2022

Figure 3

Yiran Li*, Rodrigo P. Baptista, Xiaohan Mei, Jessica C. Kissinger. 2022. Small and intermediate size structural RNAs in the unicellular parasite as revealed by sRNA-seq and comparative genomics. Microbial Genomics. May 10;8(5).

Figure 1

Beatrice Amos, Cristina Aurrecoechea, Matthieu Barba, Ana Barreto, Evelina Y Basenko, Wojciech Bażant, Robert Belnap, Ann S Blevins, Ulrike Böhme, John Brestelli, Brian P Brunk, Mark Caddick, Danielle Callan, Lahcen Campbell, Mikkel B Christensen, George K Christophides, Kathryn Crouch, Kristina Davis, Jeremy DeBarry, Ryan Doherty, Yikun Duan, Michael Dunn, Dave Falke, Steve Fisher, Paul Flicek, Brett Fox, Bindu Gajria, Gloria I Giraldo-Calderón, Omar S Harb, Elizabeth Harper, Christiane Hertz-Fowler, Mark J Hickman, Connor Howington, Sufen Hu, Jay Humphrey, John Iodice, Andrew Jones, John Judkins, Sarah A Kelly, Jessica C Kissinger, Dae Kun Kwon, Kristopher Lamoureux, Daniel Lawson, Wei Li, Kallie Lies, Disha Lodha, Jamie Long, Robert M MacCallum, Gareth Maslen, Mary Ann McDowell, Jaroslaw Nabrzyski, David S Roos, Samuel S C Rund, Stephanie Wever Schulman, Achchuthan Shanmugasundram, Vasily Sitnik, Drew Spruill, David Starns, Christian J Stoeckert, Jr, Sheena Shah Tomko, Haiming Wang, Susanne Warrenfeltz, Robert Wieck, Paul A Wilkinson, Lin Xu, Jie Zheng. 2022. VEuPathDB:The Eukaryotic Pathogen, Vector and Host Bioinformatics Resource Center. Nucleic Acids Res. Jan 7;50(D1):D898-D911. doi.org/10.1093/nar/gkab929

Figure 4

Rodrigo P. Baptista, Yiran Li*, Adam Sateriale, Karen L. Brooks, Alan Tracey, Mandy J. Sanders, Brendan R. E. Ansell, Aaron R. Jex, Garrett W. Cooper, Ethan D. Smith, Rui Xiao, Jennifer E. Dumaine, Peter Georgeson, Bernard Pope, Matthew Berriman, Boris Striepen, James A. Cotton and Jessica C. Kissinger. 2022. Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveals expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions. Genome Research Jan;32(1):203-213. doi.org/10.1101/gr.275325.121.

 

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2021

Image of Article Page 1

Mariko S. Peterson, Chester J. Joyner, Jessica A. Brady, Jennifer S. Wood, Monica Cabrera-Mora, Celia L. Saney, Luis L. Fonseca, Wayne Cheng, Jianlin Jang, Stacey A. Lapp, 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. 2021. Clinical recovery of Macaca fascicularis infected with Plasmodium knowlesi. Malaria Journal Dec 30;20(1):486 doi.org/10.1186/s12936-021-03925-6

Figure 1

Rodrigo P. Baptista, Garrett W. Cooper and Jessica C. Kissinger. Challenges for Cryptosporidium population studies. (Review) Genes 2021, 12:894  doi.org/10.3390/genes12060894

Figure 3

Sivaranjani Namasivayam*, Rodrigo P. Baptista, Wenyuan Xiao, Erica M. Hall, Josheph 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

Figure 3

Yiran Li*, Rodrigo Baptista, Adam Sateriale, Boris Striepen, Jessica C Kissinger. 2021. Analysis of Long Non-Coding RNA in Cryptosporidium parvum Reveals Significant Stage-Specific Antisense Transcription. Front. Cell. Infect. Microbiol 10:608298. doi: 10.3389/fcimb.2020.608298 (BioRxiv DOI: 10.1101/2020.09.19.304907)

 
 
Rodrigo P. Baptista, Yiran Li*, Adam Sateriale, Mandy J. Sanders, Karen L Brooks, Alan Tracey, Brendan R. E. Ansell, Aaron R. Jex, Garret W. Cooper, Ethan D. Smith, Rui Xiao, Jennifer E. Dumaine, Matthew Berriman, Boris Striepen, James A. Cotton and Jessica C. Kissinger. 2021. Consistent, comparative and evidence-based genome annotation for the closely-related species, Cryptosporidium parvumC. hominis and C. tyzzeri. BioRxiv DOI: 10.1101/2021.01.29.428682.

 

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2020

Figure 1

Yiran Li*, R.P. Baptista and J.C. Kissinger. 2020. Non-Coding RNAs in the Apicomplexa: an update. (In Press, Trends in Parasitology, available online https://doi.org/10.1016/j.pt.2020.07.006)

article

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 

Figure

Warrenfeltz S, Kissinger JC and EuPathDB Team. (2020) 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.  

 

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2019

Pipeline for processing studies

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 [epub]

Fig 2. Plasmodium cynomolgi relapses cause distinct changes in host transcriptomes related to B cells.

 

Chester J. Joyner, Cristiana F. A. Brito, Celia L. Saney, Regina Joice Cordy, Maren L. Smith, Stacey A. Lapp, Monica Cabrera-Mora, Shuya Kyu, Nicolas Lackman, Mustafa V. Nural, Jeremy D. DeBarry , the MaHPIC Consortium, Jessica C. Kissinger, Mark P. Styczynski, Frances Eun-Hyung Lee, Tracey J. Lamb, and Mary R. Galinski. Humoral immunity prevents clinical malaria during Plasmodium relapses without reducing transmission potential. (2019) PLoS Pathog 15(9): e1007974. doi.org/10.1371/journal.ppat.1007974   

https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1007901

Baptista, R. P. and Kissinger, J.C. Is reliance upon an inaccurate eukaryotic genome sequence sabotaging your experiments? (2019) PLoS Pathog 15(9): e1007901. doi.org/10.1371/journal.ppat.1007901

graphical abstract

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. Protective immunity in a genetically tractable natural mouse model of cryptosporidiosis Cell Host & Microbe (2019), https://doi.org/10.1016/j.chom.2019.05.006
 
https://insight.jci.org/articles/view/125156/figure/7
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. Distinct amino acid and lipid perturbations characterize acute versus chronic malaria JCI Insight 2019;4(9):e125156 doi.org/10.1172/jci.insight.125156
 
https://www.nature.com/articles/s41564-019-0438-1
Jessica C. Kissinger. Evolution of Cryptosporidium. News & Views. (2019) Nature Microbiology. doi.org/10.1038/s41564-019-0438-1
 

 

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2018

Warrenfeltz S, Basenko EY, Crouch K, Harb OS, Kissinger JC, Roos DS, Shanmugasundram A, Silva-Franco F. EuPathDB: The Eukaryotic Pathogen Genomics Database Resource. Methods Mol Biol. Editor, Martin Kollmar. 2018;1757:69-113. doi: 10.1007/978-1-4939-7737-6_5. PMID:29761457

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 and Christiane Hertz-Fowler. FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. 2018. J. 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. Microb Genom. 2018 Feb 14. doi: 10.1099/mgen.0.000156 [epub]

Jessica C. Kissinger, Karen E. Hermetz, Keith M. Woods, Steve J. Upton. Enrichment of Cryptosporidium parvum from in vitro culture as measured by total RNA and subsequent sequence analysis. Mol Biochem Parasitol. 2017 Dec 29.. doi: 10.1016/j.molbiopara.2017.12.004115

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2017

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 familyParasitology. 2017 Jul 19:1-14. doi: 10.1017/S0031182017001329

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 mBio 8:e01846-17. https://doi.org/10.1128/mBio.01846-17.

Nathan M. Chasen, Beejan Asady, Leandro Lemgruber; Rossiane C. Vommaro, Jessica C. Kissinger, Isabelle Coppens, and Silvia N.J. Moreno. A Glycosylphosphatidylinositol-Anchored Carbonic Anhydrase-Related Protein of Toxoplasma gondii Is Important for Rhoptry Biogenesis and Virulence. 2017 mSphere doi:10.1128/mSphere.00027-17

Yan Tang, Chester J. Joyner, Monica Cabrera- Mora, 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 data analysis implicates monocytes in the disruption of erythropoiesis during acute malaria in macaquesMalaria Journal 16:384 doi.org/10.1186/s12936-017-2029-z

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. arXiv:1706.07992

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 experimentsNucleic Acids Research. 2017 doi.org/10.1093/nar/gkx1027

Ousman Mahmud and Jessica C. Kissinger. Evolution of the Apicomplexan Sugar Transporter Gene Family Repertoire. International Journal of Genomics 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; AchchuthanShanmugasundram; 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

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2016

Olukemi O. Ifeonu, Raphael Simon, Sharon M. Tennant, Abhineet S. Sheoran, Maria C. Daly, Victor Felix, Jessica C. Kissinger, Giovanni Widmer, Myron M. Levine, Saul Tzipori and Joana C. Silva Cryptosporidium hominis Gene Catalog: a resource for the selection of novel Cryptosporidium vaccine candidates. Database (2016) doi: 10.1093/database/baw137

Joyner C, Moreno A, Meyer EV, Cabrera-Mora M; MaHPIC Consortium, Kissinger JC, Barnwell JW, Galinski MR. Plasmodium cynomolgi infections in rhesus macaques display clinical and parasitological features pertinent to modelling vivax malaria pathology and relapse infections. Malar J. 2016 Sep 2;15(1):451.

Chien JT, Pakala SB, Geraldo JA, Lapp SA, Humphrey JC, Barnwell JW, Kissinger JC, Galinski MR. High-Quality Genome Assembly and Annotation for Plasmodium coatneyi, Generated Using Single-Molecule Real-Time PacBio Technology. Genome Announc. 2016 Sep 1;4(5). pii: e00883-16. doi: 10.1128/genomeA.00883-16.

Ifeonu OO, Chibucos M, Orvis J, Su Q, Elwin K, Guo F, Zhang H, Xiao L, Sun M, Chalmers RM, Fraser CM, Zhu G, Kissinger JC, Widmer G, Silva JC. Annotated draft genome sequences of three species of CryptosporidiumC. meleagridis isolate UKMEL1, C. baileyi isolate TAMU-09Q1, and C. hominis isolates TU502_2012 and UKH1. Pathog Dis. 2016 Aug 12. PMID: 27519257

Jessica C. Kissinger. An unsettling picture emerges from population genomic studies of Plasmodium vivax. Nature Genetics 48(8):825-826 (2016) doi:10.1038/ng.3630

Nyasa RB, Kimbi HK, Zofou D, DeBarry JD, Kissinger JC, Titanji VP. An evolutionary approach to identify potentially protective B cell epitopes involved in naturally acquired immunity to malaria and the role of EBA-175 in protection amongst denizens of Bolifamba, Cameroon. Malar J. 2016 May 20;15(1):281. doi: 10.1186/s12936-016-1337-z

Staffan Bensch, Björn Canbäck, Jeremy D. DeBarry, Thomas Johansson, Olof Hellgren, Jessica C. Kissinger, Vaidas Palinauskas, Elin Videvall and Gediminas Valkiūnas. Before malaria was malaria: the genome of Haemoproteus tartakovskyi resolves the phylogenetic position of Plasmodium falciparum. 2016 Genome Biology & Evolution, 2016 doi:10.1093/gbe/evw081

H. Lorenzi, A. Khan, M. Behnke, S. Namasivayam, S. Seshadri, M. Hadjithomas, S. Karamycheva, D. Pinney, B. Brunk, J. Ajioka, D. Azjenberg, J.C. Boothroyd, J. Boyle, M.L. Darde, J.P. Dubey, M. Grigg, D. Howe, K. Kim,B. Rosenthal, J. Saeij, C.L. Su, M. White, XQ Zhu, J. Parkinson, L. Liu, J.C. Kissinger, D.S. Roos, L.D. Sibley. Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes. 2016 Nat Commun. 2016 Jan 7;7:10147. doi: 10.1038/ncomms10147

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2015

Yi Yan, Brian Adam, Mary Galinski, Jessica C. Kissinger, Alberto Moreno and Juan B. Gutierrez. Mathematical model of susceptibility, resistance, and resilience in the within-host dynamics between a Plasmodium parasite and the immune system.  Mathematical BioSciences, 2015 Dec;270 (Pt B):213-23. doi: 10.1016/j.mbs.2015.10.003.

Buscaglia, C.A., Kissinger, J.C. and F. Agüero. Neglected Tropical Diseases in the Post-Genomic Era. Invited Review, Trends Genet. 2015 Oct;31(10):539-55. doi: 10.1016/j.tig.2015.06.002.

Yin W, Kissinger JC, Moreno A, Galinski MR, Styczynski MP. From genome-scale data to models of infectious disease: A Bayesian network-based strategy to drive model development. Math Biosci. 2015 Jun 17. pii: S0025-5564(15)00124-8. doi: 10.1016/j.mbs.2015.06.006.

Tomasz Blazejewski, Nirvana Nursimulu, Viviana Pszenny, Sriveny Dangoudoubiyam, Sivaranjani Namasivayam, Melissa A. Chiasson, Kyle Chessman, Michelle Tonkin, Swapna Seshadri, Stacy S. Hung, Stacy M. Ricklefs, Martin J. Boulanger, Steve F. Porcella, Joshua Bridgers, Jessica C. Kissinger, Daniel K. Howe, Michael E. Grigg, and John Parkinson. Systems based analysis of the Sarcocystis neurona genome identifies pathways that differentiate tissue-invading from enteric coccidian parasites. MBio 2015 doi: 10.1128/mBio.02445-14

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2014

Kevin Lee, Weiwei Yin, Dalia Arafat, Yan Tang, Karan Uppal, Monica Cabrera-Mora, Alberto Moreno, Esmeralda Meyer, Jeremy DeBarry, Suman Pakala, Vishal Nayak, Jessica C. Kissinger, Dean Jones, Mary Galinski, Mark Styczynski, and Greg Gibson. Integration of Transcriptomics and Metabolomics in a Rhesus Macaque Drug Administration Study Front. Cell Dev. Biol., 08 October 2014 | doi: 10.3389/fcell.2014.00054

Jenna Oberstaller, Yoanna Pumpalova, Ariel Schieler, Manuel Llinás, Jessica C. Kissinger. The Cryptosporidium parvum ApiAP2 gene family: insights into the evolution of the apicomplexan AP2 regulatory systems. Nucleic Acids Research 2014 1 doi: 10.1093/nar/gku500

Vivien G. Dugan, Scott J. Emrich, Gloria I. Giraldo-Calderón, Omar S. Harb, Ruchi M. Newman, Brett E. Pickett, Lynn M. Schriml, Timothy B. Stockwell, Christian J. Stoeckert Jr, Dan E. Sullivan, Indresh Singh, Doyle V. Ward, Alison Yao, Jie Zheng, Tanya Barrett, Bruce Birren, Lauren Brinkac, Vincent M. Bruno, Elizabet Caler, Sinéad Chapman, Frank H. Collins, Christina A. Cuomo, Valentina Di Francesco, Scott Durkin, Mark Eppinger, Michael Feldgarden, Claire Fraser, W. Florian Fricke, Maria Giovanni, Matthew R. Henn, Erin Hine, Julie Dunning Hotopp, Ilene Karsch-Mizrachi, Jessica C. Kissinger, Eun Mi Lee, Punam Mathur, Emmanuel F. Mongodin, Cheryl I. Murphy, Garry Myers, Daniel E. Neafsey, Karen E. Nelson, William C. Nierman, Julia Puzak, David Rasko, David S. Roos, Lisa Sadzewicz, Joana C. Silva, Bruno Sobral, R. Burke Squires, Rick L. Stevens, Luke Tallon, Herve Tettelin, David Wentworth, Owen White, Rebecca Will, Jennifer Wortman, Yun Zhang, Richard H. Scheuermann. Standardized Metadata for Human Pathogen/Vector Genomic Sequences. PLoS One 2014 DOI: 10.1371/journal.pone.0099979

Jeremy D. DeBarry and Jessica C. Kissinger. Innovation through duplication in the reduced genomes of twelve parasites. PLoS One 2014 DOI: 10.1371/journal.pone.0099213

Jorge L. Salinas, Jessica C. Kissinger, Dean P. Jones, Mary R. Galinski. Metabolomics in the Fight Against Malaria. Memórias do Instituto Oswaldo Cruz 2014 Vol 109 DOI: 10.1590/0074-0276140043

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2013

Jenna Oberstaller, Sandeep J. Joseph and Jessica C. Kissinger. Genome-wide upstream motif analysis of Cryptosporidium parvum genes clustered by expression profile. BMC Genomics.2013, 14:516. DOI: 10.1186/1471-2164-14-516

Lucchi NW, Oberstaller J, Kissinger JC, Udhayakumar V. Malaria diagnostics and surveillance in the post-genomic era. Public Health Genomics. 2013;16(1-2):37-43. doi: 10.1159/000345607. Epub 2013 Mar 18. PMID: 23548716

Patel JC, Oberstaller J, Xayavong M, Narayanan J, DeBarry JD, Srinivasamoorthy G, Villegas L, Escalante AA, DaSilva A, Peterson DS, Barnwell JS, Kissinger JC, Udhayakumar V and Lucchi NW. Real-Time Loop-Mediated Isothermal Amplification (RealAmp) for the Species- Specific Identification of Plasmodium vivax. PLoS ONE 8(1): e54986. doi:10.1371/journal.pone.0054986

Jeremy DeBarry, Segun Fatumo and Jessica C. Kissinger. The Apicomplexan Genomic Landscape - The Evolutionary Context of Plasmodium. (Book Chapter) Malaria Parasites: Comparative Genomics, Evolution and Molecular Biology Edited by: Jane M. Carlton, Susan L. Perkins and Kirk W. Deitsch ISBN: 978-1-908230-07-2 Publisher: Caister Academic Press (February 2013)

Cristina Aurrecoechea, Ana Barreto, John Brestelli, Brian P. Brunk, Shon Cade, Ryan Doherty, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Omar S. Harb, Mark Heiges, Sufen Hu, John Iodice, Jessica C. Kissinger, Eileen T. Kraemer, Wei Li, Deborah F. Pinney, Brian Pitts, David S. Roos, Ganesh Srinivasamoorthy, Christian J. Stoeckert Jr., Haiming Wang, Susanne Warrenfeltz. EuPathDB: The Eukaryotic Pathogen Database. Nucl. Acids Res. (2013) 41 (D1): D684-D691. doi: 10.1093/nar/gks1113

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2012

Adhemar Zerlotini, Eric Aguiar, Fudong Yu, Huayong Xu, Yixue Li, Neil Young, Robin Gasser, Anna Protasio, Matt Berriman, David Roos, Jessica Kissinger, Guilherme Oliveira. SchistoDB: An Updated Resource for the Three Key Schistosomes of Humans Nucleic Acids Research, 2012, 1–4 doi:10.1093/nar/gks1087

Alok Dhamanaskar, Michael E. Cotterell, Chaitanya Guttula, John A. Miller, Jessica C. Kissinger, Jie Zheng, and Christian J. Stoeckert, Jr. Suggestions for Galaxy Workflow Design Using Ontologically Annotated Web Services Formal Ontology in Information Systems - Proceedings of the Seventh International Conference (FOIS 2012) Volume 239 29-42, 2012

Satomi Kato and JC Kissinger.  Cryptosporidium: Comparative Genomics and Pathogenesis. in "Evolution of Virulence in Eukaryotic Microbes" Editors, David Sibley, Barbara J. Howlett, and Joseph Heitman,  Wiley-Blackwell, pp 518 2012

Zhu-Hong Li, Javier G. De Gaudenzi, Vanina E. Alvarez, Haiming Wang, Jessica Kissinger, Alberto C. Frasch, Roberto Docampo. A 43-nt U-rich element in the 3' untranslated region of a large number of Trypanosoma cruzi transcripts is important for mRNA abundance in intracellular amastigotes J. Biol. Chem 2012 doi:10.1074/jbc.M111.338699

Lucchi, N.W., Poorak, M., Oberstaller, J., DeBarry, J., Srinivasamoorthy, G., Goldman, I., Xayavong, M., DaSilva, A., Peterson, D.S., Barnwell, J., Kissinger, J.C., Udhayakumar, V. A new single-step PCR assay for the detection of the zoonotic malaria parasite Plasmodium knowlesiPLoS ONE. 2012 7(2): e31848. doi:10.1371/journal.pone.0031848

Y. Wang, H. Tang, J.D. DeBarry, X. Tan, J. Li, X. Wang, T. Lee, H. Jin, B. Marler, H. Guo, J.C. Kissinger and A.H. Paterson MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012, 1-14. doi: 10.1093/nar/gkr1293 [Epub ahead of print, Jan 4, 2012]

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2011

Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S, Harb OS, Kissinger JC, Li W, Nayak V, Pinney DF, Stoeckert CJ Jr, Roos DS. FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res. 2011 Nov 7. [Epub ahead of print]

Rui Wang, Chaitanya Guttula, Maryam Panahiazar, Haseeb Yousaf, John A. Miller, Eileen T. Kraemer and Jessica C. Kissinger, Web Service Composition using Service Suggestions In: Proceedings of the 2011 IEEE International Workshop on Formal Methods in Services and Cloud Computing (FM-S&C ) in conjunction with the 2011 IEEE International Conference on Web Services (ICWS), Washington, DC (July 2011) pp. 482-489.

Sharmi Thor, Deborah Hilt, Jessica C Kissinger, Andrew Paterson, Mark Jackwood. Recombination in avian gamma-coronaviruses. Viruses 2011, 3(9), 1777-1799; doi:10.3390/v3091777

J. E. Phillips, M. W. Jackwood, E. T. McKinley, S. W. Thor, D. A. Hilt, N. D. Acevedo1, S. M. Williams, J. C. Kissinger, A. H. Paterson, J. S. Robertson, C. Lemke. Changes in Nonstructural Protein 3 are Associated with Attenuation in Avian Coronavirus. Virus Genes, Epub Sept 10

Chaitanya Guttula, Alok Dhamanaskar, Rui Wang, John A. Miller, Jessica C. Kissinger, Jie Zheng and Christian J. Stoeckert, Jr., Enriching the Ontology for Biomedical Investigations (OBI) to Improve its Suitability for Web Service Annotations. In Proceedings of the 2011 International Conference on Biomedical Ontology (ICBO) Buffalo, New York (July 2011) pp. 246-258.

Steve Fischer, Cristina Aurrecoechea, Brian P. Brunk, Xin Gao, Omar S. Harb, Eileen T. Kraemer, Cary Pennington, Charles Treatman, Jessica C. Kissinger, David S. Roos and Christian J. Stoeckert. The Strategies WDK: a graphical search interface and web development kit for functional genomics databases. DATABASE - The Journal of Biological Databases and Curation 2011 10.1093/database/bar027

Enid T. McKinley, Mark W. Jackwood, Deborah A. Hilt, Jessica C. Kissinger, Andrew H. Paterson, Jon S. Robertson, Cornelia Lemke. Attenuated live vaccine usage affects accurate measures of virus diversity and evolutionary rates in avian coronavirus infectious bronchitis virus. Virus Research 158 (2011) 225–234

Jessica C Kissinger and Jeremy DeBarry. Genome cartography: charting the apicomplexan genome. Trends in Parasitology 27 (2011), pp. 345-354 DOI information: 10.1016/j.pt.2011.03.006

A. Demas, J. Oberstaller, J. DeBarry, N.W. Lucchi, G. Srinivasamoorthy, D. Sumari, A.M. Kabanywanyi, L. Villegas, A. A. Escalante, S.P. Kachur, J.W. Barnwell, D.S. Peterson, V. Udhayakumar, and J.C. Kissinger. Applied genomics: Data mining reveals species-specific malaria diagnostic targets more sensitive than 18S rRNA. J. Clinical Microbiology 2011; 49(7):2411-8

J. DeBarry and J.C. Kissinger. Jumbled Genomes: Missing Apicomplexan Synteny. Molecular Biology and Evolution 2011 28(10):2855-71; doi: 10.1093/molbev/msr103

C. Aurrecoechea, A. Barreto, J. Brestelli, B.P. Brunk, E. V. Caler, S. Fischer, B. Gajria, X. Gao, A. Gingle, G. Grant, O.S. Harb, M. Heiges, F. J. Iodice, J.C. Kissinger, E.T. Kraemer, W. Li, V. Nayak, C. Pennington, D.F. Pinney, D.S. Roos, C. Ross, G. Srinivasamoorthy, C.J. Stoeckert Jr., C. Treatman, H. Wang. AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species. Nucleic Acids Research, 2010, 1–8 doi:10.1093/nar/gkq1006

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2010

H. Wang, J. DeBarry, J. C. Kissinger SynView - Synteny Browser with GBrowse Integration. A Practical Guide to Bioinformatics Analysis 2010 iConcept Press Ltd.

S. J. Joseph, J. A. Fernandez-Robledo, M. J. Gardner, N.M. El-Sayed, C-H. Kuo, E. J. Schott, H. Wang, J. C. Kissinger and G. R. Vasta. The Alveolate Perkinsus marinus: Biological Insights from EST Gene Discovery BMC Genomics 2010, 11:228

M.W. Jackwood, T.O. Boynton, D.A. Hilt, E.T. McKinley, J.C. Kissinger, A.H. Paterson, J. Robertson, C. Lemke, A.W. McCall, S.M. Williams, J.W. Jackwood and L. Byrd. Emergence of a group 3 coronavirus through recombination. Virology 2010 Mar 1;398(1):98-108.

C. Aurrecoechea, J. Brestelli, B.P. Brunk, S. Fischer, B. Gajria, J. Gao, A. Gingle, G. Grant, O.S. Harb, M. Heiges, F. Innamorato, J. Iodice, J.C. Kissinger, E.T. Kraemer, W. Li, J.A. Miller, V. Nayak, C. Pennington, D.F. Pinney, D.S. Roos, C. Ross, G. Srinivasamoorthy, C.J. Stoeckert Jr., R. Thibodeau, C. Treatman, H. Wang. EuPathDB: a Portal to Eukaryotic Pathogen Databases. Nucleic Acids Research, 2010 Jan;38(Database issue):D415-9. Epub 2009 Nov 13

M. Aslett, C. Aurrecoechea, M. Berriman, J. Brestelli, B. P. Brunk, M. Carrington, D. P. Depledge, S. Fischer, B. Gajria, X. Gao, M. J. Gardner, A. Gingle, G. Grant, O. S. Harb, M. Heiges, C. Hertz-Fowler, R. Houston, F. Innamorato, J. Iodice, J. C. Kissinger, E. Kraemer, W. Li, F. Logan, J. A. Miller, S. Mitra, P. J. Myler, V. Nayak, C. Pennington, I. Phan, D. F. Pinney, G. Ramasamy, M. Rogers, D. S. Roos, C. Ross, D. Sivam, D. F. Smith, G. Srinivasamoorthy, C. J. Stoeckert Jr., S. Subramanian, R. Thibodeau, A. Tivey, C. Treatman, G. Velarde, H. Wang (2010) TriTrypDB: A Functional Genomic Resource for the Trypanosomatidae. Nucleic Acids Research, 2010 Jan;38(Database issue):D457-62. Epub 2009 Oct 20

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2009

K. Storm, E. Kraemer, C. Aurrecoechea, M. Heiges, C. Pennington and J.C. Kissinger (2009) Web Site Evolution: Usability Evaluation Using Time Series Analysis of Selected Episode Graphs. 11th IEEE International Symposium on Web Systems Evolution (WSE'09), Edmonton, Canada (September 2009) 

R. Wang, D. Brewer, S. Shastri, S. Swayampakula, J. A. Miller, E. T. Kraemer and J. C. Kissinger, "Adapting the Galaxy Bioinformatics Tool to Support Semantic Web Service Composition," Proceedings of the 3-rd IEEE International Workshop on Scientific Workflows (SWF'09), in conjunction with the 2009 IEEE International Conference on Web Services (ICWS'09), Los Angeles, California (July 2009) pp. 283-290.

Wang, Z. X. Gao, C. He, J.A. Miller, J.C. Kissinger, M. Heiges, C. Aurrecoechea, E.T. Kraemer and C. Pennington (2009). An Evaluation of Multiple Approaches for Federating Biological Data. Journal of Information Technology Research, 2(2):42-64

B. Balu, C. Chauhan, S. P. Maher, D. A. Shoue, J. C. Kissinger, M. J. Fraser Jr and J. H. Adams. (2009) piggyBac is an effective tool for functional analysis of the Plasmodium falciparum genome. BMC Microbiology 2009, 9:83

Mullapudi, N. , Joseph, S. and J. C. Kissinger. (2009) Identification and Functional characterization of cis-regulatory elements in the apicomplexan parasite Toxoplasma gondiiGenome Biology Apr 7;10(4): R34

Aurrecoechea C., Brestelli J., Brunk B., Dommer J., Fischer S., Gajria B., Gao X., Gingle A., Grant G., Harb O., Heiges M., Innamarato F., Iodice J., Kissinger J.C., Kraemer E., Li W., Miller J., Nayak V., Roos D., Stoeckert C. (2009) PlasmoDB: A functional genomic database for malaria parasites. Nucleic Acids Research Jan;37(Database issue) :D539-43

Zerlotini A., Heiges M., Wang H., Moraes R., Dominitini A., Ruiz J., Kissinger J.C., Oliveira G. (2009) SchistoDB: a Schistosoma mansoni genome resource Nucleic Acids Research Jan; 37 (Database issue) :D579-82

C. Aurrecoechea, J. Brestelli, B.P. Brunk, J.M. Carlton, J. Dommer, S. Fischer, B. Gajria, J. Gao, A. Gingle, G. Grant, O.S. Harb, M. Heiges, F. Innamorato, J. Iodice, J.C. Kissinger, E. Kraemer, W. Li, J.A. Miller, H.G. Morrison, V. Nayak, C. Pennington, D.F. Pinney, D.S. Roos, C. Ross, C.J. Stoeckert Jr., S. Sullivan, C. Treatman, H. Wang. (2009) GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lambliaand Trichomonas vaginalis Nucleic Acids Research, Jan; 37 (Database issue) :D526-30

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2008

Kuo, C-H, Wares, J.P. and J.C. Kissinger. (2008) The Apicomplexan whole genome phylogeny: an analysis of incongruence among trees Mol Biol Evol. Dec; 25(12) :2689-98

Mendes,P.N., B. McKnight, A.P. Sheth and J.C. Kissinger. (2008) TcruziKB: Enabling Complex Queries for Genomic Data Exploration. ICSC, pp. 432-439, 2008 IEEE International Conference on Semantic Computing 

Z. Wang, J. Miller, J.C. Kissinger, R. Wang, D. Brewer and C. Aurrecoechea, "WS-BioZard: A Wizard for Composing Bioinformatics Web Services," Proceedings of the 2-nd IEEE International Workshop on Scientific Workflows (SWF'08) 

Kuo, C.H and J.C. Kissinger. (2008) Consistent and contrasting properties of lineage-specific gene in the apicomplexan parasites Plasmodium and TheileriaBMC Evolutionary Biology 2008, 8:108

Sanderson SJ, Xia D, Prieto H, Yates J, Heiges M, Kissinger JC, Bromley E, Lal K, Sinden RE, Tomley F, Wastling JM. (2008) Determining the protein repertoire of Cryptosporidium parvum sporozoites. Proteomics 2008, 8, 0000-0000. DOI 10.1002/pmic.200700804

B. Gajria, A. Bahl, J. Brestelli, J. Dommer, S. Fischer, X. Gao, M. Heiges, J. Iodice, *, A.J. Mackey, D. F. Pinney, D.S. Roos, C.J. Stoeckert Jr, H. Wang and B.P. Brunk. (2008) ToxoDB: an integrated Toxoplasma gondii database resource.  Nucleic Acids Research, Jan;36 (Database issue) :D553-6

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2007

Wang Z., Gao X., He C., Miller J.A., Kissinger J.C., Heiges M., Aurrecoechea C., Kraemer E. and Pennington C., "A Comparison of Federated Databases with Web Services for the Integration of Bioinformatics Data," Proceedings of the 2007 International Conference on Bioinformatics & Computational Biology (BIOCOMP'07), Las Vegas, Nevada (June 2007) pp. 334-338.

Mullapudi, N., Lancto, C., Abrahamsen, M., Kissinger, J.C. (2007) Identification of putative cis-regulatory elements in Cryptosporidium parvum by de novo pattern finding. BMC Genomics 2007, 8:13 

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. Special Issue: The African Journal of Medicine and Medical Sciences, 36 Suppl. 15-18

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2006

Chapman, B.A., Bowers J.E., Feltus F.A., Kissinger J.C. and Paterson A.H. Buffering crucial functions may impart cyclicality to angiosperm polyploidization Proc Natl Acad Sci U S A. 2006 February 21; 103(8): 2730¨C2735.

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 cruziNAR 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. 

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2004

Huang, J., N. Mullapudi, C.A. Lancto, M. Scott, M.S. Abrahamsen and Kissinger J.C. (2004) Cryptosporidium parvumPhylogenomic evidence for organelle loss, intracellular and horizontal gene transfer. Genome Biology 5(11):R88

Striepen, B. and Kissinger, J.C. (2004) Genomics meets transgenics in search of the elusive Cryptosporidium drug target. Trends in Parasitology 20(8):355-358

Gunasekera AM, Patankar S, Schug J, Eisen G, Kissinger J.C., Roos D, Wirth DF. (2004) Widespread distribution of antisense transcripts in the Plasmodium falciparum genome. Mol Biochem Parasitol. Jul;136(1):35-42. 

Vidigal, T.H.D.A., L. Spatz, Kissinger J.C., 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 spacer sequences of the ribosomal DNA in Biomphalaria tenagophila complex (Mullusca: Planorbidae). Memorias do Oswaldo Cruz 99(2):153-158

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. Proc. Natl. Acad. Sci., USA 101(9):3154-3159. 

Huang, J., N. Mullapudi, T. Sicheritz-Ponten and J.C. Kissinger. (2004) A Glimpse into 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:D329-331.

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

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2003

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 

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2002

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 

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

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2001

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

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2000

Vidigal, T.H.D.A. J.C. Kissinger, R.L. Caldeira, E.C.R. Pires, E. Monteiro, A.J.G. Simpson and O.S. Carvalho. (2000) Phylogenetic relationships among Brazilian Biomphalaria species (Mollusca:Planorbidae) based upon analysis of ribosomal ITS2 sequences. Parasitology 121(6):611-620

Drozdowicz, Y.M., J.C. Kissinger, and P.A. Rea. (2000) A new category of H+-pyrophosphatase: AVP2, a sequence-divergent, monovalent cation-insensitive H+-translocating inorganic pyrophosphatase from Arabidopsis thaliana. Plant Physiology 123:353-362

Krautz, G.M, J.C. Kissinger and A.U. Krettli. (2000) The Targets of the Lytic Antibody Response against Trypanosoma cruzi. Parasitology Today 16(1):31-34 

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1999

Roos, D.S., M.J. Crawford, R.G.K. Donald, J.C. Kissinger, L.J. Klimczak and B. Striepen. (1999) Origin, targeting, and function of the apicomplexan plastid. Current Opinions in Microbiology 2:426-432.

Roos, D.S., M.J. Crawford, R.G.K. Donald, L.M. Fohl, K.M. Hager, J.C. Kissinger, M.G. Reynolds, B. Striepen, and W.J. Sullivan Jr. (1999) Transport and Trafficking: Toxoplasma as a model for PlasmodiumNovartis Foundation Symposium 226:176-198.

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1998

Kissinger, J.C., W.E. Collins,  J. Li, and T.F. McCutchan. (1998) Plasmodium inui is not closely related to other Quartan Plasmodium Species. J. Parasitol. 84(2):278-282

Kissinger, J.C., and R. Raff. (1998) Evolutionary Changes in Sites and Timing of Expression of Actin Genes in Embryos of the Direct- and Indirect-Developing Sea Urchins, Heliocidaris erythrogramma and H. tuberculata .Development, Genes and Evolution 208(2):82-93 

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1997

Carreno, R.A., J.C. Kissinger, T.F. McCutchan and J.R. Barta. (1997) Phylogenetic analysis of haemosporinid parasites (Apicomplexa: Haemosporina) and their co-evolution with vectors and intermediate hosts. Archiv für Protistenkunde 148:245-252

Bolker, J.A., M. Butler, J.C. Kissinger, and M.A. Riley.  (1997) Addressing the Gender Gap in Evolutionary Biology. Trends. Ecol. & Evol. Vol 12(2) p. 46-47

Li, J., R.R. Gutell, S.H. Damberger, R.A. Wirtz, J.C. Kissinger, M.J. Rogers, J. Sattabongkot and Thomas F. McCutchan. (1997) Regulation and trafficking of distinct sets of ribosomal RNAs during the Plasmodium vivaxdevelopmental cycle J. Mol. Biol. 269:203-213 

Kissinger, J.C., J.H. Hahn and R. Raff. (1997) Rapid evolution in a conserved gene family: Evolution of the actin gene family in the Sea Urchin Genus Heliocidaris and Related Genera. Mol. Biol. Evol.  14:654-665. 

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1989-1996

McCutchan, T. F., J.C. Kissinger, M.G. Touray, M. J. Rogers, J. Li, M. Sullivan, E.M. Braga, A.U. Krettli, L. H. Miller. (1996) Comparison of Circumsporozoite Proteins form Avian and Mammalian Malarias: Biological and Phylogenetic Implications. PNAS Vol. 93 p.11889-11894. 

Popodi, E., J.C. Kissinger, M.E. Andrews and R. Raff.  (1996) Sea Urchin Hox Genes: Insights into the ancestral Hox cluster. Mol. Biol. Evol. 13: 1078-1086. 

Hahn, H-H., J.C. Kissinger and R. Raff. (1995). Structure and Evolution of the CyI actin genes in the Direct- and Indirect-Developing Sea Urchins Heliocidaris erythrogramma and H. tuberculata Gene 153:219-224. 

Sahm, D., J.C. Kissinger, M. Gilmore, P.Murray, R. Mulder, S. Solliday, and B. Clarke.  (1989). In-vitro susceptibility studies of vancomycin-resistant Enterococcus faecalis. Antimicrobial Agents and Chemotherapy. Sept: 1588-1591

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Book Chapters

Omar Harb Jessica C. Kissinger and David S. Roos on behalf of the EuPathDB group (2020). ToxoDB: the functional genomic resource for Toxoplasma and related organisms. In:Toxoplasma gondii 3rd Edition. Edited by Louis Weiss and Kami Kim. Academic Press. ISBN 978-0-12-815041-2, 1244 pages.

Jeremy DeBarry, Segun Fatumo and Jessica C. Kissinger. (2013) The Apicomplexan Genomic Landscape - The Evolutionary Context of Plasmodium. In “Malaria Parasites: Comparative Genomics, Evolution and Molecular Biology,” Editors, Jane M. Carlton, Susan L. Perkins and Kirk W. Deitsch ISBN: 978-1-908230-07-2 Publisher: Caister Academic Press

Satomi Kato and JC Kissinger. (2012) Cryptosporidium: Comparative Genomics and Pathogenesis. in "Evolution of Virulence in Eukaryotic Microbes" Editors, David Sibley, Barbara J. Howlett, and Joseph Heitman, ISBN: 1118038185 Wiley-Blackwell

H. Wang, J. DeBarry, J. C. Kissinger (2010) SynView - Synteny Browser with GBrowse Integration. A Practical Guide to Bioinformatics Analysis, iConcept Press Ltd.

Lorenza Putignani, Sanya J. Sanderson, Cristina Russo, Jessica Kissinger, Donato Menichella and Jonathan M. Wastling, Proteomic and genomic approaches to understanding the "power plant" of Cryptosporidium 2009 CABI publishing.

Kissinger, J.C. (2007) Genomics. In: Cryptosporidium and Cryptosporidiosis. Edited by Ron Fayer and Lihua Xiao. Taylor and Francis. Publisher CRC 2007 ISBN 1420052268

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

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

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., Totowa, New Jersey

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.

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