Publications

Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses.

  • MBio. 2014 May 20;5(3):e01174-14. doi: 10.1128/mBio.01174-14.
  • Menachery VD, Eisfeld AJ, Schäfer 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 BJ, Schepmoes AA, Shukla AK, Metz TO, Smith RD, Waters KM, Katze MG, Kawaoka Y, Baric RS

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

  • mSystems. 2016 May 10; DOI: http://dx.doi.org/10.1128/mSystems.00043-16
  • Nakayasu ES, Nicora CD, Sims AC, Burnum-Johnson KE, Kim YM, Kyle JE, Matzke MM, Shukla AK, Chu RK, Schepmoes AA, Jacobs JM, Baric RS, Webb-Robertson BJ, Smith RD, Metz TO

Multi-task consensus clustering of genome-wide transcriptomes from related biological conditions.

  • Bioinformatics. 2016 May 15;32(10):1509-17. doi: 10.1093/bioinformatics/btw007. Epub 2016 Jan 21.
  • Niu Z, Chasman D, Eisfeld AJ, Kawaoka Y, Roy S

Systems biology: A tool for charting the antiviral landscape.

  • Virus Res. 2016 Jun 15;218:2-9. doi: 10.1016/j.virusres.2016.01.005. Epub 2016 Jan 12.
  • Bowen JR, Ferris MT, Suthar MS

A CRISPR screen defines a signal peptide processing pathway required by flaviviruses.

  • Nature. 2016 Jul 7;535(7610):164-8.
  • Zhang R, Miner JJ, Gorman MJ, Rausch K, Ramage H, White JP, Zuiani A, Zhang P, Fernandez E, Zhang Q, Dowd KA, Pierson TC, Cherry S, Diamond MS.

Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens.

  • PLoS Comput Biol. 2016 Jul 12;12(7):e1005013. doi: 10.1371/journal.pcbi.1005013. eCollection 2016.
  • Chasman D, Walters KB, Lopes TJ, Eisfeld AJ, Kawaoka Y, Roy S

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus.

  • BMC Syst Biol. 2016 Sep 23;10(1):93.
  • McDermott JE, Mitchell HD, Gralinski LE, Eisfeld AJ, Josset L, Bankhead A 3rd, Neumann G, Tilton SC, Schäfer A, Li C, Fan S, McWeeney S, Baric RS, Katze MG, Waters KM