PUBLICATIONS & DATA
Genomic and proteomic data can be accessed by following the links provided in the Data column on this page or through the Katze Lab Informatics Server.
For questions about or assistance with data access, please contact: help@nida.viromics.washington.edu.
| Authors | Title | Citation | Data |
| 2009 | |||
| Chan, E.Y., M.J. Korth, and M.G. Katze | Decoding the multifaceted HIV-1 virus-host interactome | J. Biol. 8:84 | |
| Chan, E.Y., J.N. Sutton, J.M. Jacobs, A. Bondarenko, and M.G. Katze | Dynamic host energetics and cytoskeletal proteomes in HIV-1-infected human primary CD4 cells: analysis by multiplexed label-free mass spectrometry | J. Virol. 83:9283-9295 | |
| Diamond, D.L., A.J. Syder, J.M. Jacobs, C.M. Sorensen, K.-A. Walters, S.C. Proll, J.E. McDermott, M.A. Gritsenko, Q. Zhang, R. Zhao, T.O. Metz, D.G. Camp III, K.M. Waters, R.D. Smith, C.M. Rice, and M.G. Katze | Temporal proteome and lipidome profiles reveal hepatitis C virus-associated reprogramming of hepatocellular metabolism and bioenergetics | PLoS Pathog. In press. | |
| Favre, D., S. Lederer, B. Kanwar, Z.M. Ma, S. Proll, Z. Kasakow, J. Mold, L. Swainson, J.D. Barbour, C.R. Baskin, R. Palermo, C.J. Miller, M.G. Katze, and J.M. McCune | Critical loss of the balance between Th17 and T regulatory cell populations in pathogenic SIV infection | PLoS Pathog. 5:e1000295 | |
| Joyce, M.A., K.-A. Walters, S.-E. Lamb, M.M. Yeh, L.-F. Zhu, N. Kneteman, J.S. Doyle, M.G. Katze, and D.L. Tyrell | HCV induces oxidative and ER stress, and sensitizes infected cells to apoptosis in SCID/Alb-uPA mice | PLoS Pathog. 5:e1000291 | |
| Lederer, S., D. Favre, K.-A. Walters, S. Proll, B. Kanwar, Z. Kasakow, C.R. Baskin, R. Palermo, J.C. McCune, and M.G. Katze | Transcriptional profiling reveals significant distinctions in kinetics and tissue compartmentalization between pathogenic and nonpathogenic SIV infection | PLoS Pathog. 5:e1000296 | |
| Peng, X., E.C. Chan, Y. Li, D.L. Diamond, M.J. Korth, and M.G. Katze | Virus-host interactions: from systems biology to translational research | Curr. Op. Microbiol. 12:432-438 | |
| Peng, X., Y. Li, K.-A. Walters, E.R. Rosenzweig, S.L. Lederer, L.D. Aicher, S. Proll, and M.G. Katze | Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers | BMC Genomics 10:373 (A BioMed Central Highly Accessed Article) | |
| Tisoncik, J.R., S.E. Belisle, D.L. Diamond, M.J. Korth, and M.G. Katze | Is systems biology the key to preventing the next pandemic? | Future Virol. 4:553-561 | |
| Walters, K.-A. and M.G. Katze | Using high-throughput genomics to study hepatitis C: what determines the outcome of infection? | Antiviral Res. 81:198-208 | |
| Walters, K.-A., A.J. Syder, S.L. Lederer, D.L. Diamond, B. Paeper, C.M. Rice, and M.G. Katze | Genomic analysis reveals a potenital role for cell-cycle perturbation in HCV-mediated apoptosis of cultured hepatocytes | PLoS Pathog. 5:e1000269 | |
| 2008 TOP | |||
| Ajioka,R.S., J.D. Philips, R.B. Weiss, D.M. Dunn, M.W. Smit, S.C. Proll, M.G. Katze, and J.P. Kushner | Down-regulation of hepcidin in porphyria cutanea tarda | Blood 112:4723-4728 | Borozan, I., L. Chen, B. Paeper, J.E. Heathcote, A.M. Edwards, M. Katze, Z. Zhang, and I.D. McGilvray | MAID: an effect-sized based model for microarray data integration across laboratories and platforms | BMC Bioinformatics 9:305 |
| Katze, M.G., J.L. Fornek, R.E. Palermo, K.-A. Walters, and M.J. Korth | Innate immune modulation by RNA viruses: emerging insights from functional genomics | Nature Rev. Immunol. 8:644-654 | |
| 2007 TOP | Chan, E. Y., W. J. Qian, D. L. Diamond, T. Liu, M. A. Gritsenko, M. E. Monroe, D. G. Camp, R. D. Smith, and M. G. Katze | Quantitative analysis of HIV-infected CD4+ cell proteome: dysregulated cell cycle progression and nuclear transport coincide with robust virus production | J. Virol. 81:7571-7583 | Informatics Server |
| Diamond, D. L. J. M. Jacobs, B. Paeper, S. C. Proll, M. A. Gritsenko, R. L. Carithers, A. M. Larson, D. G. Camp, R. D. Smith, and M. G. Katze | Proteomic profiling of human liver biopsies: hepatitis C virus-induced fibrosis and mitochondrial dysfunction | Hepatology46:649-657 | Informatics Server |
| Katze, M. G. and M. J. Korth | Lost in the world of functional genomics, systems biology, and translational research: Is there life after the Milstein award? | Cytokine Growth Factor Rev. 18:441-450 | |
| Lazaro, C. A., M. Chang, W. Tang, J. Campbell, D. G. Sullivan, D. R. Gretch, L. Corey, R. W. Coombs, and N. Fausto | Hepatitis C virus replication in transfected and serum-infected cultured human fetal hepatocytes | Am. J. Pathol. 170:478-489 | |
| Tan, S.-L., G. Ganji, B. Paeper, S. Proll, and M. G. Katze | Systems biology and the host response to infection | Nature Biotechnol. 25:1383-1389 | |
| Tang, W., C. Lazaro, J. Campbell, T. Parks, M. G. Katze, and N. Fausto | Response of non-transformed human hepatocytes to conditional expression of full-length hepatitis C virus open reading frame | Am. J. Pathol. 171:1831-1846 | |
| 2006 TOP | |||
| Diamond, D. L., S. C. Proll, J. M. Jacobs, E. Y. Chan, D. G. Camp II, R. D. Smith, and M. G. Katze | HepatoProteomics: applying proteomic technologies to the study of liver function and disease | Hepatology 44:299-308 | |
| Lederer, S. L., K. A. Walters, S. Proll, B. Paeper, S. Robinzon, L. Boix, N. Fausto, J. Bruiz, and M. G. Katze | Distinct cellular responses differentiating alcohol- and hepatitis C virus-induced liver cirrhosis | Virol. J. 3:98 | Informatics Server |
| Pal, S., M. C. Shuhart, L. Thomassen, S. S. Emerson, T. Su, N. Feuerborn, J. Kae, and D. R. Gretch | Intrahepatic hepatitis C virus replication correlates with chronic hepatitis C disease severity in vivo | J. Virol. 80:2280-2290 | |
| Pal, S. D. G. Sullivan, S. Kim, K. K.-Y. Lai, J. Kae, S. J. Cotler, R. L. Carithers, Jr., B. L. Wood, J. D. Perkins, and D. R. Gretch | Productive replication of hepatitis C virus in perihepatic lymph nodes in vivo: implications of HCV lymphotropism | Gastroenterology 130:1107-1116 | |
| Smith, M. W., K. A. Walters, M. J. Korth, M. Fitzgibbon, S. Proll, J. C. Thompson, M. W. Yeh, M. C. Shuhart, J. C. Furlong, P. P. Cox, D. L. Thomas, J. D. Phillips, J. P. Kushner, N. Fausto, R. L. Carithers Jr., and M. G. Katze | Gene expression patterns that correlate with hepatitis C and early progression to fibrosis in liver transplant patients | Gastroenterology 130:179-187 | Informatics Server |
| Wallace J. C., M. J. Korth, D. L. Diamond, S. C. Proll, and M. G. Katze | Virology in the 21st century: finding function with functional genomics | Future Virol. 1:47-53 | |
| Walters, K. A., M. A. Joyce, J. C. Thompson, S. Proll, J. Wallace, M. W. Smith, J. Furlong, D. L. Tyrrell, and M. G. Katze | Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis | Virol. J. 3:37 | Informatics Server |
| Walters, K. A., M. A. Joyce, J. C. Thompson, M. W. Smith, M. M. Yeh, S. Proll, L.-F. Zhu, T. J. Gao, N. M. Kneteman, D. L. Tyrrell, and M. G. Katze | Host-specific response to HCV infection in the chimeric SCID-beige/Alb-uPA mouse model: role of the innate antiviral immune respons | PLoS Pathogens 2:e59 | Informatics Server |
| Walters, K. A., M. W. Smith, S. Pal, J. C. Thompson, M. J. Thomas, M. M. Yeh, D. L. Thomas, M. Fitzgibbon, S. Proll, N. Fausto, D. R. Gretch, R. L. Carithers, M. C. Shuhart, and M. G. Katze | Identification of a specific gene expression pattern associated with HCV-induced pathogenesis in HCV- and HCV/HIV- infected individuals | Virology 350:453-464 | Informatics Server |
| 2005 TOP | |||
| Desiere, F., E. W. Deutsch, A. I. Nesvizhskii, P. Mallick, N. L. King, J. K. Eng, A. Aderem, R. Boyle, E. Brunner, S. Donohoe, N. Fausto, E. Hafen, L. Hood, M. G. Katze, K. A. Kennedy, F. Kregenow, H. Lee, B. Lin, D. Martin, J. A. Ranish, D. J. Rawlings, L. E. Samelson, Y. Shiio, J. D. Watts, B. Wollscheid, M. E. Wright, W. Yan, L. Yang, E. C. Yi, H. Zhang, and R. Aebersold | Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry | Genome Biol. 6:R9 | |
| Jacobs, J. M., D. L. Diamond, E. Y. Chan, M. A. Gritsenko, W. Qian, M. Stastna, T. Baas, D. G. Camp II, R. L. Carithers Jr., R. D. Smith, and M. G. Katze | Proteome analysis of liver cells expressing a full- length hepatitis C virus (HCV) replicon and biopsy specimens of posttransplantation liver from HCV- infected patients | J. Virol. 79:7558-7569 | Informatics Server NCRR Proteomics |
| Korth M. J., J. C. Kash, J. C. Furlong, and M. G. Katze | Virus infection and the interferon response: a global view through functional genomics | Methods Mol. Med. 116:37-55 | |
| Reiss, D. J., I. Avila-Campillo, V. Thorsson, B. Schwikowski, and T. Galitski | Tools enabling the elucidation of molecular pathways active in human disease: application to hepatitis C virus infection | BMC Bioinformatics 6:154 | |
| 2004 TOP | |||
| Coito, C., D. L. Diamond, P. Neddermann, M. J. Korth, and M. G. Katze | High-throughput screening of the yeast kinome: identification of human serine/threonine protein kinases that phosphorylate the hepatitis C virus NS5A protein | J. Virol. 78:3502-3513 | |
| Prinz, S., I. Avila-Campillo, C. Aldridge, A. Srinivasan, K. Dimitrov, A. F. Siegel, and T. Galitski | Control of yeast filamentous-form growth by modules in an integrated molecular network | Genome Res. 14:380-390 | |
| Yan, W., H. Lee, E. W. Deutsch, C. A. Lazaro, W. Tang, E. Chen, N. Fausto, M. G. Katze, and R. Aebersold | A dataset of human liver proteins identified by protein profiling via isotope coded affinity tag (ICAT) and tandem mass spectrometry | Mol. Cell Proteomics 3:1039-1041 | |
| Yan, W., H. Lee, E. C. Yi, D. Reiss, P. Shannon, B. K. Kwieciszewski, C. Coito, X. J. Li, A. Keller, J. Eng, T. Galitski, D. R. Goodlett, R. Aebersold, and M. G. Katze | System-based proteomic analysis of the interferon response in human liver cells | Genome Biol. 5:R54 | |
| Zhang, H., W. Yan, and R. Aebersold | Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes | Curr. Opin. Chem. Biol. 8:66-75 | |
| 2003 TOP | |||
| Smith, M. W., Z. N. Yue, G. K. Geiss, N. Y. Sadovnikova, V. S. Carter, L. Boix, C.A. Lazaro, G. B. Rosenberg, R. E. Bumgarner, N. Fausto, J. Bruix, and M. G. Katze | Identification of novel tumor markers in hepatitis C virus-associated hepatocellular carcinoma | Cancer Res. 63:859-864 | Informatics Server |
| Smith, M. W., Z. N. Yue, M. J. Korth, H. A. Do, L. Boix, N. Fausto, J. Bruix, R.L. Jr. Carithers, and M. G. Katze | Hepatitis C virus and liver disease: global transcriptional profiling and identification of potential markers | Hepatology 38:1458-1467 | Informatics Server |