A Systems Biology Approach to Emerging Respiratory Viral Diseases
EMSL Project ID
33200
Abstract
This Systems Biology Program will comprehensively analyze and model the molecular and cellular events and pathogen-host interactions that occur during the course of respiratory virus infection. Our Research Project will focus on two NIAID Priority Pathogens: influenza virus and severe acute respiratory syndrome associated coronavirus (SAR-CoV). Technology cores include a Transcriptional Analysis Core, led by Dr. Michael Katze (University of Washington), and a Proteomics and Metabolomics Core led by Dr. Richard Smith (Pacific Northwest National Laboratory; PNNL). A Mathematical Modeling and Informatics Core will provide systems for data integration, analysis, and dissemination. Computational modeling will be conducted by Dr. Shannon McWeeney (OHSU) and Dr. Katrina Waters (PNNL). This multidisciplinary research team will apply a systems biology approach to experimental systems that will use highly pathogenic wild-type viruses and engineered viruses with attenuated pathogenicity due to modifications or deletions of specific viral genes. Our goal is to comprehensively analyze and model the virus-host interactions and cellular response networks induced by these viruses and to identify differences and commonalities in the host response to diverse respiratory pathogens. Our findings may provide novel targets for therapeutic intervention or suggest alternative vaccine strategies.
Project Details
Start Date
2009-02-03
End Date
2012-02-05
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Gao X, Q Zhang, D Meng, G Isaac, R Zhao, TL Fillmore, RK Chu, J Zhou, K Tang, Z Hu, RJ Moore, RD Smith, MG Katze, and TO Metz. 2012. "A reversed-phase capillary ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) method for comprehensive top-down/bottom-up lipid profiling." Analytical and Bioanalytical Chemistry 402(9):2923-2933.
Matzke MM, KM Waters, TO Metz, JM Jacobs, A Sims, R Baric, JG Pounds, and BJM Webb-Robertson. 2011. "Improved Quality Control Processing of Peptide-centric LC-MS Proteomics Data." Bioinformatics.
Tisoncik-Go J ,Gasper D J,Kyle J E,Eisfeld A J,Selinger C ,Hatta M ,Morrison J ,Korth M J,Zink E M,Kim YM ,Schepmoes A A,Nicora C D,Purvine S O,Weitz K K,Peng X ,Green R ,Tilton S C,Webb-Robertson BJ M,Waters K M,Metz T O,Smith R D,Kawaoka Y ,Suresh M ,Josset L ,Katze M G 2016. "Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism" Cell Host & Microbe 19(2):254-66. 10.1016/j.chom.2016.01.002
Wang M, JJ Carver, VV Phelan, LM Sanchez, N Garg, Y Peng, DD Nguyen, JD Watrous, CA Kapono, T Luzzatto-Knaan, C Porto, A Bouslimani, AV Melnik, MJ Meehan, WT Liu, M Crusemann, PD Boudreau, E Esquenazi, M Sandoval-Calderon, R Kersten, LA Pace, RA Quinn, KR Duncan, CC Hsu, DJ Floros, RG Gavilan, K Kleigrewe, TR Northen, RJ Dutton, D Parrot, EE Carlson, B Aigle, CF Michelsen, L Jelsbak, C Sohlenkamp, PA Pevzner, A Edlund, JS Mclean, J Piel, BT Murphy, L Gerwick, CC Liaw, YL Yang, HU Humpf, M Maansson, RA Keyzers, AC Sims, A Johnson, AM Sidebottom, BE Sedio, A Klitgaard, CB Larson, CA Boya P, D Torres-Mendoza, D Gonzalez, JR, DB Silva, LM Marques, DP Demarque, E Pociute, EC O'Neill, E Briand, EJ Helfrich, EA Granatosky, E Glukhov, F Ryffel, H Houson, H Mohimani, JJ Kharbush, Y Zeng, JA Vorholt, KL Kurita, P Charusanti, KL McPhail, KF Nielsen, L Vuong, M Elfeki, MF Traxler, N Engene, N Koyama, OB Vining, R Baric, RR Silva, SJ Mascuch, S Tomasi, S Jenkins, V Macherla, T Hoffman, V Agarwal, PG Williams, J Dai, R Neupane, J Gurr, AM Rodriguez, A Lamsa, C Zhang, K Dorrestein, BM Duggan, J Almaliti, PM Allard, P Phapale, LF Nothias, T Alexandrov, M Litaudon, JL Wolfender, JE Kyle, TO Metz, T Peryea, DT Nguyen, D VanLeer, P Shinn, A Jadhav, R Muller, KM Waters, W Shi, X Liu, L Zhang, R Knight, PR Jensen, BO Palsson, K Pogliano, RG Linington, M Gutierrez, NP Lopes, WH Gerwick, BS Moore, PC Dorrestein, and N Bandeira. 2016. "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking." Nature Biotechnology 34(8):828-837. doi:10. 1038/nbt. 3597
Webb-Robertson BJM, LA McCue, KM Waters, MM Matzke, JM Jacobs, TO Metz, SM Varnum, and JG Pounds. 2010. "Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-based Proteomics Data." Journal of Proteome Research 9(11):5748-5756.