Bacteriorhodopsin (bR) is a light-driven proton pump, which is a membrane protein with seven transmembrane helices and a prosthetic group of retinal. The structure of bR has been determined at high resolution, and the homology modeling of G-protein coupled receptors, which have seven transmembrane helices, is usually carried out based on the structure of bR as the structure template. However, t...

The ?ech and Rips constructions of persistent homology are stable with respect to perturbations the input data. However, neither is robust outliers, both can be insensitive topological structure high-density regions A natural solution consider 2-parameter persistence. This paper studies stability homology: we show that several related density-sensitive bifiltrations from data satisfy properties...

The present study characterized Argulus spp. infecting the cultured carps using 18S rRNA gene sequences, estimated the genetic similarity among Argulus spp. and established their phylogenetic relationship. Of the 320 fish samples screened, 34 fish (10.6%) had Argulus infection. The parasitic frequency index (PFI) was observed to be high (20%) in Hypophthalmichthys molitrix and Labeo bata. The f...

The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on genome-wide scales. New models are needed to quantitatively interpret this data at a global scale. Here we introduce the use of tools from topological data a...

UNLABELLED POPE (Phylogeny, Ortholog and Paralog Extractor) provides an integrated platform for automatic ortholog identification. Intermediate steps can be visualized, modified and analyzed in order to assess and improve the underlying quality of orthology and paralogy assignments. AVAILABILITY POPE is available for download from the website: http://www.well.ox.ac.uk/~tota/pope.

Sequence analysis and phylogenetic study of hemagglutinin (HA) gene of H9N2 subtype of avian influenza virus isolates (outbreaks of 1998-2002) in Tehran province (Iran) were studied. Two sets of forward and reverse primers in highly conserved regions, based on sequences of HA gene in Genbank, were designed. PCR products of a 430-bp fragment of 16 isolates were sequenced and then were aligned wi...