Jan Badura

• Poznań University of Technology

RNA molecules are essential in regulating biological processes such as gene expression, cellular differentiation, and development. Accurately predicting RNA secondary structures and designing sequences that fold into specific configurations remain significant challenges in computational biology, with far-reaching implications for medicine, syntheti...

RNA molecules play vital roles in many biological processes, such as gene regulation or protein synthesis. The adoption of a specific secondary and tertiary structure by RNA is essential to perform these diverse functions, making RNA a popular tool in bioengineering therapeutics. The field of RNA design responds to the need to develop novel RNA mol...

This paper concludes the Brilliant Challenges contest. Participants had to design interesting optimization problems and publish them using the Optil.io platform. It was the first widely-advertised contest in the area of operational research where the objective was to submit the problem definition instead of the algorithmic solutions. Thus, it is a...

Motivation There are very few methods for de novo genome assembly based on the overlap graph approach. It is considered as giving more exact results than the so-called de Bruijn graph approach but in much greater time and of much higher memory usage. It is not uncommon that assembly methods involving the overlap graph model are not able to successf...

The pseudoknot is a specific motif of the RNA structure that highly influences the overall shape and stability of a molecule. It occurs when nucleotides of two disjoint single-stranded fragments of the same chain, separated by a helical fragment, interact with each other and form base pairs. Pseudoknots are characterized by great topological divers...

We propose a new method for analyzing a set of parameters in a multiple criteria ranking method. Unlike the existing techniques, we do not use any optimization method, instead incorporating and extending a Segmenting Description (SD) approach. The algorithm rewrites a set of initial inequalities into an equivalent SD system by means of three fundam...

We propose a new method for analyzing a set of parameters in a multiple criteria ranking method. Unlike the existing techniques, we do not use any optimization technique, instead incorporating and extending a Segmenting Description approach. While considering a value-based preference disaggregation method, we demonstrate the usefulness of the intro...

Next generation sequencers produce billions of short DNA sequences in a massively parallel manner, which causes a great computational challenge in accurately reconstructing a genome sequence de novo using these short sequences. Here, we propose the GRASShopPER assembler, which follows an approach of overlap-layout-consensus. It uses an efficient GP...

Assemblies obtained for the data set Homo sapiens chromosome 14. (DOCX)

Scaffolding of the data set Homo sapiens chromosome 14 for the assemblers GRASShopPER, SOAPdenovo2 and SGA with the combination of scaffolders SSPACE and SOAPdenovo2. (DOCX)

Assemblies obtained for the data set Candidatus Microthrix parvicella strain Bio17-1. (DOCX)

Assemblies obtained for the data set Caenorhabditis elegans strain N2. (DOCX)

Scaffolding of the data set Candidatus Microthrix parvicella strain Bio17-1 for the assemblers GRASShopPER, SOAPdenovo2 and SGA with the combination of scaffolders SSPACE and SOAPdenovo2. (DOCX)

Scaffolding of the data set Caenorhabditis elegans strain N2 for the assemblers GRASShopPER, SOAPdenovo2 and SGA with the combination of scaffolders SSPACE and SOAPdenovo2. (DOCX)

Algorithm parameters. The list of GRASShopPER parameters. Description of how to run GRASShopPER. Parameters of all the methods used throughout computational experiment. (DOCX)

Reliable and trustworthy evaluation of algorithms is a challenging process. Firstly, each algorithm has its strengths and weaknesses, and the selection of test instances can significantly influence the assessment process. Secondly, the measured performance of the algorithm highly depends on the test environment architecture, i.e., CPU model, availa...

Reliable and trustworthy evaluation of algorithms is a challenging process. Firstly, each algorithm has its strengths and weaknesses, and the selection of test instances can significantly influence the assessment process. Secondly, the measured performance of the algorithm highly depends on the test environment architecture, i.e., CPU model, availa...

Online judges are systems designed for the reliable evaluation of algorithm source code submitted by users, which is next compiled and tested in a homogeneous environment. Online judges are becoming popular in various applications. Thus, we would like to review the state of the art for these systems. We classify them according to their principal ob...

Online judges are systems designed for the reliable evaluation of algorithm source code submitted by users, which is next compiled and tested in a homogeneous environment. Online judges are becoming popular in various applications. Thus, we would like to review the state of the art for these systems. We classify them according to their principal ob...

Evaluation as a Service, in brief, is defined as a paradigm of keeping the evaluation data in the cloud and allowing to access them via dedicated interfaces. Here, we present Optil.io, an online platform that allows users to reliably evaluate metaheuristic-based algorithms, designed to solve complex optimization problems, in a secure cloud-based in...

The main objective of the presented research is to design a platform for continuous evaluation of optimization algorithms using crowdsourcing technique. The resulting platform, called Optil.io, runs in a cloud using platform as a service model and allows researchers from all over the world to collaboratively solve computational problems. This is th...