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  • Katze Lab
    biology approaches to define and model virus host interactions innate immune signaling and the varied strategies used by viruses to evade cellular defense mechanisms We study a wide range of viral pathogens including influenza virus SARS coronavirus Ebola virus hepatitis C virus and human and simian immunodeficiency viruses We are also spearheading efforts to develop genomic resources for nonhuman primate ferret and Syrian hamster models of human virus infection Announcements

    Original URL path: http://viromics.washington.edu/ (2016-01-01)
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  • Katze Lab
    studies include cultured cell lines primary differentiated human tracheobronchial epithelial cells and mouse ferret and macaque models of infection SARS and MERS Coronaviruses Severe acute respiratory syndrome SARS first emerged in Hong Kong in November 2002 and quickly spread to 27 countries resulting in over 8 000 cases and 774 deaths Since the emergence of SARS and the subsequent identification of SARS coronavirus as the etiologic agent the virus has largely disappeared The possibility remains however for another SARS outbreak or for the emergence of new forms of coronavirus as has occurred in the Middle East MERS coronavirus Our goal is to use cell culture and animal models of infection together with high throughput technologies to increase our knowledge of SARS and MERS pulmonary pathogenesis and to identify sets of genes whose expression patterns in response to infection may suggest novel targets for antiviral therapies SIV and HIV 1 Funded through a contract from the Division of AIDS National Institute of Allergy and Infectious Diseases our lab serves as the national Nonhuman Primate Core Functional Genomics Laboratory for AIDS Vaccine Research and Development We use genomic and proteomic profiling to evaluate macaque models of AIDS and AIDS vaccine studies Blood samples are taken prior to immunization at multiple points during the immunization phase and at multiple points following viral challenge Expression profiles are then analyzed for features that correlate with innate or acquired immunity or with attenuation of disease Our long term goal is to identify gene expression signatures that define successful vaccination and differentiate vaccine candidates in a qualitative fashion Ebola Virus Ebola viruses are members of the filovirus family and the etiologic agents of an exceptionally severe form of viral hemorrhagic fever Preventive or therapeutic measures are not available for these viruses and care is limited to supportive

    Original URL path: http://viromics.washington.edu/research.html (2016-01-01)
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  • Katze Lab
    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 Authors Chang S T P Sova X Peng J Weiss G L Law R E Palermo and M G Katze Citation mBio 2 5 e00134 11 Data GEO accession GSE38006 Read Me Gene Locus Ref Seq Title A chemokine gene expression signature derived from meta analysis predicts the pathogenicity of viral respiratory infections Authors Chang S T N Tchitchek D Ghosh A Benecke and M G Katze Citation BMC Syst Biol 5 202 A BioMed Central Highly Accessed Article Title Functional genomics reveals the induction of inflammatory response and metalloproteinase gene expression during lethal Ebola virus infection Authors Cilloniz C H Ebihara C Ni G Neumann M J Korth S M Kelly Y Kawaoka H Feldmann and M G Katze Citation J Virol 85 9060 9068 Data Microarray Data Title A single N66S mutation in the PB1 F2 protein of influenza A virus increases virulence by inhibiting the early interferon response in vivo Authors Conenello G J R Tisoncik E Rosenzweig Z T Varga P Palese and M G Katze Citation J Virol 85 652 662 Data GEO accession GSE35940 Title Virus infection rapidly activates the P58IPK pathway delaying peak kinase activation to enhance viral replication Authors Goodman A G B C Tanner S T Chang and M G Katze Citation Virology 417 27 36 Title Host regulatory network response to infection with highly pathogenic H5N1 avian influenza virus Authors Li C A Bankhead III A J Eisfeld Y Hatta S Jeng J H Chang L D Aicher S Proll A L Ellis G L Law K Waters G Neumann M G Katze S McWeeney and Y Kawaoka Citation J Virol 85 10955 10967 Data GEO accession GSE28166 Title Differential microRNA expression and virulence of avian 1918 reassotant and reconstructed 1918 influenza A viruses Authors Li Y J Li S E Belisle C R Baskin T M Tumpey and M G Katze Citation Virology 321 105 113 Title 2009 pandemic H1N1 virus causes disease and upregulation of genes related to inflammatory and immune response cell death and lipid metabolism in pigs Authors Ma W S E Belisle D Mosier X Li E Stigger Rosser Q Liu C Qiao J Elder R Webbey M G Katze and J A Richt Citation J Virol 85 11626 11637 Data GEO accession GSE35738 Title Conserved host response to highly pathogenic avial influenza virus infection in human cell culture mouse and macaque model systems Authors 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 Citation BMC Syst Biol 5 190 Data GEO accession GSE33142 GSE28166 Calu 3 data GSE33263 mouse data and GSE33351 macaque data Title Network based prediction and analysis of HIV dependency factors Authors Murali T M M D Dyer D Badger B M Tyler and M G Katze Citation PLoS Comp Bio 9 7 e1002164 Title Genomic analysis reveals pre and post challenge differences in a rhesus macaque AIDS vaccine trial insights into mechanisms of vaccine efficacy Authors Palermo R E L J Patterson L D Aicher M J Korth M Robert Guroff and M G Katze Citation J Virol 85 1099 1116 Title Functional genomics reveals an essential and specific role for STAT1 in protection of the central nervous system following herpes simplex virus corneal infection Authors Pasieka T J C Cilloniz V S Carter P Rosato M G Katze and D A Leib Citation J Virol 85 12972 12981 Data GEO accession GSE35943 Title Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection Authors 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 Citation mBio 2 6 e00198 11 Data GEO accession GSE36971 Title Systems virology identifies a mitochondrial fatty acid oxidation enzyme dodecenoyl CoA delta isomerase DCI required for HCV replication and likely pathogenesis Authors Rasmussen A L D L Diamond J E McDermott X Gao T O Metz M Matzke V S Carter S E Belisle M J Korth K M Waters R D Smith and M G Katze Citation J Virol 85 11646 11654 Data Supplemental Data Title Pandemic swine origin H1N1 influenza A isolates show heterogeneous virulence in macaques Authors 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 Citation J Virol 85 1214 1233 Data GEO accession GSE31694 Title The NS1 protein of influenza A virus suppresses interferon regulated activation of antigen presentation and immune proteasome pathways Authors Tisoncik J R R Billharz S Burmakina S E Belisle S C Proll M J Korth A García Sastre and M G Katze Citation J Gen Virol 92L2093 2104 Data GEO accession GSE39202 Title Genome sequencing and comparison of two nohuman primate animal models the cynomolgus and Chinese rhesus macaques Authors 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 Citation Nature Biotechnol 29 1019 1023 2010 Publications Title Genomic profiling of TNF alpha receptor and IL1 receptor knockout mice reveals a link between TNF alpha signaling and increased severity of 1918 pandemic influenza virus infection Authors Belisle S E J R Tisoncik M J Korth V S Carter S C Proll D E Swayne M Pantin Jackwood T M Tumpey and M G Katze Citation J Virol 84 12576 12588 Title Macaque proteome response to highly pathogenic avian influenza and 1918 reassortant influenza virus infections Authors 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 Citation J Virol 84 12058 12068 Title Lethal dissemination of H5N1 influenza virus is associaed with dysregulation of inflammation and lipoxin signaling in a mouse model of infection Authors Cilloniz C M J Pantin Jackwood C Ni A G Goodman X Peng S C Proll V S Carter E R Rosenzweig K J Szretter J M Katz M J Korth D E Swayne T M Tumpey and M G Katze Citation J Virol 84 7613 7624 Data GEO accession GSE48890 Microarray Data Title Progressive renal injury from transgenic expression of human carbonic anhydrase IV folding mutants is enhanced by deficiency of P58IPK Authors Datta R G N Shah T S Rubbelke A Waheed M Rauchman A G Goodman M G Katze and W S Sly Citation Proc Natl Acad Sci USA 107 6448 6452 Title Temporal proteome and lipidome profiles reveal hepatitis C virus associated reprogramming of hepatocellular metabolism and bioenergetics Authors 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 Citation PLoS Pathog 6 e1000719 Data Supplemental Data Title The interferon alpha beta receptor provides protection against influenza virus replication but is despensible for inflammatory response signaling Authors Goodman A G H Zeng S C Proll X Peng C Cilloniz V S Carter M J Korth T M Tumpey and M G Katze Citation J Virol 84 2027 2037 Data GEO accession GSE37665 Title Viral replication rate regulates clinical outcome and CD8 T cell responses during highly pathogenic H5N1 influenza virus infection in mice Authors Hatta Y K Hershberger K Shinya S C Proll R R Dubielzig M Hatta M G Katze Y Kawaoka and M Suresh Citation PLoS Pathog 6 e1001139 Title MicroRNA expression and virulence in pandemic influenza virus infected mice Authors Li Y E Y Chan J Li C Ni X Peng E Rosenzweig T M Tumpey and M G Katze Citation J Virol 84 3023 3032 Title Unique signatures of non coding RNA expression in response to virus infection and altered innate immune signaling Authors 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 Citation mBio 1 5 e00206 10 Title What is systems biology Authors Tisoncik J and M G Katze Citation Future Microbiol 5 139 141 Title Extrapulmonary tissue responses in cynomolgus macaques Macaca fascicularis infected with highly pathogenic avian influenza A H5N1 virus Authors Tolnay A E C R Baskin T M Tumpey P J Sabourin C L Sabouirin J P Long J A Pyles R A Albrecht A Garcia Sastre M G Katze and H Bielefeldt Ohmann Citation Arch Virol 155 905 914 Title Transcriptomic analysis reveals a mechanism for a pre fibrotic phenotype in STAT1 knockout mice during SARS coronavirus infection Authors Zornetzer G A M B Frieman E R Rosenzweig M J Korth C Page R S Baric and M G Katze Citation J Virol 84 11297 11309 Data GEO accession GSE36016 2009 Publications Title Early and sustained innate immune response defines pathology and death in highly pathogenic influenza infected nonhuman primates Authors 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 Citation Proc Natl Acad Sci USA 106 3455 3460 Data Microarray Data Title The NS1 protein of the 1918 pandemic influenza virus blocks host interferon and lipid metabolism pathways Authors Billharz R H Zeng S C Proll M J Korth S Lederer R Albrecht A G Goodman E Rosenzweig T M Tumpey A Garcia Sastre and M G Katze Citation J Virol 83 10557 10570 Data GEO accession GSE37829 GEO accession GSE37951 Title Decoding the multifacted HIV 1 virus host interactome Authors Chan E Y M J Korth and M G Katze Citation J Biol 8 84 Title Dynamic host energetics and cytoskeletal proteomes in HIV 1 infected human primary CD4 cells analysis by multiplexed label free mass spectrometry Authors Chan E Y J N Sutton J M Jacobs A Bondarenko and M G Katze Citation J Virol 83 9283 9285 Data Supplemental Data Title Lethal influenza virus infection in macaques is associated with early disregulation of inflammatory related genes Authors 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 Citation PLoS Pathog 5 e1000604 Data Microarray Data Title Copy number variation of CCL3 like genes affects rate of progression to simian AIDS in rhesus macaques Macaca mulatta Authors 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 Citation PLoS Genet 5 e1000346 Title Unraveling the complexities of the interferon response during SARS CoV infection Authors de Lang A T Baas S L Smits M G Katze A D M E Osterhaus and B L Haagmans Citation Future Virol 4 71 78 Title Critical loss of the balance between Th17 and T regulatory cell populations in pathogenic SIV infection Authors 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 Citation PLoS Pathog 5 e1000295 Title A single amino acid substitution in a polymerase protein of an H5N1 influenza virus is associated with systemic infection and impaired T cell activation in mice Authors Fornek J L L Gillim Ross C Santos V Carter J M Ward L I Cheng S Proll M G Katze and K Subbarao Citation J Virol 83 11102 11115 Data Microarray Data Title P58IPK a novel CHID member of the host innate immune defense response against pathogenic virus infection Authors Goodman A G J L Fornek G R Medigeshi L A Perrone X Peng M D Dyer S C Proll S E Knoblaugh V S Carter M J Korth J A Nelson T M Tumpey and M G Katze Citation PLoS Pathog 5 e1000438 Data Microarray Data Title Genomics Hepatitis C virus gets personal Authors Iadonato S P Katze M G Citation Nature 8 357 8 Data Title HCV induces oxidative and ER stress and sensitizes infected cells to apoptosis in SCID Alb uPA mice Authors 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 Citation PLoS Pathog 5 e1000291 Data Microarray Data Title Resources for genetic management and genomics research on non human primates at the National Primate Research Centers NPRCs Authors Kanthaswamy S J P Capitanio C J Dubay B Ferguson T Folks J C Ha C E Hotchkiss Z P Johnson M G Katze L S Kean H M Kubisch S Lank L A Lyons G M Miller J Nylander D H O Connor R E Palermo D G Smith E J Vallender R W Wiseman and J Rogers Citation J Med Primatol 38 17 23 Title Transcriptional profiling reveals significant distinctions in kinetics and tissue compartmentalization between pathogenic and nonpathogenic SIV infection Authors 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 Citation PLoS Pathog 5 e1000296 Data Microarray Data Title Host responses to wild type and attenuated herpes simplex virus infection in the absence of STAT1 Authors Pasieka T J C Cilloniz B Lu T H Teal S C Proll M G Katze and D A Leib Citation J Virol 83 2075 2087 Data Microarray Data Title Virus host interactions from systems biology to translational research Authors Peng X E C Chan Y Li D L Diamond M J Korth and M G Katze Citation Curr Op Microbiol 12 432 438 Title Computational identification of hepatitis C virus associated microRNA mRNA regulatory modules in human livers Authors Peng X Y Li K A Walters E R Rosenzweig S L Lederer L D Aicher S Proll and M G Katze Citation BMC Genomics 10 373 A BioMed Central Highly Accessed Article Data Supplemental Data Title Impaired cholesterol biosynthesis in a neuronal cell line persistently infected with measles virus Authors Robinzon S A Dafa Berger M D Dyer B Paeper S C Proll T H Teal S Rom D Fishman B Rager Zisman and M G Katze Citation J Virol 83 5495 5504 Data Microarray Data Title Early upregulation of ARDS associated cytokines promote lethal disease in an aged mouse model of SARS CoV infection Authors Rockx B T Baas G A Zornetzer B Haagmans T Sheahan M Frieman M D Dyer T H Teal S Proll J van den Brand R Baric and M G Katze Citation J Virol 83 7062 7074 Data Microarray Data Title Is systems biology the key to preventing the next pandemic Authors Tisoncik J R S E Belisle D L Diamond M J Korth and M G Katze Citation Future Virol 4 553 561 Title Using high throughput genomics to study hepatitis C what determines the outcome of infection Authors Walters K A and M G Katze Citation Antiviral Res 81 198 208 Title Genomic analysis reveals a potenital role for cell cycle perturbation in HCV mediated apoptosis of cultured hepatocytes Authors Walters K A A J Synder S L Lederer D L Diamond B Paeper C M Rice and M G Katze Citation PLoS Pathog 5 e1000269 Data Microarray Data 2008 Publications Title Down regulation of hepcidin in porphyria cutanea tarda Authors 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 Citation Blood 112 4723 4728 NIDA Data Microarray Data Title Genomic analysis reveals age dependent innate immune responses to SARS coronavirus Authors Baas T A Roberts T H Teal L Vogel J Chen T M Tumpey M G Katze and K Subbarao Citation J Virol 82 9465 9476 Data Microarray Data Title MAID an effect sized based model for microarray data integration across laboratories and platforms Authors Borozan I L Chen B Paeper J E Heathcote A M Edwards M Katze Z Zhang and I D McGilvray Citation BMC Bioinformatics 9 305 Title Innate immune modulation by RNA viruses emerging insights from functional genomics Authors Katze M G J L Fornek R E Palermo K A Walters and M J Korth Citation Nature Rev Immunol 8 644 654 Title UPR pathways combine to prevent hepatic steatosis caused by ER stress mediated suppression of transcriptional master regulators Authors Rutkowski D T J Wu S H Back M U Callaghan S P Ferris J Iqbai R Clark H Miao J R Hassler J Fornek M G Katze M M Hussain B Song J Swathirajan J Wang G D Y Yau and R J Kaufman Citation Dev Cell 15 829 840 2007 Publications Title Functional genomic and serological analysis of the protective immune response resulting from vaccination of macaques with an NS1 truncated influenza virus Authors 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 Citation J Virol 81 11817 11827 Data Microarray Data Title Quantitative analysis of HIV 1 infected CD4 cell proteome dysregulated cell cycle progression and nuclear transport coincide with robust virus production Authors 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 Citation J Virol 81 7571 7583 Title Functional genomics highlights differential induction of antiviral pathways in the lungs of SARS CoV infected macaques Authors de Lang A T Baas T Teal L M Leijten B Rain A D Osterhaus B L Haagmans and M G Katze Citation PLoS Pathog 3 e112 Data Microarray Data Title Proteomic profiling of human liver biopsies hepatitis C virus induced fibrosis and mitochondrial dysfunction Authors 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 Citation Hepatology 46 649 657 Data Supplemental Data Title Use of functional genomics to understand influenza virus host interactions Authors Fornek J L M J Korth and M G Katze Citation Adv Virus Res 70 81 100 Title Establishment and maintenance of the innate antiviral response to West Nile Virus involves both RIG I and MDA5 signaling through IPS 1 Authors Frederickson B L B C Keller J Fornek M G Katze and M Gale Jr Citation J Data Microarray Data Virol 82 609 616 Title Evolutionary and biomedical insights from the rhesus macaque genome Authors Gibbs R J Rogers M G Katze et al Citation Science 316 222 234 Title The cellular protein P58IPK regulates influenza virus mRNA translation and replication through a PKR mediated mechanism Authors Goodman A G J A Smith S Balachandran O Perwitasari S C Proll M J Thomas M J Korth G N Barber L A Schiff and M G Katze Citation J Virol 81 2221 2230 Title Lost in the world of functional genomics systems biology and translational research Is there life after the Milstein award Authors Katze M G and M J Korth Citation Cytokine Growth Factor Rev 18 441 450 Title Aberrant innate immune response in lethal infection of macaques with the 1918 influenza virus Authors 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 Citation Nature 445 319 323 Data ArrayExpress Microarray Data Title Functional genomics analyses of differential macaque peripheral blood mononuclear cell infections by human immunodeficiency virus 1 and simian immunodeficiency virus Authors Li Y E Y Chan and M G Katze Citation Virology 366 137 149 NIDA Data Microarray Data Title Distinct RIG I and MDA5 signaling by RNA viruses in innate immunity Authors Loo Y M J Fornek N Crochet G Bajwa O Perwitasari L Martinez Sobrido S Akira M A Gill A Garcia Sastre M G Katze and M Gale Jr Citation J Virol 82 335 345 Data Microarray Data Title The role of p58IPK in protecting the stressed endoplasmic reticulum Authors Rutkowski D T S W Kang A G Goodman J L Garrison J Taunton M G Katze R J Kaufman and R S Hegde Citation Mol Biol Cell 18 3681 3691 Title Systems biology and the host response to infection Authors Tan S L G Ganji B Paeper S Proll and M G Katze Citation Nature Biotechnol 25 1383 1389 Title Response of non transformed human hepatocytes to conditional expression of full length hepatitis C virus open reading frame Authors Tang W C Lazaro J Campbell T Parks M G Katze and N Fausto Citation Am J Pathol 171 1831 1846 Data Microarray Data Title High density rhesus macaque oligonucleotide microarray design using early stage rhesus genome sequence information and human genome annotations Authors 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 Citation BMC Genomics 8 28 Data ArrayExpress Microarray Data 2006 Publications Title Integrated molecular signature of disease analysis of influenza virus infected macaques through functional genomics and proteomics Authors 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 Citation J Virol 80 10813 10828 Data NCRR Proteomics Microarray Data Title SARS CoV virus host interactions and comparative etiologies of acute respiratory distress syndrome as determined by transcriptional and cytokine profiling of formalin fixed paraffin embedded tissues Authors Baas T J Taubenberger P Y Chong P Chui and M G Katze Citation J Interferon Cytokine Res 26 309 317 Title HepatoProteomics applying proteomic technologies to the study of liver function and disease Authors Diamond D L S C Proll J M Jacobs E Y Chan D G Camp R D Smith and M G Katze Citation Hepatology 44 299 308 Title Hijacking of the host cell response and translational control during influenza virus infection Authors Kash J C A G Goodman M J Korth and M G Katze Citation Virus Res 119 111 120 Title Global suppression of the host antiviral response by Ebola and Marburgviruses increased antagonism of the type 1 interferon response is associated with enhanced virulence Authors Kash J C E Muhlberger V Carter O Grosch O Perwitasari S C Proll M J Thomas F Weber H D Klenk and M G Katze Citation J Virol 80 3009 3020 Data Microarray Data Title Genomic analysis of increased host immune and cell death responses induced by 1918 influenza virus Authors Kash J C T M Tumpey S C Proll V Carter O Perwitasare M J Thomas C F Basler P Palese J K Taubenberger A Garcia Sastre D E Swayne and M G Katze Citation Nature 443 578 581 Data Microarray Data Title Insights into influenza virus host interactions through global gene expression profiling cell culture systems to animal models p 341 360 In Y Kawaoka ed Influenza virology current topics Authors Korth M J J C Kash C R Baskin and M G Katze Citation Horizon Scientific Press Wymondham U K Title Suppression of proinflammatory signal transduction and gene expression by the dual nucleic acid binding domains of the vaccinia virus E3L proteins Authors Langland J O J C Kash V Carter M J Thomas M G Katze and B L Jacobs Citation J Virol 80 10083 10095 Data Microarray Data ArrayExpress Title Distinct cellular responses differentiating alcohol and hepatitis C virus induced liver cirrhosis Authors Lederer S L K A Walters S Proll B Paeper S Robinzon L Boix N Fausto J Bruix and M G Katze Citation Virol J 3 98 Data Microarray Data Title Cotranslocational degradation protects the stressed endoplasmic reticulum from protein overload Authors Oyadomari S C Yun E A Fisher N Kreglinger G Kreibich M Oyadomari H P Harding A G Goodman H Harant J L Garrison J Taunton M G Katze and D Ron Citation Cell 126 727 739 Title Functional genomics analysis of herpes simplex virus type 1 counteraction of the host innate response Authors Pasieka T J T Baas V S Carter S C Proll D A Leib and M G Katze Citation J Virol 80 7600 7612 Data Microarray Data Title Reovirus induces and benefits from an integrated cellular stress response Authors Smith J A S C Schmechel A Raghavan M Abelson C Reilly M G Katze R J Kaufman P R Bohjanen and L A Schiff Citation J Virol 80 2019 2033 Title Gene expression patterns that correlate with hepatitis C and early progression to fibrosis in liver transplant recipients Authors Smith M W K A Walters M J Korth M Fitzgibbon S C Proll J C Thompson M M Yeh M C Shuhart J C Furlong P P Cox D L Thomas J D Phillips J P Kushner N Fausto R L Carithers and M G Katze Citation Gastroenterol 130 179 187 Data Microarray Data Title Functional gene analysis of individual response to challenge with simian immunodeficiency virus SIVmac239 in Macaca mulatta peripheral blood mononuclear cell culture Authors Thomas M J M B Agy S C Proll B W Paeper Y Li K L Jensen M J Korth and M G Katze Citation Virology 348 242 252 Data Microarray Data Title Use of human nasal cannulas during bronchoscopy procedures as a simple method for maintaining adequate oxygen saturation in pigtailed macaques Macaca nemestrina Authors Thomas M J L R Flanary B A Brown M G Katze and C R Baskin Citation J Am Assoc Lab Anim Sci 45 44 48 Title Virology in the 21st century finding function with functional genomics Authors Wallace J C M J Korth D L Diamond S C Proll and M G Katze Citation Future Virol 1 47 53 Title Application of functional genomics to the chimeric mouse model of HCV infection optimization of microarray protocols and genomics analysis Authors 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 Citation Virol J 3 37 Data Microarray Data Title Host specific response to HCV infection in the chimeric SCID beige Alb uPA mouse model role of the innate antiviral immune response Authors 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 Knetman D L Tyrrell and M G Katze Citation PLOS Pathogens 2 591 601 Data Microarray Data Title Identification of a specific gene expression pattern associated with HCV induced pathogenesis in HCV and HCV HIV infected individuals Authors 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 Jr M C Shuhart and M G Katze Citation Virology 350 453 464 Data Microarray Data 2005 Publications Title Integration with the human genome of peptide sequences obtained by high throughput mass spectrometry Authors 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 Citation Genome Biol 6 R9 Title Adaptation of near real time biosensor systems for monitoring of cabin air quality p 1 16 In C Winder ed Proceedings of the contaminated air protection conference University of New South Wales Sydney Authors Furlong C E R C Stevens S D Soelberg N Yee G Geiss M G Katze S Near S Yee and T Chinowsky Citation Title Proteome analysis of liver cells expressing a full length hepatitis C virus HCV replicon and biopsy specimens of posttransplantation liver from HCV infected patients Authors 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 Citation J Virol 79 7558 7569 Data NCRR Proteomics Title Virus infection and the interferon response a global view through functional genomics Authors Korth M J J C Kash J C Furlong and M G Katze Citation Methods Mol Med 116 37 55 Title Pancreatic cell failure in mice with a deletion mutation of the endoplasmic reticulum molecular chaperone gene P58IPK Authors Ladiges W C S E Knoblaugh J F Morton M J Korth B L Sopher C R Baskin A MacAuley A G Goodman R C LeBoeuf and M G Katze Citation Diabetes 54 1071 1081 Title Analysis of the Macaca mulatta transcriptome and the sequence divergence between Macaca and human Authors 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 Citation Genome Biol 6 R60 Data ArrayExpress Title Nef induces multiple genes involved in cholesterol synthesis and uptake in human immunodeficiency virus type 1 infected T cells Authors van t Wout AB Swain JV Schindler M Rao U Pathmajeyan MS Mullins JI Kirchhoff F Citation J Virol 79 10053 8 Data Microarray Data 2004 Publications Title Integration of clinical data pathology and cDNA microarrays in influenza virus infected pigtailed macaques Macaca nemestrina Authors Baskin C R A García Sastre T M Tumpey H Bielefeldt Ohmann V S Carter E Nistal Villán and M G Katze Citation J Virol 78 10420 10432 Data Microarray Data Title High throughput screening of the yeast kinome identification of human serine theronine kinases that phosphorylate the hepatitis C virus NS5A protein Authors Coito C D L Diamond P Neddermann M J Korth and M G Katze Citation J Virol 78 3502 3513 Title The host response to West Nile Virus infection limits viral spread through the activation of the interferon regulatory factor 3 pathway Authors Fredericksen B L M Smith M G Katze P Y Shi and M Gale Jr Citation J Virol 78 7737 7747 Data Microarray Data Title Global host immune response pathogenesis and transcriptional profiling of type A influenza viruses expressing the hemagglutinin and neuraminidase genes from the 1918 pandemic virus Authors Kash J C C F Basler A García Sastre V Carter R Billharz D E Swayne R M Przygodzki J K Taubenberger M G Katze and T M Tumpey Citation J Virol 78 9499 9511 Data Microarray Data Title A dataset of human liver proteins identified by protein profiling via isotope coded affinity tag ICAT and tandem mass spectrometry Authors Yan W H Lee E W Deutsch C A Lazaro W Tang E Chen N Fausto M G Katze and R Aebersold Citation Mol Cell Proteomics 3 1039 1041 Title System based proteomic analysis of the interferon response in human liver cells Authors 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 Citation Genome Biol 5 R54 2003 Publications Title Gene expression profiling of the cellular transcriptional network regulated by alpha beta interferon and its partial attenuation by the hepatitis C virus nonstructural 5A protein Authors Geiss G K V S Carter Y He B K Kwieciszewski T Holzman M J Korth C A Lazaro N Fausto R E Bumgarner and M G Katze Citation J Virol 77 6367 6375 Data Microarray Data Title The regulation of hepatitis C virus HCV internal ribosome entry site mediated translation by HCV replicons and nonstructural proteins Authors He Y W Yan C Coito Y Li M Gale and M G Katze Citation J Gen Virol 84 535 543 Data Supplemental Data Title Identification of novel tumor markers in hepatitis C virus associated hepatocellular carcinoma Authors 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 Citation Cancer Res 63 859 864 Data Microarray Data Title Hepatitis C virus and liver disease global transcriptional profiling and identification of potential markers Authors Smith M W Z N Yue M J Korth H A Do L Boix N Fausto J Bruix R L Carithers Jr and M G Katze Citation Hepatology 38 1458 1467 Data Microarray Data Title Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4 T cell lines Authors van t Wout A B G K Lehrman S A Mikheeva G C O Keeffe M G Katze R E Bumgarner G K Geiss and J I Mullins Citation J Virol 77 1392 1402 Data Microarray Data 2002 Publications Title P52rIPK regulates the molecular co chaperone P58IPK to mediate control of the RNA dependent protein kinase in response to cytoplasmic stress Authors Gale M Jr C M Blakely A Darveau P R Romano M J Korth and M G Katze Citation Biochemistry 41 11878 11887 Title Cellular transcriptional profiling in influenza A virus infected lung epithelial cells the role of the nonstructural NS1 protein in the evasion of the host innate defense and its potential contribution to pandemic influenza Authors Geiss G K M Salvatore T M Tumpey V S Carter X Wang C F Basler J K Taubengerger R E Bumgarner P Palese M G Katze and A García Sastre Citation Proc Natl Acad Sci USA 99 10736 10741 Data Microarray Data Supplemental Data Title To interfere and to anti interfere the interplay between hepatitis C virus and interferon Authors He Y and M G Katze Citation Viral Immunol 15 95 119 Title Subversion of cell signaling pathways by hepatitis C virus nonstructural 5A protein via interaction with Grb2 and

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  • Katze Lab
    Clues to Respiratory Diseases Mouse model suggests varied genetic dispositions to Ebola Dr Rasmussenn and Dr Katze discuss their publication in Science Senator Patty Murray praises Katze lab during Ebola hearing Ebola questions answered Are hospitals in this region prepared Discussion of federal government response to Ebola Dr Katze answers viewer questions about Ebola on Q13 FOX October 10 2014 Dr Katze questions US Ebola response Conversation about Ebola transmission on New Day Northwest October 6 2014 Dr Katze explains local Ebola research on Q13 FOX September 28 2014 Ebola outbreak Not just a one off event Katze says Dr Katze interviewed by KING 5 August 6 2014 Tactics of new Middle East virus suggest treating by altering lung cells response to infection Cell response to new coronavirus unveils possible paths to treatments UW to collaborate on biodefense drug development New targets for the control of HIV predicted using a novel computational analysis New class of biomolecules triggered in response to respiratory virus infection Personalising medicine to prevent pandemics University Week Hepatitis C virus reprograms liver cell metabolic functions Video Dr Katze featured in Dual Use Research A Dialogue UW will lead 13 million collaborative vaccine project UW scientists partner

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  • Katze Lab
    Her postdoctoral work identified critical host molecules regulating HCV and HIV infection both in vitro and in patients She also employs systems methods to identify features of pathogenesis and identify potential drug targets for many emerging or highly pathogenic viruses including dengue Ebola Lassa Lujo Middle East CoV and H7N9 influenza She holds a BA from Smith College and a MA M Phil and PhD in Microbiology from Columbia University Pavel Sova Ph D Research Scientist ps44 uw edu Pavel Sova came to Katze lab in 2009 as a virologist He has an extensive experience working with viruses including HIV Epstein Barr virus human cytomegalovirus adenovirus vaccinia virus flu and dengue virus Prior to joining the Katze lab in addition to his work with viruses he has been involved in cancer genomics epigenomics focusing on development of methylation biomarkers for early detection of cervical cancer in genomics of nonhuman primates and in development of oncolytic adenoviral vectors When not in the lab Pavel enjoys climbing or skiing Cascade peaks and volcanoes and spending time with his family Jenny Tisoncik Go Ph D Senior Research Scientist tisoncik uw edu Dr Go is applying systems approaches to the study of pathogen host interactions In particular she is interested in modeling the acute phase response during H1N1 pandemic influenza infection for a global understanding of transcriptome regulation leading to viral pathogenesis and severe respiratory disease Toward this end she is directing collaborative multidisciplinary projects in functional genomics including microarray and next generation sequencing studies utilizing in vitro and in vivo model systems and providing biological interpretation of high throughput omics datasets She obtained her Ph D in Microbiology and Immunology from the University of Illinois at Chicago where she examined influenza NA inhibitor resistance Dr Go maintains an active interest in science education and has been actively engaged in student science research mentoring programs Hongjie Wang Ph D Research Scientist wanghj uw edu Hongjie Wang is a molecular biologist interested in virus host interaction He received his Ph D from the University of Helsinki Prior to joining the Katze lab he worked on the field of adenovirus for 10 years Outside work he enjoys hiking and sitting by the campfire with his daughter Research Scientists Kristi Barker Research Scientist klbarker uw edu Kristi received a B S in Biology from the University of Texas at San Antonio and a M S in Biochemistry and Molecular Biology at Colorado State University Her graduate work focused on epigenetic regulation of gene expression in yeast Her first job was at The Center For Personalized Diagnostics at Arizona State University where she studied disease biomarkers protein post translational modifications and protein protein interactions using microarrays Kristi is excited to have moved to Seattle with an opportunity to learn new concepts in the Katze lab When not working she enjoys running yoga and hanging out with her two dogs Victoria Carter Research Scientist victoria uw edu Victoria joined the Katze lab in 1999 She brought with her 12

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  • Katze Lab
    a minimum of 4 years of experience in scientific research preferably in a life sciences biotechnical industry Master s degree in microbiology immunology bioinformatics or biostatistics is a plus A clear understanding of modern functional genomics is imperative Familiarity with statistical analysis and study design experience in implementing statistical strategies for various study designs to ensure correct application and interpretation of statistical models Experience with the analysis of high throughput data microarray NGS metabolomics proteomics etc including familiarity with statistical and bioinformatics tools Ability to builds successful collaborations with internal and external partners Ability to anticipate problems conflicts and provide resolution through creative problem solving High level of interpersonal skills as well as excellent communication and presentation skills Experience with LIMs is a plus Please email CV and cover letter to Xinxia Peng xinxiap uw edu SENIOR PROJECT MANAGER POSITION The Katze Lab currently has an outstanding opportunity for a Senior Project Manager The successful candidate will plan organize and supervise the research direction of multiple projects related to HIV SIV and nonhuman primate models This candidate should have a strong background in immunodeficiency virus biology immunology and vaccine development We seek virologists immunologists whose research interests include cellular and molecular immunology innate immunity nonhuman primate genomics and or host pathogen interaction The responsibilities include Plan organize and supervise the work of a staff of scientists and technicians including subordinate team leaders This will entail the direction of multiple projects related to HIV SIV and immunodeficiency virus host interactions Act as project manager and liaison with collaborators both academic and clinical at the local national and international level Develop strategies to achieve overall objectives and evaluate progress and results obtained as well as identify new areas of research activities Maintain up to date knowledge of new technical methods and developments affecting the research of the laboratory Evaluate and interpret experimental results Responsible for the development and preparation of scientific publications and presentations as well as participate in the development and preparation of grant proposals Act as a liaison with outside researchers in academic and industrial settings Cultivate collaborations with scientific thought leaders particularly with scientists in the pharmaceutical industry and biotechnology We are seeking individuals with the following qualifications Ph D in microbiology immunology biology or related field plus a minimum of 8 years of experience in scientific research preferably in a life sciences biotechnical industry A clear understanding of modern functional genomics Familiarity with statistical analysis and study design experience in implementing statistical strategies for various study designs to ensure correct application and interpretation of statistical models Familiarity with the analysis of high throughput data microarray NGS metabolomics proteomics etc including statistical and bioinformatics tools Ability to build successful collaborations with internal and external partners Ability to anticipate problems conflicts and provide resolution through creative problem solving High level of interpersonal skills as well as excellent communication and presentation skills Please email CV and cover letter to Michael Katze honey uw edu BIOINFORMATICS POSTDOCTORAL POSITION As a Bioinformatics Postdoctoral

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  • Genomics Services
    and Washington Science Sound Genomics The Katze lab offers Illumina Next Generation Sequencing and Data Analysis as a fee for service for researchers internal and external to the University of Washington Platforms available for sequencing include the Illumina NextSeq500 and MiSeq We offer standard library preparations for RNA seq applications However we can accommodate all library types prepared with Illumina adaptors for sequencing For more information on services and pricing

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  • Katze Lab
    paths to treatments China Virus and Washington Science CONTACT THE LAB Principal Investigator Michael G Katze Ph D Phone 206 732 6135 Fax 206 732 6056 E mail honey uw edu Lab Administrator Rose Howard Phone 206 732 6183 Fax 206 732 6056 E mail rmhoward uw edu Program Coordinator Jacqueline Perry Phone 206 732 6057 Fax 206 732 6056 E mail jacqp uw edu Data Access For questions related

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