A5077512966- DNA and Biological Computing
- Advanced biosensing and bioanalysis techniques
- DNA and Nucleic Acid Chemistry
- Chemical Synthesis and Analysis
- Escherichia coli research studies
- Gene Regulatory Network Analysis
- Gene expression and cancer classification
- Celiac Disease Research and Management
- Virology and Viral Diseases
- Algorithms and Data Compression
- Genomics and Chromatin Dynamics
- Zoonotic diseases and public health
- Cellular Automata and Applications
- Biochemical and Molecular Research
- Evolution and Genetic Dynamics
- Systemic Lupus Erythematosus Research
- Acute Lymphoblastic Leukemia research
- Bayesian Methods and Mixture Models
- Gut microbiota and health
- COVID-19 epidemiological studies
- Monoclonal and Polyclonal Antibodies Research
- semigroups and automata theory
- Helicobacter pylori-related gastroenterology studies
- Stochastic processes and statistical mechanics
- Viral Infections and Immunology Research
University of Łódź
2013-2024
Institute of Informatics of the Slovak Academy of Sciences
2008
Silesian University of Technology
2008
Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic inflammation affecting up to 2.0% of adults around the world. The molecular background RA has not yet been fully elucidated, but classified as a in which genetic one most significant risk factors. One hallmark impaired DNA repair observed patient-derived peripheral blood mononuclear cells (PBMCs). aim this study was correlate phenotype defined efficiency double-strand break (DSB) with genotype limited...
Machine learning (ML) algorithms can handle complex genomic data and identify predictive patterns that may not be apparent through traditional statistical methods. They become popular tools for medical applications including prediction, diagnosis or treatment of diseases like rheumatoid arthritis (RA). RA is an autoimmune disease in which genetic factors play a major role. Among the most important predisposing to development this serving as markers are HLA-DRB non-HLA genes single nucleotide...
The branch of informatics that deals with construction and operation computers built DNA, is one the research directions which investigates issues related to use DNA as hardware software. This concept assumes due their biological origin mainly for intelligent, personalized targeted diagnostics frequently therapy. Important elements this are (1) retrieval unique sequences using machine learning methods and, based on results process, (2) construction/design smart diagnostic biochip projects....
In this paper we propose a biomolecular implementation of the push-down automaton (one theoretical models computing device with unbounded memory) using DNA molecules. The idea improved was inspired by Cavaliere et al. (2005).
In the paper we present a theoretical analysis of extension finite automaton built on DNA (introduced by Shapiro team) to an arbitrary number states and symbols. implementation use new idea several restriction enzymes ins
The development of conventional, silicon-based computers has several limitations, including some related to the Heisenberg uncertainty principle and von Neumann "bottleneck". Biomolecular based on DNA proteins are largely free these disadvantages and, along with quantum computers, reasonable alternatives their conventional counterparts in applications. idea a computer proposed by Ehud Shapiro's group at Weizmann Institute Science was developed using one restriction enzyme as hardware...
The Binary State Speciation and Extinction (BiSSE) model is a branching process based that allows the diversification rates to be controlled by binary trait. We develop general approach, on BiSSE model, for predicting pathogenicity in bacterial populations from microsatellites profiling data. A comprehensive approach E. coli proposed using state-dependent combined with TRS-PCR profiling. Additionally, we have evaluated possibility of estimating parameters genetic analyzed real dataset (from...
A major challenge in DNA computing area is to design autonomous and programmable biomolecular devices built on DNA. The significant achievement the field of nanodevices was a laboratory implementation 2-state finite automaton based one restriction enzyme FokI [3]. Although this practical represents proof concept for with molecules, it has limited computational power. enables construction an automata at most 3-states. We propose use several enzymes (instead one) which act autonomously test...
Abstract Great advances in biotechnology have allowed the construction of a computer from DNA. One proposed solutions is biomolecular finite automaton, simple two-state DNA without memory, which was presented by Ehud Shapiro’s group at Weizmann Institute Science. The main problem with this computer, biomolecules carry out logical operations, its complexity – increasing number states automata. In study, we constructed (in laboratory conditions) six-state that uses two endonucleases (e.g. Acu...
Biomolecular computers, along with quantum may be a future alternative for traditional, silicon-based computers. Main advantages of biomolecular computers are massive parallel processing data, expanded capacity storing information and compatibility living organisms (first attempts using in cancer therapy through blocking improper genetic described Benenson et al.(2004). However, have several drawbacks including time-consuming procedures preparing input, problems detecting output signals...
The authors present a solution to the problem of generating maximum possible number symbols for biomolecular computer using restriction enzyme BbvI and ligase as hardware, transition molecules built double-stranded DNA software. presented offers an answer open question, in algorithm form, maximal that makes use BbvI.
The increasingly expanding genomic databases generate the need for new tools their processing and further use. In paper, a bioinformatics tool, which is search engine of microsatellite elements—trinucleotide repeat sequences (TRS) in files FASTA type—is presented. An innovative approach was applied consists connecting—within one engine—both mapping TRS motifs extracting that are found between mapped motifs. Accordingly, we present hereby tool called TRS-omix, comprises searching information...
We apply multitype continuous time Markov branching models to study pathogenicity in E. coli, a bacterium belonging the genus Escherichia.First, we examine briey properties of processes and also survey some fundamental limit theorems regarding behavior such under various conditions.These are then applied discrete, state dependent order analyze published clinical data set consisting 251 strains coli.We use well established methods, incorporating maximum likelihood techniques, estimate...