Related papers: Predicting Knot or Catenane Type of Site-Specific …
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base pairs while the DNA is usually several millions of base pairs long.…
Splicing sites provide unique statistics in human genome due to their large number and reasonably complete annotation. Analyses of the cumulative SNPs distribution in splicing sites reveal a few interesting observations. While a degree of…
Gene assembly in ciliates is an extremely involved DNA transformation process, which transforms a nucleus, the micronucleus, to another functionally different nucleus, the macronucleus. In this paper we characterize which loop recombination…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…
We present a method to determine Fashion DNA, coordinate vectors locating fashion items in an abstract space. Our approach is based on a deep neural network architecture that ingests curated article information such as tags and images, and…
Modellers of large scale genome rearrangement events, in which segments of DNA are inverted, moved, swapped, or even inserted or deleted, have found a natural syntax in the language of permutations. Despite this, there has been a wide range…
Medication recommendation targets to provide a proper set of medicines according to patients' diagnoses, which is a critical task in clinics. Currently, the recommendation is manually conducted by doctors. However, for complicated cases,…
Recent advances in neural networks have been successfully applied to many tasks in online recommendation applications. We propose a new framework called cone latent mixture model which makes use of hand-crafted state being able to factor…
Spiking Neural Networks (SNN) are models for "realistic" neuronal computation, which makes them somehow different in scope from "ordinary" deep-learning models widely used in AI platforms nowadays. SNNs focus on timed latency (and possibly…
By exploiting the exquisite selectivity of DNA hybridization, DNA-Coated Colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the…
Although rare, an increasing number of proteins have been observed to contain entanglements in their native structures. To gain more insight into the significance of protein knotting, researchers have been investigating protein knot…
An example of a nonspecific molecular bond is the affinity of any positive charge for any negative charge (like-unlike), or of nonpolar material for itself when in aqueous solution (like-like). This contrasts specific bonds such as the…
Despite the remarkable success of deep learning systems over the last decade, a key difference still remains between neural network and human decision-making: As humans, we cannot only form a decision on the spot, but also ponder,…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Long range charge transfer experiments in DNA oligomers and the subsequently measured -- and very diverse -- transport response of DNA wires in solid state experiments exemplifies the need for a thorough theoretical understanding of charge…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
The art of tying knots is exploited in nature and occurs in multiple applications ranging from being an essential part of scouting programs to engineering molecular knots. Biomolecular knots, such as knotted proteins, bear various cellular…
A recommender system's basic task is to estimate how users will respond to unseen items. This is typically modeled in terms of how a user might rate a product, but here we aim to extend such approaches to model how a user would write about…