Related papers: Comparative genomics study of inverted repeats in …
In eukaryotes, DNA replication is initiated along each chromosome at multiple sites called replication origins. Locally, each replication origin is "licensed", or specified, at the end of the M and the beginning of G1 phases of the cell…
The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional…
We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to…
Diatoms, a major group of microalgae, play a critical role in global carbon cycling and primary production. Despite their ecological significance, comprehensive genomic resources for diatoms are limited. To address this, we have annotated…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth…
Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-…
Characterizing the differential excision of mRNA is critical for understanding the functional complexity of a cell or tissue, from normal developmental processes to disease pathogenesis. Most transcript reconstruction methods infer…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
This paper considers the problem of matching fragment to organism using its complete genome. Our method is based on the probability measure representation of a genome. We first demonstrate that these probability measures can be modelled as…
Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…
This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be…
Advances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacterium ${\it Escherichia coli}$, for $\approx$ 65$\%$ of the promoters we remain completely ignorant of…
We provide, on an extensive dataset and using several different distances, confirmation of the hypothesis that CGR patterns are preserved along a genomic DNA sequence, and are different for DNA sequences originating from genomes of…
We have investigated the deviation from the standard recombination process, using the ACBAR 2008 and the WMAP 3 year data. In this investigation, we have considered the possibility of the accelerated recombination as well as the delayed…
Gene regulation in Eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory…
Circular RNAs (circRNAs) are important components of the non-coding RNA regulatory network. Previous circRNA identification primarily relies on high-throughput RNA sequencing (RNA-seq) data combined with alignment-based algorithms that…