This multi-method study presents an exercise in applied discourse analysis conducted within the broad framework of systemic-functional linguistics. The theoretical part of the work explores the relationship between one functional component of language, Halliday's notion of Theme, and the characterisation of a particular genre, the scientific research article (RA). Relevant literature on a variety of views of genre and Theme in the traditions of English for Academic Purposes (FAP) and systemic-functional linguistics is reviewed. The integration of these two levels of functional description is used as a basis for exploring the way in which Theme and generic structure relate to 'successful' processes and products of scientific research communication. The particular educational setting for the applied part of this work is the writing of first scientific RAs in English by NNS (non-native speaker) novice researchers. The primary method of study adopted here is corpus-based and initial discourse-functional analysis and description of marked and unmarked thematic choices are based on a corpus of 36 published RAs in the physical and life sciences written by 'experienced' NSs. This corpus represents a base 'norm' of thematic usage against which other corpora are compared, namely, published RAs written by 'experienced' NNS scientists and unpublished first and final RA drafts written by NNS novices. Major findings indicated that 'appropriate' thematic selections in the RA genre are constrained by the changing rhetorical purposes, signalled by means of moves, which operate throughout the different stages of scientific RA discourse; thus, the textual metafunction of Theme plays a significant role in the characterisation and dynamic wi thin-text structuring of the scientific RA genre. Furthermore, background surveys by means of questionnaires and interviews of the participants in the process of international research communication, in particular, of 'expert' NS journal editors, confirmed that 'appropriate' thematic control was clearly associated with the judgement of the merits of NNSs' RAs, and thereby, their 'successful' publication. With the pedagogical application of such theoretical insights in mind, the use of the teaching/research tool of Propositional Clusters (PCs) was explored in the EAP classroom as a heuristic for raising NNS novices' awareness about the manipulation of Theme in drafting and redrafting RA sections. Data collected from PCs exercises indicated their potential to raise awareness about the role of 'appropriate' thematic control in helping to create 'successful' texts. This study contributes to our understanding of aspects of the functional relationship between elements of discourse structure and lexica-grammatical components such as Theme/Subject. In addition, reflecting the social-semiotic perspective of a systemic-functional framework, this work strongly emphasises the social-constructionist nature of the processes involved in international research communication through the medium of the scientific research article.