Oleksiy Karpenko

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OBJECTIVE Predictions of the binding ability of antigen peptides to major histocompatibility complex (MHC) class II molecules are important in vaccine development. The variable length of each binding peptide complicates this prediction. METHODOLOGY Motivated by the search properties of the ant colony system (ACS), a method for the identification of an(More)
UNLABELLED BACKGROUND Fibromyalgia (FM) is a clinical syndrome characterized by chronic pain and allodynia. The diagnosis of FM has been one of exclusion as a test to confirm the diagnosis is lacking. Recent data highlight the role of the immune system in FM. Aberrant expressions of immune mediators, such as cytokines, have been linked to the(More)
Several computational methods for the prediction of major histocompatibility complex (MHC) class II binding peptides embodying different strengths and weaknesses have been developed. To provide reliable prediction, it is important to design a system that enables the integration of outcomes from various predictors. The construction of a meta-predictor of(More)
RATIONALE Strategies to stage and treat cancer rely on a presumption of either localized or widespread metastatic disease. An intermediate state of metastasis termed oligometastasis(es) characterized by limited progression has been proposed. Oligometastases are amenable to treatment by surgical resection or radiotherapy. METHODS We analyzed microRNA(More)
MOTIVATION The highly coordinated expression of thousands of genes in an organism is regulated by the concerted action of transcription factors, chromatin proteins and epigenetic mechanisms. High-throughput experimental data for genome wide in vivo protein-DNA interactions and epigenetic marks are becoming available from large projects, such as the model(More)
Prediction of class II major histocompatibility complex (MHC)-peptide binding is a challenging task due to variable length of binding peptides. Different computational methods have been developed; however, each has its own strength and weakness. In order to provide reliable prediction, it is important to design a system that enables the integration of(More)
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