Related papers: Minimum length RNA folding trajectories
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA…
Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called…
A long series of recent results and breakthroughs have led to faster and better distributed approximation algorithms for single source shortest paths (SSSP) and related problems in the CONGEST model. The runtime of all these algorithms,…
The contact map of a protein fold is a graph that represents the patterns of contacts in the fold. It is known that the contact map can be decomposed into stacks and queues. RNA secondary structures are special stacks in which the degree of…
We consider a new problem of designing a network with small $s$-$t$ effective resistance. In this problem, we are given an undirected graph $G=(V,E)$, two designated vertices $s,t \in V$, and a budget $k$. The goal is to choose a subgraph…
In this paper we present a selfcontained analysis and description of the novel {\it ab initio} folding algorithm {\sf cross}, which generates the minimum free energy (mfe), 3-noncrossing, $\sigma$-canonical RNA structure. Here an RNA…
We study the electrical distribution network reconfiguration problem, defined as follows. We are given an undirected graph with a root vertex, demand at each non-root vertex, and resistance on each edge. Then, we want to find a spanning…
It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model. In contrast, ensemble based quantities such…
Link state routing protocols such as OSPF or IS-IS currently use only best paths to forward IP packets throughout a domain. The optimality of sub-paths ensures consistency of hop by hop forwarding although paths, calculated using Dijkstra…
In this paper, we propose an end-to-end deep learning model, called E2Efold, for RNA secondary structure prediction which can effectively take into account the inherent constraints in the problem. The key idea of E2Efold is to directly…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
This paper give a simple linear-time algorithm that, given a weighted digraph, finds a spanning tree that simultaneously approximates a shortest-path tree and a minimum spanning tree. The algorithm provides a continuous trade-off: given the…
The Nearest Neighbor model is the $\textit{de facto}$ thermodynamic model of RNA secondary structure formation and is a cornerstone of RNA structure prediction and sequence design. The current functional form (Turner 2004) contains…
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…
Given a flow network, the Minimum Flow Decomposition (MFD) problem is finding the smallest possible set of weighted paths whose superposition equals the flow. It is a classical, strongly NP-hard problem that is proven to be useful in RNA…
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…
We present TT2NE, a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. TT2NE guarantees to find the minimum free energy…
Computing distances and finding shortest paths in massive real-world networks is a fundamental algorithmic task in network analysis. There are two main approaches to solving this task. On one hand are traversal-based algorithms like…
An influential result by Dor, Halperin, and Zwick (FOCS 1996, SICOMP 2000) implies an algorithm that can compute approximate shortest paths for all vertex pairs in $\tilde{O}(n^{2+O\left(\frac{1}{k}\right )})$ time, ensuring that the output…