AIMC Topic: Sequence Analysis, DNA

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DeepDualEnhancer: A Dual-Feature Input DNABert Based Deep Learning Method for Enhancer Recognition.

International journal of molecular sciences Nov 1, 2024
Enhancers are cis-regulatory DNA sequences that are widely distributed throughout the genome. They can precisely regulate the expression of target genes. Since the features of enhancer segments are difficult to detect, we propose DeepDualEnhancer, a ...
Promoter Regions, Genetic Enhancer Elements, Genetic Computational Biology Sequence Analysis, DNA Humans Neural Networks, Computer Deep Learning Genomics Algorithms
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An Integrated Multi-Model Framework Utilizing Convolutional Neural Networks Coupled with Feature Extraction for Identification of 4mC Sites in DNA Sequences.

Computers in biology and medicine Oct 28, 2024
N4-methylcytosine (4mC) is a chemical modification that occurs on one of the four nucleotide bases in DNA and plays a vital role in DNA expression, repair, and replication. It also actively participates in the regulation of cell differentiation and g...
Sequence Analysis, DNA Humans DNA Cytosine Neural Networks, Computer
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Generative language models on nucleotide sequences of human genes.

Scientific reports Sep 27, 2024
Language models, especially transformer-based ones, have achieved colossal success in natural language processing. To be precise, studies like BERT for natural language understanding and works like GPT-3 for natural language generation are very impor...
Computational Biology Sequence Analysis, DNA Humans Natural Language Processing Base Sequence
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Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities.

Trends in microbiology Sep 12, 2024
Increasing evidence suggests that the human microbiome plays an important role in cancer risk and treatment. Untargeted 'omics' techniques have accelerated research into microbiome-cancer interactions, supporting the discovery of novel associations a...
Humans Machine Learning Neoplasms Microbiota Metagenomics Computational Biology Sequence Analysis, DNA
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Utilizing Deep Neural Networks to Fill Gaps in Small Genomes.

International journal of molecular sciences Aug 4, 2024
With the widespread adoption of next-generation sequencing technologies, the speed and convenience of genome sequencing have significantly improved, and many biological genomes have been sequenced. However, during the assembly of small genomes, we st...
Genome, Fungal Neurospora crassa Genomics Algorithms Sequence Analysis, DNA Saccharomyces cerevisiae Deep Learning Neural Networks, Computer Schizosaccharomyces High-Throughput Nucleotide Sequencing Software
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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...
Promoter Regions, Genetic Software Animals Computational Biology Sequence Analysis, DNA Mice Humans Neural Networks, Computer
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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...
Computational Biology Transcription Factors Animals Gene Regulatory Networks Humans Neural Networks, Computer Databases, Genetic Algorithms Sequence Analysis, DNA
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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...
Sequence Analysis, DNA Data Compression Deep Learning Genomics Humans Neural Networks, Computer Algorithms
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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...
Nucleotides DNA Machine Learning Nanotechnology Sequence Analysis, DNA
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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...
Humans Machine Learning Sequence Analysis, DNA Chromosome Mapping Algorithms
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