PhD, Chemical Engineering, University of California
BS, Chemical Engineering, University of Florida
Larkin, C.I., Dunn, M.D., Shoemaker, J.E., Klimstra, W.B., & Faeder, J.R. (2025). A detailed kinetic model of Eastern equine encephalitis virus replication in a susceptible host cell. In Antia, R. (Ed.). PLoS Comput Biol, 21(6), e1013082.Public Library of Science (PLoS). doi: 10.1371/journal.pcbi.1013082.
Larkin, C.I., Dunn, M.D., Shoemaker, J.E., Klimstra, W.B., & Faeder, J.R. (2024). A detailed kinetic model of Eastern equine encephalitis virus replication in a susceptible host cell. In bioRxiv. doi: 10.1101/2024.12.13.628424.
Liparulo, T.S., & Shoemaker, J.E. (2024). Mathematical Modeling Suggests That Monocyte Activity May Drive Sex Disparities during Influenza Infection. Viruses, 16(6), 837.MDPI. doi: 10.3390/v16060837.
Luciani, L.L., Miller, L.M., Zhai, B., Clarke, K., Hughes Kramer, K., Schratz, L.J., Balasubramani, G.K., Dauer, K., Nowalk, M.P., Zimmerman, R.K., Shoemaker, J.E., & Alcorn, J.F. (2023). Blood Inflammatory Biomarkers Differentiate Inpatient and Outpatient Coronavirus Disease 2019 From Influenza. Open Forum Infect Dis, 10(3), ofad095.Oxford University Press (OUP). doi: 10.1093/ofid/ofad095.
Ackerman, E.E., Weaver, J.J.A., & Shoemaker, J.E. (2022). Mathematical Modeling Finds Disparate Interferon Production Rates Drive Strain-Specific Immunodynamics during Deadly Influenza Infection. Viruses, 14(5), 906.MDPI. doi: 10.3390/v14050906.
Aponte-Serrano, J.O., Weaver, J.J.A., Sego, T.J., Glazier, J.A., & Shoemaker, J.E. (2021). Multicellular spatial model of RNA virus replication and interferon responses reveals factors controlling plaque growth dynamics. In Kosakovsky Pond, S.L. (Ed.). PLoS Comput Biol, 17(10), e1008874.Public Library of Science (PLoS). doi: 10.1371/journal.pcbi.1008874.
Aponte-Serrano, J.O., Weaver, J.J.A., Sego, T.J., Glazier, J.A., & Shoemaker, J.E. (2021). Multicellular Spatial Model of RNA Virus Replication and Interferon Responses Reveals Factors Controlling Plaque Growth Dynamics. 2021.03.16.435618.Cold Spring Harbor Laboratory. doi: 10.1101/2021.03.16.435618.
Getz, M., Wang, Y., An, G., Asthana, M., Becker, A., Cockrell, C., Collier, N., Craig, M., Davis, C.L., Faeder, J.R., Ford Versypt, A.N., Mapder, T., Gianlupi, J.F., Glazier, J.A., Hamis, S., Heiland, R., Hillen, T., Hou, D., Islam, M.A., Jenner, A.L., Kurtoglu, F., Larkin, C.I., Liu, B., Macfarlane, F., Maygrundter, P., Morel, P.A., Narayanan, A., Ozik, J., Pienaar, E., Rangamani, P., Saglam, A.S., Shoemaker, J.E., Smith, A.M., Weaver, J.J.A., & Macklin, P. (2021). Iterative community-driven development of a SARS-CoV-2 tissue simulator. bioRxiv, 2020.04.02.019075.Cold Spring Harbor Laboratory. doi: 10.1101/2020.04.02.019075.
Gregg, R.W., Shabnam, F., & Shoemaker, J.E. (2021). Agent-based modeling reveals benefits of heterogeneous and stochastic cell populations during cGAS-mediated IFNβ production. In Pier Luigi, M. (Ed.). Bioinformatics, 37(10), 1428-1434.Oxford University Press (OUP). doi: 10.1093/bioinformatics/btaa969.
Noh, H., Hua, Z., Chrysinas, P., Shoemaker, J.E., & Gunawan, R. (2021). DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks. BMC Bioinformatics, 22(1), 108.Springer Nature. doi: 10.1186/s12859-021-04046-2.
Ostaszewski, M., Niarakis, A., Mazein, A., Kuperstein, I., Phair, R., Orta-Resendiz, A., Singh, V., Aghamiri, S.S., Acencio, M.L., Glaab, E., Ruepp, A., Fobo, G., Montrone, C., Brauner, B., Frishman, G., Monraz Gómez, L.C., Somers, J., Hoch, M., Kumar Gupta, S., Scheel, J., Borlinghaus, H., Czauderna, T., Schreiber, F., Montagud, A., Ponce de Leon, M., Funahashi, A., Hiki, Y., Hiroi, N., Yamada, T.G., Dräger, A., Renz, A., Naveez, M., Bocskei, Z., Messina, F., Börnigen, D., Fergusson, L., Conti, M., Rameil, M., Nakonecnij, V., Vanhoefer, J., Schmiester, L., Wang, M., Ackerman, E.E., Shoemaker, J.E., Zucker, J., Oxford, K., Teuton, J., Kocakaya, E., Summak, G.Y., Hanspers, K., Kutmon, M., Coort, S., Eijssen, L., Ehrhart, F., Rex, D.A.B., Slenter, D., Martens, M., Pham, N., Haw, R., Jassal, B., Matthews, L., Orlic-Milacic, M., Senff Ribeiro, A., Rothfels, K., Shamovsky, V., Stephan, R., Sevilla, C., Varusai, T., Ravel, J.M., Fraser, R., Ortseifen, V., Marchesi, S., Gawron, P., Smula, E., Heirendt, L., Satagopam, V., Wu, G., Riutta, A., Golebiewski, M., Owen, S., Goble, C., Hu, X., Overall, R.W., Maier, D., Bauch, A., Gyori, B.M., Bachman, J.A., Vega, C., Grouès, V., Vazquez, M., Porras, P., Licata, L., Iannuccelli, M., Sacco, F., Nesterova, A., Yuryev, A., de Waard, A., Turei, D., Luna, A., Babur, O., Soliman, S., Valdeolivas, A., Esteban-Medina, M., Peña-Chilet, M., Rian, K., Helikar, T., Puniya, B.L., Modos, D., Treveil, A., Olbei, M., De Meulder, B., Ballereau, S., Dugourd, A., Naldi, A., Noël, V., Calzone, L., Sander, C., Demir, E., Korcsmaros, T., Freeman, T.C., Augé, F., Beckmann, J.S., Hasenauer, J., Wolkenhauer, O., Wilighagen, E.L., Pico, A.R., Evelo, C.T., Gillespie, M.E., Stein, L.D., Hermjakob, H., D'Eustachio, P., Saez-Rodriguez, J., Dopazo, J., Valencia, A., Kitano, H., Barillot, E., Auffray, C., Balling, R., Schneider, R., & COVID-19 Disease Map Community. (2021). COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol, 17(10), e10387.Springer Nature. doi: 10.15252/msb.202110387.
Ackerman, E.E., & Shoemaker, J.E. (2020). Network Controllability-Based Prioritization of Candidates for SARS-CoV-2 Drug Repositioning. Viruses, 12(10), 1087.MDPI. doi: 10.3390/v12101087.
Fukuyama, S., Iwatsuki-Horimoto, K., Kiso, M., Nakajima, N., Gregg, R.W., Katsura, H., Tomita, Y., Maemura, T., da Silva Lopes, T.J., Watanabe, T., Shoemaker, J.E., Hasegawa, H., Yamayoshi, S., & Kawaoka, Y. (2020). Pathogenesis of Influenza A(H7N9) Virus in Aged Nonhuman Primates. J Infect Dis, 222(7), 1155-1164.Oxford University Press (OUP). doi: 10.1093/infdis/jiaa267.
Liou, J.J., Shoemaker, J.E., & Vande Geest, J.P. (2020). Mechanobiology of the Optic Nerve Head in Primary Open-Angle Glaucoma. In Mechanobiology. (pp. 47-64).Elsevier. doi: 10.1016/b978-0-12-817931-4.00003-0.
Sato, R., Makino-Okamura, C., Lin, Q., Wang, M., Shoemaker, J.E., Kurosaki, T., & Fukuyama, H. (2020). Repurposing the psoriasis drug Oxarol to an ointment adjuvant for the influenza vaccine. Int Immunol, 32(8), 499-507.Oxford University Press (OUP). doi: 10.1093/intimm/dxaa012.
Wang, M., Luciani, L.L., Noh, H., Mochan, E., & Shoemaker, J.E. (2020). TREAP: A New Topological Approach to Drug Target Inference. Biophys J, 119(11), 2290-2298.Elsevier. doi: 10.1016/j.bpj.2020.10.021.
Weaver, J.J.A., & Shoemaker, J.E. (2020). Mathematical Modeling of RNA Virus Sensing Pathways Reveals Paracrine Signaling as the Primary Factor Regulating Excessive Cytokine Production. PROCESSES, 8(6), 719.MDPI. doi: 10.3390/pr8060719.
Ackerman, E.E., Alcorn, J.F., Hase, T., & Shoemaker, J.E. (2019). A dual controllability analysis of influenza virus-host protein-protein interaction networks for antiviral drug target discovery. BMC Bioinformatics, 20(1), 297.Springer Nature. doi: 10.1186/s12859-019-2917-z.
Gregg, R.W., Sarkar, S.N., & Shoemaker, J.E. (2019). Mathematical modeling of the cGAS pathway reveals robustness of DNA sensing to TREX1 feedback. J Theor Biol, 462, 148-157.Elsevier. doi: 10.1016/j.jtbi.2018.11.001.
Perkins, E.J., Gayen, K., Shoemaker, J.E., Antczak, P., Burgoon, L., Falciani, F., Gutsell, S., Hodges, G., Kienzler, A., Knapen, D., McBride, M., Willett, C., Doyle, F.J., & Garcia-Reyero, N. (2019). Chemical hazard prediction and hypothesis testing using quantitative adverse outcome pathways. ALTEX, 36(1), 91-102.ALTEX Edition. doi: 10.14573/altex.1808241.
Wang, M., Fukuyama, S., Kawaoka, Y., & Shoemaker, J.E. (2019). Predicting Host Immune Cell Dynamics and Key Disease-Associated Genes Using Tissue Transcriptional Profiles. PROCESSES, 7(5), 301.MDPI. doi: 10.3390/pr7050301.
Ackerman, E.E., Kawakami, E., Katoh, M., Watanabe, T., Watanabe, S., Tomita, Y., Lopes, T.J., Matsuoka, Y., Kitano, H., Shoemaker, J.E., & Kawaoka, Y. (2018). Network-Guided Discovery of Influenza Virus Replication Host Factors. In Bloom, J.D., & Harwood, C.S. (Eds.). mBio, 9(6), 10.1128/mbio.02002-10.1128/mbio.02018.American Society for Microbiology. doi: 10.1128/mBio.02002-18.
Gregg, R.W., Sarkar, S., & Shoemaker, J.E. (2018). Examining Dynamic Emergent Properties of the DNA Sensing Pathway. IFAC-PapersOnLine, 51(19), 112-113.Elsevier. doi: 10.1016/j.ifacol.2018.09.017.
Mochan, E., Ackerman, E.E., & Shoemaker, J.E. (2018). A Systems and Treatment Perspective of Models of Influenza Virus-Induced Host Responses. PROCESSES, 6(9), 138.MDPI. doi: 10.3390/pr6090138.
Noh, H., Shoemaker, J.E., & Gunawan, R. (2018). Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection. Nucleic Acids Res, 46(6), e34.Oxford University Press (OUP). doi: 10.1093/nar/gkx1314.
Wang, M., Fukuyama, S., Kawaoka, Y., & Shoemaker, J.E. (2018). Predicting host immune cell dynamics using tissue gene expression. IFAC-PapersOnLine, 51(19), 5-6.Elsevier. doi: 10.1016/j.ifacol.2018.09.005.
Fukuyama, S., Katsura, H., Zhao, D., Ozawa, M., Ando, T., Shoemaker, J.E., Ishikawa, I., Yamada, S., Neumann, G., Watanabe, S., Kitano, H., & Kawaoka, Y. (2015). Multi-spectral fluorescent reporter influenza viruses (Color-flu) as powerful tools for in vivo studies. Nat Commun, 6(1), 6600.Springer Nature. doi: 10.1038/ncomms7600.
Lopes, T.J.S., Shoemaker, J.E., Matsuoka, Y., Kawaoka, Y., & Kitano, H. (2015). Identifying problematic drugs based on the characteristics of their targets. Front Pharmacol, 6, 186.Frontiers. doi: 10.3389/fphar.2015.00186.
Shoemaker, J.E., Fukuyama, S., Eisfeld, A.J., Zhao, D., Kawakami, E., Sakabe, S., Maemura, T., Gorai, T., Katsura, H., Muramoto, Y., Watanabe, S., Watanabe, T., Fuji, K., Matsuoka, Y., Kitano, H., & Kawaoka, Y. (2015). An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation. In Whelan, S. (Ed.). PLoS Pathog, 11(6), e1004856.Public Library of Science (PLoS). doi: 10.1371/journal.ppat.1004856.
Zhao, D., Fukuyama, S., Sakai-Tagawa, Y., Takashita, E., Shoemaker, J.E., & Kawaoka, Y. (2015). C646, a Novel p300/CREB-Binding Protein-Specific Inhibitor of Histone Acetyltransferase, Attenuates Influenza A Virus Infection. Antimicrob Agents Chemother, 60(3), 1902-1906.American Society for Microbiology. doi: 10.1128/AAC.02055-15.
Muramoto, Y., Shoemaker, J.E., Le, M.Q., Itoh, Y., Tamura, D., Sakai-Tagawa, Y., Imai, H., Uraki, R., Takano, R., Kawakami, E., Ito, M., Okamoto, K., Ishigaki, H., Mimuro, H., Sasakawa, C., Matsuoka, Y., Noda, T., Fukuyama, S., Ogasawara, K., Kitano, H., & Kawaoka, Y. (2014). Disease severity is associated with differential gene expression at the early and late phases of infection in nonhuman primates infected with different H5N1 highly pathogenic avian influenza viruses. In Dermody, T.S. (Ed.). J Virol, 88(16), 8981-8997.American Society for Microbiology. doi: 10.1128/JVI.00907-14.
Watanabe, T., Kawakami, E., Shoemaker, J.E., Lopes, T.J.S., Matsuoka, Y., Tomita, Y., Kozuka-Hata, H., Gorai, T., Kuwahara, T., Takeda, E., Nagata, A., Takano, R., Kiso, M., Yamashita, M., Sakai-Tagawa, Y., Katsura, H., Nonaka, N., Fujii, H., Fujii, K., Sugita, Y., Noda, T., Goto, H., Fukuyama, S., Watanabe, S., Neumann, G., Oyama, M., Kitano, H., & Kawaoka, Y. (2014). Influenza virus-host interactome screen as a platform for antiviral drug development. Cell Host Microbe, 16(6), 795-805.Elsevier. doi: 10.1016/j.chom.2014.11.002.
Matsuoka, Y., Matsumae, H., Katoh, M., Eisfeld, A.J., Neumann, G., Hase, T., Ghosh, S., Shoemaker, J.E., Lopes, T.J.S., Watanabe, T., Watanabe, S., Fukuyama, S., Kitano, H., & Kawaoka, Y. (2013). A comprehensive map of the influenza A virus replication cycle. BMC Syst Biol, 7(1), 97.Springer Nature. doi: 10.1186/1752-0509-7-97.
Schaefer, M.H., Lopes, T.J.S., Mah, N., Shoemaker, J.E., Matsuoka, Y., Fontaine, J.F., Louis-Jeune, C., Eisfeld, A.J., Neumann, G., Perez-Iratxeta, C., Kawaoka, Y., Kitano, H., & Andrade-Navarro, M.A. (2013). Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. In Rzhetsky, A. (Ed.). PLoS Comput Biol, 9(1), e1002860.Public Library of Science (PLoS). doi: 10.1371/journal.pcbi.1002860.
Shoemaker, J.E., Fukuyama, S., Eisfeld, A.J., Muramoto, Y., Watanabe, S., Watanabe, T., Matsuoka, Y., Kitano, H., & Kawaoka, Y. (2012). Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs. BMC Syst Biol, 6(1), 117.Springer Nature. doi: 10.1186/1752-0509-6-117.
Shoemaker, J.E., Lopes, T.J.S., Ghosh, S., Matsuoka, Y., Kawaoka, Y., & Kitano, H. (2012). CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data. BMC Genomics, 13(1), 460.Springer Nature. doi: 10.1186/1471-2164-13-460.
Lopes, T.J.S., Schaefer, M., Shoemaker, J., Matsuoka, Y., Fontaine, J.F., Neumann, G., Andrade-Navarro, M.A., Kawaoka, Y., & Kitano, H. (2011). Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases. Bioinformatics, 27(17), 2414-2421.Oxford University Press (OUP). doi: 10.1093/bioinformatics/btr414.
Luni, C., Shoemaker, J.E., Sanft, K.R., Petzold, L.R., & Doyle, F.J. (2010). Confidence from uncertainty--a multi-target drug screening method from robust control theory. BMC Syst Biol, 4(1), 161.Springer Nature. doi: 10.1186/1752-0509-4-161.
Shoemaker, J.E., Gayen, K., Garcia-Reyero, N., Perkins, E.J., Villeneuve, D.L., Liu, L., & Doyle, F.J. (2010). Fathead minnow steroidogenesis: in silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk. BMC Syst Biol, 4(1), 89.Springer Nature. doi: 10.1186/1752-0509-4-89.
Shoemaker, J.E., & Doyle, F.J. (2008). Identifying fragilities in biochemical networks: robust performance analysis of Fas signaling-induced apoptosis. Biophys J, 95(6), 2610-2623.Elsevier. doi: 10.1529/biophysj.107.123398.
Shoemaker, J., Reeves, G.T., Gupta, S., Pilyugin, S.S., Egli, T., & Narang, A. (2003). The dynamics of single-substrate continuous cultures: the role of transport enzymes. J Theor Biol, 222(3), 307-322.Elsevier. doi: 10.1016/s0022-5193(03)00036-5.
Ackerman, E.E., Mochan, E., & Shoemaker, J.E. (2019). Strain-Specific Immune Response to Influenza Virus Infection. In IFAC-PapersOnLine, 52(26), (pp. 101-106).Elsevier. doi: 10.1016/j.ifacol.2019.12.243.
Hill, A., Shoemaker, J., Ardila, C., & Vande Geest, J.P. (2018). Differential ECM Related Gene Expression in The Human Lamina Cribrosa in Populations at Increased Risk for Primary Open Angle Glaucoma. In INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE, 59(9).