AIMC Topic: DNA

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A Novel Adaptive Linear Neuron Based on DNA Strand Displacement Reaction Network.

IEEE/ACM transactions on computational biology and bioinformatics
Analog DNA strand displacement circuits can be used to build artificial neural network due to the continuity of dynamic behavior. In this study, DNA implementations of novel catalysis, novel degradation and adjustment reaction modules are designed an...

CapsProm: a capsule network for promoter prediction.

Computers in biology and medicine
Locating the promoter region in DNA sequences is of paramount importance in bioinformatics. This problem has been widely studied in the literature, but it has not yet been fully resolved. Some researchers have shown remarkable results using convoluti...

Intelligent and robust DNA robots capable of swarming into leakless nonlinear amplification in response to a trigger.

Nanoscale horizons
Nonlinear DNA signal amplification with an enzyme-free isothermal self-assembly process is uniquely useful in nanotechnology and nanomedicine. However, progress in this direction is hampered by the lack of effective design models of leak-resistant DN...

Rewritable two-dimensional DNA-based data storage with machine learning reconstruction.

Nature communications
DNA-based data storage platforms traditionally encode information only in the nucleotide sequence of the molecule. Here we report on a two-dimensional molecular data storage system that records information in both the sequence and the backbone struct...

Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning.

Nature biotechnology
Protein-ligand interactions are increasingly profiled at high throughput using affinity selection and massively parallel sequencing. However, these assays do not provide the biophysical parameters that most rigorously quantify molecular interactions....

Identification of DNA N4-methylcytosine sites based on multi-source features and gradient boosting decision tree.

Analytical biochemistry
N4-methylcytosine (4 mC) is an important and common methylation which widely exists in prokaryotes. It plays a crucial role in correcting DNA replication errors and protecting host DNA against degradation by restrictive enzymes. Hence, the accurate i...

Advances in Designer DNA Nanorobots Enabling Programmable Functions.

Chembiochem : a European journal of chemical biology
The advent of DNA nanotechnology has paved the way for the development of nanoscale robotics capable of executing smart and sophisticated tasks in a programmed and automatic manner. The programmability and customizable functionality of designer DNA n...

DNA Memristors and Their Application to Reservoir Computing.

ACS synthetic biology
This paper introduces memristors realized by molecular and DNA reactions. Molecular memristors process one input molecule, generate two output molecules, and are realized using two molecular reactions with two different rate constants. The DNA memris...

A nonlinear neural network based on an analog DNA toehold mediated strand displacement reaction circuit.

Nanoscale
The DNA toehold mediated strand displacement reaction is one of the semi-synthetic biology technologies for next-generation computers. In this article, we present a framework for a novel nonlinear neural network based on an engineered biochemical cir...

Molecular Visualization of Early-Stage Acute Kidney Injury with a DNA Framework Nanodevice.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)
DNA nanomachines with artificial intelligence have attracted great interest, which may open a new era of precision medicine. However, their in vivo behavior, including early diagnosis and therapeutic effect are limited by their targeting efficiency. ...