.S. Roos, and J.C. Kissinger. (2006) Parasite Databases and Data Mining Approaches. In: Bioinformatics in Tropical Disease Research: A Practical Approach. H. del Portillo, A. Gruber, A. Durham and C. Hyuong Editors. NCBI Electronic Book (In Press - this will be a 2007 chapter)

Whetzel, P., Date, S.V., Essien, K., Fraunholz, M.J., Gajria, B., Grant, G.R., Iodice, J., Kissinger, J.C., Labo, P.T., Milgram, A.J., Roos, D.S. and C.J. Stoeckert. (2006) PlasmoDB: The Plasmodium Genomics and Functional Genomics Resource. In: In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins. Edited by Nicola Mulder. Nova Science Publishers. Hauppauge, NY

Huang, J. and Kissinger, J.C. (2006) "Lateral and intracellular gene transfer in the Apicomplexa: the scope and functional consequences" In: Genome Evolution in Eukaryotic Microbes. Edited by Laura A. Katz and Debashish Bhattacharya. (Oxford University Press)

Whetzel, Patricia, Bindu Gajria, Jessica C. Kissinger, Christian J. Stoeckert Jr., and David S. Roos (2005) PlasmoDB: The Plasmodium Genome Resource in Malaria: Parasite Biology, Pathogenesis, and Protection, Second Edition, Edited by Irwin W. Sherman. ASM Press

Roos, D.S., J.A. Darling, M.G. Reynolds, K.M. Hager, B.S. Striepen and J.C. Kissinger. (1999) Toxoplasma as a model parasite: apicomplexan biochemistry, cell biology, molecular genetics, genomics and beyond. Biology of Parasitism. C. Tschudi and E. Pearce Editors. Kluwer Academic Publishers, Boston, Massachusettes.

Papers

Mullapudi, N., Lancto, C., Abrahamsen, M., Kissinger, J.C. (2007) Identification of putative cis-regulatory elements in Cryptosporidium parvum by de novo pattern finding. In press, BMC Genomics

Z. Szabó, A. Oliveira Stahl, S-V. Albers, J. C. Kissinger, Arnold J.M. Driessen and M. Pohlschröder (2007) Identification of diverse archaeal proteins with class III signal peptides cleaved by distinct archaeal prepilin peptidases. Journal of Bacteriology doi:10.1128/JB.01547-06

Aurrecoechea, C., Heiges, M., Wang, H., Wang, Z., Fischer, S., Rhodes, P., Miller, J., Kraemer E., Stoeckert, C.J., Roos, D.S. and Kissinger, J.C. (2007) ApiDB: Integrated Resources for the Apicomplexan Bioinformatics Resource Center. Nucleic Acids Research doi:10.1093/nar/gkl880

Nash, O., Huynh, C., Doumbia, S., Kissinger, J.C., Isokpehi, R.D., Olorunsogo, O.O. (2007) Building Bioinformatics Capacity in West Africa. (In press)

Stoeckert, C.J., Fischer, S., Kissinger, J.C., Heiges, M., Aurrecoechea, C., Garija, B. and Roos D.S. (2006) PlasmoDB 5.0: new looks, new genomes Trends in Parasitology 22(12), 543-546

Paterson, A.H., Chapman, B.A., Kissinger, J.C., Bowers, J.E., Feltus, F.A, Estill, J.C.(2006) Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends in Genetics 22(11), 597-602

Wang, H., Su, Y., Mackey, A., Kraemer, E., and Kissinger, J.C. (2006) SynView: A GBrowse-compatible Approach to Visualizing Comparative Genome Data. Bioinformatics 22, 2308-2309

Kissinger, J.C. (2006) A Tale of three genomes - the kinetoplastids have arrived. Trends in Parasitology 22(6)

Agüero, F., Zheng, W, Weatherly, D.B., Mendes, P. and Kissinger. J.C. (2006) TcruziDB: An integrated, post-genomics community resource for Trypanosoma cruzi. NAR 34:D428-D431

Heiges, M., Wang, H., Robinson E., Aurrecoechea C., Gao X., Kaluskar N., Rhodes P., Wang S., He C., Su Y., Miller J., Kraemer E., and Kissinger J.C. (2006) CryptoDB: a Cryptosporidium bioinformatics resource update Nucleic Acids Res., Jan 2006; 34: D419 - D422.

Huang, J., N. Mullapudi, C.A. Lancto, M. Scott, M.S. Abrahamsen and J.C. Kissinger. Cryptosporidium parvum: Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer. Genome Biology 5(11):R88

Striepen,B. and Kissinger,J.C. (2004) Genomics Meets Transgenics in Search of the Slusive Cryptosporidium Drug Target. Trends in Parasitology 20(8):355-8
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Gunasekera AM, Patankar S, Schug J, Eisen G, Kissinger J, Roos D, Wirth DF.
Links (2004) Widespread distribution of antisense transcripts in the Plasmodium falciparum genome.
Mol Biochem Parasitol. 2004 Jul;136(1):35-42.

Vidigal, T.H.D.A., L. Spatz, J.C. Kissinger, R.A.F. Redondo, E.C.R. Pires, A.J.G. Simpson and O.S. Carvalho. (2004) Analysis of the first and second internal transcribed space sequences of the ribosomal DNA in Biomphalaria tenagophila complex (Mullusca: Planorbidae). Memorias Oswaldo Cruz 99(2):153-158

Kissinger, J.C., and D.S. Roos. (2004) Getting the most out of bioinformatics resources  In: Genomes and the Molecular Cell Biology of Malaria Parasites A. Waters and C. Janse (eds.) Horizon Scientific Press, Norfolk, UK.

Striepen,B., A.J.P. Pruijssers, J. Huang, C. Li, M.J. Gubbels, N.N. Umejiego, L. Hedstrom and J.C. Kissinger. (2004) Multiple gene transfers in the evolution of parasite nucleotide biosynthesis. PNAS 101(9):3154-3159.

Huang, J., N. Mullapudi, T. Sicheritz-Ponten and J.C. Kissinger. (2004) A Glimpse in the pattern and scale of Gene transfer in the Apicomplexa. International J. for Parasitology 34:265-274

Stwora-Wojczyk, M.M., J.C. Kissinger, S.L. Spitalnik and B.S. Wojczyk. (2004) O-glycosylation in Toxoplasma gondii and Cryptosporidium parvum: Identification and analysis of a family of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases. International J. for Parasitology 34: 309-322

D. Puiu, S. Enomoto G.A. Buck, M. Abrahamsen and J.C. Kissinger. (2004) CryptoDB: The Cryptosporidium genome resource. Nucleic Acids Research 32:D329-D331.

Luchtan, M., Warade, C., Weatherly, B., Tarleton, R.L. and Kissinger, J.C..  (2004) TcruziDB: An integrated Trypanosoma cruzi genome resource. Nucleic Acids Research 32:D344-D346.

Milgram,A.J., Gajria,B., Kissinger,J.C., Pearson,D.S. and Roos,D.S. (2003) Plasmodium falciparum GenePlot. CD-ROM Insert, Plasmodium genome:Scientific achievement and medical opportunity. Nature, 421(6926).

Li, L., B.P. Brunk, J.C. Kissinger, D. Pape, J. Martin, T. Wylie, M. Dante, K. Tang, R. Cole, S. J. Fogarty, D.K.Howe, P. Liberator, C. Diaz, M. White, M.E. Jerome, E.A. Johnson, J.A. Radke, R. Waterson, S. Clifton, D.S. Roos, and L. D. Sibley. (2003) Gene Discovery in the Apicomplexa as Revelaed by EST Sequencing and Assembly of a Comparative Gene Database. Genome Research 13:443-454.

Su, C., D. Evans, R. Cole, J.C. Kissinger, J.W. Ajioka and L.D. Sibley. Recent expansion of Toxoplasma through enhanced oral transmission. (2003) Science, 299:414-416

Bahl, A., Brunk, B., Crabtree, J., Fraunholz, M. J., Gajria, B., Grant, G. R., Ginsburg, H., Gupta, D., Kissinger, J. C., Labo, P., Li, L., Mailman, M. D., Milgram, A. J., Pearson, D. S., Roos, D. S., Schug, J, Stoeckert, C. J. Jr., Whetzel, P. (2003) PlasmoDB: The Plasmodium Genome Resource. A database integrating experimental and computational data. Nucleic Acids Res. 31:212-215

Kissinger, J.C., B. Gajria, L. Li, I. Paulsen and D. Roos. (2003) ToxoDB: Accessing the Toxoplasma gondii Genome. Nucleic Acids Res. 31:234-236

Vidigal, T.H.D.A., K. G. Magalhaes, J.C. Kissinger, R.L. Caldeira, A.J.G. Simpson and O.S. Carvalho. (2002) A multiplex-PCR approach to identification of the Brazilian intermediate hosts of Schistosoma mansoni. Memorias do Instituto Oswaldo Cruz 97(Suppl. I):95-97

Kissinger, J.C., B.P. Brunk, J. Crabtree, M.J. Fraunholz, B. Gajria, A.J. Milgram, D.S. Pearson, J. Schug, A. Bahl, S.J. Diskin, H. Ginsburg, G. R. Grant, D. Gupta, P. Labo, L. Li, M. Mailman, S.K. McWeeney, P. Whetzel, C.J. Stoeckert Jr., and D.S. Roos. (2002) PlasmoDB: the Plasmodium genome database. Designing and mining a eukaryotic genomics resource. Nature 419:490-492

Rose, R.W., T. Brueser, J.C. Kissinger and M. Pohlschroder. (2002) Twin Arginine Translocation: A Way Out for Halophilic Archaea. Molecular Microbiology 45(4):943-950

Kissinger, J.C., P.C.A. de Souza, C.O. Soares, T.F. McCutchan and A.U. Krettli. (2002) Molecular Phylogenetic analysis of the avian malarial parasite Plasmodium (Novyella) juxtanucleare. Journal of Parasitology 88:769-773

Bahl A., B. Brunk, R.L. Coppel, J. Crabtree, S.J. Diskin, M.J. Fraunholz, G.R. Grant, D. Gupta, R.L. Huestis, J.C.Kissinger, P. Labo, L. Li, S.K. McWeeney, A.J. Milgram, D.S. Roos, J. Schug, and C.J. Stoeckert Jr. (2002) PlasmoDB: The Plasmodium Genome Resource. Nucleic Acids Research 30 (1):87-90

Kissinger, J.C., M.J. Crawford, D.S. Roos and J. Ajioka. (2002) Toxoplasma gondii: A Model for Evolutionary Genomics and Chemotherapy. Pathogen Genomics: Impact on Human Health. K. J. Shaw Editor. Humana Press Inc.

Roos, D.S., M.J. Crawford, R.G.K. Donald, M. Fraunholz, O.S. Harb, C.Y. He, J.C. Kissinger, M.K. Shaw, and B. Striepen.(2002) Mining the Plasmodium genome database to define organellar function: What does the apicoplast do? Philosophical Transactions Royal Society of London, B Biological Sciences 357(1417):35-46

Schein, A.T., J.C. Kissinger and L.H. Ungar. (2001) Chloroplast transit peptide prediction: a peek inside the black box. Nucleic Acids Research 29 (16):e82

Tarleton, R.L. and J.C. Kissinger. (2001) Parasite Genomics: Current Status and Future Prospects. Current Opinions in Immunology 13:395-402

Fast, N. M., J.C. Kissinger, J.C., D.S. Roos, and P.J. Keeling. (2001) Nuclear-encoded Plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids. Molecular Biology and Evolution 18(3):418-426

The Plasmodium Genome Database Collaborative. PlasmoDB: An integrative database of the Plasmodium falciparum genome. (2001) Tools for accessing and analyzing finished and unfinished sequence data. Nucleic Acids Research 29(1):66-69

Akopyants, N.S., S.W. Cliston, J. Martin, D. Pape, T. Wylie, L. Li, J.C. Kissinger, D.S. Roos and S.M. Beverley. (2001) A survey of the Leishmania major Friedlin strain V1 genome by shotgun sequencing: a resource for DNA microarrays and expression profiling. Molecular Biochemical Parasitology 113(2):337-40