Related papers: Identifying RNA contacts from SHAPE-MaP by partial…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
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,…
Predicting bioactivity and physical properties of molecules is a longstanding challenge in drug design. Most approaches use molecular descriptors based on a 2D representation of molecules as a graph of atoms and bonds, abstracting away the…
Processing information on 3D objects requires methods stable to rigid-body transformations, in particular rotations, of the input data. In image processing tasks, convolutional neural networks achieve this property using…
The interaction between Ribonucleic Acids (RNAs) and proteins, also called RNA Protein Interaction (RPI), plays an important role in the life activities of organisms, including in various regulatory processes, such as gene splicing, gene…
In this paper, we propose a computationally efficient approach -- space(Sparse PArtial Correlation Estimation)-- for selecting non-zero partial correlations under the high-dimension-low-sample-size setting. This method assumes the overall…
We present a novel approach to constraint-based causal discovery, that takes the form of straightforward logical inference, applied to a list of simple, logical statements about causal relations that are derived directly from observed…
This work derives closed-form expressions computing the expectation of co-presence and of number of co-occurrences of nodes on paths sampled from a network according to general path weights (a bag of paths). The underlying idea is that two…
A contact map is a simple representation of the structure of proteins and other chain-like macromolecules. This representation is quite amenable to numerical studies of folding. We show that the number of contact maps corresponding to the…
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…
While dealing with matching shapes to their parts, we often apply a tool known as functional maps. The idea is to translate the shape matching problem into "convenient" spaces by which matching is performed algebraically by solving a least…
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…
Background: In the Nearest-Neighbor Thermodynamic Model, a standard approach for RNA secondary structure prediction, the energy of the multiloops is modeled using a linear entropic penalty governed by three branching parameters. Although…
Effective application of mathematical models to interpret biological data and make accurate predictions often requires that model parameters are identifiable. Approaches to assess the so-called structural identifiability of models are…
Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in sequencing technologies. The prohibitive sizes of the…
The graph structure of a Bayesian network (BN) can be learned from data using the well-known score-and-search approach. Previous work has shown that incorporating structured representations of the conditional probability distributions…
Interacting RNA complexes are studied via bicellular maps using a filtration via their topological genus. Our main result is a new bijection for RNA-RNA interaction structures and linear time uniform sampling algorithm for RNA complexes of…
We propose the Part-based Recurrent Multi-view Aggregation network(PREMA) to eliminate the detrimental effects of the practical view defects, such as insufficient view numbers, occlusions or background clutters, and also enhance the…
Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample…
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…