Genomics
Summary: Linear mixed models are a commonly used statistical approach in genome-wide association studies when population structure is present. However, naive permutations to empirically estimate the null distribution of a statistic of…
Prediction of mRNA gene-expression profiles directly from routine whole-slide images (WSIs) using deep learning models could potentially offer cost-effective and widely accessible molecular phenotyping. While such WSI-based gene-expression…
Nonlinear data visualization using t-distributed stochastic neighbor embedding (t-SNE) enables the representation of complex single-cell transcriptomic landscapes in two or three dimensions to depict biological populations accurately.…
In this paper, we examine the computational complexity of enumeration in certain genome rearrangement models. We first show that the Pairwise Rearrangement problem in the Single Cut-and-Join model (Bergeron, Medvedev, & Stoye, J. Comput.…
The task of understanding and interpreting the complex information encoded within genomic sequences remains a grand challenge in biological research and clinical applications. In this context, recent advancements in large language model…
Large language models (LLMs) are having transformative impacts across a wide range of scientific fields, particularly in the biomedical sciences. Just as the goal of Natural Language Processing is to understand sequences of words, a major…
Background: Genomic instability is a hallmark of cancer, leading to many somatic alterations. Identifying which alterations have a system-wide impact is a challenging task. Nevertheless, this is an essential first step for prioritizing…
The global surge in the cases of gastric cancer has prompted an investigation into the potential of gut microbiota as a predictive marker for the disease. The alterations in gut diversity are suspected to be associated with an elevated risk…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Background: Allium vegetables (garlic and onion) are one of the flavorings in people's daily diets. Observational studies suggest that intake of allium vegetables may be correlated with a lower incidence of digestive system cancers.…
Expanding genetic codes from natural standard nucleotides to artificial non-standard nucleotides marks a significant advancement in synthetic biology, with profound implications for biotechnology and medicine. Decoding the biological…
Gene and RNA editing methods, technologies, and applications are emerging as innovative forms of therapy and medicine, offering more efficient implementation compared to traditional pharmaceutical treatments. Current trends emphasize the…
This paper provides a comprehensive survey of data structures for representing k-mer sets, which are fundamental in high-throughput sequencing analysis. It categorizes the methods into two main strategies: those using fingerprinting and…
One of the major challenges arising from single-cell transcriptomics experiments is the question of how to annotate the associated single-cell transcriptomic profiles. Because of the large size and the high dimensionality of the data,…
This paper provides a comprehensive review of recent advancements in k-mer-based data structures representing collections of several samples (sometimes called colored de Bruijn graphs) and their applications in large-scale sequence indexing…
Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed…
Age-related macular degeneration (AMD) is a major cause of blindness in older adults, severely affecting vision and quality of life. Despite advances in understanding AMD, the molecular factors driving the severity of subretinal scarring…
Understanding the genetic underpinnings of complex traits and diseases has been greatly advanced by genome-wide association studies (GWAS). However, a significant portion of trait heritability remains unexplained, known as ``missing…
Genomic data I used in many fields but, it has become known that most of the platforms used in the sequencing process produce significant errors. This means that the analysis and inferences generated from these data may have some errors…
Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run…