AIMC Topic: DNA
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Intelligent and robust DNA robots capable of swarming into leakless nonlinear amplification in response to a trigger.
Nanoscale horizons
May 31, 2022
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
May 27, 2022
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
May 23, 2022
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
May 21, 2022
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
May 16, 2022
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
May 13, 2022
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
May 5, 2022
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)
May 4, 2022
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. ...
Deep6mAPred: A CNN and Bi-LSTM-based deep learning method for predicting DNA N6-methyladenosine sites across plant species.
Methods (San Diego, Calif.)
Apr 25, 2022
DNA N6-methyladenine (6mA) is a key DNA modification, which plays versatile roles in the cellular processes, including regulation of gene expression, DNA repair, and DNA replication. DNA 6mA is closely associated with many diseases in the mammals and...
FCNGRU: Locating Transcription Factor Binding Sites by Combing Fully Convolutional Neural Network With Gated Recurrent Unit.
IEEE journal of biomedical and health informatics
Apr 14, 2022
Deciphering the relationship between transcription factors (TFs) and DNA sequences is very helpful for computational inference of gene regulation and a comprehensive understanding of gene regulation mechanisms. Transcription factor binding sites (TFB...
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