Genomics
Sequence diversity is one of the major challenges in the design of diagnostic, prophylactic and therapeutic interventions against viruses. DiMA is a novel tool that is big data-ready and designed to facilitate the dissection of sequence…
Artificial Intelligence (AI) has emerged as a key driver of precision agriculture, facilitating enhanced crop productivity, optimized resource use, farm sustainability, and informed decision-making. Also, the expansion of genome sequencing…
Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to study individual cellular distinctions and uncover unique cell characteristics. However, a significant technical challenge in scRNA-seq analysis is the occurrence of…
Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases…
Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture…
Locations of DNA replication initiation in prokaryotes, called "origins of replication", are well-characterized. However, a mechanistic understanding of the sequence-dependence of the local unzipping of double-stranded DNA, the first step…
Genotype imputation enhances genetic data by predicting missing SNPs using reference haplotype information. Traditional methods leverage linkage disequilibrium (LD) to infer untyped SNP genotypes, relying on the similarity of LD structures…
Mammalian gut microbiomes are essential for host functions like digestion, immunity, and nutrient utilization. This study examines the gut microbiome of horses, donkeys, and their hybrids, mules and hinnies, to explore the role of…
Fescue toxicity causes reduced growth and reproductive issues in cattle grazing endophyte-infected tall fescue. To characterize the gut microbiota and its response to fescue toxicosis, we collected fecal samples before and after a 30-days…
MotifbreakR is a software tool that scans genetic variants against position weight matrices of transcription factors (TF) to determine the potential for the disruption of TF binding at the site of the variant. It leverages the Bioconductor…
RNA sequencing techniques, like bulk RNA-seq and Single Cell (sc) RNA-seq, are critical tools for the biologist looking to analyze the genetic activity/transcriptome of a tissue or cell during an experimental procedure. Platforms like…
Molecular biologists frequently interpret gene lists derived from high-throughput experiments and computational analysis. This is typically done as a statistical enrichment analysis that measures the over- or under-representation of…
At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segments using sequence alignment algorithms. Calculating the…
In this paper, we introduce QuST-LLM, an innovative extension of QuPath that utilizes the capabilities of large language models (LLMs) to analyze and interpret spatial transcriptomics (ST) data. In addition to simplifying the intricate and…
Heaps' or Herdan's law is a linguistic law describing the relationship between the vocabulary/dictionary size (type) and word counts (token) to be a power-law function. Its existence in genomes with certain definition of DNA words is…
Due to the sequential sample arrival, changing experiment conditions, and evolution of knowledge, the demand to continually visualize evolving structures of sequential and diverse single-cell RNA-sequencing (scRNA-seq) data becomes…
Mobile genetic elements (MGEs) are as ubiquitous in nature as they are varied in type, ranging from viral insertions to transposons to incorporated plasmids. Horizontal transfer of MGEs across bacterial species may also pose a significant…
The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state of the art for computational prediction of genetic variant impact, particularly those relevant to disease. The five complete editions of the CAGI community…
Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the…
Motivation Modern molecular sequence analysis increasingly relies on automated and robust software tools for interpretation, annotation, and biological insight. The Analysis of Orthologous Collections (AOC) application automates the…