Related papers: A stitch in time: Efficient computation of genomic…
We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence. Our…
A basic principle in crystal structure determination is that there should be proper distances between adjacent atoms. Therefore, detection of atom bumping is of fundamental significance in structure determination, especially in the direct…
Two new algorithms are described for matching two dimensional coordinate lists of point sources that are signifcantly faster than previous methods. By matching rarely occurring triangles (or more complex shapes) in the two lists, and by…
After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies between less than one to a few kT. This causes the opening of intermittent…
The classical method of determining the atomic structure of complex molecules by analyzing diffraction patterns is currently undergoing drastic developments. Modern techniques for producing extremely bright and coherent X-ray lasers allow a…
Motivation: The comparison of diverse genomic datasets is fundamental to understanding genome biology. Researchers must explore many large datasets of genome intervals (e.g., genes, sequence alignments) to place their experimental results…
Motivation: Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes…
Currently, identification of crystallization pathways in polymers is being carried out using molecular simulation-based data on a preset cut-off point on a single order parameter (OP) to define nucleated or crystallized regions. Aside from…
In this work we describe a fast and stable algorithm for the computation of the orthogonal moments of an image. Indeed, orthogonal moments are characterized by a high discriminative power, but some of their possible formulations are…
We propose a fast algorithm for evaluating the moments of Bingham distribution. The calculation is done by piecewise rational approximation, where interpolation and Gaussian integrals are utilized. Numerical test shows that the algorithm…
The maximal clique problem, to find the maximally sized clique in a given graph, is classically an NP-complete computational problem, which has potential applications ranging from electrical engineering, computational chemistry,…
We developed a low-energy model that can be used at any time to describe the dynamics of DNA bubbles at temperatures below the melting point. The Schr\"odinger equation associated with this problem is solved in imaginary time with a quantum…
Background: The computation of the statistical properties of motif occurrences has an obviously relevant practical application: for example, patterns that are significantly over- or under-represented in the genome are interesting candidates…
Recent years have seen deep neural networks (DNNs) becoming wider and deeper to achieve better performance in many applications of AI. Such DNNs however require huge amounts of memory to store weights and intermediate results (e.g.,…
We present a new approach for solving (minimum disagreement) correlation clustering that results in sublinear algorithms with highly efficient time and space complexity for this problem. In particular, we obtain the following algorithms for…
The DNA molecule is modeled by a parabola embedded chain with long-range interactions between twisted base pair dipoles. A mechanism for bubble generation is presented and investigated in two different configurations. Using random normally…
A distributed algorithm performs local computations on pieces of input and communicates the results through given communication links. When processing a massive graph in a distributed algorithm, local outputs must be configured as a…
The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without…
In high-dimensional generalized linear models, it is crucial to identify a sparse model that adequately accounts for response variation. Although the best subset section has been widely regarded as the Holy Grail of problems of this type,…
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…