The article is devoted to the analysis of publication activity of the flagship university (scientometric indicators of teachers and researchers) as one of the key indicators for assessing the contribution of the flagship university to the social and economic development of the region. While solving the research tasks, the authors defined the list of scientometric indicators for assessing scientific results, analyzed the scientometric indicators of development of Yaroslav-the-Wise Novgorod State University (Veliky Novgorod) for the past three years, determined the importance of a further increase in publication activity of the university for a positive influence on the regional development. The authors consider the strategy for transformation and integration of the flagship university into the University-Region ecosystem of the regional innovative development fixed at federal and regional levels, in order to introduce advanced and knowledge-intensive technologies into the digital economy of the territory. The authors described the first results obtained within the indicated collaboration and the performance of the university as an autonomous strategic agent of regional transformations. The authors outlined the main directions of innovative development of Yaroslav-the-Wise Novgorod State University and the Novgorod Region as an advanced scientific and technological center (in the field of intelligent electronics among others), the center for developing social, anthropologic, cultural, urban and other studies which determine current and future directions of the university's publication activity. The authors note an increase in scale and effectiveness of research due to the interaction between the region and the flagship university, which manifests itself both in the growth of publication activity and in an increased volume of attracted grant funds which, in turn, are the source of financing scientific publications. The number of publications co-authored with residents of other states and industrial partners increased. To obtain results, the authors used a comparative method (quantitative and qualitative analysis), modern tools for bibliometric analysis, forecasting, an economic and statistic method.