基因组学
Many people are familiar with the physico-chemical properties of gene sequences. In this paper I present a mathematical perspective: how do mathematical principles such as information theory, coding theory, and combinatorics influence the…
We show, that the specific distribution of gene's length, which is observed in natural genomes, might be a result of a growth process, in which a single length scale $L(t)$ develops that grows with time as $t^{1/3}$. This length scale could…
The increasing availability of high throughput data arising from gene expression studies leads to the necessity of methods for summarizing the available information. As annotation quality improves it is becoming common to rely on the Gene…
We describe here the new concept of $\epsilon$-Homomorphisms of Probabilistic Regulatory Gene Networks(PRN). The $\epsilon$-homomorphisms are special mappings between two probabilistic networks, that consider the algebraic action of the…
In protein-protein interaction networks certain topological properties appear to be recurrent: networks maps are considered scale-free. It is possible that this topology is reflected in the protein structure. In this paper we investigate…
Human chromosome 21 is the only chromosome in human genome that exhibits oscillation of (G+C)-content of cycle length of hundreds kilobases (500 kb near the right telomere). We aim at establishing the existence of similar periodicity in…
We investigate the application of hierarchical classification schemes to the annotation of gene function based on several characteristics of protein sequences including phylogenic descriptors, sequence based attributes, and predicted…
The extraction of information form high-throughput experiments is a key aspect of modern biology. Early in the development of microarray technology, researchers recognized that the size of the datasets and the limitations of both…
Upon growth on dinitrogen, the filamentous cyanobacterium Nostoc PCC 7120 initiates metabolic and morphological changes. We analyzed the expression of 1249 genes from major metabolic categories under nitrogen fixing and non-nitrogen fixing…
Linear discrimination, from the point of view of numerical linear algebra, can be treated as solving an ill-posed system of linear equations. In order to generate a solution that is robust in the presence of noise, these problems require…
We cloned, expressed and purified the Escherichia coli yhbO gene product, which is homolog to the Bacillus subtilis general stress protein 18 (the yfkM gene product), the Pyrococcus furiosus intracellular protease PfpI, and the human…
Recombination is an important event in the evolution of HIV. It affects the global spread of the pandemic as well as evolutionary escape from host immune response and from drug therapy within single patients. Comprehensive computational…
In this report, correlation of the pixels comprising a microarray spot is investigated. Subsequently, correlation statistics namely: Pearson correlation and Spearman rank correlation are used to segment the foreground and background…
On the basis of epidemiological studies, infection was suggested to play a role in the etiology of human cancer. While for some cancers such a role was indeed demonstrated, there is no direct biological support for the role of viral…
Transfer-RNA genes in archaea often have introns intervening between exon sequences. The structural motif at the boundary between exon and intron is the bulge-helix-bulge. Computational investigations of these boundary structures in H.…
Gene expression data matrices often contain missing expression values. In this paper, we describe a new algorithm, named improved fixed rank approximation algorithm (IFRAA), for missing values estimations of the large gene expression data…
A new N-dimensional vector space of DNA sequences over the Galois field of the 64 codons (GF(64)) was recently presented. Now, in order to include deletions and insertions (indel mutations), we have defined a new Galois field over the set…
The unicellular cyanobacterium Synechococcus PCC 7942 has been used as a model organism for studies of prokaryotic circadian rhythms, carbon-concentrating mechanisms, response to a variety of nutrient and environmental stresses, and cell…
We describe a stochastic birth-and-death model of evolution of horizontally transferred genes in microbial populations. The model is a generalization of the stochastic model described by Berg and Kurland and includes five parameters: the…
In this work, we discovered a fundamental connection between selection for protein stability and emergence of preferred structures of proteins. Using standard exact 3-dimensional lattice model we evolve sequences starting from random ones…