Distinguished Research Professor Ph.D. (1995) Indiana University 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. Kissinger Lab Website 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) Honors & Awards Lamar Dodd Creative Research Award, UGA, 2024 Fulbright US Scholar, Fulbright Scholar Program, 2022 Fellow, American Association for the Advancement of Science, 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 Select Professional Service Deputy Director, African Centers of Excellence Global Council (ACE) (2021 – Present) Global Council Member, NIAID ACE (2019 – 2021) 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) Visit Kissinger's ORCID 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-doctoral Fellow & 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 "Bioinformatics resources for kinetoplastid organisms and their hosts", Wellcome Trust (2020-2025), 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 Selected Publications Selected Publications: Recent Publications (*= Graduate student; # = Undergraduate student) Sriveny Dangoudoubiyam, Jamie Norris, *Sivaranjani namasivayam, Rodrigo de Paula Baptista, Naila Cannes do Nascimento, Joseph Camp, Christopher L. Schardl, Jessica C. Kissinger and Daniel K. Howe. Temporal gene expression during asexual development of the apicomplexan Sarcocystis neurona. 2024. (In revision, mSphere). Bayona-Vásquez NJ, Sullivan AH, Beaudry MS, Khan A, Baptista RP, Petersen K, Bhuiyan MIU, Brian Brunelle, Robinson G, Chalmers RM, Grigg ME, Kissinger JC, Glenn TC. Whole genome targeted enrichment and sequencing in Cryptosporidium SPP. 2024. bioRxiv. Pre-print doi:10.1101/2024.03.29.586458 (submitted). *Lasya R Penumarthi, Rodrigo Baptista, Megan S Beaudry, Travis C Glenn and Jessica C Kissinger. A new chromosome-level genome assembly and annotation of Cryptosporidium meleagridis 2024. bioRxiv. Pre-print doi:10.1101/2024.02.16.580748 (Submitted). Rodrigo de Paula Baptista, *Rui Xiao, *Yiran Li, Travis C. Glenn and Jessica C. Kissinger. New T2T assembly of Cryptosporidium parvum IOWA annotated with reference genome gene identifiers (2024) bioRxiv. Pre-print doi:10.1101/2023.06.13.544219v1 (Submitted). *Fiifi Dadzie, Megan Beaudry, Alex Deyanov, Haley Slani, Mihn Q. Duong, Randi Turner, Asis Khan, Cesar Arias, Jessica C. Kissinger, Travis Glenn, Rodrigo de Paula Baptista. Evaluating the Benefits and Limits of Multiple Displacement Amplification in Whole-Genome Oxford Nanopore Sequencing. (2024) bioRxiv. Pre-print doi:10.1101/2024.02.09.579537 (Submitted) *Fiifi Agyabeng-Dadzie, *Rui Xiao and Jessica C. Kissinger. Cryptosporidium Genomics – Current Understanding, Advances, and Applications. Solicited Review. (2024) Current Tropical Medicine Reports doi: 10.1007/s40475-024-00318-y Evelina Y. Basenko, Achchuthan Shanmugasundram, Ulrike Böhme, David Starns, Paul Wilkinson, Helen R. Davison, Kathryn Crouch, Gareth Maslen, Omar Harb, Beatrice Amos, Mary Ann McDowell, Jessica C. Kissinger, David S. Roos, Andrew Jones. What’s new in FungiDB, a web-based bioinformatics platform for omics scale data analysis for fungal and oomycete species. (2024) Genetics. Mar 26:iyae035. doi: 10.1093/genetics/iyae035 Nigel Yarlett, Mary Morada, Deborah A. Schaefer, Kevin Ackman, Elizabeth Carranza, Rodrigo de Paula Baptista, Michael W. Riggs and Jessica C. Kissinger. Genomic and virulence analysis of in vitro cultured Cryptosporidium parvum. (2024) PLoS Pathog 20(2):e1011992. doi: 10.1371/journal.ppat.1011992 Jorge Alvarez-Jarreta, Beatrice Amos, Cristina Aurrecoechea, Saikou Bah, Matthieu Barba, Ana Barreto, Evelina Y Basenko, Robert Belnap, Ann Blevins, Ulrike Böhme, John Brestelli, Stuart Brown, Danielle Callan, Lahcen I. Campbell, George K. Christophides, Kathryn Crouch, Helen R. Davison, Jeremy DeBarry, Richard Demko, Ryan Doherty, Yikun Duan, Walter Dundore, Sarah Dyer, Dave Falke, Steve Fisher, Bindu Gajria, Daniel Galdi, Gloria I. Giraldo-Calderón, Omar S. Harb, Elizabeth Harper, Danica Helb, Connor Howington, Sufen Hu, Jay Humphrey, John Iodice, Andrew Jones, John Judkins, Sarah A. Kelly, Jessica C. Kissinger, Nupur Kittur, Dae Kun Kwon, Kristopher Lamoureux, Wei Li, Disha Lodha, Robert M. MacCallum, Gareth Maslen, Mary Ann McDowell8, Jeremy Myers, Mustafa Veysi Nural, David S. Roos, Samuel S.C. Rund, Achchuthan Shanmugasundram, Vasily Sitnik, Drew Spruill, David Starns, Sheena Shah Tomko, Haiming Wang, Susanne Warrenfeltz, Robert Wieck, Paul A. Wilkinson, Jie Zheng. (2024) VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Research, doi.org/10.1093/nar/gkad1003 Sebastian Shaw, Ian S. Cohn, Rodrigo P. Baptista, Guoqin Xia, Bruno Melillo, *Fiifi Agyabeng-Dadzie, Jessica C. Kissinger and Boris Striepen. (2023) Genetic crosses within and between species of Cryptosporidium, bioRxiv 2023.08.04.551960; doi: 10.1101/2023.08.04.551960; PNAS doi: 10.1073/pnas.2313210120 *Sivaranjani Namasivayam, Cheng Sun, Assiatu B Barrie, Wenyuan Xiao, #Erica M. Hall, *Jenna Oberstaller, Cedric Feschotte, Jessica C Kissinger and Ellen J Pritham. Massive invasion of organellar DNA drives nuclear genome evolution in Toxoplasma. (2023). PNAS doi:10.1073/pnas.2308569120). 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.
