Related papers: The Enhanced Double Digest Problem for DNA Physica…

The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…

This paper addresses the problem of learning binary hash codes for large scale image search by proposing a novel hashing method based on deep neural network. The advantage of our deep model over previous deep model used in hashing is that…

Analysis of single-molecule micromanipulation experiments of DNA unzipping process shows some features of the force-distance curve, namely two consequent plateaus in the area of ${\sim}12-14pN$ dependent on nucleotide sequence structure, as…

The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…

DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…

Double-strand DNA breaks (DSBs) are a form of DNA damage that can cause abnormal chromosomal rearrangements. Recent technologies based on high-throughput experiments have obvious high costs and technical challenges.Therefore, we design a…

We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of…

Deep convolutional neural networks (CNNs) have shown excellent performance in object recognition tasks and dense classification problems such as semantic segmentation. However, training deep neural networks on large and sparse datasets is…

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.,…

The maximum graph bisection problem is a well known graph partition problem. The problem has been proven to be NP-hard. In the maximum graph bisection problem it is required that the set of vertices is divided into two partition with equal…

Nowadays, Cellular Neural Networks (CNN) are practically implemented in parallel, analog computers, showing a fast developing trend. Physicist must be aware that such computers are appropriate for solving in an elegant manner practically…

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…

DNA polymerase (DNAP) is a dual-purpose enzyme that plays two opposite roles in two different situations during DNA replication. It plays its normal role as a {\it polymerase} catalyzing the elongation of a new DNA molecule by adding a…

Map Space Exploration is the problem of finding optimized mappings of a Deep Neural Network (DNN) model on an accelerator. It is known to be extremely computationally expensive, and there has been active research looking at both heuristics…

Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…

We consider the problem of storing and retrieving information from synthetic DNA media. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on their collection of substrings…

The seriation problem seeks to reorder a set of elements given pairwise similarity information, so that elements with higher similarity are closer in the resulting sequence. When a global ordering consistent with the similarity information…

Due to its longevity and enormous information density, DNA is an attractive medium for archival data storage. Thanks to rapid technological advances, DNA storage is becoming practically feasible, as demonstrated by a number of experimental…

The vast parallelism, exceptional energy efficiency and extraordinary information inherent in DNA molecules are being explored for computing, data storage and cryptography. DNA cryptography is a emerging field of cryptography. In this paper…

Technologies for sequencing (reading) and synthesizing (writing) DNA have progressed on a Moore's law-like trajectory over the last three decades. This has motivated the idea of using DNA for data storage. Theoretically, DNA-based storage…