Related papers: Comprehensive assessment of error correction metho…
Wide-field, multi-band surveys now detect millions of unresolved sources in nearby galaxy clusters, yet separating globular clusters (GCs) from foreground stars and background galaxies remains challenging. Scalable, automated classification…
The newly developed deep-sequencing technologies make it possible to acquire both quantitative and qualitative information regarding transcript biology. By measuring messenger RNA levels for all genes in a sample, RNA-seq provides an…
In forensic genetics, short tandem repeats (STRs) are used for human identification (HID). Degraded biological trace samples with low amounts of short DNA fragments (low-quality DNA samples) pose a challenge for STR typing. Predefined…
In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when…
Background: Single-cell RNA sequencing (scRNA-seq) enables gene expression profiling at cellular resolution but is inherently affected by sparsity caused by dropout events, where expressed genes are recorded as zeros due to technical…
RNAs are essential molecules that carry genetic information vital for life, with profound implications for drug development and biotechnology. Despite this importance, RNA research is often hindered by the vast literature available on the…
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…
Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in sequencing technologies. The prohibitive sizes of the…
Motivation: Next-generation sequencing tools have enabled producing of huge amount of genomic information at low cost. Unfortunately, presence of sequencing errors in such data affects quality of downstream analyzes. Accuracy of them can be…
Next-generation sequencing (NGS) technologies have enabled affordable sequencing of billions of short DNA fragments at high throughput, paving the way for population-scale genomics. Genomics data analytics at this scale requires overcoming…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
DNA has many valuable characteristics that make it suitable for a long-term storage medium, in particular its durability and high information density. DNA can be stored safely for hundreds of years with virtually no degradation, in contrast…
Objectives: The vast and complex nature of human genomic sequencing data presents challenges for effective analysis. This review aims to investigate the application of Natural Language Processing (NLP) techniques, particularly Large…
Next Generation Sequencing (NGS) technology has resulted in massive amounts of proteomics and genomics data. This data is of no use if it is not properly analyzed. ETL (Extraction, Transformation, Loading) is an important step in designing…
Storing digital data in synthetic DNA faces challenges in ensuring data reliability in the presence of edit errors--deletions, insertions, and substitutions--that occur randomly during various stages of the storage process. Current…
The study of functional genomics--particularly in non-model organisms has been dramatically improved over the last few years by use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
Background: High-throughput techniques bring novel tools but also statistical challenges to genomic research. Identifying genes with differential expression between different species is an effective way to discover evolutionarily conserved…
Synthetic DNA can in principle be used for the archival storage of arbitrary data. Because errors are introduced during DNA synthesis, storage, and sequencing, an error-correcting code (ECC) is necessary for error-free recovery of the data.…