AIMC Topic: DNA

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DeepBarcoding: Deep Learning for Species Classification Using DNA Barcoding.

IEEE/ACM transactions on computational biology and bioinformatics Aug 8, 2022
DNA barcodes with short sequence fragments are used for species identification. Because of advances in sequencing technologies, DNA barcodes have gradually been emphasized. DNA sequences from different organisms are easily and rapidly acquired. There...
Neural Networks, Computer Deep Learning Sequence Analysis, DNA DNA DNA Barcoding, Taxonomic
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Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization.

Chemical reviews Jul 29, 2022
Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review...
Artificial Intelligence DNA Catalysis Alkynes Amination
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BERT-Promoter: An improved sequence-based predictor of DNA promoter using BERT pre-trained model and SHAP feature selection.

Computational biology and chemistry Jul 14, 2022
A promoter is a sequence of DNA that initializes the process of transcription and regulates whenever and wherever genes are expressed in the organism. Because of its importance in molecular biology, identifying DNA promoters are challenging to provid...
Machine Learning Natural Language Processing DNA Promoter Regions, Genetic
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DNA: Deeply Supervised Nonlinear Aggregation for Salient Object Detection.

IEEE transactions on cybernetics Jul 4, 2022
Recent progress on salient object detection mainly aims at exploiting how to effectively integrate multiscale convolutional features in convolutional neural networks (CNNs). Many popular methods impose deep supervision to perform side-output predicti...
Neural Networks, Computer DNA
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Single-cell specific and interpretable machine learning models for sparse scChIP-seq data imputation.

PloS one Jul 1, 2022
MOTIVATION: Single-cell Chromatin ImmunoPrecipitation DNA-Sequencing (scChIP-seq) analysis is challenging due to data sparsity. High degree of sparsity in biological high-throughput single-cell data is generally handled with imputation methods that c...
Machine Learning Animals Mice Genomics Sequence Analysis, DNA Cluster Analysis DNA
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Hyb4mC: a hybrid DNA2vec-based model for DNA N4-methylcytosine sites prediction.

BMC bioinformatics Jun 29, 2022
BACKGROUND: DNA N4-methylcytosine is part of the restrictive modification system, which works by regulating some biological processes, for example, the initiation of DNA replication, mismatch repair and inactivation of transposon. However, using expe...
Neural Networks, Computer DNA
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Using deep learning to detect digitally encoded DNA trigger for Trojan malware in Bio-Cyber attacks.

Scientific reports Jun 10, 2022
This article uses Deep Learning technologies to safeguard DNA sequencing against Bio-Cyber attacks. We consider a hybrid attack scenario where the payload is encoded into a DNA sequence to activate a Trojan malware implanted in a software tool used i...
Software Deep Learning Sequence Analysis, DNA DNA Computer Security
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Characterizing collaborative transcription regulation with a graph-based deep learning approach.

PLoS computational biology Jun 6, 2022
Human epigenome and transcription activities have been characterized by a number of sequence-based deep learning approaches which only utilize the DNA sequences. However, transcription factors interact with each other, and their collaborative regulat...
Humans Deep Learning Protein Binding Transcription Factors DNA Gene Expression Regulation Binding Sites Chromatin
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A Novel Adaptive Linear Neuron Based on DNA Strand Displacement Reaction Network.

IEEE/ACM transactions on computational biology and bioinformatics Jun 3, 2022
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...
Neural Networks, Computer Algorithms Computer Simulation DNA Neurons
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CapsProm: a capsule network for promoter prediction.

Computers in biology and medicine Jun 1, 2022
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...
Neural Networks, Computer Software Computational Biology DNA Promoter Regions, Genetic
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