Distinguished Research Professor Ph.D. (1995) Indiana University Fellow, American Association for the Advancement of Science, 2021 Fulbright US Scholar, Fulbright Scholar Program, 2021 Fellow, American Society for Tropical Medicine & Hygiene, 2020 Distinguished Research Professor, UGA, 2017 Richard F. Reiff Internationalization Award, UGA, 2016 SEC Academic Leadership Development Program Fellow, 2015-2016 Faculty Excellence in Diversity Award, UGA, 2013 Creative Research Medal, UGA, 2009 Kavli Fellow, Frontiers of Science 2005-2006, 2008 Visit the Kissinger Lab Website & ORCID Research Interests How do eukaryotic and organellar genome sequences evolve? Our lab is interested in parasite genomics and the biology of genome evolution. The nuclear and organellar genome sequences of parasitic eukaryotes are often highly-reduced, devoid of recognizable mobile elements and riddled with intracellular and lateral gene transfers. Our approach is to apply molecular, computational and phylogenetic tools to the analysis of complete parasite genome sequences. Projects include the development of tools for data integration, data mining, comparative genomics and the systems biology of host-pathogen interactions. Kissinger is a member of the NIH/NIAID Bioinformatic Resource Center, VEuPathDB.org leadership team. Research focuses on the apicomplexan protist pathogens, Toxoplasma gondii and several species of Cryptosporidium and Plasmodium. Researchers in our group work at the bench, the computer, or both. Podcasts People, Parasites and Plagues (Episode 7 - Petabytes of problematic pathogens) People, parasites and Plagues (Mini-Episode - A career in science) The Genetics Podcast (Episode 85 - Large-scale parasite genomics and the power of multi-omic data) Talking Biotech Podcast (Episode 371: November 2022 - The Genomes of Parasites) Select Professional Service Deputy Director, African Centers of Excellence Global Council (ACE) (2021 – Present) Global Council Member, NIAID ACE (2019 – 2021) Advisory Committee, NIH D43 BRECA, Makerere Univ. (2019-2022) Director, Institute of Bioinformatics (IOB), (2010-2019) Scientific Advisory Group, Institute Pasteur de Tunis, EU2020 PHINDaccess (2018 – 2022) Editor, Microbial Genomics (2015 - 2020) Member, Editorial Board of Academic Editors, PeerJ (2012 – 2020) External Advisory Committee, Louisiana NIH INBRE (2011 – 2017) Education Education: 1989 A.B. cum laude University of Chicago 1995 PhD Molecular, Cellular & Developmental Biology, Indiana University, Mentor: Rudy Raff 1995-1996 NSF/Sloan post-doctoral Fellow NIH/NIAID/LPD, Mentor: Tom McCutchan 1996-1998 CNPq post-doctoral Fellow CPqRR-FIOCRUZ, Brazil 1998-2002 Post-doc/Lecturer UPENN, Mentor: David Roos Research Research Areas: Molecular Genetics Genomics and Bioinformatics Evolutionary Genetics Research Interests: Systems biology of host-pathogen interactions, Nuclear and organellar genome evolution in eukaryotic parasites, Databases, Ontologies, Data mining and Data integration of 'omics (genome, transcriptome, proteome, metabolome, lipidome), clinical, immunological, epidemiological and experimental metadata. Grants: Grant Support NIH 75N93019R00028, “Center for Influenza Disease and Emergence Research (CIDER)” (2021-2028) Role: Co-I NIH R01AI148667, “Capturing the genomic variation present in Cryptosporidium and cryptosporidiosis” (2020-2024) Role: Joint-PI with Travis Glenn "Ensuring Access and Appropriate/Effective Use of Clinical & Epidemiological Datasets for Enteric Pathogens," Bill & Melinda Gates Foundation (2020-2023), Role: Co-I NIH R21AI144779-01A1, “Detailed analysis of Cryptosporidium non-coding gene expression” (2020 – 2022), Role: PI "Bioinformatics resources for kinetoplastid organisms and their hosts", Wellcome Trust (2020-2024), Role: Co-applicant with Andy Jones & David Roos “Integrated Informatics Resources for Eukaryotic Microbial Pathogens and Invertebrate Vectors of Disease” i.e. VEuPathDB.org, NIH/NIAID (2019-2024), Role: Co-I FungiDB: An integrated bioinformatics resource for fungi and oomycetes", Wellcome Trust (2018-2023), Role: Co-Applicant with Andy Jones & David Roos Selected Publications Selected Publications: Recent Publications (*= Graduate student; # = Undergraduate student) Achchuthan Shanmugasundram, David Starns, Ulrike Böhme, Beatrice Amos, Paul Wilkinson, Omar S. Harb, Susanne Warrenfeltz, Jessica C. Kissinger, Mary Ann McDowell, David S. Roos, Kathryn Crouch and Andrew R. Jones. (2023) TriTrypDB: an integrated functional genomics resource for kinetoplastida. PloS NTD doi: 10.1371/journal.pntd.0011058 Danielle N. Farinella, Sukhpreet Kaur, ViLinh Tran, Monica Cabrera-Mora, Chester J. Joyner, Stacey A. Lapp, Suman Pakala, Mustafa V. Nural, Jeremy D. DeBarry, MaHPIC Consortium, Jessica C. Kissinger, Dean P. Jones, Alberto Moreno, Mary R. Galinski, Regina Joice Cordy. (2023) Malaria disrupts the rhesus macaque gut microbiome. Frontiers Cellular and Infection Microbiology. doi: 10.3389/fcimb.2022.1058926 Jeremy D. DeBarry, Mustafa V. Nural, Suman B. Pakala, Vishal Nayak, Susanne Warrenfeltz, Jay Humphrey, Stacey A. Lapp, Monica Cabrera-Mora, Cristiana F. A. Brito, Jianlin Jiang, Celia L. Saney, Allison Hankus, Hannah M. Stealey#, Megan B. DeBarry, Nicolas Lackman, Noah Legall#, Kevin Lee, Yan Tang, Anuj Gupta, Elizabeth D. Trippe, Robert R. Bridger, Daniel Brent Weatherly, Mariko S. Peterson, Xuntian Jiang, ViLinh Tran, Karan Uppal, Luis L. Fonseca, Chester J. Joyner, Ebru Karpuzoglu, Regina J. Cordy, Esmeralda V. S. Meyer, Lance L. Wells, Daniel S. Ory, F. Eun-Hyung Lee, Rabindra Tirouvanziam, Juan B. Gutiérrez, Chris Ibegbu, Tracey J. Lamb, Jan Pohl, Sarah T. Pruett, Dean P. Jones, Mark P. Styczynski, Eberhard O. Voit, Alberto Moreno, Mary R. Galinski & Jessica C. Kissinger. 2022. MaHPIC malaria systems biology data from Plasmodium cynomolgi sporozoite longitudinal infections in macaques. Scientific Data doi: 10.1038/s41597-022-01755-y. Mariko S. Peterson, Chester J. Joyner, Stacey A. Lapp, Jessica A. Brady, Jennifer S. Wood, Monica Cabrera-Mora, Celia L. Saney, Luis L. Fonseca, Jianlin Jiang, Stephanie R. Soderberg, Mustafa V. Nural, Jay Humphrey, Allison Hankus, Deepa Machiah, Ebru Karpuzoglu, Jeremy D. DeBarry, MaHPIC Consortium, Rabindra Tirouvanziam, Jessica C. Kissinger, Alberto Moreno, Sanjeev Gumber, Eberhard O. Voit, Juan B. Gutierrez, Regina Joice Cordy and Mary R. Galinski. 2022. Plasmodium knowlesi cytoadhesion involves SICA variant proteins. Frontiers in Cellular and Infection Microbiology. doi: 10.3389/fcimb.2022.888496. Yiran Li*, Rodrigo P. Baptista, Xiaohan Mei and Jessica C. Kissinger. 2022. Small and intermediate size structural RNAs in the unicellular parasite Cryptosporidium parvum as revealed by sRNA-Seq and comparative genomics. Microbial Genomics. doi: 10.1099/mgen.0.000821. Rodrigo P. Baptista, Yiran Li*, Adam Sateriale, Mandy J. Sanders, Karen L. Brooks, Alan Tracey, Brendan R. E. Ansell, Aaron R. Jex, Garrett W. Cooper, Ethan D. Smith, Rui Xiao, Jennifer E. Dumaine, Matthew Berriman, Boris Striepen, James A. Cotton and Jessica C. Kissinger. 2022. Long-read assembly and comparative and evidence-based reanalysis of Cryptosporidium genome sequences reveal new biological insights. Genome Res. 2022 doi: 10.1101/gr.275325.121. Amos B, Aurrecoechea C, Barba M, Barreto A, Basenko EY, Bażant W, Belnap R, Blevins AS, Böhme U, Brestelli J, Brunk BP, Caddick M, Callan D, Campbell L, Christensen MB, Christophides GK, Crouch K, Davis K, DeBarry J, Doherty R, Duan Y, Dunn M, Falke D, Fisher S, Flicek P, Fox B, Gajria B, Giraldo-Calderón GI, Harb OS, Harper E, Hertz-Fowler C, Hickman MJ, Howington C, Hu S, Humphrey J, Iodice J, Jones A, Judkins J, Kelly SA, Kissinger JC, Kwon DK, Lamoureux K, Lawson D, Li W, Lies K, Lodha D, Long J, MacCallum RM, Maslen G, McDowell MA, Nabrzyski J, Roos DS, Rund SSC, Schulman SW, Shanmugasundram A, Sitnik V, Spruill D, Starns D, Stoeckert CJ, Tomko SS, Wang H, Warrenfeltz S, Wieck R, Wilkinson PA, Xu L, Zheng J. 2022. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Res. 2022 Jan 7;50(D1):D898-D911. doi: 10.1093/nar/gkab929. Rodrigo P. Baptista, Garrett W. Cooper# and Jessica C. Kissinger. 2021. Challenges for Cryptosporidium population studies. Genes 2021, 12:894 doi.org/10.3390/genes12060894 Sivaranjani Namasivayam*, Wenyuan Xiao*, Rodrigo P. Baptista, Erica M. Hall#, Joseph S. Doggett, Karin Troell and Jessica C. Kissinger. 2021. A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia. Genome Research, doi:10.1101/gr.266403.120 Peterson MS, Joyner CJ, Brady JA, Wood JS, Cabrera-Mora M, Saney CL, Fonseca LL, Cheng WT, Jiang J, Lapp SA, Soderberg SR, Nural MV, Humphrey JC, Hankus A, Machiah D, Karpuzoglu E, DeBarry JD; MaHPIC-Consortium, Tirouvanziam R, Kissinger JC, Moreno A, Gumber S, Voit EO, Gutiérrez JB, Cordy RJ, Galinski MR. 2021. Clinical recovery of Macaca fascicularis infected with Plasmodium knowlesi. Malar J. 2021 Dec 30;20(1):486. doi: 10.1186/s12936-021-03925-6. Wang W., Peng D., Baptista R.P., Li Y.*, Mining T., Kissinger J.C. and Tarleton R.L. 2021. Gene family expansion and diversification in Trypanosoma cruzi 2021. PLoS Pathogens doi.org/10.1371/journal.ppat.1009254 Li, Yiran*, Baptista R.P., A. Sateriale, B. Striepen and Kissinger J.C. 2020. Long Non-coding RNAs During Cryptosporidium parvum Development as Revealed by Stranded RNA-Seq. Front. Cell. Infect. Microbiol. 10:608298. doi: 10.3389/fcimb.2020.608298 J.H. Butler, Baptista R.P, Valenciano, A.L., Conrad, M. R.M., Kissinger J.C., Tumwebaze, P.K., Rosenthal P.J., Cooper R.A., Yue J., Zhou B. and Cassera M.B. 2020. “Mutations in Plasmodium falciparum Pro-drug Activation and Resistance Esterase Mediate Resistance to a Sub-class of Sesquiterpene Dimer Antimalarial Natural Products” ACS Infect Dis. Nov 13;6(11):2994-3003 doi: 10.1021/acsinfecdis.0c00487 Yiran Li*, R.P. Baptista and J.C. Kissinger. 2020. Non-coding RNAs in the Apicomplexa: an update. Trends in Parasitology. Oct;36(10):835-849 DOI:10.1016/j.pt.2020.07.006. Jeremy D. DeBarry, Jessica C. Kissinger, Mustafa V. Nural, Suman B. Pakala, Jay C. Humphrey, Esmeralda V. S. Meyer, Regina Joice Cordy, Monica Cabrera-Mora, Elizabeth D. Trippe, Jacob B. Aguilar, Ebru Karpuzoglu, Yi H. Yan, Jessica A. Brady, Allison N. Hankus, Nicolas Lackman, Alan R. Gingle, Vishal Nayak, Alberto Moreno, Chester J. Joyner,Juan B. Gutierrez, Mary R. Galinski, and the MaHPIC Consortium. 2020. Guidelines for Supporting a Systems Biology Cyberinfrastructure. 19:24 pp-1-12 DOI:10.5334/dsj-2020-024 Loic Favennec, Giovanni Widmer, David Carmena, Martin Kvac, Rachel M. Chalmers, Jessica C. Kissinger, Lihua Xiao, Adam Sateriale, Borist Striepen, Fabrice Laurent, Sonia Lacroix Lamande and Gilles Gargala. 2020. Update on Cryptosporidium spp.: Highlights from the Seventh International Giardia and Cryptosporidium Conference. Parasite Vol. 27(14) DOI: 10.1051/parasite/2020011 Warrenfeltz S, Kissinger JC; EuPathDB Team. Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org. Methods Mol Biol. 2020;2052:139-192. doi: 10.1007/978-1-4939-9748-0_10. PubMed PMID: 31452162. Emmanuel Ruhamyankaka, Brian P. Brunk, Grant Dorsey, Omar S. Harb, Danica A. Helb, John Judkins, Jessica C. Kissinger, Brianna Lindsay, David S. Roos, Christian J. Stoeckert, Jie Zheng, Sheena Shah Tomko. ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies. 2019 Open Res 2019, 3:1661 doi.org/10.12688/gatesopenres.13087.1 Joyner CJ, Brito CFA, Saney CL, Joice Cordy R, Smith ML, Lapp SA, Cabrera-Mora M, Kyu S, Lackman N, Nural MV, DeBarry JD; MaHPIC Consortium, Kissinger JC, Styczynski MP, Lee FE, Lamb TJ, Galinski MR. Humoral immunity prevents clinical malaria during Plasmodium relapses without eliminating gametocytes. PLoS Pathog. 2019 Sep 19;15(9):e1007974. doi: 10.1371/journal.ppat.1007974. PubMed PMID: 31536608. Baptista RP, Kissinger JC. Is reliance on an inaccurate genome sequence sabotaging your experiments? PLoS Pathog. 2019 Sep 12;15(9):e1007901. doi: 10.1371/journal.ppat.1007901. PubMed PMID: 31513692 Adam Sateriale, Jan Slapeta, Rodrigo Baptista, Julie B. Engiles, Jodi A. Gullicksrud, Gillian T. Herbert, Carrie F. Brooks, Emily M. Kugler, Jessica C. Kissinger, Christopher A. Hunter, and Boris Striepen. A Genetically Tractable, Natural Mouse Model of Cryptosporidiosis Offers Insights into Host Protective Immunity, Cell Host & Microbe 2019, https://doi.org/10.1016/j.chom.2019.05.006 Cordy RJ, Patrapuvich R, Lili LN, Cabrera-Mora M, Chien J-T, Tharp GK, Khadka M, Meyer EVS, Lapp SA, Joyner CJ, Garcia A, Banton S, Tran V, Luvira V, Rungin S, Saeseu T, Rachaphaew N, Pakala S, DeBarry JD, MaHPIC Consortium, Kissinger JC, Ortland EA, Bosinger SE, Barnwell JW, Jones DP, Uppal K, Li S, Sattabongkot J, Moreno A, Galinski MR. 2019; Distinct amino acid and lipid perturbations characterize acute versus chronic malaria JCI Insight 2019;4(9):e125156 doi.org/10.1172/jci.insight.125156 Jessica C. Kissinger. Evolution of Cryptosporidium. News & Views. (2019) Nature Microbiology. https://doi.org/10.1038/s41564-019-0438-1 Warrenfeltz S, Basenko EY, Crouch K, Harb OS, Kissinger JC, Roos DS, Shanmugasundram A, and Silva-Franco F. EuPathDB: The Eukaryotic Pathogen Genomics Database Resource. 2018. Methods Mol Biol. 2018;1757:69-113. doi: 10.1007/978-1-4939-7737-6_5. Evelina Y. Basenko, Jane A. Pulman, Achchuthan Shanmugasundram, Omar S. Harb, Kathryn Crouch, David Starns, Susanne Warrenfeltz, Cristina Aurrecoechea, Christian J. Stoeckert Jr., Jessica C. Kissinger, David S. Roos, Christiane Hertz-Fowler. FungiDB: An integrated bioinformatic resource for fungi and oomycetes. 2018. Journal of Fungi 2018, 4(1), 39; doi:10.3390/jof4010039 Rodrigo P. Baptista, João Luis R. Cunha, Jeremy DeBarry, Egler Chiari, Jessica C. Kissinger, Daniella C. Bartholomeu and Andréa M. Macedo. Assembly of highly-repetitive genomes using short reads: The genome of DTU III Trypanosoma cruzi strain 231, 2018 Microb Genom. 2018 Feb 14. doi: 10.1099/mgen.0.000156 Jessica C. Kissinger, Karen E. Hermetz, Keith M. Woodsd, Steve J. Upton. Enrichment of Cryptosporidium parvum from in vitro culture as measured by total RNA and subsequent sequence analysis. 2018 Mol Biochem Parasitol. doi: 10.1016/j.molbiopara.2017.12.004115 Animesh Dhara, Rodrigo de Paula Baptista, Jessica C. Kissinger, E. Charles Snow and Anthony P. Sinai, Ablation of an OTU-family deubiquitinase exposed the underlying regulation governing the plasticity of cell cycle progression in Toxoplasma gondii 2017 mBio 8:e01846-17 John Brestelli, Francislon S. Oliveira, Shon Cade, Jie Zheng, John Iodice, Steve Fischer, Cristina Aurrecoechea, Jessica C. Kissinger, Brian P. Brunk, Christian J. Stoeckert Jr., Gabriel R. Fernandes, David S. Roos, Daniel P. Beiting. MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. BioRxiv and Nov 2017 Nucleic Acids Research, gkx1027 Elizabeth D. Trippe, Jacob B. Aguilar, Yi H. Yan, Mustafa V. Nural, Jessica A. Brady, Mehdi Assefi, Saeid Safaei, Mehdi Allahyari, Seyedamin Pouriyeh, Mary R. Galinski, Jessica C. Kissinger, Juan B. Gutierrez. A Vision for Health Informatics: Introducing the SKED Framework. An Extensible Architecture for Scientific Knowledge Extraction from Data. 2017 arXiv Yan Tang, Chester J. Joyner, Monica Cabrera-Mora, Celia L. Saney, Stacey A. Lapp, Mustafa V. Nural, Suman B. Pakala, Jeremy D. DeBarry, Stephanie Soderberg, the MaHPIC Consortium, Jessica C. Kissinger, Tracey J. Lamb, Mary R. Galinski and Mark P. Styczynski. Integrative analysis associates monocytes with insufficient erythropoiesis during acute Plasmodium cynomolgi malaria in rhesus macaques. Malar J. 2017 Sep 22;16(1):384. doi: 10.1186/s12936-017-2029-z S. A. Lapp, J-T. Chien, S. Pakala, J.A. Geraldo, G. Batugedara, F. Ay, J. Humphrey, J.D. DeBarry, K.G. Le Roch, M.R. Galinski and J.C. Kissinger. PacBio assembly of a Plasmodium knowlesi genome sequence with Hi-C correction and manual annotation of the SICAvar gene family Parasitology. 2017 Jul 19:1-14. doi: 10.1017/S0031182017001329 Nathan M. Chasen, Beejan Asady, Leandro Lemgruber; Rossiane C. Vommaro, Jessica C. Kissinger, Isabelle Coppens, and Silvia N.J. Moreno. A GPI-anchored Carbonic Anhydrase-Related Protein of Toxoplasma gondii is Important for Rhoptry Biogenesis and Virulence. 2017. mSphere. 2017 May 17;2(3). pii: e00027-17. doi: 10.1128/mSphere.00027-17 Ousman Mahmud* and Jessica C. Kissinger. Evolution of the Apicomplexan Sugar Transporter Gene Family Repertoire, International Journal of Genomics, vol. 2017, Article ID 1707231. 2017. doi:10.1155/2017/1707231 Cristina Aurrecoechea; Ana Barreto; Evelina Y. Basenko; John Brestelli; Brian P. Brunk; Shon Cade; Kathryn Crouch; Ryan Doherty; Dave Falke; Steve Fischer; Bindu Gajria; Omar S. Harb; Mark Heiges; Christiane Hertz-Fowler; Sufen Hu; John Iodice; Jessica C. Kissinger; Cris Lawrence; Wei Li; Deborah F. Pinney; Jane A. Pulman; David S. Roos; Achchuthan Shanmugasundram; Fatima Silva-Franco; Sascha Steinbiss; Christian J. Stoeckert Jr; Drew Spruill; Haiming Wang; Susanne Warrenfeltz; Jie Zheng. EuPathDB: the eukaryotic pathogen genomics database resource Nucleic Acids Research. 2017 doi: 10.1093/nar/gkw1105
