| Influenza virus-host interactome screen as a platform for antiviral drug development T Watanabe, E Kawakami, JE Shoemaker, TJS Lopes, Y Matsuoka, ... Cell host & microbe 16 (6), 795-805, 2014 | 279 | 2014 |
| Control theory and systems biology PA Iglesias, BP Ingalls MIT press, 2010 | 220 | 2010 |
| A comprehensive map of the influenza A virus replication cycle Y Matsuoka, H Matsumae, M Katoh, AJ Eisfeld, G Neumann, T Hase, ... BMC systems biology 7, 1-18, 2013 | 164 | 2013 |
| CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data JE Shoemaker, TJS Lopes, S Ghosh, Y Matsuoka, Y Kawaoka, H Kitano BMC genomics 13, 1-11, 2012 | 126 | 2012 |
| Multi-spectral fluorescent reporter influenza viruses (Color-flu) as powerful tools for in vivo studies S Fukuyama, H Katsura, D Zhao, M Ozawa, T Ando, JE Shoemaker, ... Nature communications 6 (1), 6600, 2015 | 105 | 2015 |
| Adding protein context to the human protein-protein interaction network to reveal meaningful interactions MH Schaefer, TJS Lopes, N Mah, JE Shoemaker, Y Matsuoka, ... PLoS computational biology 9 (1), e1002860, 2013 | 100 | 2013 |
| COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms M Ostaszewski, A Niarakis, A Mazein, I Kuperstein, R Phair, ... Molecular systems biology 17 (10), e10387, 2021 | 80 | 2021 |
| Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases TJS Lopes, M Schaefer, J Shoemaker, Y Matsuoka, JF Fontaine, ... Bioinformatics 27 (17), 2414-2421, 2011 | 70 | 2011 |
| 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 … Y Muramoto, JE Shoemaker, MQ Le, Y Itoh, D Tamura, Y Sakai-Tagawa, ... Journal of virology 88 (16), 8981-8997, 2014 | 55 | 2014 |
| Iterative community-driven development of a SARS-CoV-2 tissue simulator M Getz, Y Wang, G An, M Asthana, A Becker, C Cockrell, N Collier, ... BioRxiv, 2020.04. 02.019075, 2020 | 52 | 2020 |
| Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection H Noh, JE Shoemaker, R Gunawan Nucleic acids research 46 (6), e34-e34, 2018 | 43 | 2018 |
| An ultrasensitive mechanism regulates influenza virus-induced inflammation JE Shoemaker, S Fukuyama, AJ Eisfeld, D Zhao, E Kawakami, S Sakabe, ... PLoS pathogens 11 (6), e1004856, 2015 | 42 | 2015 |
| Chemical hazard prediction and hypothesis testing using quantitative adverse outcome pathways EJ Perkins, K Gayen, JE Shoemaker, P Antczak, L Burgoon, F Falciani, ... Alternatives to animal experimentation 36 (1), 91-102, 2019 | 39 | 2019 |
| Identifying fragilities in biochemical networks: robust performance analysis of Fas signaling-induced apoptosis JE Shoemaker, FJ Doyle Biophysical Journal 95 (6), 2610-2623, 2008 | 34 | 2008 |
| Fathead minnow steroidogenesis: in silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk JE Shoemaker, K Gayen, N Garcia-Reyero, EJ Perkins, DL Villeneuve, ... BMC systems biology 4, 1-17, 2010 | 29 | 2010 |
| C646, a novel p300/CREB-binding protein-specific inhibitor of histone acetyltransferase, attenuates influenza A virus infection D Zhao, S Fukuyama, Y Sakai-Tagawa, E Takashita, JE Shoemaker, ... Antimicrobial agents and chemotherapy 60 (3), 1902-1906, 2016 | 28 | 2016 |
| Network-guided discovery of influenza virus replication host factors EE Ackerman, E Kawakami, M Katoh, T Watanabe, S Watanabe, Y Tomita, ... MBio 9 (6), 10.1128/mbio. 02002-18, 2018 | 26 | 2018 |
| Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs JE Shoemaker, S Fukuyama, AJ Eisfeld, Y Muramoto, S Watanabe, ... BMC systems biology 6, 1-14, 2012 | 26 | 2012 |
| Confidence from uncertainty-A multi-target drug screening method from robust control theory C Luni, JE Shoemaker, KR Sanft, LR Petzold, FJ Doyle BMC systems biology 4, 1-10, 2010 | 21 | 2010 |
| The dynamics of single-substrate continuous cultures: the role of transport enzymes J Shoemaker, GT Reeves, S Gupta, SS Pilyugin, T Egli, A Narang Journal of theoretical biology 222 (3), 307-322, 2003 | 21 | 2003 |
