This special issue collects five papers that were presented at the Mini EURO Conference on Computational Biology, Bioinformatics and Medicine organized by the EURO Working Group on Operational Research in Computational Biology, Bioinformatics and Medicine (EURO-CBBM). The Conference was held in Rome on September 2008 and included presentations of 61 talks selected on the basis of extended abstracts and three invited talks. The objective of the conference was to bring together researchers developing and using state-of-the art modeling and optimization approaches to solve problems in computational biology, bioinformatics and medicine. The conference program was planned with the objective of establishing an effective forum for the exchange and for the discussion of current research, issues and future trends in the above mentioned areas. The meeting was structured into 15 sessions on Protein Structure Analysis, Protein Structure Prediction, Structural Bioinformatics, Motif Recognition, Image Analysis, Dynamic Models, Networks, Data Mining Methods, DNA Sequencing, Optimization and Feature Extraction Methods and Microarray Analysis. Out of 61 presentations, 11 were evaluated for publication in the special issue. After two rounds of reviewing process, five papers were selected for publication. The first paper is “A Logic-Based Approach to Polymer Sequence Analysis” by R. Bruni. This paper presents an improved propositional logic based approach for the estimation of protein sequences from mass spectroscopy results. The correspondence