Revealing miRNAs patterns by employing matrix representations and energy analysis.

MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression. Despite their relatively short length (about 21 nucleotides), they can regulate thousands of transcripts within a cell. Due to their low complementarity to targets, studying their activity and binding region preferences (3'UTR, 5'UTR, or CDS) is challenging.

Multifarious aspects of the chaos game representation and its applications in biological sequence analysis.

Chaos game representation (CGR) has been successfully applied in bioinformatics for over 30 years. Since then, many further extensions were announced. Numerical encoding of biological sequences is especially convenient in the visualisation process, free-alignment methods and input preparation for machine learning techniques.

The importance of atomic partial charges in the reproduction of intermolecular interactions for the triacetin - a model of glycerol backbone.

Lipids play a central role within the cell. They not only encompass it but are also engaged in many processes such as cellular transport and energy production. Despite ongoing advances in experimental studies, computer simulations are a viable method to trace their behavior at the atomic level and on an elusive time scale.

Optimal Solution to the Torsional Coefficient Fitting Problem in Force Field Parametrization.

Molecular modeling is an excellent tool for studying biological systems on the atomic scale. Depending on objects, which may be proteins, nucleic acids, or lipids, different force fields are recommended. The phospholipid bilayers constitute an example, in which behavior is extensively studied using molecular dynamics simulations due to limitations of experimental methods.

The robustness of the chaos game representation to mutations and its application in free-alignment methods.

Numerical representation of biological sequences plays an important role in bioinformatics and has many practical applications. One of the most popular approaches is the chaos game representation. In this paper, the authors propose a novel look into chaos game construction - an analytical description of this procedure.

DNA microarray integromics analysis platform.

Background: The study of interactions between molecules belonging to different biochemical families (such as lipids and nucleic acids) requires specialized data analysis methods. This article describes the DNA Microarray Integromics Analysis Platform, a unique web application that focuses on computational integration and analysis of "multi-omics" data. Our tool supports a range of complex analyses, including - among others - low- and high-level analyses of DNA microarray data, integrated analysis of transcriptomics and lipidomics data and the ability to infer miRNA-mRNA interactions.

Quantification of airborne birch (Betula sp.) pollen grains and allergens in Krakow.

Introduction: Birch (Betula sp.) pollen grains are the main cause of seasonal allergies in northern and central Europe. The allergen particles released from the grains are often well distributed in the air.

Telemedical database of Hodgkin's disease.

The creation of a complex telemedical system oriented towards childhood Hodgkin's disease has been undertaken at the Department of Bioinformatics and Telemedicine of the Jagiellonian University Medical College in cooperation with the Department of Oncology and Pediatric Hematology of the Polish-American Institute of Pediatrics, JU MC. Data collecting, data processing and data transmission is aimed to aid and/or supervise surgical and drug treatment. The Tele-Database of Childhood Hodgkin's Disease (TDCHD) is not a simple Internet database project.