The fast growth of data in the academic field has contributed to making recommendation systems for scientific papers more popular. Content-based filtering (CBF), a pivotal technique in recommender systems (RS), holds particular significance in the realm of scientific publication recommendations. In a content-based scientific publication RS, recommendations are composed by observing the features of users and papers. Content-based recommendation encompasses three primary steps, namely, item representation, user modeling, and recommendation generation. A crucial part of generating recommendations is the user modeling process. Nevertheless, this step is often neglected in existing content-based scientific publication RS. Moreover, most existing approaches do not capture the semantics of user models and papers. To address these limitations, in this paper we present a transparent Recommendation and Interest Modeling Application (RIMA), a content-based scientific publication RS that implicitly derives user interest models from their authored papers. To address the semantic issues, RIMA combines word embedding-based keyphrase extraction techniques with knowledge bases to generate semantically-enriched user interest models, and additionally leverages pretrained transformer sentence encoders to represent user models and papers and compute their similarities. The effectiveness of our approach was assessed through an offline evaluation by conducting extensive experiments on various datasets along with user study (N = 22), demonstrating that (a) combining SIFRank and SqueezeBERT as an embedding-based keyphrase extraction method with DBpedia as a knowledge base improved the quality of the user interest modeling step, and (b) using the msmarco-distilbert-base-tas-b sentence transformer model achieved better results in the recommendation generation step.