Dorota Bielinska-Waz

In this paper, an alignment-free bioinformatics technique, termed the 20D-Dynamic Representation of Protein Sequences, is utilized to investigate the similarity/dissimilarity between Baculovirus and Echinococcus multilocularis genome sequences. In this method, amino acid sequences are depicted as 20D-dynamic graphs, comprising sets of “material poi...

Objective: A new diagnostic graphical tool-classification maps-supporting the detection of Age-Related Macular Degeneration (AMD) has been constructed. Methods: The classification maps are constructed using the ordinal regression model. In the ordinal regression model, the ordinal variable (the dependent variable) is the degree of the advancemen...

The 4D-Dynamic Representation of DNA/RNA Sequences, an alignment-free bioinformatics method recently developed by us, has been used to study the genetic diversity of Echinococcus multilocularis in red foxes in Poland. Sequences of three mitochondrial genes, i.e., NADH dehydrogenase subunit 2 (nad2), cytochrome b (cob), and cytochrome c oxidase subu...

The aim of the studies is to show that graphical bioinformatics methods are good tools for the description of genome sequences of viruses. A new approach to the identification of unknown virus strains is proposed. Methods Biological sequences have been represented graphically through 2D and 3D-Dynamic Representations of DNA/RNA Sequences - theoret...

Due to the multidimensional structure of the results of similarity studies, their analysis is often difficult. Therefore, a compact and transparent presentation of these results is essential. The purpose of the present study is to propose a graphical representation of the results of similarity analysis in studies on the quality of life. The results...

A non-standard bioinformatics method, 4D-Dynamic Representation of DNA/RNA Sequences, aiming at an analysis of the information available in nucleotide databases, has been formulated. The sequences are represented by sets of "material points" in a 4D space - 4D-dynamic graphs. The graphs representing the sequences are treated as "rigid bodies" and c...

The aim of this work is to present new classification maps in health informatics and to show that they are useful in data analysis. A statistical method, correspondence analysis, has been applied for obtaining these maps. This approach has been applied to studies on expectations and worries related to the retirement threshold. For this purpose two...

Similarity studies in different areas of computational science are briefly reviewed. In particular, a new method called by us 2D-dynamic Representation of DNA/RNA Sequences aiming at similarity studies of biological sequences is described. It is shown that similarity studies are also a convenient tool to study the retirement threshold in social sci...

A review of classification studies in various ares of science is presented. A computational biology method, 3D-dynamic Representation of DNA/RNA Sequences, which allows for the creation of classification maps, is outlined. A new classification map in social science, obtained using the computational statistics method Correspondence Analysis, is show...

Methods of bioinformatics in which the biological sequences (DNA, RNA, protein) are represented by sets of material points in 2D, 3D, or 20D space, and described by values analogous to the ones used in the dynamics, as e.g. moments of inertia, are reviewed. A new application of the 3D method, called by us 3D-Dynamic Representation of DNA/RNA Sequen...

A new theoretical method for the virus identifcation has been proposed. The 2D-Dynamic Representation of DNA/RNA Sequences has been applied to the prediction of influenza A virus subtypes. We have shown that the method can be successfully combined with novel supervised machine learning algorithms, such as C5.0. The descriptors of the 2D-Dynamic Rep...

A graphical representation of DNA sequences in which the distribution of a particular base is represented by a set of discrete lines has been formulated. The methodology of this approach has been borrowed from two areas of physics: spectroscopy and dynamics. Consequently, the set of discrete lines is referred to as the spectrum. Next, the spectrum...

2D-dynamic representation of DNA/RNA sequences has been applied for the characterization of the complete genome sequence of Zika virus. Graphically, the 2D-dynamic graphs evolve with time. Numerically, applying descriptors related to the 2D-dynamic graphs, correct classification of the sequences has been obtained. These descriptors have been shown...

A method, called 3D-dynamic representation of DNA sequences , and its application to the classification of the DNA sequences is briefly reviewed. Some new classification diagrams obtained using this method are also shown. The method constitutes an alignment free tool of the comparison of the DNA sequences. It allows for both graphical and numerical...

2D-dynamic representation of DNA sequences is briefly reviewed. Some new examples of 2D-dynamic graphs which are the graphical tool of the method are shown. Using the examples of the complete genome sequences of the Zika virus it is shown that the present method can be applied for the study of the evolution of viral genomes.

If it is a terrifying thought that life is at the mercy of the multiplication of these minute bodies [microbes], it is a consoling hope that Science will not always remain powerless before such enemies... — Louis Pasteur The global public health management today faces a wide range of challenges from ecological and environmental changes. Global wa...

Background: The recent epidemic of Zika virus infections in South and Latin America have raised serious concern on its ramifications for the population in the Americas and spread of the virus worldwide. The Zika virus disease is a relatively new phenomenon for which sufficient and comprehensive data and investigative reports have not been availabl...

A new method of comparison of protein sequences has been formulated. The sequence of amino acids is represented by a set of point masses in a 20D space. The distribution of points in the space is obtained by applying the method of a walk in the 20D space. Projections of the 20D representation into 2D or 3D spaces illustrate the distribution of part...

Similarity/dissimilarity analysis of DNA sequences is performed using 3D-dynamic representation. The sequences are represented by material points in a 3D-space. Descriptors related to such 3D-dynamic graphs are calculated. A new normalized similarity measure is introduced for a comparison of the sequences. The method is applied to β-globin genes of...

A new 3D graphical representation of DNA sequences is introduced. This representation is called 3D-dynamic representation. It is a generalization of the 2D-dynamic dynamic representation. The sequences are represented by sets of "material points" in the 3D space. The resulting 3D-dynamic graphs are treated as rigid bodies. The descriptors character...

We propose spectral density distribution moments as molecular descriptors. We apply the new descriptors for developing a QSPR model that predicts the logarithmic values of subcooled liquid vapor pressure. We consider the infrared spectra of chloronaphthalenes.

A new tool of the classification of DNA sequences is introduced. The method is based on 2D-dynamic graphs and their descriptors. Using the descriptors created by centers of masses, moments of inertia, angles between the x axis and the principal axis of inertia of the 2D-dynamic graphs one can obtain classification diagrams in which similar sequence...

Statistical properties of the hyperchaotic Qi system are studied. The theory, recently formulated and applied for the damped driven pendulum, is used in this investigation. Asymmetry coefficients, related to the statistical moment of distributions composed from the time-series, are shown to behave in a different way for periodic, chaotic and hyperc...

We introduce spectral density distribution moments as molecular descriptors. We demonstrate that these descriptors correctly represent the molecular structure. To prove the correctness of the new descriptors, we consider the IR spectra of 76 chloronaphthalenes. We show that the consecutive substitutions of the hydrogen atoms by the chlorine atoms a...

Frequencies and intensities of molecular spectra are used to construct a new kind of molecular descriptors. In this work two kinds of descriptors have been defined: one is a linear combinations of squares of the frequencies and another one – a linear combination of squares of the intensities. If the frequencies and the intensities are interpreted a...

New approaches aiming at a detailed similarity/dissimilarity analysis of DNA sequences are formulated. Several corrections that enrich the information which may be derived from the alignment methods are proposed. The corrections take into account the distributions along the sequences of the aligned bases (neglected in the standard alignment methods...

The aim of this paper is to introduce a new tool for a simple identification of spectral types. We use methods of statistical spectroscopy, in particular the method of intensity-distribution moments. The statistical approach revealed a characteristic behavior of moments of the stellar spectra for different spectral types. The transition from one sp...

A 2D-graphical representation of DNA sequences is presented. In this representation, the DNA sequence is represented by a four-component (A, C, T, G) spectrum taken as a superposition of Gaussian functions. The maxima of single Gaussians are determined by the positions of the bases in the sequence. Distribution moments of the four-component functio...

The aim of this paper is to present a new simple indicator of chaos derived from the dynamics of the motion. For this purpose statistical methods are used. A function describing the motion of the analyzed system (in the example under consideration, the time dependence of the angle of a damped driven pendulum, omega(t)) is recorded in time intervals...

The aim of this paper is to present a new method of classification of the stellar spectra. The parameters characterizing the spectra are moments of intensity distributions. Statistical Theory of Spectra is used as a tool for the classification of the stellar spectra. The method of using distribution moments has been already proposed by the present...

Statistical spectroscopy is applied to the theory of molecular similarity. Statistical moments of the intensity distributions are considered as a new kind of descriptors, in particular atomic or molecular ones. A model spectrum is taken as a sum of two Gaussian distributions characterized by different parameters. The linear correlations between dis...

This paper aims at an application of the statistical theory of spectra to the classification of chemical compounds. It has been shown that the moments of the intensity distributions may be used as molecular descriptors. The new descriptors have been tested using spectra of nitriles and amides. The dependence of the accuracy of the classification on...

Multi-dimensional aspects of similarity studies of DNA/RNA sequences are emphasized. The new graphical representation presented in our recent papers and its descriptors are used as numerical examples of the multi-dimensionality.

This paper aims at demonstrating the applicability of statistical spectroscopy and genetic algorithms to the similarity studies. Statistical moments of the intensity distributions are used as a basis for defining similarity distances between pairs of model spectra. Model spectrum is taken as a sum of two Gaussian distributions characterized by diff...

Similarity studies of DNA sequences using 2D-dynamic graphs are performed. The orientation of the graphs in 2D-space is proposed as a descriptor. Mass overlaps and comparison of the positions of the graphs are proposed as similarity measures of pairs of sequences.

We propose the statistical moments of mass-density distributions (created for two orthogonal directions) as new descriptors of DNA sequences. The distributions are derived using a 2D-dynamic representation technique proposed in our previous paper in which the sequence is coded by a set of point masses properly distributed in 2D-space.

A new 'dynamic' 2D-graphical representation of DNA sequences is presented. The model is based on 2D-plots that have been used before and are easy to visualize, but it removes many degeneracies present in the previous approaches. The moments of inertia of the 'dynamic' graphs are proposed as a new kind of descriptor for DNA sequences.

In this chapter, new statistical approaches were developed to characterize molecular similarity based on spectroscopy.

he influence of spatial confinement on the structure and spectra of the Rydberg HeH molecule is analysed at the level of the variational full configuration interaction approach. The confining potential is assumed to have cylindrical symmetry, with the symmetry axis of the potential overlapping with the molecular bond. In the direction perpendicular...

Statistical moments of the intensity distributions are used as molecular descriptors. They are used as a basis for defining similarity distances between two model spectra. Parameters which carry the information derived from the comparison of shapes of the spectra and are related to the number of properties taken into account, are defined.

The applicability of the perturbation theory to studies on the effect of confinement is discussed in the context of the influence of spatial confinement on the Rydberg Heft molecule. In the analysis the confining potential is assumed to have cylindrical symmetry, with symmetry axis of the potential overlapping with the molecular axis. In the direct...

The effect of spatial confinement in the presence of plasma environment on the dipole allowed transition properties for the first five helium-like atoms (He through C4(+)) is studied. The Debye screening describes the effect of plasma. Additionally, the effect of a spatial confinement (as, for example, it is in the case of atoms surrounded by liqui...

Ab initio potential energy curves of the Rydberg NeH molecule in the presence of cylindrical spatial confinement were computed by the method of multi-reference configuration interaction with extended basis sets. The influence of the applied potential to the structures and spectra of the ground and excited states of NeH was analysed in terms of pert...

Spectra of hydrogenlike atoms embedded in a Debye plasma are investigated. The state energies and the transition rates are studied using a fully relativistic formalism based on the Dirac equation. The effect of the plasma is described by introducing an exponential screening to the nuclear Coulomb potential (the Debye screening). Systematic trends w...

Systematic investigation have been performed for the dynamic polarizabilities, energy levels, oscillator strengths and transition probabilities for the first few members of helium isoelectronic series He, Li+, Be2+, B3+ and C4+ embedded in the Debye plasma. The effect of plasma is described by introducing an exponential screening (the Debye screeni...

The properties of spectra of atoms and molecules confined by an external potential are analyzed. The effects of spatial confinement are studied using quantum-chemical models. The confinement of the system is described by an external one-particle potential. Two-electron atoms confined in a spherically symmetric harmonic oscillator potential are inve...

Structure and spectral properties of the hydrogen molecule confined in a spherically symmetric harmonic oscillator potential were studied using the configuration interaction method. Increased strength of the confining potential exerts significant influence on the geometry of the molecule as well as on the vibronic transitions between the electronic...

Spectra of two electrons confined in a spherically symmetric potential of mixed Coulomb and harmonic form are studied using the Hartree-Fock and configuration interaction methods. The model studied corresponds to a two-electron atom confined in a harmonic oscillator potential. The spectral consequences of the interplay between the effects of the co...

Relativistic Quantum Defect Orbital (RQDO) calculations have been performed in the LS coupling scheme on electric quadrupole (E2) transitions between levels belonging to several astrophysically important configurations of Ni XVIII. A number of line strengths are reported and compared with the ones found in the literature. A good agreement with the...

The relativistic quantum defect orbital (RQDO) formalism is applied to electric quadrupole (E2) transitions for the first time. The RQDO calculations have been performed in the LSJ-coupling scheme on E2 transitions between levels belonging to several astrophysically important configurations of Fe XVI. A number of line strengths are reported and com...

Formulae for the evaluation of the expectation values of rq between the relativistic quantum defect orbital theory wavefunctions are derived. Their recursive structure leads to the development of explicit relations between the formulae for different values of q . The formulae may be considered as a relativistic quantum defect orbital theory general...

Spectra of several types of finite Heisenberg lattices have been studied using methods of statistical spectroscopy. In particular, spectral density distributions, discrete spectra generated from the spectral density distribution moments, and the distributions of spacings between the neighboring energy levels have been analyzed. The densities have b...

The method of moments, derived from the statistical theory of spectra, has been used to generate envelopes of the electronic bands in diatomic molecules. Adequately accurate envelopes have been generated using a trial function with adjustable asymptotic behaviour. In the cases considered, the Gram-Charlier-type expansions are divergent.

Shapes of molecular electronic bands are studied using the methods of the statistical theory of spectra. It is demonstrated that while the Gram-Charlier and Edgeworth type expansions give a correct description of the molecular bands in the case of harmonic-oscillator-like potentials, they are inappropriate if departure from harmonicity is considera...

Perturbation methods are generally used for solving wave operator equations associated with the determination of effective Hamiltonians. In many cases the standard Rayleigh-Schrodinger and Brillouin-Wigner series either converge slowly or diverge. Therefore it is necessary to modify or to renormalize the standard wave equations. FOE that purpose de...

An approach aimed at approximating the extreme (the lowest and/or the highest) eigenvalues of matrices representing many-electron model Hamiltonians from a knowledge of several spectral density distribution moments is proposed. A detailed discussion of the Heisenberg spin Hamiltonian spectrum is presented as an example of an application. This is th...

Methods of the statistical theory of spectra are applied to the description of the vibronic spectra of molecules and solids. Explicit expressions for envelopes of electronic bands are derived. Several examples are elaborated to illustrate the theory.

The quantum-defect-orbital method has been reformulated in order to include both relativistic effects and the electron correlation described by a core polarization potential. All quantities appearing in this formulation may be evaluated analytically. A comparison with experimental results demonstrates, on one hand, the significance of the relativit...