Access to data associated with specfic publications 

Genomic and proteomic data can be accessed by following the links provided in the Data column on this page or through the Publicly Available Data and Resources links on the Systems Virology Home page.

For questions about or assistance with data access, please contact: Lynn Law gllaw@u.washington.edu


Systems Virology Publications 
AuthorsTitleCitationData
2013

Palermo RE, Tisoncik-Go J, Korth MJ, Katze MG.

 Old world monkeys and new age science: the evolution of nonhuman primate systems virology. ILAR J.2013;54(2):166-80. doi: 10.1093/ilar/ilt039. 

Korth MJ, Tchitchek N, Benecke AG, Katze MG

Systems approaches to influenza-virus host interactions and the pathogenesis of highly virulent and pandemic viruses.

 Semin Immunol. 2013 Oct 31;25(3):228-39. doi: 10.1016/j.smim.2012.11.001. Epub 2012 Dec 5

.PMC3596458

 

de Wit E, Rasmussen AL, Falzarano D, Bushmaker T, Feldmann F, Brining DL, Fischer ER, Martellaro C, Okumura A, Chang J, Scott D, Benecke AG, Katze MG, Feldmann H, Munster VJ

 Middle East respiratory syndrome coronavirus (MERS-CoV) causes transient lower respiratory tract infection in rhesus macaques.

Proc Natl Acad Sci U S A. 2013 Sep 23.

 

PMC3799368
 

Falzarano D, de Wit E, Rasmussen AL, Feldmann F, Okumura A, Scott DP, Brining D, Bushmaker T, Martellaro C, Baseler L, Benecke AG, Katze MG, Munster VJ, Feldmann H.

Treatment with interferon-α2b and ribavirin improves outcome in MERS-CoV-infected rhesus macaques. Nat Med. 2013 Sep 8. doi: 10.1038/nm.3362. GSE47957

Law GL, Tisoncik-Go J, Korth MJ, Katze MG.

 Drug repurposing: a better approach for infectious disease drug discovery?

 Curr Opin Immunol. 2013 Sep 5. pii: S0952-7915(13)00132-5. doi: 10.1016/j.coi.2013.08.004.

 
Lisa Gralinski, Armand Bankhead, Sophia Jeng, Vineet Menachery, Sean Proll, Sarah Belisle, Melissa Matzke, Bobbie-Jo Webb-Robertson, Maria Luna, Anil Shukla, Martin Ferris, Meagan Bolles, Jean Chang, Lauri Aicher, Katrina Waters, Richard Smith, Thomas Metz, G. Law, Michael Katze, Shannon McWeeney, and Ralph Baric Mechanisms of SARS-CoV Induced Acute Lung Injury mBIO, 2013  vol. 4 no. 4 e00271-13 doi: 10.1128/mBio.00271-13 GSE33266
Nicolas Tchitchek, Amie J. Eisfeld, Jennifer Tisoncik-Go, Laurence Josset, Lisa E. Gralinski, Christophe Bécavin4, Susan C. Tilton, Bobbie-Jo Webb-Robertson, Martin T. Ferris, Allison L. Totura, Chengjun Li, Gabriele Neumann, Thomas O. Metz, Richard D. Smith, Katrina M. Waters, Ralph Baric, Yoshihiro Kawaoka, Michael G. KatzeSpecific Mutations in H5N1 Mainly Impact the Magnitude and Velocity of the Host Response in Mice BMC Systems Biology 2013, 7:69 doi:10.1186/1752-0509-7-69

Metadata

GSE37569, GSE33263, GSE33263GSE43301, GSE44445GSE43302, GSE44441

Vineet D. Menachery and Ralph S. Baric Bugs in the system  Immunological Reviews 15 Aug 2013 
Hugh D. Mitchell, Amie J. Eisfeld, Amy C. Sims, Jason E. McDermott, Melissa M. Matzke, Bobbi-Jo M. Webb-Robertson, Susan C. Tilton, Nicolas Tchitchek, Laurence Josset, Chengjun Li, Amy L. Ellis, Jean H. Chang, Robert A. Heegel, Maria L. Luna, Athena A. Schepmoes, Anil K. Shukla, Thoams O. Metz, Gabriele Neumann, Arndt G. Benecke, Richard D. Smith, Ralph S. Baric, Yoshihiro Kawaoka, Michael G. Katze, Katrina M. WatersA Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory VirusesPLoS ONE 8(7): e69374. doi:10.1371/journal.pone.0069374

GSE33267, GSE37827, GSE28166, GSE37571GSE40844

SuperSeries accession GSE47963

Selinger C, Katze MG Mathematical models of viral latency. Curr Opin Virol. 2013 Aug;3(4):402-7. doi: 10.1016/j.coviro.2013.06.015. Epub 2013 Jul 26. 
Law GL, Korth MJ, Benecke AG, Katze MG.Systems virology: host-directed approaches to viral pathogenesis and drug targetingNat Rev Microbiol. 2013 Jun 3. doi: 10.1038/nrmicro3036.
 
 Gibbs DL, Baratt A, Baric RS, Kawaoka Y, Smith RD, Orwoll ES, Katze MG, McWeeney SK. Protein co-expression network analysis (ProCoNA) J Clin Bioinforma. 2013 Jun 1;3(1):11. [Epub ahead of print] 
Amy C. Sims, Susan C. Tilton, Vineet D. Menachery, Lisa E. Gralinski, Alexandra Schäfer, Melissa M. Matzke, Bobbie-Jo M. Webb-Robertson, Jean Chang, Maria L. Luna, Casey E. Long, Anil K. Shukla, Armand R. Bankhead III, Susan E. Burkett, Gregory Zornetzer, Chien-Te Kent Tseng, Thomas O. Metz, Raymond Pickles, Shannon McWeeney, Richard D. Smith, Michael G. Katze, Katrina M. Waters, Ralph S. Baric
Release of SARS-CoV Nuclear Import Block Enhances Host Transcription in Human Lung CellsJournal of Virology 87(7):3885-902
GEO accession# GSE33267

Josset L, Go JT, Katze MG.

Moving H5N1 studies into the era of systems biology Virus Res. 2013 Mar 14.  [Epub ahead of print]  

Laurence Josset, Vineet D. Menachery, Lisa E. Gralinski, Sudhakar Agnihothram, Pavel Sova, Victoria S. Carter, Boyd L. Yount, Rachel L. Graham, Ralph S. Baric and Michael, G. Katze

Cell host-response to infection with novel human coronavirus EMC predicts potential antivirals and important differences with SARS -coronavirus mBio DOI: 10.1128/mBio.00165-13 (2013)

 GEO accession# GSE45042

  Supplemental Data

2012
Cheung, C.Y., E.Y. Chan, A. Krasnoselsky, D. Purdy, A.T. Navare, J.T. Bryan, C.K.L. Leung, K.P.Y. Hui, J.S.M. Peiris, and M.G. Katze
H5N1 virus causes significant perturbations in host proteome very early in influenza virus-infected primary human monocyte-derived macrophages J. Infect. Dis.206:640-645 Supplemental Data
Gao, X., Q. Zhang, D. Meng, G. Isaac, R. Zhao, T.L. Filmore, R.K. Chu, J. Zhou, K. Tang, Z. Hu, R.J. Moore, R.D. Smith, M.G. Katze, and T.O. MetzA reversed-phase capillary ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) method for comprehensive top-down/bottom-up lipid profiling Anal. Bioanal. Chem. 402:2923-2933 
Jones, D.C., W.L. Ruzzo, X. Peng, and M.G. KatzeA new approach to bias correction in RNA-seq Bioinformatics 28:921-928 
Jones, D.C., W.L. Ruzzo, X. Peng, and M.G. KatzeCompression of next-generation sequencing reads aided by highly-efficient de novo assemblyNucleic Acids Res. 2012 Aug 16. 
Josset, L., J. Belser, M. Pantin-Jackwood, J. Chang, S. Chang, S. Belisle, T. Tumpey, and M. KatzeImplication of inflammatory macrophages, nuclear receptors and interferon regulatory factors in increased virulence of pandemic 2009 H1N1 influenza A virus after host adaptation
 J. Virol. 86:7192-7206
 GEO accession # GSE36328
Josset, L., F. Engelmann, K. Haberthur, S. Kelly, B. Park, Y. Kawaoka, A. García-Sastre, M.G. Katze, and I. MessaoudiIncreased viral loads and exacerbated innate host response in aged macaques infected with 2009 pandemic H1N1 influenza virus J. Virol. 86:11115-11127  GEO accession # GSE38502
Kangas LJ, Metz TO, Isaac G, Schrom BT, Ginovska-Pangovska B, Wang L, Tan L, Lewis RR, Miller JH 
In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipid
Bioinformatics 2012 Jul 1;28(13):1705-13
 
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.76:16-32
 
Tisoncik-Go, J., S.E. Belisle, N. Tchitchek, T.M. Tumpey, W. Ma, J.A. Richt, D. Safronetz, H. Feldmann, and M.G. Katze2009 pandemic H1N1 influenza virus elicits similar clincal course but differential host transcriptional response in mouse, macaque, and swine infection modelsBMC Genomics 2012 Nov 15;13(1):627.  GEO Series GSE40092
2011

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. 85:1214-1233  GEO accession # GSE31694

Aderem A, Adkins JN, Ansong C, Galagan J, Kaiser S, Korth MJ, Law GL, McDermott JG, Proll SC, Rosenberger C, Schoolnik G, Katze MG

A systems biology approach to infectious disease research: innovating the pathogen-host research paradigm MBio. 2:e00325-10 

Mark R. Denison, Rachel L. Graham, Eric F. Donaldson, Lance D. Eckerle and Ralph S. Baric

Coronaviruses:An RNA proofreading machine regulates replication fidelity and diversity. RNA Biology 8(2):270-9 

Armand Bankhead III, Emiliano Mancini, Amy C. Sims, Ralph S. Baric, Shannon McWeeney, Peter M.A. Sloot

A Simulation Framework to Investigate in vitro Viral Infection Dynamics.

Procedia Computer Science

doi:10.1016/j.procs.2011.04.195

 

Bradel-Tretheway BG, Mattiacio JL, Krasnoselsky A, Stevenson C, Purdy D, Dewhurst S, Katze MG

Comprehensive Proteomic Analysis of Influenza Virus Polymerase Complex Reveals a Novel Association with Mitochondrial Proteins and RNA Polymerase Accessory Factors

 J. Virol. 85(17):8569-81

 

 Melissa M. Matzke; Katrina M. Waters; Thomas O. Metz; Jon M. Jacobs; Amy C. Sims; Ralph S. Baric; Joel G. Pounds; Bobbie-Jo M. Webb-Robertson

Improved quality control processing of peptide-centric LC-MS proteomics data

 Bioinformatics 27(20):2866-72

 

Chengjun Li, Armand Bankhead III, Amie J. Eisfeld, Yasuko Hatta, Sophia Jeng, Jean H. Chang, Lauri D. Aicher, Sean Proll, Amy L. Ellis, G. Lynn Law, Katrina Waters, Gabriele Neumann, Michael G. Katze Shannon McWeeney, Yoshihiro Kawaoka

 

Host Regulatory Network Response to Infection with Highly Pathogenic H5N1 Avian Influenza Virus


 J Virol. 85(21):10955-67

 GEO accession # GSE28166 

Peng, X., L. Gralinski, M.T. Ferris, M.B. Frieman, M.J. Thomas, S. Proll, M.J. Korth, J.R. Tisoncik, M. Heise, S. Luo, G.P. Schroth, T.M. Tumpey, C. Li, Y. Kawaoka, R.S. Baric, and M.G. Katze

Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection

mBio 2(6):e00198-11

 

Jason E McDermott,Harish Shankaran, Amie J Eisfeld, Sarah E Belisle, Gabriele Neumann, Chengjun Li, Shannon McWeeney, Carol Sabourin, Yoshihiro Kawaoka, Michael G Katze and Katrina M Waters

Conserved host response to highly pathogenic avian 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)  

Bobbie-Jo M. Webb-Robertson, Melissa M. Matzke, Jon M. Jacobs, Joel G. Pounds, Katrina M. Waters

A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors

Proteomics 11(24):4736-41 

 

 

Stewart T Chang, Nicolas Tchitchek, Debashis Ghosh, Arndt Benecke and Michael G Katze

A chemokine gene expression signature derived from meta-analysis predicts the pathogenicity of viral respiratory infections BMC Syst. Biol. 5:202 (A BioMed Central Highly Accessed Article)
 

2010

Zornetzer, G.A., M.B. Frieman, E.R. Rosenzweig, M.J. Korth, C. Page, R.S. Baric, and M.G. Katze

Transcriptomic analysis reveals a mechanism for a pre-fibrotic phenotype in STAT1 knockout mice during SARS-coronavirus infection

J. Virol. 84:11297-11309

 GEO accession # GSE36016

Tisoncik, J. and M.G. Katze

What is systems biology? 

Future Microbiol.5(2), 39-141

 

Peng, X., L. Gralinski, C.D. Armour, M.T. Ferris, M.J. Thomas, S. Proll, B.G. Bradel-Tretheway, M.J. Korth, J.C. Castle, M.C. Biery, H.K. Bouzek, D.R. Haynor, M.B. Frieman, M. Heise, C.K.Raymond, R.S. Baric, and M.G. Katze

Unique signatures of non-coding RNA expression in response to virus infection and altered innate immune signaling

mBio 1(5):e00206-10

 

Hatta, Y., K. Hershberger, K. Shinya, S.C. Proll, R.R. Dubielzig, M. Hatta, M.G. Katze, Y. Kawaoka, and M. Suresh

Viral replication rate regulates clinical outcome and CD8 T cell responses during highly pathogenic H5N1 influenza virus infection in mice

PLoS Pathog. 6:e1001139

 

Webb-Robertson BJ, McCue LA, Waters KM, Matzke MM, Jacobs JM, Metz TO, Varnum SM, Pounds JG.

Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data

J Proteome Res 9(11):5748-56

 

2009

J R Tisoncik, SE Belisle, DL Diamond, MJ Korth, MG Katze

Is systems biology the key to preventing the next pandemic?

Future Viol. 4 (6):553-561