Related papers: RawAlign: Accurate, Fast, and Scalable Raw Nanopor…

Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e., without basecalling). However, existing solutions cannot interpret raw signals…

Nanopore sequencing technologies continue to advance rapidly, offering critical benefits such as real-time analysis, the ability to sequence extremely long DNA fragments (up to millions of bases in a single read), and the option to…

Nanopore sequencing can read substantially longer sequences of nucleic acid molecules, called reads, than other sequencing methods, which has led to advances in genomic analysis such as the gapless human genome assembly. By analyzing the…

The advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data…

Motivation: Detection of structural variants (SV) from the alignment of sample DNA reads to the reference genome is an important problem in understanding human diseases. Long reads that can span repeat regions, along with an accurate…

The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…

Nanopore based sequencing has demonstrated significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multi-layered…

Nanopore sequencing is a widely-used high-throughput genome sequencing technology that can sequence long fragments of a genome into raw electrical signals at low cost. Nanopore sequencing requires two computationally-costly processing steps…

Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…

In nanopore sequencing, electrical signal is measured as DNA molecules pass through the sequencing pores. Translating these signals into DNA bases (base calling) is a highly non-trivial task, and its quality has a large impact on the…

Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The accuracy and speed of basecalling have critical implications…

Instruction tuning is a supervised fine-tuning approach that significantly improves the ability of large language models (LLMs) to follow human instructions. We propose SelfCodeAlign, the first fully transparent and permissive pipeline for…

Translocation event detection from raw nanopore current signals is a fundamental step in nanopore signal analysis. Traditional data analysis methods rely on user-defined parameters to extract event information, making the interpretation of…

Miniature DNA sequencing hardware has begun to succeed in mobile contexts, driving demand for efficient machine learning at the edge. This domain leverages deep learning techniques familiar from speech and time-series analysis for both…

Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…

Nanopore sequencing enables real-time long-read DNA sequencing with reads exceeding 10 kilobases, but inherent error rates of 12-15 percent present significant computational challenges for read alignment. The critical seed chaining step…

Nanopore genome sequencing is the key to enabling personalized medicine, global food security, and virus surveillance. The state-of-the-art base-callers adopt deep neural networks (DNNs) to translate electrical signals generated by nanopore…

We investigate usage of dynamic time warping (DTW) algorithm for aligning raw signal data from MinION sequencer. DTW is mostly using for fast alignment for selective sequencing to quickly determine whether a read comes from sequence of…

Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…

Neural visual decoding is a central problem in brain computer interface research, aiming to reconstruct human visual perception and to elucidate the structure of neural representations. However, existing approaches overlook a fundamental…