Genomics
The continuing advances of omic technologies mean that it is now more tangible to measure the numerous features collectively reflecting the molecular properties of a sample. When multiple omic methods are used, statistical and computational…
This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ5). FASTA/FASTQ files have several current limitations, such as their large file sizes,…
Cell proliferation and migration highly relate to normal tissue self-healing, therefore it is highly significant for artificial controlling. Recently, vibrational strong coupling between biomolecules and Mid-infrared (MIR) light photons has…
The accumulation of somatic mutations is a driver of cancer and has long been associated with ageing. Due to limitations in quantifying mutation burden with age in non-cancerous tissues, the impact of somatic mutations in other ageing…
Motivation: There is accumulating evidence showing the important roles of bacteriophages (phages) in regulating the structure and functions of the microbiome. However, lacking an easy-to-use and integrated phage analysis software hampers…
The regulAS software package is a bioinformatics tool designed to support computational biology researchers in investigating regulatory mechanisms of splicing alterations through integrative analysis of large-scale RNA-Seq data from cancer…
This paper will argue that one of the biggest challenges for livestock genomics is to make whole-genome sequencing and functional genomics applicable to breeding practice. It discusses potential explanations for why it is so difficult to…
Prokaryotic gene prediction plays an important role in understanding the biology of organisms and their function with applications in medicine and biotechnology. Although the current gene finders are highly sensitive in finding long genes,…
Mapper, a topological algorithm, is frequently used as an exploratory tool to build a graphical representation of data. This representation can help to gain a better understanding of the intrinsic shape of high-dimensional genomic data and…
Motivation: Enhancers are important cis-regulatory elements that regulate a wide range of biological functions and enhance the transcription of target genes. Although many feature extraction methods have been proposed to improve the…
Fetal neuroinflammation and prenatal stress (PS) may contribute to lifelong neurological disabilities. Astrocytes and microglia, among the brain's non-neuronal glia cell populations, play a pivotal role in neurodevelopment, predisposition…
Accurately inferring the root causes of disease from sequencing data can improve the discovery of novel therapeutic targets. However, existing root causal inference algorithms require perfectly measured continuous random variables. Single…
Colon cancer is a prevalent gastrointestinal malignancy arising in the colon. Ulcerative colitis(UC) is one of the risk factors of colorectal cancer. The detection of under-expressed biomarkers and molecular mechanisms in UC and colon…
The spatial positioning of chromosomes relative to functional nuclear bodies is intertwined with genome functions such as transcription. However, the sequence patterns and epigenomic features that collectively influence chromatin spatial…
Genome-wide association studies (GWAS) are commonly employed to study the genetic basis of complex traits and diseases, and a key question is how much heritability could be explained by all variants in GWAS. One widely used approach that…
Numerous epidemiological studies suggest febrile infections could confer long-term immunity to certain types of cancers, though the precise mechanisms for this phenomenon remain unclear. Systemic heat-shock responses to fever may be key to…
Possessing the five-year durability rate of nearly 5%, currently, the fourth leading cause for cancer-related deaths is pancreatic cancer. Previously, several works have resolved that early diagnosis performs a meaningful function in…
Modelling gene-gene epistatic interactions when computing genetic risk scores is not a well-explored subfield of genetics and could have potential to improve risk stratification in practice. Though applications of machine learning (ML) show…
Shaped by natural selection and other evolutionary forces, an organism's evolutionary history is reflected through its genome sequence, content of functional elements and organization. Consequently, organisms connected through phylogeny,…
With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the…