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MaHPIC Publications

Luiz Gustavo Gardinassi, Jianguo Xia, Sandra Safo, Shuzhao Li. Bioinformatics tools for the interpretation of metabolomics data. 2017. Current Pharmacological Reports. (In Press)

Tang Y, Joyner CJ, Cabrera-Mora M, Lapp SA, Nural MV, Pakala SB, DeBarry JD, Soderberg S, the MaHPIC consortium, Kissinger JC, Lamb TJ, Galinski MR, Styczynski MP.  Integrative analysis associates monocytes with insufficient erythropoiesis during acute Plasmodium cynomolgi malaria in rhesus macaques. 2017. Malaria Journal (In Press)

Gardinassi LG, Cordy RJ, Lacerda MVG, Salinas JL, Monteiro WM, Melo GC, Siqueira AM, Val FF, Tran V, Jones DP, Galinski MR, Li S.  Metabolome-Wide Association Study of Peripheral Parasitemia in Plasmodium vivax Malaria.  2017. International Journal of Medical Microbiology (In Press)

Fonseca LL, Joyner CJ, MaHPIC Consortium, Galinski MR, Voit EO.  A model of Plasmodium vivax concealment based on Plasmodium cynomolgi infections in Macaca mulatta.  2017. Malaria Journal (In Press)

Anderson DC, Lapp SA, Barnwell JW, Galinski MR.  A Large Scale Plasmodium vivax-Saimiri boliviensis Trophozoite-schizont Transition Proteome.  2017.  PLOS ONE. 2017 Aug 22;12(8):e0182561.  doi: 10.1371/journal.pone.0182561. PubMed Central PMID: 28829774.   

Uppal K, Salinas JL, Monteiro WM, Val F, Cordy RJ, Liu K, Melo GC, Siqueira AM, Magalhaes B, MaHPIC Consortium, Galinski MR, Lacerda MVG, Jones DP. Plasma metabolomics reveals membrane lipids, aspartate/asparagine and nucleotide metabolism pathway differences associated with chloroquine resistance in Plasmodium vivax malaria.  PLoS One.  2017 Aug 16. doi: 10.1371/journal.pone.0182819. PubMed Central PMID: 28813452.

Lapp SA, Geraldo JA, Chien JT, Ay F, Pakala SB, Batugendra G, Humphrey J, MaHPIC consortium, DeBarry JD, Le Roch KG, Galinski MR, Kissinger JC.  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. Epub ahead of print. PubMed Central PMID: 28720171.

Galinski MR, Lapp SA, Peterson MS, Ay F, Joyner CJ, Le Roch KG, Fonseca LL, Voit EO, MaHPIC consortium.  Plasmodium knowlesi: A superb in vivo nonhuman primate model of antigenic variation in malaria.  Parasitology.  2017 Jul 17:1-16. doi: 10.1017/S0031182017001135. Epub ahead of print. PMID: 28712361.

Joyner C, the MaHPIC Consortium, Wood JS, Moreno A, Garcia A, Galinski MR. Severe and Complicated Cynomolgi Malaria in a Rhesus Macaque Resulted in Similar Histopathological Changes as Those Seen in Human Malaria.  American Journal of Tropical Medicine and Hygiene.  2017 Jun 5. doi:10.4269/ajtmh.16-0742.

Voit EO. The Best Models of Metabolism. WIREs Systems Biology.  2017 May 19.  doi: 10.1002/wsbm.1391.

Faraji M, Voit EO. Nonparametric dynamic modeling.  Math Biosci. 2017 May. Epub 2016 Aug 30. pii: S0025-5564(16)30113-4. doi: 10.1016/j.mbs.2016.08.004.  PubMed PMID: 27590775.

Qi Z, Roback JD, Voit EO.  Effects of Storage Time on Glycolysis in Donated Human Blood Units. Metabolites. 2017 Mar 29;7(2). pii: E12. doi: 10.3390/metabo7020012. PubMed PMID: 28353627.

Faraji M, Voit EO.  Stepwise Inference of Likely Dynamic Flux Distributions from Metabolic Time Series Data. Bioinformatics.  2017 Mar 7. doi: 10.1093/bioinformatics/btx126.  Epub ahead of print.  PubMed PMID: 28334199.

Qi Z, Voit EO. Inference of cancer mechanisms through computational systems analysis. Mol Biosyst. 2017 Feb 28; 13(3): 489-497. doi: 10.1039/c6mb00672h. PubMed PMID: 28112324; PubMed Central PMCID: PMC5330810.

Uppal K, Walker DI, Jones DP. xMSannotator: An R Package for Network-Based Annotation of High-Resolution Metabolomics Data. Anal Chem.  2017 Jan 17; 89(2): 1063-1067. doi: 10.1021/acs.analchem.6b01214.  Epub 2017 Jan 4.  PubMed PMID 27977166.

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 infectionsMalar J. 2016 Sep 2;15(1):451. doi: 10.1186/s12936-016-1480-6. PubMed PMID: 27590312; PubMed Central PMCID: PMC5010691.

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. PubMed PMID: 27587810; PubMed Central PMCID: PMC5009967.

Fonseca LL, Alezi HS, Moreno A, Barnwell JW, Galinski MR, Voit EO.  Quantifying the removal of red blood cells in Macaca mulatta during a Plasmodium coatneyi infection. Malar J. 2016 Aug 12;15(1):410. doi: 10.1186/s12936-016-1465-5. PubMed PMID: 27520455; PubMed Central PMCID: PMC4983012.

Yan Y, Adam B, Galinski MR, Kissinger JC, Moreno A, Gutierrez JB. Mathematical model of susceptibility, resistance, and resilience in the within-host dynamics between a Plasmodium parasite and the immune system. Math Biosci. 2015 Dec;270(Pt B):213-23. doi: 10.1016/j.mbs. 2015.10.003. Epub 2015 Oct 23. PubMed PMID: 26505135.

Gutierrez JB, Galinski MR, Cantrell S, Voit EO.  From within host dynamics to the epidemiology of infectious disease: Scientific overview and challenges.  Math Biosci.  2015. doi: 10.1016/j.mbs.2015.10.002. Epub 2015 Oct 16.

Fonseca LL, Voit EO: Comparison of mathematical frameworks for modeling erythropoiesis in the context of malaria infection.  Math Biosci.2015 Dec;270(Pt B):224-36. doi:10.1016/j.mbs.2015.08.020.  Epub 2015 Sep 8.  PubMed PMID: 26362230; PubMed Central PMCID: PMC4679698.

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 Dec. doi: 10.1016/j.mbs.2015.06.006. Epub 2015 Jun 17.  PubMed PMID: 26093035; PubMed Central PMCID: PMC4679518.

Li S, Todor A, Luo R. Blood transcriptomics and metabolomics for personalized medicine. Comput Struct Biotechnol J. 2015 Oct 31;14:1-7. doi: 10.1016/j.csbj.2015.10.005.  PubMed PMID: 26702339; PubMed Central PMCID: PMC4669660.

Yin W, Garimalla S, Moreno A, Galinski MR, Styczynski MP.  A tree-like Bayesian structure learning algorithm for small-sample datasets from complex biological model systems.  BMC Systems Biology.  2015 Aug 28. doi:10.1186/s12918-015-0194-7.  PubMed PMID: 26310492; PubMed Central PMCID: PMC4551520. 

Moreno A, Joyner C.  Malaria vaccine clinical trials: what's on the horizon.  Current Opin Immunol.  2015 Aug.  doi:10.1016/j.coi.2015.06.008.  Epub 2015 Jul 13.  PubMed PMID: 26172291; PubMed Central PMCID: PMC4553069.

Uppal K, Soltow QA, Promislow DE, Wachtman LM, Quyyumi AA, Jones DP.  MetabNet: An R Package for Metabolic Association Analysis of High-Resolution Metabolomics Data.  Front Bioeng Biotechnol 2015 Jun 11. doi: 10.3389/fbioe.2015.00087. PubMed PMID: 26125020; PubMed Central PMCID: PMC4464066.

Joyner C, Barnwell JW, Galinski MR. No more monkeying around: primate malaria model systems are key to understanding Plasmodium vivax liver-stage biology, hypnozoites, and relapses.Front Microbiol 2015, 6:145. doi:10.3389/fmicb.2015.00145. 

Lapp SA, Mok S, Zhu L, Wu H, Preiser PR, Bozdech Z, Galinski MR.  Plasmodium knowlesi gene expression differs in ex vivo compared to in vitro blood-stage cultures.  Malar J.  2015 Mar 13; 14:110. doi:10.1186/s12936-015-0612-8. PubMed PMID: 25880967; PubMed Central PMCID: PMC4369371.

Anderson DC, Lapp SA, Akinyi S, Meyer EVS, Barnwell JW, Korir-Morrison C, Galinski MR.  Plasmodium vivax trophozoite-stage proteomes.  J Proteomics.  2015 Feb 6; 115:157–176. doi:10.1016/j.jprot.2014.12.010.  Epub 2014 Dec 27.  PubMed PMID: 25545414; PubMed Central PMCID: PMC4436379.

Lee KJ, Yin W, Arafat D, Tang Y, Uppal K, Tran V, Cabrera-Mora M, Lapp S, Moreno A, Meyer E, DeBarry JD, Pakala S, Nayak V, Kissinger JC, Jones DP, Galinski MR, Styczynski MP, Gibson G.  Comparative transcriptomics and metabolomics in a rhesus macaque drug administration study Front Cell Dev Biol.  2014 Oct 8; 2:54. doi:10.3389/fcell.2014.00054. PubMed PMID: 25453034; PubMed Central PMCID: PMC4233942.

Salinas JL, Kissinger JC, Jones DP, Galinski MR.  Metabolomics in the fight against malaria.  Mem Inst Oswaldo Cruz.  2014 Aug; 109:589–597. doi: 10.1590/0074-0276140043. PubMed PMID: 25185001; PubMed Central PMCID: PMC4156452.

Lapp SA, Korir-Morrison C, Jiang J, Bai Y, Corredor V, Galinski MR.  Spleen-dependent regulation of antigenic variation in malaria parasites: Plasmodium knowlesi SICAvar expression profiles in splenic and asplenic hosts.  PLoS ONE.  2013 Oct 18; 8(10):e78014. doi:10.1371/journal.pone.0078014.  PubMed PMID: 24205067; PubMed Central PMCID: PMC3799730.

Submitted for Publication 2017:

Kissinger JC, DeBarry JD, Nural MN, Pakala SB, Humphrey JC, Meyer EV, Cordy RJ, Cabrera-Mora M, Trippe ED, Aguilar JB, Karpuzoglu E, Yan YH, Brady JA, Hankus AN, Lackman N, Gingle AR, Nayak V, Moreno A, Joyner CJ, Gutierrez JB, Galinski MR, and the MaHPIC Consortium. 10 Simple rules for supporting a systems biology cyberinfrastructure

Gardinassi LG, Arevalo-Herrera M, Herrera S, Cordy RJ, Tran V, Smith MR, Johnson MS, Chacko B, Liu KH, Darley-Usmar VM, Go YM, MaHPIC consortium, Jones DP, Galinski MR, Li S.  Molecular signatures of clinical tolerance to Plasmodium vivax revealed by integrative metabolomics and transcriptomics.

Taghavian O, Jain A, Joyner CJ, Ketchum S, Nakajima R, Jasinskas A, Liang L, Fong R, King C, Greenhouse B, Murphy M, Bailey J, Galinski MR, Barnwell JW, Plowe CV, Davies DH, Felgner PL.  Antibody profiling by proteome microarray with multiplex isotype detection reveals overlap between human and Aotus nancymaae controlled malaria infections. 

Tang Y, Gupta A, Garimalla S, the MaHPIC consortium, Galinski MR, Styczynski MP, Fonseca LL, Voit EO.  Metabolic Modeling Helps Interpret Transcriptomic changes during a Complex Disease.

Trippe ED, Aguilar JB, Yan YH, Nural MV, Brady JA, Assefi M, Safaei S, Allahyari M, Pouriyeh S, Galinski MR, Kissinger JC, Gutierrez JB.  A Vision for Health Informatics: Introducing the SKED Framework.

Allahyari M, Pouriyeh S, Assefi M, Safaei S, Trippe ED, Gutierrez JB, Kochut K.  A Brief Survey of Text Mining: Classification, Clustering and Extraction Techniques.

Chien JT, Tseng C, Gutierrez JB, Galinski MR.  Applying Data Science in Malaria Research: From Infections and Disease, to Knowledge and Insights.

Uppal K, Go YM, Jones DP.  xMWAS: an R package for data-driven integration and differential network analysis.  

Aguilar JB, Gutierrez JB.  An Epidemiological Model of Malaria Accounting for Asymptomatic Carriers.  

Yan YH, Trippe ED, Gutierrez JB.  A Method for Massively Parallel Analysis of Time Series.  

Coming Soon:

Cordy RJ et al.  Global metabolic profiles differentiate acute and chronic malaria in rhesus macaques and humans.

Tang Y et al.  Multi-omics Characterization, Integration, and Analysis of Malaria Infection in a Non-Human Primate Model.