PhD, Chemical Engineering, University of California
BS, Chemical Engineering, University of Florida
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-BASEL, 14(5), 906.MDPI AG. 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. PLOS COMPUTATIONAL BIOLOGY, 17(10), e1008874.Public Library of Science (PLoS). doi: 10.1371/journal.pcbi.1008874.
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.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 IFN beta production. 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 plus : elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks. BMC BIOINFORMATICS, 22(1), 108.Springer Science and Business Media LLC. 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., Gomez, L.C.M., Somers, J., Hoch, M., Gupta, S.K., Scheel, J., Borlinghaus, H., Czauderna, T., Schreiber, F., Montagud, A., de Leon, M.P., Funahashi, A., Hiki, Y., Hiroi, N., Yamada, T.G., Draeger, A., Renz, A., Naveez, M., Bocskei, Z., Messina, F., Boernigen, 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., Ribeiro, A.S., 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., Groues, 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., Pena-Chilet, M., Rian, K., Helikar, T., Puniya, B.L., Modos, D., Treveil, A., Olbei, M., De Meulder, B., Ballereau, S., Dugourd, A., Naldi, A., Noel, V., Calzone, L., Sander, C., Demir, E., Korcsmaros, T., Freeman, T.C., Auge, 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., & Community, C.D.M. (2021). COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. MOLECULAR SYSTEMS BIOLOGY, 17(10), e10387.EMBO. 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-BASEL, 12(10), 1087.MDPI AG. doi: 10.3390/v12101087.
Fukuyama, S., Iwatsuki-Horimoto, K., Kiso, M., Nakajima, N., Gregg, R.W., Katsura, H., Tomita, Y., Maemura, T., Lopes, T.J.D.S., Watanabe, T., Shoemaker, J.E., Hasegawa, H., Yamayoshi, S., & Kawaoka, Y. (2020). Pathogenesis of Influenza A(H7N9) Virus in Aged Nonhuman Primates. JOURNAL OF INFECTIOUS DISEASES, 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. INTERNATIONAL IMMUNOLOGY, 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. BIOPHYSICAL JOURNAL, 119(11), 2290-2298.Elsevier BV. 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 AG. 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 Science and Business Media LLC. 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. JOURNAL OF THEORETICAL BIOLOGY, 462, 148-157.Elsevier BV. 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., III, D.F.J., & Garcia-Reyero, N. (2019). Chemical Hazard Prediction and Hypothesis Testing Using Quantitative Adverse Outcome Pathways. ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION, 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 AG. 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. MBIO, 9(6), 1-14.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 BV. 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 AG. 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 RESEARCH, 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 BV. doi: 10.1016/j.ifacol.2018.09.005.
Zhao, D., Fukuyama, S., Sakai-Tagawa, Y., Takashita, E., Shoemaker, J.E., & Kawaoka, Y. (2016). C646, a Novel p300/CREB-Binding Protein-Specific Inhibitor of Histone Acetyltransferase, Attenuates Influenza A Virus Infection. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 60(3), 1902-1906.American Society for Microbiology. doi: 10.1128/AAC.02055-15.
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. NATURE COMMUNICATIONS, 6(1), 6600.Springer Science and Business Media LLC. 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. FRONTIERS IN PHARMACOLOGY, 6, 186.Frontiers Media SA. 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. PLOS PATHOGENS, 11(6), e1004856.Public Library of Science (PLoS). doi: 10.1371/journal.ppat.1004856.
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. JOURNAL OF VIROLOGY, 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 BV. 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 SYSTEMS BIOLOGY, 7(1), 97.Springer Science and Business Media LLC. 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. PLOS COMPUTATIONAL BIOLOGY, 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 SYSTEMS BIOLOGY, 6(1), 117.Springer Science and Business Media LLC. 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 Science and Business Media LLC. 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., & III, D.F.J. (2010). Confidence from uncertainty - A multi-target drug screening method from robust control theory. BMC SYSTEMS BIOLOGY, 4(1), 161.Springer Science and Business Media LLC. doi: 10.1186/1752-0509-4-161.
Shoemaker, J.E., Gayen, K., Garcia-Reyero, N., Perkins, E.J., Villeneuve, D.L., Liu, L., & III, D.F.J. (2010). Fathead minnow steroidogenesis: in silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk. BMC SYSTEMS BIOLOGY, 4(1), 89.Springer Science and Business Media LLC. doi: 10.1186/1752-0509-4-89.
Shoemaker, J.E., & III, D.F.J. (2008). Identifying fragilities in biochemical networks: Robust performance analysis of Fas signaling-induced apoptosis. BIOPHYSICAL JOURNAL, 95(6), 2610-2623.Elsevier BV. 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. JOURNAL OF THEORETICAL BIOLOGY, 222(3), 307-322.Elsevier BV. doi: 10.1016/S0022-5193(03)00036-5.
Aponte-Serrano, J.O., Weaver, J.J.A., Sego, T.J., Glazier, J.A., & Shoemaker, J.E. Multicellular Spatial Model of RNA Virus Replication and Interferon Responses Reveals Factors Controlling Plaque Growth Dynamics. Cold Spring Harbor Laboratory. doi: 10.1101/2021.03.16.435618.
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 BV. doi: 10.1016/j.ifacol.2019.12.243.