MOTIVATION Proteins underlay the functioning of a cell and the wiring of proteins in protein-protein interaction network (PIN) relates to their biological functions. Proteins with similar wiring in the PIN (topology around them) have been shown to have similar functions. This property has been successfully exploited for predicting protein functions. Topological similarity is also used to guide ...

We describe a method for estimating species trees that relies on replicated subsampling of large data matrices. One application of this method is phylogeographic research, which has long depended on large datasets that sample intensively from the geographic range of the focal species; these datasets allow systematicists to identify cryptic diversity and understand how contemporary and historica...

Considering a commutative unital quantale L as the truth value table and using the tool of L-generalized convergence structures of stratified L-filters, this paper introduces a kind of fuzzy upper topology, called fuzzy S-upper topology, on L-preordered sets. It is shown that every fuzzy join-preserving L-subset is open in this topology. When L is a complete Heyting algebra, for every completel...

in this paper‎, ‎we introduce a new model of point free topology‎ ‎for point-set topology‎. ‎we study the basic concepts in this‎ ‎structure and will find that it is naturally close to point-set‎ ‎topology‎.‎

In the network querying problem, one is given a protein complex or pathway of species A and a protein-protein interaction network of species B; the goal is to identify subnetworks of B that are similar to the query in terms of sequence, topology, or both. Existing approaches mostly depend on knowledge of the interaction topology of the query in the network of species A; however, in practice, th...

this paper introduces a new approach to topology, based on category theory and universal algebra, and called categorically-algebraic (catalg) topology. it incorporates the most important settings of lattice-valued topology, including poslat topology of s.~e.~rodabaugh, $(l,m)$-fuzzy topology of t.~kubiak and a.~v{s}ostak, and $m$-fuzzy topology on $l$-fuzzy sets of c.~guido. moreover, its respe...

Background and Purpose: Hyphal wall protein 1 (HWP1) is an important adhesin which usually is expressed on the germ tube and hyphal surface produced by different Candida species. The hyphal wall protein-coding gene (HWP1) was evaluated as a novel identification and phylogenetic marker in Candida tropicalis, C. orthopsilosis, C. parapsilosis and C. glabrata. Materials and Methods: Initially, fo...

Under a coalescent model for within-species evolution, gene trees may differ from species trees to such an extent that the gene tree topology most likely to evolve along the branches of a species tree can disagree with the species tree topology. Gene tree topologies that are more likely to be produced than the topology that matches that of the species tree are termed anomalous, and the region o...

let g = (v,e) be a locally finite graph, i.e. a graph in which every vertex has finitely many adjacent vertices. in this paper, we associate a topology to g, called graphic topology of g and we show that it is an alexandroff topology, i.e. a topology in which intersec- tion of every family of open sets is open. then we investigate some properties of this topology. our motivation is to give an e...