AIMC Topic: Sequence Analysis, DNA
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GraphPro: An interpretable graph neural network-based model for identifying promoters in multiple species.
Computers in biology and medicine
Aug 2, 2024
Promoters are DNA sequences that bind with RNA polymerase to initiate transcription, regulating this process through interactions with transcription factors. Accurate identification of promoters is crucial for understanding gene expression regulation...
PPRTGI: A Personalized PageRank Graph Neural Network for TF-Target Gene Interaction Detection.
IEEE/ACM transactions on computational biology and bioinformatics
Jun 5, 2024
Transcription factors (TFs) regulation is required for the vast majority of biological processes in living organisms. Some diseases may be caused by improper transcriptional regulation. Identifying the target genes of TFs is thus critical for underst...
GenCoder: A Novel Convolutional Neural Network Based Autoencoder for Genomic Sequence Data Compression.
IEEE/ACM transactions on computational biology and bioinformatics
Jun 5, 2024
Revolutionary advances in DNA sequencing technologies fundamentally change the nature of genomics. Today's sequencing technologies have opened into an outburst in genomic data volume. These data can be used in various applications where long-term sto...
Precision Basecalling of Single DNA Nucleotide from Overlapped Transmission Readouts with Machine Learning Aided Solid-State Nanogap.
ACS applied materials & interfaces
May 31, 2024
DNA sequencing with the quantum tunneling technique heralds a paradigm shift in genetic analysis, promising rapid and accurate identification for diverging applications ranging from personalized medicine to security issues. However, the widespread di...
GEMA: A Genome Exact Mapping Accelerator Based on Learned Indexes.
IEEE transactions on biomedical circuits and systems
May 28, 2024
In this article, we introduce GEMA, a genome exact mapping accelerator based on learned indexes, specifically designed for FPGA implementation. GEMA utilizes a machine learning (ML) algorithm to precisely locate the exact position of read sequences w...
Using a hybrid neural network architecture for DNA sequence representation: A study on N-methylcytosine sites.
Computers in biology and medicine
May 27, 2024
N-methylcytosine (4mC) is a modified form of cytosine found in DNA, contributing to epigenetic regulation. It exists in various genomes, including the Rosaceae family encompassing significant fruit crops like apples, cherries, and roses. Previous inv...
Assessment and classification of COVID-19 DNA sequence using pairwise features concatenation from multi-transformer and deep features with machine learning models.
SLAS technology
May 23, 2024
The 2019 novel coronavirus (renamed SARS-CoV-2, and generally referred to as the COVID-19 virus) has spread to 184 countries with over 1.5 million confirmed cases. Such a major viral outbreak demands early elucidation of taxonomic classification and ...
Development of a two-layer machine learning model for the forensic application of legal and illegal poppy classification based on sequence data.
Forensic science international. Genetics
May 22, 2024
Poppies are beneficial plants with a variety of applications, including medicinal, edible, ornamental, and industrial purposes. Some Papaver species are forensically significant plants because they contain opium, a narcotic substance. Internationally...
Fundamentals for predicting transcriptional regulations from DNA sequence patterns.
Journal of human genetics
May 10, 2024
Cell-type-specific regulatory elements, cataloged through extensive experiments and bioinformatics in large-scale consortiums, have enabled enrichment analyses of genetic associations that primarily utilize positional information of the regulatory el...
A culture-independent approach, supervised machine learning, and the characterization of the microbial community composition of coastal areas across the Bay of Bengal and the Arabian Sea.
BMC microbiology
May 10, 2024
BACKGROUND: Coastal areas are subject to various anthropogenic and natural influences. In this study, we investigated and compared the characteristics of two coastal regions, Andhra Pradesh (AP) and Goa (GA), focusing on pollution, anthropogenic acti...
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