相关论文: Uniform generation of RNA-RNA interaction structur…
Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops. This shape-projection preserves the…
In this paper we present a sampling framework for RNA structures of fixed topological genus. We introduce a novel, linear time, uniform sampling algorithm for RNA structures of fixed topological genus $g$, for arbitrary $g>0$. Furthermore…
A topological RNA structure is derived from a diagram and its shape is obtained by collapsing the stacks of the structure into single arcs and by removing any arcs of length one. Shapes contain key topological, information and for fixed…
In this paper we present a combinatorial proof of a relation between the generating functions of unicellular and bicellular maps. This relation is a consequence of the Schwinger-Dyson equation of matrix theory. Alternatively it can be…
The topological filtration of interacting RNA complexes is studied and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that for two interacting…
In this paper we study $\gamma$-structures filtered by topological genus. $\gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A…
In this paper we study properties of topological RNA structures, i.e.~RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological…
In this paper we compute the bivariate generating function of $\gamma$-matchings over two backbones, filtered by the number of arcs and the topological genus. $\gamma$-matchings over two backbones are chord-diagrams, obtained via…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
We present a general setting for structure-sequence comparison in a large class of RNA structures that unifies and generalizes a number of recent works on specific families on structures. Our approach is based on tree decomposition of…
We present a unified pipeline for univariate time series classification via complex networks and persistent homology. A time series is mapped to a graph through one of five constructions across three families (visibility (natural and…
Long non-coding RNA, microRNA, and messenger RNA enable key regulations of various biological processes through a variety of diverse interaction mechanisms. Identifying the interactions and cross-talk between these heterogeneous RNA classes…
A major goal in genomics is to properly capture the complex dynamical behaviors of gene regulatory networks (GRNs). This includes inferring the complex interactions between genes, which can be used for a wide range of genomics analyses,…
We present a novel topological classification of RNA secondary structures with pseudoknots. It is based on the topological genus of the circular diagram associated to the RNA base-pair structure. The genus is a positive integer number,…
Single-cell RNA sequencing (scRNA-seq) technology provides high-throughput gene expression data to study the cellular heterogeneity and dynamics of complex organisms. Graph neural networks (GNNs) have been widely used for automatic cell…
The enumeration of maps and the study of uniform random maps have been classical topics of combinatorics and statistical physics ever since the seminal work of Tutte in the sixties. Following the bijective approach initiated by Cori and…
Combinatorial enumeration of various RNA secondary structures and protein contact maps, is of great interest for both combinatorists and computational biologists. Enumeration of protein contact maps has considerable difficulties due to the…
We introduce the Insertion Chain Complex, a higher-dimensional extension of insertion graphs, as a new framework for analyzing finite sets of words. We study its topological and combinatorial properties, in particular its homology groups,…
Designing RNA molecules that interact with specific proteins is a critical challenge in experimental and computational biology. Existing computational approaches require a substantial amount of previously known interacting RNA sequences for…
The problem of estimating the structure of a graph from observed data is of growing interest in the context of high-throughput genomic data, and single-cell RNA sequencing in particular. These, however, are challenging applications, since…