A5036768913- Genomics and Phylogenetic Studies
- Algorithms and Data Compression
- DNA and Biological Computing
- RNA and protein synthesis mechanisms
- Genome Rearrangement Algorithms
- Advanced biosensing and bioanalysis techniques
- Advanced Graph Theory Research
- Cancer Genomics and Diagnostics
- Chromosomal and Genetic Variations
- Protein Structure and Dynamics
- Limits and Structures in Graph Theory
- Complexity and Algorithms in Graphs
- Machine Learning in Bioinformatics
- RNA Research and Splicing
- Bacteriophages and microbial interactions
- Genomics and Chromatin Dynamics
- Bioinformatics and Genomic Networks
- RNA Interference and Gene Delivery
- semigroups and automata theory
- Graph theory and applications
- Gene expression and cancer classification
- Biomedical Text Mining and Ontologies
- Biotin and Related Studies
- Fractal and DNA sequence analysis
- 3D Modeling in Geospatial Applications
Poznań University of Technology
2010-2024
Institute of Bioorganic Chemistry, Polish Academy of Sciences
2009-2018
University of Luxembourg
2013
Polish Academy of Sciences
2002-2003
The problem addressed in this paper is concerned with DNA sequencing by hybridization. An algorithm proposed that solves a computational phase of approach the presence both positive and negative errors resulting from hybridization experiment. No priori knowledge nature source these required. extensive set experiments showed behaves surprisingly well if only appear. general case, where occur, can be also solved satisfactorily for an error rate up to 10%.
Abstract Motivation: A new heuristic algorithm for solving DNA sequencing by hybridization problem with positive and negative errors. Results: providing better solutions than algorithms known from the literature based on tabu search method. Contact: blazewic@sol.put.poznan.pl * To whom correspondence should be addressed.
A formulation of a new problem the restriction map construction based on simplified digestion experiment and development an algorithm for solving both ideal noisy data cases introduced problem.A partial digest branch cut finding solution problem.
Experimental co-expression data and protein-protein interaction networks are frequently used to analyze the interactions among genes or proteins. Recent studies have investigated methods integrate these two sources of information. We propose a new method obtained through DNA microarray analysis (MA) (PPI) network data, apply it Arabidopsis thaliana. The proposed identifies small subsets highly interacting Based on basis co-localization mRNA developmental expression, we show that groups...
In this paper, a tabu-search algorithm enhanced by scatter search is presented. The solves the DNA sequencing problem with negative and positive errors, yielding outcomes of high quality. We compare new method two other metaheuristic approaches: previous hybrid genetic algorithm, also an old branch-and-bound approach.
Abstract 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 so-called Bruijn approach but in much greater time and of higher memory usage. not uncommon that involving model able to successfully compute datasets, mainly due limitation a computer. This was reason developing last decades Bruijn-based methods, fast fairly accurate. However, latter can fail longer or repetitive genomes, they...
Reconstruction of the original DNA sequence in sequencing by hybridization approach (SBH) requires computational support due to a large number possible combinations.One can notice lack algorithms admitting false-negative data and giving addition all solutions. In this paper, new method has been proposed. An algorithm based on its idea (for general case, when some are missing, like real experiment) implemented tested. Authentic sequences have used for testing. A parallel version also The...
An algorithm is proposed to provide the tool for an automatic resonance assignment of 2D–NOESY spectra RNA duplexes. The algorithm, based on a certain subproblem Hamiltonian path, reduces number possible connections between resonances within aromatic and anomeric region spectra. Appropriate pathways H6/H8 H1′ were obtained by subsequent implementation experimental data as limiting factors. Predictive power was tested both simulated DNA
We study the simplified partial digest problem (SPDP), which is a mathematical model for new method of genome mapping. This easy laboratory implementation and robust with respect to experimental errors. SPDP NP-hard in strong sense. present an O(n2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> ) time enumerative algorithm (ENUM) O(n xmlns:xlink="http://www.w3.org/1999/xlink">2q</sup> dynamic programming error-free SPDP, where n number...
Studies conducted during the last decade unexpectedly revealed several new biological functions of RNA molecules. The involvement in many complex processes requires highly effective systems controlling its accumulation. In this context, mechanisms degradation appear as one most important factors influencing activity. Here, we present our first attempt to describe process using bioinformatics methods. Based on obtained data, propose a formulation problem, called Partial Degradation Problem...
The progress of research in the area computational biology, visible last decades, brought, among others, a new insight into complexity issues. latter, previously studied mainly on ground computer science or operational research,