Literature cited, project 2017J2RMTN

Posted on by
  1. Berni Canani, , De Filippis, F., et al. 2017. Appl. Environ. Microbiol. 83: e01206-17.  https://dx.doi.org/10.1128/AEM.01206-17.
  2. Bokulich, N. A., Mills, D.A. 2013. Appl. Environmen. Microbiol. 79: 2519–226.  https://dx.doi.org/10.1128/AEM.03870-12.
  3. Callahan, B. J., McMurdie, P. J., Holmes, S. P.. 2017. ISME J. 11: 2639–4263. https://dx.doi.org/10.1038/ismej.2017.119.
  4. Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A.J.A., Holmes, S. P. 2016. Nature Meth. 13: 581–583. https://dx.doi.org/10.1038/nmeth.3869.
  5. De Filippis, F., Parente, E., Ercolini, D. 2017a. Microbial Biotechnol. 10: 91–102. https://dx.doi.org/10.1111/1751-7915.12421.
  6. De Filippis, F., Laiola, M., Blaiotta, G., Ercolini, D.. 2017b. Appl. Environ. Microbiol., 83: e00905–17. https://dx.doi.org/10.1128/AEM.00905-17.
  7. De Filippis, F., Parente, E., Danilo Ercolini. Ann. Rev. Food Sci. Technol. 9. https://dx.doi.org/10.1146/annurev-food-030117-012312.
  8. De Filippis, F., Parente, E., Zotta, T., Ercolini, D. 2018b. J. Food Microbiol. 265: 9–17. https://dx.doi.org/10.1016/j.ijfoodmicro.2017.10.028.
  9. EFSA (2015). The food classification and description system FoodEx 2 (revision 2). Supporting publication 2015:EN-804. http://www.efsa.europa.eu/en/supporting/pub/215e.htm
  10. Emerson, J. B., Adams, R. I., Betancourt Román C. M., Brooks, B., Coil, D. A., Dahlhausen, Holly H. Ganz, K., et al. 2017. Microbiome 5: 86. https://dx.doi.org/10.1186/s40168-017-0285-3.
  11. Erkus, O., de Jager, V.C.L., Geene, R. T. C. M., van Alen-Boerrigter, I., Hazelwood, L., van Hijum, S. A .F. T., Kleerebezem, M., Smid, E. J. 2016. Int. J. Food Microbiol. 228: 1–9. https://dx.doi.org/10.1016/j.ijfoodmicro.2016.03.027.
  12. Faust, K., Raes, J. 2016. F1000Research 5: 1519–14. https://dx.doi.org/10.12688/f1000research.9050.2.
  13. Fouhy, F., Clooney, A. G., Stanton, C., Claesson, M.J., Cotter, P. D. 2016. BMC Microbiol. 16: 123. https://dx.doi.org/10.1186/s12866-016-0738-z.
  14. Garofalo, C., Osimani, A., Milanovic, V., Aquilanti, L., De Filippis, F., Stellato, G., Di Mauro, S., Turchetti, B., Buzzini, P., Ercolini, D., Clementi, F., 2015. Food Microbiol. 49: 123-133. https://dx.doi.org/10.1016/j.fm.2015.01.017
  15. Humblot, C., Guyot, J.-P. 2009. Appl. Environ. Microbiol. 75: 4354–4361. https://dx.doi.org/10.1128/AEM.00451-09.
  16. Kuuliala, L., Al Hage, Y., Ioannidis, A.-G., Sader, M., Kerckhof, F.-M., Vanderroost, M., Boon, N. et al. 2018. Food Microbiol. 70: 232–44. https://dx.doi.org/10.1016/j.fm.2017.10.011.
  17. Layeghifard, M., Hwang, D. M., Guttman, D. S. 2017. Trends Microbiol. 25: 217–28. https://dx.doi.org/10.1016/j.tim.2016.11.008.
  18. Levy, S.E., Myers, R.M. 2016. Annu. Rev. Genom. Hum. Genet. 17:95-115. https://dx.doi.org/10.1146/annurev-genom-083115-022413
  19. McDonald, D., Price, M.N., Goodrich, J., et al. 2012. ISME J. 6(3): 610-618. https://dx.doi.org/1038/ismej.2011.139.
  20. McMurdie, P. J., Susan Holmes. 2015. Bioinformatics 31: 282–283. https://dx.doi.org/10.1093/bioinformatics/btu616.
  21. Mitchell, A. L., Scheremetjew, M., Denise, H., Potte, S., Tarkowska, A., Qureshi, M., Salazar, G. A., et al. 2018. Nucleic Acids Research 46: D726–35. https://dx.doi.org/10.1093/nar/gkx967.
  22. Nature Editorial 2016. Nature Microbiology 1: 16112. https://dx.doi.org/10.1038/nmicrobiol.2016.112
  23. Parente, E., Cocolin, L., De Filippis, F., Zotta, T., Ferrocino, I., O’Sullivan, O., Neviani, E., De Angelis, M., Cotter, P. D., Ercolini, D. 2016. Int. J. Food Microbiol. 219 28–37. https://dx.doi.org/10.1016/j.ijfoodmicro.2015.12.001.
  24. Parente, E., Zotta, T., Faust, K., De Filippis, F., Ercolini, D. 2018. Food Microbiol. 73: 49-60. https://dx.doi.org/10.1016/j.fm.2017.12.010.
  25. Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P. et al. 2013. Nucl. Ac. Res. 41 (Database issue): D590–96.  https://dx.doi.org/10.1093/nar/gks1219.
  26. Qin J, et al. 2010. Nature. 464: 59-65. https://dx.doi.org/10.1038/nature08821.
  27. Quince, C., Walker, A.W., Simpson, J.T., Loman, N.J., Segata, N. 2017. Nat. Biotechnol. 35: 833-844. https://dx.doi.org/10.1038/nbt.3935.
  28. Sedlar, K., Kupkova, K., Provaznik, I. 2017. Comput. Struct. Biotecnol. J. 15: 48-55.  https://dx.doi.org/1016/j.csbj.2016.11.005.
  29. Singer, Esther, Bill Andreopoulos, Robert M Bowers, Janey Lee, Shweta Deshpande, Jennifer Chiniquy, Doina Ciobanu, et al. 2016. Scientific Data 3: 160081. https://dx.doi.org/10.1038/sdata.2016.81.
  30. Stellato, G., De Filippis, F., La Storia, A., Ercolini, D. 2015. and Envirn. Microbiol. 81:7893-7904. https://dx.doi.org/10.1128/AEM.02294-15.
  31. Thompson, L. R, Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J. et al. 2017. Nature 104: 457-465. https://dx.doi.org/10.1038/nature24621.
  32. Vandeputte, D., Tito, R.Y., Vanleeuwen, R., Falony, G., Raes, J. 2017. FEMS Microbiol. Rev. 41: S154–67. https://dx.doi.org/10.1093/femsre/fux027.
  33. Zhou, J., He, Z., Yang, Y., Deng, Y., Tringe, S. G., Alvarez-Cohen. L. 2015. mBio 6 (1). https://dx.doi.org/10.1128/mBio.02288-14.