Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA: Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med. 2012, 367 (19): 1814-1820. 10.1056/NEJMoa1211721.
Article
CAS
PubMed
Google Scholar
Bermingham A, Chand MA, Brown CS, Aarons E, Tong C, Langrish C, Hoschler K, Brown K, Galiano M, Myers R, Pebody RG, Green HK, Boddington NL, Gopal R, Price N, Newsholme W, Drosten C, Fouchier RA, Zambon M: Severe respiratory illness caused by a novel coronavirus, in a patient transferred to the United Kingdom from the Middle East, September 2012. Euro Surveill. 2012, 17 (40): 20290-
CAS
PubMed
Google Scholar
Raj VS, Mou H, Smits SL, Dekkers DH, Muller MA, Dijkman R, Muth D, Demmers JA, Zaki A, Fouchier RA, Thiel V, Drosten C, Rottier PJ, Osterhaus AD, Bosch BJ, Haagmans BL: Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC. Nature. 2013, 495 (7440): 251-254. 10.1038/nature12005.
Article
CAS
PubMed
Google Scholar
Scobey T, Yount BL, Sims AC, Donaldson EF, Agnihothram SS, Menachery VD, Graham RL, Swanstrom J, Bove PF, Kim JD, Grego S, Randell SH, Baric RS: Reverse genetics with a full-length infectious cDNA of the Middle East respiratory syndrome coronavirus. Proc Natl Acad Sci U S A. 2013, 110 (40): 16157-16162. 10.1073/pnas.1311542110.
Article
CAS
PubMed Central
PubMed
Google Scholar
Mielech AM, Kilianski A, Baez-Santos YM, Mesecar AD, Baker SC: MERS-CoV papain-like protease has deISGylating and deubiquitinating activities. Virology. 2014, 450–451: 64-70.
Article
PubMed
Google Scholar
Niemeyer D, Zillinger T, Muth D, Zielecki F, Horvath G, Suliman T, Barchet W, Weber F, Drosten C, Muller MA: Middle East respiratory syndrome coronavirus accessory protein 4a is a type I interferon antagonist. J Virol. 2013, 87 (22): 12489-12495. 10.1128/JVI.01845-13.
Article
CAS
PubMed Central
PubMed
Google Scholar
Siu KL, Yeung ML, Kok KH, Yuen KS, Kew C, Lui PY, Chan CP, Tse H, Woo PC, Yuen KY, Jin DY: Middle East respiratory syndrome coronavirus 4a protein is a double-stranded RNA-binding protein that suppresses PACT-induced activation of RIG-I and MDA5 in innate antiviral response. J Virol. 2014, 88 (9): 4866-4876. 10.1128/JVI.03649-13.
Article
PubMed Central
PubMed
Google Scholar
Chan RW, Chan MC, Agnihothram S, Chan LL, Kuok DI, Fong JH, Guan Y, Poon LL, Baric RS, Nicholls JM, Peiris JS: Tropism of and innate immune responses to the novel human betacoronavirus lineage C virus in human ex vivo respiratory organ cultures. J Virol. 2013, 87 (12): 6604-6614. 10.1128/JVI.00009-13.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lau SK, Lau CC, Chan KH, Li CP, Chen H, Jin DY, Chan JF, Woo PC, Yuen KY: Delayed induction of proinflammatory cytokines and suppression of innate antiviral response by the novel Middle East respiratory syndrome coronavirus: implications for pathogenesis and treatment. J Gen Virol. 2013, 94 (Pt 12): 2679-2690.
Article
CAS
PubMed
Google Scholar
Kindler E, Jonsdottir HR, Muth D, Hamming OJ, Hartmann R, Rodriguez R, Geffers R, Fouchier RA, Drosten C, Muller MA, Dijkman R, Thiel V: Efficient replication of the novel human betacoronavirus EMC on primary human epithelium highlights its zoonotic potential. mBio. 2013, 4 (1): e00611-e00612.
Article
CAS
PubMed Central
PubMed
Google Scholar
Josset L, Menachery VD, Gralinski LE, Agnihothram S, Sova P, Carter VS, Yount BL, Graham RL, Baric RS, Katze MG: Cell Host Response to Infection with Novel Human Coronavirus EMC Predicts Potential Antivirals and Important Differences with SARS Coronavirus. mBio. 2013, 4 (3): e00165-13.
Article
CAS
PubMed Central
PubMed
Google Scholar
Faure E, Poissy J, Goffard A, Fournier C, Kipnis E, Titecat M, Bortolotti P, Martinez L, Dubucquoi S, Dessein R, Gosset P, Mathieu D, Guery B: Distinct Immune Response in Two MERS-CoV-Infected Patients: Can We Go from Bench to Bedside?. PLoS One. 2014, 9 (2): e88716-10.1371/journal.pone.0088716.
Article
PubMed Central
PubMed
Google Scholar
Cotten M, Watson SJ, Kellam P, Al-Rabeeah AA, Makhdoom HQ, Assiri A, Al-Tawfiq JA, Alhakeem RF, Madani H, Alrabiah FA, Al Hajjar S, Al-nassir WN, Albarrak A, Flemban H, Balkhy HH, Alsubaie S, Palser AL, Gall A, Bashford-Rogers R, Rambaut A, Zumla AI, Memish ZA: Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study. Lancet. 2013, 382 (9909): 1993-2002. 10.1016/S0140-6736(13)61887-5.
Article
PubMed Central
PubMed
Google Scholar
Agnihothram S, Gopal R, Yount BL, Donaldson EF, Menachery VD, Graham RL, Scobey TD, Gralinski LE, Denison MR, Zambon M, Baric RS: Evaluation of Serologic and Antigenic Relationships Between Middle Eastern Respiratory Syndrome Coronavirus and Other Coronaviruses to Develop Vaccine Platforms for the Rapid Response to Emerging Coronaviruses. J Infect Dis. 2014, 209 (7): 995-1006. 10.1093/infdis/jit609.
Article
CAS
PubMed Central
PubMed
Google Scholar
Edelsbrunner H, Letscher D, Zomorodian A: Topological persistence and simplication. Discrete Comput Geom. 2002, 28: 511-533. 10.1007/s00454-002-2885-2.
Article
Google Scholar
Edelsbrunner H, Harer JL: Computational Topology: An Introduction. 2009, Providence: American Mathematical Society
Book
Google Scholar
Singh G, Mémoli F, Carlsson G: Topological Methods for the Analysis of High Dimensional Data Sets and 3D Object Recognition. Eurographics Symposium on Point-Based Graphics 2007. 2007, Prague: The Eurographics Assocation
Google Scholar
Sims AC, Tilton SC, Menachery VD, Gralinski LE, Schafer A, Matzke MM, Webb-Robertson BJ, Chang J, Luna ML, Long CE, Shukla AK, Bankhead AR, Burkett SE, Zornetzer G, Tseng CT, Metz TO, Pickles R, McWeeney S, Smith RD, Katze MG, Waters KM, Baric RS: Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells. J Virol. 2013, 87 (7): 3885-3902. 10.1128/JVI.02520-12.
Article
CAS
PubMed Central
PubMed
Google Scholar
Totura AL, Baric RS: SARS coronavirus pathogenesis: host innate immune responses and viral antagonism of interferon. Curr Opin Virol. 2012, 2 (3): 264-275. 10.1016/j.coviro.2012.04.004.
Article
CAS
PubMed
Google Scholar
Tao X, Hill TE, Morimoto C, Peters CJ, Ksiazek TG, Tseng CT: Bilateral entry and release of Middle East respiratory syndrome coronavirus induces profound apoptosis of human bronchial epithelial cells. J Virol. 2013, 87 (17): 9953-9958. 10.1128/JVI.01562-13.
Article
CAS
PubMed Central
PubMed
Google Scholar
Chen L-C, Chen C-C, Liang Y, Tsang N-M, Chang Y-S, Hsueh C: A novel role for TNFAIP2: its correlation with invasion and metastasis in nasopharyngeal carcinoma. Mod Pathol. 2011, 24 (2): 175-184. 10.1038/modpathol.2010.193.
Article
CAS
PubMed
Google Scholar
Platanias LC, Fish EN: Signaling pathways activated by interferons. Exp Hematol. 1999, 27 (11): 1583-1592. 10.1016/S0301-472X(99)00109-5.
Article
CAS
PubMed
Google Scholar
Park H, Li Z, Yang XO, Chang SH, Nurieva R, Wang YH, Wang Y, Hood L, Zhu Z, Tian Q, Dong C: A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17. Nat Immunol. 2005, 6 (11): 1133-1141. 10.1038/ni1261.
Article
CAS
PubMed Central
PubMed
Google Scholar
Malicet C, Giroux V, Vasseur S, Dagorn JC, Neira JL, Iovanna JL: Regulation of apoptosis by the p8/prothymosin alpha complex. Proc Natl Acad Sci U S A. 2006, 103 (8): 2671-2676. 10.1073/pnas.0508955103.
Article
CAS
PubMed Central
PubMed
Google Scholar
Jiang YF, Vaccaro MI, Fiedler F, Calvo EL, Iovanna JL: Lipopolysaccharides induce p8 mRNA expression in vivo and in vitro. Biochem Biophys Res Commun. 1999, 260 (3): 686-690. 10.1006/bbrc.1999.0953.
Article
CAS
PubMed
Google Scholar
Vasseur S, Hoffmeister A, Garcia-Montero A, Mallo GV, Feil R, Kuhbandner S, Dagorn JC, Iovanna JL: p8-deficient fibroblasts grow more rapidly and are more resistant to adriamycin-induced apoptosis. Oncogene. 2002, 21 (11): 1685-1694. 10.1038/sj.onc.1205222.
Article
CAS
PubMed
Google Scholar
Kreisel D, Sugimoto S, Tietjens J, Zhu J, Yamamoto S, Krupnick AS, Carmody RJ, Gelman AE: Bcl3 prevents acute inflammatory lung injury in mice by restraining emergency granulopoiesis. J Clin Invest. 2011, 121 (1): 265-276. 10.1172/JCI42596.
Article
CAS
PubMed Central
PubMed
Google Scholar
Deng X, Xu M, Yuan C, Yin L, Chen X, Zhou X, Li G, Fu Y, Feghali-Bostwick CA, Pang L: Transcriptional regulation of increased CCL2 expression in pulmonary fibrosis involves nuclear factor-kappaB and activator protein-1. Int J Biochem Cell Biol. 2013, 45 (7): 1366-1376. 10.1016/j.biocel.2013.04.003.
Article
CAS
PubMed
Google Scholar
Held KS, Chen BP, Kuziel WA, Rollins BJ, Lane TE: Differential roles of CCL2 and CCR2 in host defense to coronavirus infection. Virology. 2004, 329 (2): 251-260. 10.1016/j.virol.2004.09.006.
Article
CAS
PubMed
Google Scholar
Wathelet MG, Orr M, Frieman MB, Baric RS: Severe acute respiratory syndrome coronavirus evades antiviral signaling: role of nsp1 and rational design of an attenuated strain. J Virol. 2007, 81 (21): 11620-11633. 10.1128/JVI.00702-07.
Article
CAS
PubMed Central
PubMed
Google Scholar
Seto T, Yoshitake M, Ogasawara T, Ikari J, Sakamoto A, Hatano M, Hirata H, Fukuda T, Kuriyama T, Tatsumi K, Tokuhisa T, Arima M: Bcl6 in pulmonary epithelium coordinately controls the expression of the CC-type chemokine genes and attenuates allergic airway inflammation. Clin Exp Allergy. 2011, 41 (11): 1568-1578. 10.1111/j.1365-2222.2011.03836.x.
Article
CAS
PubMed
Google Scholar
Mizutani T, Fukushi S, Murakami M, Hirano T, Saijo M, Kurane I, Morikawa S: Tyrosine dephosphorylation of STAT3 in SARS coronavirus-infected Vero E6 cells. FEBS Lett. 2004, 577 (1–2): 187-192.
Article
CAS
PubMed
Google Scholar
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-alpha2b and ribavirin improves outcome in MERS-CoV-infected rhesus macaques. Nat Med. 2013, 19 (10): 1313-1317. 10.1038/nm.3362.
Article
CAS
PubMed Central
PubMed
Google Scholar
Falzarano D, de Wit E, Feldmann F, Rasmussen AL, Okumura A, Peng X, Thomas MJ, van Doremalen N, Haddock E, Nagy L, LaCasse R, Liu T, Zhu J, McLellan JS, Scott DP, Katze MG, Feldmann H, Munster VJ: Infection with MERS-CoV Causes Lethal Pneumonia in the Common Marmoset. PLoS Pathog. 2014, 10 (8): e1004250-10.1371/journal.ppat.1004250.
Article
PubMed Central
PubMed
Google Scholar
Zhao J, Li K, Wohlford-Lenane C, Agnihothram SS, Fett C, Gale MJ, Baric RS, Enjuanes L, Gallagher T, McCray PB, Perlman S: Rapid generation of a mouse model for Middle East respiratory syndrome. Proc Natl Acad Sci U S A. 2014, 111 (13): 4970-4975. 10.1073/pnas.1323279111.
Article
CAS
PubMed Central
PubMed
Google Scholar
Agnihothram S, Yount BL, Donaldson EF, Huynh J, Menachery VD, Gralinski LE, Graham RL, Becker MM, Tomar S, Scobey TD, Osswald HL, Whitmore A, Gopal R, Ghosh AK, Mesecar A, Zambon M, Heise M, Denison MR, Baric RS: A Mouse Model for Betacoronavirus Subgroup 2c Using a Bat Coronavirus Strain HKU5 Variant. mBio. 2014, 5 (2): e00047-14-10.1128/mBio.00047-14.
Article
PubMed Central
PubMed
Google Scholar
Law GL, Tisoncik-Go J, Korth MJ, Katze MG: Drug repurposing: a better approach for infectious disease drug discovery?. Curr Opin Immunol. 2013, 25 (5): 588-592. 10.1016/j.coi.2013.08.004.
Article
CAS
PubMed Central
PubMed
Google Scholar
Menachery VD, Eisfeld AJ, Schafer A, Josset L, Sims AC, Proll S, Fan S, Li C, Neumann G, Tilton SC, Chang J, Gralinski LE, Long C, Green R, Williams CM, Weiss J, Matzke MM, Webb-Robertson B-J, Schepmoes AA, Shukla AK, Metz TO, Smith RD, Waters KM, Katze MG, Kawaoka Y, Baric RS: Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses. mBio. 2014, 5 (3): e01174-01114-
Article
Google Scholar
Johnson WE, Li C, Rabinovic A: Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007, 8 (1): 118-127. 10.1093/biostatistics/kxj037.
Article
PubMed
Google Scholar
Tausz A: phom: Persistent Homology in R, Version 1.0.1. 2011, Available at CRAN http://cran.r-project.org
Google Scholar
Carlsson G, Zomorodian A, Collins A, Guibas L: Persistence Barcodes for Shapes. Eurographics Symposium on Geometry Processing. Edited by: Scopigno R, Zorin D. 2004, New York: ACM
Google Scholar
Kruskal JB: Nonmetric Multidimensional Scaling: A Numerical Method. Psychometrika. 1964, 29 (2): 115ff-10.1007/BF02289694.
Article
Google Scholar
Smyth G: Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions using R and Bioconductor. Edited by: Gentleman RVC, Dudoit S, Irizarry R, Huber W. 2005, New York: Springer
Google Scholar
Rozen S, Skaletsky H: Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 2000, 132: 365-386.
CAS
PubMed
Google Scholar
Livak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001, 25 (4): 402-408. 10.1006/meth.2001.1262.
Article
CAS
PubMed
Google Scholar
Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A: Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013, 14: 128-10.1186/1471-2105-14-128.
Article
PubMed Central
PubMed
Google Scholar
Zambelli F, Pesole G, Pavesi G: Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes. Nucleic Acids Res. 2009, 37 (Web Server issue): W247-W252.
Article
CAS
PubMed Central
PubMed
Google Scholar