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In higher eukaryotes, transfer RNAs (tRNAs) with the same anticodon are encoded by multiple nuclear genes, and little is known about how mutations in these genes affect translation and cellular homeostasis. Similarly, the surveillance systems that respond to such defects in higher eukaryotes are not clear. Here, we discover that loss of GTPBP2, a novel(More)
Ab initio protein structure prediction is an important problem for which several algorithms have been developed. Algorithms differ by how they represent 3D protein conformations (on-lattice, off-lattice, coarse-grain or fine-grain model), by the energy model they consider, and whether they are heuristic or exact algorithms. This paper presents a local(More)
Given an RNA sequence and two designated secondary structures A, B, we describe a new algorithm that computes a nearly optimal folding pathway from A to B. The algorithm, RNAtabupath, employs a tabu semi-greedy heuristic, known to be an effective search strategy in combinatorial optimization. Folding pathways, sometimes called routes or trajectories, are(More)
The Quasigroup Completion Problem (QCP) is a very challenging benchmark among combinatorial problems, and the focus of much recent interest in the area of constraint programming. [5] reports that QCPs of order 40 could not be solved by pure constraint programming approaches, but could sometimes be solved by hybrid approaches combining constraint programming(More)
We perform a systematic comparison of SAT and CSP models for a challenging combinatorial problem, quasigroup completion (QCP). Our empirical results clearly indicate the superiority of the 3D SAT encoding (Kautz et al. 2001), with various solvers, over other SAT and CSP models. We propose a partial explanation of the observed performance. Analytically, we(More)
Epithelial morphogenesis generates the shape of tissues, organs and embryos and is fundamental for their proper function. It is a dynamic process that occurs at multiple spatial scales from macromolecular dynamics, to cell deformations, mitosis and apoptosis, to coordinated cell rearrangements that lead to global changes of tissue shape. Using time lapse(More)
Synthetic biology is a rapidly emerging discipline with long-term ramifications that range from single-molecule detection within cells to the creation of synthetic genomes and novel life forms. Truly phenomenal results have been obtained by pioneering groups--for instance, the combinatorial synthesis of genetic networks, genome synthesis using BioBricks,(More)
Chemical and enzymatic footprinting experiments, such as shape (selective 2'-hydroxyl acylation analyzed by primer extension), yield important information about RNA secondary structure. Indeed, since the [Formula: see text]-hydroxyl is reactive at flexible (loop) regions, but unreactive at base-paired regions, shape yields quantitative data about which RNA(More)