Related papers: RNA-LEGO: Combinatorial Design of Pseudoknot RNA
We analytically explore the scaling properties of a general class of nested subgraphs in complex networks, which includes the $K$-core and the $K$-scaffold, among others. We name such class of subgraphs $K$-nested subgraphs due to the fact…
We study counter expressed gene networks constructed from gene-expression data obtained from many types of cancers. The networks are synthesized by connecting vertices belonging to each others' list of K-farthest-neighbors, with K being an…
In this paper, we introduce polynomial time algorithms that generate random $k$-noncrossing partitions and 2-regular, $k$-noncrossing partitions with uniform probability. A $k$-noncrossing partition does not contain any $k$ mutually…
RNA structure prediction is a challenging problem, especially with pseudoknots. Recently, there has been a shift from the classical minimum free energy-based methods (MFE) to partition function-based ones that assemble structures using…
Algorithm of construction of all knots, links with given number of crosses on diagram of knot, link is offered. This algorithm is based on simple proposition, that there is a representation of knot (link) as closure of braid with n threads…
We view the folding of RNA-sequences as a map that assigns a pattern of base pairings to each sequence, known as secondary structure. These preimages can be constructed as random graphs (i.e. the neutral networks associated to the structure…
We study the impact of forbidding short cycles to the edge density of $k$-planar graphs; a $k$-planar graph is one that can be drawn in the plane with at most $k$ crossings per edge. Specifically, we consider three settings, according to…
A tangled-diagram over $[n]=\{1,...,n\}$ is a graph of degree less than two whose vertices $1,...,n$ are arranged in a horizontal line and whose arcs are drawn in the upper halfplane with a particular notion of crossings and nestings.…
We are giving tables of quasi-alternating knots with $8\le n \le 12$ crossings. As the obstructions for a knot to be quasialternating we used homology thickness with regards to Khovanov homology, odd homology, and Heegaard-Floer homology…
In a DNA sequence, we have the celebrated Watson-Crick complement $\overline{T}=A$, $\overline{A}=T$, $\overline{C}=G$, and $\overline{G}=C$. Given an integer $m\ge 2$, a secondary structure in a DNA sequence refers to the existence of two…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
The maximum number of non-crossing straight-line perfect matchings that a set of $n$ points in the plane can have is known to be $O(10.0438^n)$ and $\Omega^*(3^n)$. The lower bound, due to Garc\'ia, Noy, and Tejel (2000) is attained by the…
In 1926, Levi showed that, for every pseudoline arrangement $\mathcal{A}$ and two points in the plane, $\mathcal{A}$ can be extended by a pseudoline which contains the two prescribed points. Later extendability was studied for arrangements…
In this paper we study canonical $\gamma$-structures, a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A $\gamma$-structure is composed by specific building…
We further develop the large $ N $ formalism presented by some of us in earlier works in order to recursively calculate the partition function of a singly pseudoknotted RNA. We demonstrate that this calculation takes time proportional to…
We study the richness of the ensemble of graphical structures (i.e., unlabeled graphs) of the one-dimensional random geometric graph model defined by $n$ nodes randomly scattered in $[0,1]$ that connect if they are within the connection…
RNA-Seq technology offers new high-throughput ways for transcript identification and quantification based on short reads, and has recently attracted great interest. The problem is usually modeled by a weighted splicing graph whose nodes…
We give a correspondence between graphs with a given degree sequence and fillings of Ferrers diagrams by nonnegative integers with prescribed row and column sums. In this setting, k-crossings and k-nestings of the graph become occurrences…
Given a set of $n$ men represented by $n$ points lying on a line, and $n$ women represented by $n$ points lying on another parallel line, with each person having a list that ranks some people of opposite gender as his/her acceptable…
In this paper we present a complete characterization of the smallest sets that block all the simple spanning trees (SSTs) in a complete geometric graph. We also show that if a subgraph is a blocker for all SSTs of diameter at most 4, then…