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Jason E. Shoemaker - Publications

Affiliations: 
chemical engineering University of California, Santa Barbara, Santa Barbara, CA, United States 
 chemical & petroleum engineering University of Pittsburgh, Pittsburgh, PA, United States 
Website:
http://www.shoemakerlab.pitt.edu/
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26 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Noh H, Hua Z, Chrysinas P, Shoemaker JE, Gunawan R. DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks. Bmc Bioinformatics. 22: 108. PMID 33663384 DOI: 10.1186/s12859-021-04046-2  0.528
2020 Ackerman EE, Shoemaker JE. Network Controllability-Based Prioritization of Candidates for SARS-CoV-2 Drug Repositioning. Viruses. 12. PMID 32993136 DOI: 10.3390/v12101087  0.337
2020 Fukuyama S, Iwatsuki-Horimoto K, Kiso M, Nakajima N, Gregg RW, Katsura H, Tomita Y, Maemura T, da Silva Lopes TJ, Watanabe T, Shoemaker JE, Hasegawa H, Yamayoshi S, Kawaoka Y. Pathogenesis of influenza A(H7N9) virus in aged non-human primates. The Journal of Infectious Diseases. PMID 32433769 DOI: 10.1093/Infdis/Jiaa267  0.3
2020 Sato R, Makino-Okamura C, Lin Q, Wang M, Shoemaker J, Kurosaki T, Fukuyama H. Repurposing the Psoriasis Drug Oxarol to an ointment adjuvant for the influenza vaccine. International Immunology. PMID 32060507 DOI: 10.1093/Intimm/Dxaa012  0.313
2019 Ackerman EE, Alcorn JF, Hase T, Shoemaker JE. A dual controllability analysis of influenza virus-host protein-protein interaction networks for antiviral drug target discovery. Bmc Bioinformatics. 20: 297. PMID 31159726 DOI: 10.1186/S12859-019-2917-Z  0.418
2019 Ackerman EE, Mochan E, Shoemaker JE. Strain-Specific Immune Response to Influenza Virus Infection Ifac-Papersonline. 52: 101-106. DOI: 10.1016/J.Ifacol.2019.12.243  0.344
2018 Ackerman EE, Kawakami E, Katoh M, Watanabe T, Watanabe S, Tomita Y, Lopes TJ, Matsuoka Y, Kitano H, Shoemaker JE, Kawaoka Y. Network-Guided Discovery of Influenza Virus Replication Host Factors. Mbio. 9. PMID 30563907 DOI: 10.1128/Mbio.02002-18  0.395
2018 Gregg RW, Sarkar SN, Shoemaker JE. Mathematical Modeling of the cGAS Pathway Reveals Robustness of DNA Sensing to TREX1 Feedback. Journal of Theoretical Biology. PMID 30395807 DOI: 10.1016/J.Jtbi.2018.11.001  0.337
2018 Perkins EJ, Gayen K, Shoemaker JE, Antczak P, Burgoon L, Falciani F, Gutsell S, Hodges G, Kienzler A, Knapen D, McBride M, Willett C, Doyle FJ, Garcia-Reyero N. Chemical hazard prediction and hypothesis testing using quantitative adverse outcome pathways. Altex. PMID 30332685 DOI: 10.14573/Altex.1808241  0.444
2018 Noh H, Shoemaker JE, Gunawan R. Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection. Nucleic Acids Research. PMID 29325153 DOI: 10.1093/Nar/Gkx1314  0.59
2018 Wang M, Fukuyama S, Kawaoka Y, Shoemaker JE. Predicting host immune cell dynamics using tissue gene expression Ifac-Papersonline. 51: 5-6. DOI: 10.1016/J.Ifacol.2018.09.005  0.324
2015 Zhao D, Fukuyama S, Sakai-Tagawa Y, Takashita E, Shoemaker JE, Kawaoka Y. C646, a novel p300/CREB-binding protein-specific inhibitor of histone acetyltransferase, attenuates influenza A virus infection. Antimicrobial Agents and Chemotherapy. PMID 26711748 DOI: 10.1128/Aac.02055-15  0.368
2015 Lopes TJ, Shoemaker JE, Matsuoka Y, Kawaoka Y, Kitano H. Identifying problematic drugs based on the characteristics of their targets. Frontiers in Pharmacology. 6: 186. PMID 26388775 DOI: 10.3389/Fphar.2015.00186  0.355
2015 Shoemaker JE, Fukuyama S, Eisfeld AJ, Zhao D, Kawakami E, Sakabe S, Maemura T, Gorai T, Katsura H, Muramoto Y, Watanabe S, Watanabe T, Fuji K, Matsuoka Y, Kitano H, et al. An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation. Plos Pathogens. 11: e1004856. PMID 26046528 DOI: 10.1371/Journal.Ppat.1004856  0.388
2015 Fukuyama S, Katsura H, Zhao D, Ozawa M, Ando T, Shoemaker JE, Ishikawa I, Yamada S, Neumann G, Watanabe S, Kitano H, Kawaoka Y. Multi-spectral fluorescent reporter influenza viruses (Color-flu) as powerful tools for in vivo studies. Nature Communications. 6: 6600. PMID 25807527 DOI: 10.1038/Ncomms7600  0.355
2014 Watanabe T, Kawakami E, Shoemaker JE, Lopes TJ, Matsuoka Y, Tomita Y, Kozuka-Hata H, Gorai T, Kuwahara T, Takeda E, Nagata A, Takano R, Kiso M, Yamashita M, Sakai-Tagawa Y, et al. Influenza virus-host interactome screen as a platform for antiviral drug development. Cell Host & Microbe. 16: 795-805. PMID 25464832 DOI: 10.1016/J.Chom.2014.11.002  0.383
2014 Muramoto Y, Shoemaker JE, Le MQ, 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, et al. 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: 8981-97. PMID 24899188 DOI: 10.1128/Jvi.00907-14  0.365
2013 Matsuoka Y, Matsumae H, Katoh M, Eisfeld AJ, Neumann G, Hase T, Ghosh S, Shoemaker JE, Lopes TJ, Watanabe T, Watanabe S, Fukuyama S, Kitano H, Kawaoka Y. A comprehensive map of the influenza A virus replication cycle. Bmc Systems Biology. 7: 97. PMID 24088197 DOI: 10.1186/1752-0509-7-97  0.368
2013 Schaefer MH, Lopes TJ, Mah N, Shoemaker JE, Matsuoka Y, Fontaine JF, Louis-Jeune C, Eisfeld AJ, Neumann G, Perez-Iratxeta C, Kawaoka Y, Kitano H, Andrade-Navarro MA. Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. Plos Computational Biology. 9: e1002860. PMID 23300433 DOI: 10.1371/Journal.Pcbi.1002860  0.395
2012 Shoemaker JE, Lopes TJ, Ghosh S, Matsuoka Y, Kawaoka Y, Kitano H. CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data. Bmc Genomics. 13: 460. PMID 22953731 DOI: 10.1186/1471-2164-13-460  0.317
2012 Shoemaker JE, Fukuyama S, Eisfeld AJ, Muramoto Y, Watanabe S, Watanabe T, Matsuoka Y, Kitano H, Kawaoka Y. 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: 117. PMID 22937776 DOI: 10.1186/1752-0509-6-117  0.341
2011 Lopes TJ, Schaefer M, Shoemaker J, Matsuoka Y, Fontaine JF, Neumann G, Andrade-Navarro MA, Kawaoka Y, Kitano H. Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases. Bioinformatics (Oxford, England). 27: 2414-21. PMID 21798963 DOI: 10.1093/Bioinformatics/Btr414  0.325
2010 Luni C, Shoemaker JE, Sanft KR, Petzold LR, Doyle FJ. Confidence from uncertainty--a multi-target drug screening method from robust control theory. Bmc Systems Biology. 4: 161. PMID 21106087 DOI: 10.1186/1752-0509-4-161  0.513
2010 Shoemaker JE, Gayen K, Garcia-Reyero N, Perkins EJ, Villeneuve DL, Liu L, Doyle FJ. Fathead minnow steroidogenesis: in silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk. Bmc Systems Biology. 4: 89. PMID 20579396 DOI: 10.1186/1752-0509-4-89  0.496
2010 Hildebrandt S, Bagheri N, Gunawan R, Mirsky H, Shoemaker J, Taylor S, Petzold L, Doyle FJ. Systems Analysis for Systems Biology Systems Biomedicine. 249-272. DOI: 10.1016/B978-0-12-372550-9.00010-9  0.55
2008 Shoemaker JE, Doyle FJ. Identifying fragilities in biochemical networks: robust performance analysis of Fas signaling-induced apoptosis. Biophysical Journal. 95: 2610-23. PMID 18539637 DOI: 10.1529/Biophysj.107.123398  0.447
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