Genomics
The study of signatures of aging in terms of genomic biomarkers can be uniquely helpful in understanding the mechanisms of aging and developing models to accurately predict the age. Prior studies have employed gene expression and DNA…
Investigation of age-related genes is of great importance for multiple purposes, for instance, improving our understanding of the mechanism of ageing, increasing life expectancy, age prediction, and other healthcare applications. In his…
In the genome biology research, regulatory genome modeling is an important topic for many regulatory downstream tasks, such as promoter classification, transaction factor binding sites prediction. The core problem is to model how regulatory…
Microbiome studies have recently transitioned from experimental designs with a few hundred samples to designs spanning tens of thousands of samples. Modern studies such as the Earth Microbiome Project (EMP) afford the statistics crucial for…
The recent super-exponential growth in the amount of sequencing data generated worldwide has put techniques for compressed storage into the focus. Most available solutions, however, are strictly tied to specific bioinformatics formats,…
Background: The computation of the statistical properties of motif occurrences has an obviously relevant practical application: for example, patterns that are significantly over- or under-represented in the genome are interesting candidates…
Applications of single-cell RNA sequencing in various biomedical research areas have been blooming. This new technology provides unprecedented opportunities to study disease heterogeneity at the cellular level. However, unique…
Applying a ML approach to the temporal variability of the Spike protein sequence enables us to identify, classify and track emerging virus variants. Our analysis is unbiased, in the sense that it does not require any prior knowledge of the…
Motivation: Alignment-free (AF) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate…
Single-cell sequencing has a significant role to explore biological processes such as embryonic development, cancer evolution, and cell differentiation. These biological properties can be presented by a two-dimensional scatter plot.…
Current metagenome assemblers developed for short sequence reads or noisy long readswere not optimized for accurate long reads. Here we describe hifiasm-meta, a new metagenome assembler that exploits the high accuracy of recent data.…
Motivation: MicroRNAs (miRNAs) play pivotal roles in gene expression regulation by binding to target sites of messenger RNAs (mRNAs). While identifying functional targets of miRNAs is of utmost importance, their prediction remains a great…
Genomic prediction can be a powerful tool to achieve greater rates of genetic gain for quantitative traits if thoroughly integrated into a breeding strategy. In rice as in other crops, the interest in genomic prediction is very strong with…
The extraction of k-mers from sequencing reads is an important task in many bioinformatics applications, such as all DNA sequence analysis methods based on de Bruijn graphs. These methods tend to be more accurate when the used k-mers are…
Since its selection as the method of the year in 2013, single-cell technologies have become mature enough to provide answers to complex research questions. With the growth of single-cell profiling technologies, there has also been a…
The MinION is a recent-to-market handheld nanopore sequencer. It can be used to determine the whole genome of a target virus in a biological sample. Its Read Until feature allows us to skip sequencing a majority of non-target reads (DNA/RNA…
We report the detection of Nipah virus in an infectious clone format, a BSL4-level pathogen and CDC-designated Bioterrorism Agent, in raw RNA-Seq sequencing reads deposited by the Wuhan Institute of Virology (WIV) produced from five…
Background: Psoriasis is a multifactorial chronic inflammatory disorder of the skin with significant morbidity, characterized by hyper proliferation of the epidermis. Even though psoriasis etiology is not fully understood, it is believed to…
Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root…
Motivation: Omics data, such as transcriptomics or phosphoproteomics, are broadly used to get a snap-shot of the molecular status of cells. In particular, changes in omics can be used to estimate the activity of pathways, transcription…