AIMC Topic: Sequence Analysis, DNA

Clear Filters Showing 1 to 10 of 287 articles

DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks.

Nature communications
Modeling long-range DNA dependencies is crucial for understanding genome structure and function across diverse biological contexts. However, effectively capturing these dependencies, which may span millions of base pairs in tasks such as three-dimens...

Refining cancer prediction with DNA sequencing and combined machine learning approaches.

Scientific reports
A high-accuracy DNA-based cancer risk predictor was developed by blending Logistic Regression with Gaussian Naive Bayes, and its hyperparameters were optimized via grid search. Five cancer types (BRCA1, KIRC, COAD, LUAD, PRAD) were classified in a co...

ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling.

Nature communications
Accurate detection of somatic variants in tumors is of critical importance and remains challenging. Current methods typically require matched normal samples for reliable detection, which are often unavailable in real-world research and clinical scena...

OpenSpliceAI provides an efficient modular implementation of SpliceAI enabling easy retraining across nonhuman species.

eLife
The SpliceAI deep learning system is currently one of the most accurate methods for identifying splicing signals directly from DNA sequences. However, its utility is limited by its reliance on older software frameworks and human-centric training data...

Empowering low-crosstalk, dynamic-decision random access of DNA storage via 384-multiplexed nanopore signatures.

Nature communications
On-demand access to information encoded in nucleotides lies at the heart of DNA/RNA applications. However, contemporary methods for targeted retrieval using PCR amplification or bead-based extraction, rely on Watson-Crick base pairing and pre-defined...

Image-based DNA sequencing encoding for detecting low-mosaicism somatic mobile element insertions.

Nature communications
Active mobile elements in the human genome can create novel mobile element insertions (MEIs) in somatic tissues. Detection of somatic MEIs, particularly those with low mosaicism, remains a significant challenge due to sequencing artifacts and alignme...

A comprehensive benchmarking of adaptive sampling tools for nanopore sequencing.

Genome biology
BACKGROUND: Adaptive sampling is an emerging technology to enrich target reads while depleting unwanted reads during real-time nanopore sequencing. The application of different algorithms has spawned various tools for the determination of read reject...

Unsupervised Clustering of DNA Transmission Footprints Using MoS/WSe Heterojunction.

ACS applied materials & interfaces
Quantum transport-based DNA sequencing is emerging as a promising technique in genetic analysis, offering fast, precise, and scalable decoding of genetic information, holding significant potential for applications in human biology and personalized me...

Quantum Transport Informed Machine Learning Mapping of Current-Voltage Characteristics for Precision Deoxyribonucleic Acid Sequencing.

The journal of physical chemistry. A
Quantum tunneling-based DNA sequencing promises to transform genomic analysis by improving long-read accuracy and enabling high-throughput sequencing, particularly the precise measurement of electrical conductance and tunneling current signatures ass...

Skin Microbiome alterations in heroin users revealed by full-length 16S rRNA sequencing.

BMC microbiology
BACKGROUND: Identifying key characteristics of unknown suspects, such as age, height, and drug use, is essential for advancing forensic investigations.