Here are some recent publications where MicroScope has been used for genome analysis:
Jamet A, Jousset AB, Euphrasie D, Mukorako P, Boucharlat A, Ducousso A, Charbit A, Nassif X. A new family of secreted toxins in pathogenic Neisseria species.
PLoS Pathog. 2015 Jan 8;11(1):e1004592.
Rollat-Farnier PA, Santos-Garcia D, Rao Q, Sagot MF, Silva FJ, Henri H, Zchori-Fein E, Latorre A, Moya A, Barbe V, Liu SS, Wang XW, Vavre F, Mouton L. Two host clades, two bacterial arsenals: evolution through gene losses in facultative endosymbionts.
Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJ. Complex archaea that bridge the gap between prokaryotes and eukaryotes.
Nature. 2015 May 14;521(7551):173-9.
Lemire A, Goudenège D, Versigny T, Petton B, Calteau A, Labreuche Y, Le Roux F. Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters.
ISME J. 2015 Jul;9(7):1523-31.