12 Works

DNA structure, replication and genome variability correlation

Igor P. Shabalkin, Margarita V. Gudkova, Yuri V. Stukalov, Elena Y. Grigorieva, Aleksei A. Cherepanov & Pavel I. Shabalkin
The study of special features of a new molecular DNA structure synthesis based on the fact that monomers transpositions can occur in the backbone of polymer chains according to the mathematical law known as a Fibonacci numerical series and «the Golden ratio» was performed. The example of the formation of a new DNA model demonstrates that there are dimers of three types in DNA structure: • Dimers with phosphodiester bond P-O-C, [(s-p) + (s-p)]; [(p-s)+(p-s)];...

A two-stage approach for combining gene expression and mutation with clinical data improves survival prediction in myelodysplastic syndromes and ovarian cancer

Yan Li, Xinyan Zhang, Tomi Akinyemiju, Akinyemi I. Ojesina, Jeff M. Szychowski, Nianjun Liu, Bo Xu & Nengjun Yi
Motivation: Many traditional clinical prognostic factors have been known for cancer for years, but usually provide poor survival prediction. Genomic information is more easily available now which offers opportunities to build more accurate prognostic models. The challenge is how to integrate them to improve survival prediction. The common approach of jointly analyzing all type of covariates directly in one single model may not improve the prediction due to increased model complexity and cannot be easily...

Molecular taxonomy and the evolution theory in light of emerging bioinformatic and cosmological data

Sergei Y. Shchyogolev
A brief review is given of recent advances in the taxonomic study of organisms and current views on biological evolution and the origin of life. A discussion is presented on how the treelike and net components contribute to the topology of phylogenetic constructs, with account taken of the prevailing role of horizontal gene transfer in prokaryote evolution and life. Approaches are described to the rational selection and practical use of phylogenetic markers (including 16S rRNA...

Zero-inflated Negative Binomial Regression for Differential Abundance Testing in Microbiome Studies

Xinyan Zhang, Himel Mallick & Nengjun Yi
Motivation: The human microbiome plays an important role in human health and disease. The composition of the human microbiome is influenced by multiple factors and understanding these factors is critical to elucidate the role of the microbiome in health and disease and for development of new diagnostics or therapeutic targets based on the microbiome. 16S ribosomal RNA (rRNA) gene targeted amplicon sequencing is a commonly used approach to determine the taxonomic composition of the bacterial...

CELNETANALYZER: HIGH-PERFORMANCE JAVA PACKAGE FOR THE TOPOLOGICAL ANALYSIS OF CELLULAR NETWORKS

Grinev V.., Kushal D.. & Charapovich V..
Summary: A simple-to-use Java-based software package CelNetAnalyzer was developed. CelNetAnalyzer is managed through a graphical user interface and it returns a comprehensive list of the topological indices including compositional complexity, degree and neighbourhood, clustering, distance, centrality and heterogeneity indices as well as simple cycles and Shannon information entropy of undirected networks. Comparative studies have shown that due to parallelization and use of enhanced and newly developed algorithms, CelNetAnalyzer calculates these parameters significantly faster than competitors....

APPLICATIONS OF SOME NEW TRANSMUTED CUMULATIVE DISTRIBUTION FUNCTIONS IN POPULATION DYNAMICS

Kyurkchiev V.., A.I. Iliev & Kyurkchiev N..
In this note we find applications of some new cumulative distribution function transformations to construct a family of sigmoidal functions based on the Verhulst logistic function. We prove estimates for the Hausdorff approximation of the shifted Heaviside step function by means of this family. Numerical examples, illustrating our results are given.

A NOVEL ROLLING BASED DNA CRYPTOGRAPHY

Haque R.. & Saha R..
DNA Cryptography can be defined as a hiding data in terms of DNA Sequence. In this paper we propose a new DNA Encryption Technique where three different types of ordering is use to make binary data into cipher text. The main stages of this encryption technique are: Key Analysis, Data and Key Arrangement, Roll in encoding, Secondary Arrangement and Shifting. Decryption process has six main steps to obtain the original binary data from the encrypted...

AN IN-SILICO PERSPECTIVE TOWARDS TARGET ABILITY OF AVAILABLE DRUGS IN INFECTIOUS DISEASE TREATMENT: A POSSIBLE STRATEGY

Ram Rup Sarkar
Motivation: In early stage of therapeutics, several structure and ligand-based in-silico approaches have aided the modern drug discovery and design. However, such techniques are limited by availability of resolved 3D structures of targets and ligands. At the same time the growing concern of drug resistivity not only demands for new drugs but also the judicious use of presently available drugs. In such a scenario, the utilization of the already available drugs of a target molecule...

Significance of targeted exome sequencing and methods of data analysis in the diagnosis of genetic disorders leading to the development of epileptic encephalopathy

Tatyana Victorovna Kozhanova
Epilepsy is the most common serious neurological disorder, and there is a genetic basis in almost 50% of people with epilepsy. The diagnosis of genetic epilepsies makes to estimate reasons of seizures in the patient. Last decade has shown tremendous growth in gene sequencing technologies, which have made genetic tests available. The aim is to show significance of targeted exome sequencing and methods of data analysis in the diagnosis of hereditary syndromes leading to the...

BIOINFORMATICS MODEL OF THE CARAPACE SCUTE PATTERN OF THE RED-EARED SLIDER TRACHEMYS SCRIPTA ELEGANS (WIED-NEUWIED, 1839)

A. Kiladze
The scutes located on the carapace of the red-eared slider Trachemys scripta elegans (Wied-Neuwied, 1839) have been modeled. Bioinformatics modeling of carapace’s scutes were carried out by utilizing the Voronoi decomposition and Delaunay triangulation method. These two geometric techniques allow the patterns of vertebral and costal scutes to be recreated. The proposed model may have a certain value for taxonomy as well as for estimating the symmetry of the morphological structures, which is important for...

DISTANT JOINING: A SEQUENCE SAMPLING METHOD FOR COMPLEX EVOLUTIONARY HISTORIES

A.A. Morozov & Y.P. Galachyants
Motivation: Massive parallel phylogenetic analyses allow to reconstruct phylogenetic trees for every gene in genome, typically using the set of potential homologues detected via BLAST or analogue. However, if the amount of hits is too high, the dataset should be reduced to tractable size, preferably without human intervention. Currently available methods are error-prone on at least some datasets and some of them also depend on additional data which may not be available. Results: We propose...

TAXONDC: CALCULATING THE SIMILARITY VALUE OF THE 16S RRNA GENE SEQUENCES OF PROKARYOTES OR ITS REGIONS OF FUNGI

S.V. Tarlachkov & I.P. Starodumova
Summary: The TaxonDC program (Taxon Distance Calculator) performs pairwise sequence alignment followed by determining the similarity value between two or more sequences of interest. Unlike widely used programs, TaxonDC makes only pairwise alignment of input sequences that allows avoiding different similarity values depending on the sequences included in the analysis. The similarity values calculated with TaxonDC are the same compared to those calculated using popular identification oriented web-based tool EzBioCloud that makes calculated values comparable...

Resource Types

  • Text
    12

Publication Year

  • 2017
    8
  • 2016
    4

Registration Year

  • 2017
    8
  • 2016
    4

Data Centers

  • Russian Agency for Digital Standardization
    12