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@macaque.org.

Authors Title Citation Data
2012
Benecke, A., M. Gale Jr, and M.G. Katze Dynamics of innate immunity are key to chronic immune activation in AIDS Curr. Opin. HIV AIDS 7:79-85  
Jones, D.C., W.L. Ruzzo, X. Peng, and M.G. Katze A new approach to bias correction in RNA-seq Bioinformatics In Press  
Tisoncik, J.R., M.J. Korth, C.P. Simmons, J. Farrar, T.R. Martin, and M.G. Katze Into the eye of the cytokine storm Microbiol. Mol. Bio. Rev. In press  
2011 TOP
Belisle, S.E., J. Yin, D.J. Shedlock, A. Dai, J. Yan, L. Hirao, M.A. Kutzler, M.G. Lewis, S.M. Lank, J.A. Karl, D.H. O'Connor, A. Khan, N.Y. Sardesai, J. Chang, L.D. Aicher, R.E. Palermo, D.B. Wiener, M.G. Katze, and J. Boyer Long-term programming of antigen-specific immunity from gene expression signatures in the PBMC of rhesus macaques immunized with an SIV DNA vaccine. PLoS One
6:e19681		  
Chang, S.T., P Sova, X. Peng, J. Weiss, G.L. Law, R.E. Palermo, and M.G. Katze Next-generation sequencing reveals HIV-1-mediated suppression of T cell activation and RNA processing and the regulation of non-coding RNA expression in a CD4+ T cell line mBio 2(5):e00134-11  
McDermott, J.E., H. Shankaran, A.J. Eisfeld, S.E. Belisle, G. Newman, C. Li, S. McWeeney, C. Sabourin, Y. Kawaoka, M.G. Katze, and K.M. Waters Conserved host response to highly pathogenic avial influenza virus infection in human cell culture, mouse and macaque model systems BMC Syst. Biol. 5:190 GEO accession GSE33142, GSE28166 (Calu-3 data), GSE33263 (mouse data), and GSE33351 (macaque data)
Murali, T.M., M.D. Dyer, D. Badger, B.M. Tyler, and M.G. Katze Network-based prediction and analysis of HIV dependency factors PLoS Comp. Bio.9(7):e1002164  
Palermo, R.E., L.J. Patterson, L.D. Aicher, M.J. Korth, M. Robert-Guroff, and M.G. Katze Genomic analysis reveals pre- and post-challenge differences in a rhesus macaque AIDS vaccine trial: insights into mechanisms of vaccine efficacy J. Virol. 85:1099-1116  
Safronetz, D., B. Rockx, F. Feldmann, S.E. Belisle, R.E. Palermo, D. Grining, D. Gardner, S.C. Proll, A. Marzi, Y. Tsuda, R.A. LaCasse, L. Kercher, A. York, M.J. Korth, D. Long. R. Rosenke, W.L. Shupert, C.A. Aranda, J.S. Mattoon, D. Kobasa, G. Kobinger, Y. Li, J.K. Taubenberger, J.A. Richt, M. Parnell, H. Ebihara, Y. Kawaoka, M.G. Katze, and H. Feldman Pandemic swine-origin H1N1 influenza A isolates show heterogeneous virulence in macaques J. Virol. 85:1214-1223 GEO accession #GSE31694
Yan, G., G. Zhang, X. Fang, Y. Zhang, C. Li, Y. Zhang, H. Du, D.N. Cooper, Q. Li, Y. Li, J. Chen, F. Ling, P. Zhang, Z. Huang, B. Wang, Y. Meng, Y. Bai, J. Wang, T. Wang, Y. Huang, L. Wei, J. Li, Z. Wang, H. Hu, L. Le, P.D. Stenson, B. Li, E.V. Ball, N. An, Q. Huang, W. Fan, X. Zhang, Y. Li, W. Wang, M.G. Katze, B. Su, R. Nielsen, H. Yang, J. Wang, X. Wang, and J. Wang Genome sequencing and comparison of two nohuman primate animal models, the cynomolgus and Chinese rhesus macaques Nature Biotechnol. 29:1019-1023  
2010 TOP
Brown, J.N., R.E. Palermo, C.R. Baskin, M. Gritsenko, P.J. Sabourin, J.P. Long, C.L. Sabourin, H. Bielefeldt-Ohmann, A. Garcia-Sastre, R. Albrecht, T.M. Tumpey, J.M. Jacobs, R.D. Smith, and M.G. Katze Macaque proteome response to highly pathogenic avian influenza and 1918 reassortant influenza virus infections J. Virol. 84:12058-12068  
2009 TOP
Baskin, C.R., H. Bielefeldt-Ohmann, T.M. Tumpey, P.J. Sabourin, J.P. Long, A. Garcia-Sastre, A.-E. Tolnay, R. Albrecht, J.A. Pyles, P. Olson, L.D. Aicher, E.R. Rosenzweig, M.K. Kaja, E.E. Clark, M.S. Kotur, J.L. Fornek, S. Proll, R.E. Palermo, C.L. Sabourin, and M.G. Katze Early and sustained innate immune response defines pathology and death in highly pathogenic influenza-infected nonhuman primates Proc. Natl. Acad. Sci. USA 106:3455-3460 Microarray Data
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  
Cilloniz, C., K. Shina, X. Peng, M.J. Korth, S.C. Proll, L.D. Aicher, V.S. Carter, J.H. Chang, D. Kobasa, F. Feldmann, J.E. Strong, H. Feldmann, Y. Kawaoka, and M.G. Katze Lethal influenza virus infection in macaques is associated with early disregulation of inflammatory related genes PLoS Pathog. 5:e100604 Microarray Data
Degenhardt, J.D., P. de Candia, A. Chabot, S. Schwartz, L. Henderson, B. Ling, M. Hunter, Z. Jiang, R.E. Palermo, M.G. Katze, E.E. Eichler, M. Ventura, J. Rogers, P. Marx, Y. Gilad, and C.D. Bustamante Copy number variation of CCL3-like genes affects rate of progression to simian AIDS in rhesus macaques (Macaca mulatta) PLoS Genet. 5:e1000346  
de Lang, A., T. Baas, S.L. Smits, M.G. Katze, A.D.M.E. Osterhaus, and B.L. Haagmans Unraveling the complexities of the interferon response during SARS-CoV infection Future Virol. 4:71-78  
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  
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 Microarray Data
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  
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. In press.  
2008 TOP
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 Nat. Rev. Immunol. 8:644-654  
2007 TOP
Baskin, C.R., H. Bielefeldt-Ohmann, A. Garcia-Sastre, T.M. Tumpey, N. Van Hoeven, V.S. Carter, M.J. Thomas, S. Proll, A. Solorzano, R. Billharz, J.L. Fornek, S. Thomas, C.H. Chen, E.A. Clark, M.K. Kaja, and M.G. Katze Functional genomic and serological analysis of the protective immune response resulting from vaccination of macaques with an NS1-truncated influenza virus J. Virol. 81:11817-11827 Informatics Server
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-1 infected CD4+ cell proteome: dysregulated cell cycle progression and nuclear transport coincide with robust virus production. J. Virol. 81:7571-7583 Informatics Server
de Lang, A., T. Baas, T. Teal, L. M. Leijten, B. Rain, A. D. Osterhaus, B. L. Haagmans, and M. G. Katze Functional genomics highlights differential induction of antiviral pathways in the lungs of SARS-CoV-infected macaques PloS Pathog. 3:e112 Informatics Server
Li, Y., E. Y. Chan, and M. G. Katze Functional genomics analyses of differential macaque peripheral blood mononuclear cell infections by human immunodeficiency virus-1 and simian immunodeficiency virus. Virology 366:137-149 Informatics Server
Gibbs, R., J. Rogers, M. G. Katze, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222-234 Genome Project
Kobasa, D., S. M. Jones, K. Shinya, J. C. Kash, J. Copps, H. Ebihara, Y. Hatta, J. H. Kim, P. Halfmann, M. Hatta, F. Feldmann, J. B. Alimonti, L. Fernando, Y. Li, M. G. Katze, H. Feldmann, and Y. Kawaoka Aberrant innate immune response in lethal infection of macaques with the 1918 influenza virus. Nature 445:319-323 Informatics Server

Array Express
Wallace, J. C., M. J. Korth, B. W. Paeper, S. C. Proll, M. J. Thomas, C. L. Magness, S. P. Iadonato, C. Nelson, and M. G. Katze High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations BMC Genomics 8:28 Informatics Server

Array Express
2006 TOP
Baas, T., C. R. Baskin, D. L. Diamond, A. Garcia-Sastre, H. Bielefeldt-Ohmann, T. M. Tumpey, M. J. Thomas, V. S. Carter, T. H. Teal, N. Van Hoeven, S. C. Proll, J. M. Jacobs, Z. R. Caldwell, M. A. Gritsenko, R. R. Hukkanen, D. G. Camp, R. D. Smith,and M. G. Katze Integrated molecular signature of disease: analysis of influenza virus-infected macaques through functional genomics and proteomics. J. Virol. 80:10813-10828 Informatics Server

NCRR Proteomics
Thomas M. J., Flanary L. R., Brown B. A., Katze M. G., Baskin C. R. Use of human nasal cannulas during bronchoscopy procedures as a simple method for maintaining adequate oxygen saturation in pigtailed macaques (Macaca nemestrina). J. Am. Assoc. Lab Anim. Sci. 45:44-8  
Korth, M. J., J. C. Kash, C. R. Baskin, and M. G. Katze Insights into influenza virus-host interactions through global gene expression profiling: cell culture systems to animal models. p. 341-360. In: Y. Kawaoka (ed.), Contemporary topics in influenza virology. Horizon Scientific Press, Wymondham, U.K.  
Thomas, M. J., M. B. Agy, S. C. Proll, B.W. Paeper, Y. Li, K. L. Jensen, M. J. Korth, and M. G. Katze Functional gene analysis of individual response to challenge of SIVmac239 in Macaca mulatta peripheral blood mononuclear cells. Virology 348:242-52 Informatics Server
2005 TOP
Magness, C.L., P.C. Fellin, M.J. Thomas, M.J. Korth, M.B. Agy, S.C. Proll, M. Fitzgibbon, C.S. Scherer, D.G. Miner, M.G. Katze, and S.P. Iadonato Analysis of the Macaca mulatta transcriptome and the sequence divergence between Macaca and human. Genome Biol. 6:R60 Informatics Server

Array Express
2004 TOP
Baskin, C. R., A. Garcia-Sastre, T. M. Tumpey, H. Bielefeldt-Ohmann, V. S. Carter, E. Nistal-Villan, and M. G. Katze Integration of clinical data, pathology, and cDNA microarrays in influenza virus-infected pigtailed macaques (Macaca nemestrina). J. Virol. 78:10420-10432 Informatics Server

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