基因组学
Routine single-sample haplotype-resolved assembly remains an unresolved problem. Here we describe a new algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a haplotype-resolved assembly without the…
The analysis of differential gene expression from RNA-Seq data has become a standard for several research areas mainly involving bioinformatics. The steps for the computational analysis of these data include many data types and file…
Motivation: Bacteriophages (aka phages), which mainly infect bacteria, play key roles in the biology of microbes. As the most abundant biological entities on the planet, the number of discovered phages is only the tip of the iceberg.…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
Trans-splicing of leader sequences onto the 59ends of mRNAs is a widespread phenomenon in protozoa, nematodes and some chordates. Using parallel sequencing we have developed a method to simultaneously map 59splice sites and analyze the…
The lack of explainability is one of the most prominent disadvantages of deep learning applications in omics. This "black box" problem can undermine the credibility and limit the practical implementation of biomedical deep learning models.…
According to the National Cancer Institute, there were 9.5 million cancer-related deaths in 2018. A challenge in improving treatment is resistance in genetically unstable cells. The purpose of this study is to evaluate unsupervised machine…
The next-generation sequencers such as Illumina and SOLiD platforms generate a large amount of data, commonly above 10 Gigabytes of text files. Particularly, the SOLiD platform allows the sequencing of multiple samples in a single run,…
Summary: We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences. Now minimap2 v2.22 can more accurately map long reads to highly repetitive regions and align through insertions or deletions…
The spread of pandemic viruses and invasive species can be catastrophic for human societies and natural ecosystems. SARS-CoV-2 demonstrated that the speed of our response is critical, as each day of delay permitted exponential growth and…
Omics technologies are powerful tools for analyzing patterns in gene expression data for thousands of genes. Due to a number of systematic variations in experiments, the raw gene expression data is often obfuscated by undesirable technical…
Sequencing by Emergence (SEQE) is a new single-molecule nucleic acid (DNA/RNA) sequencing technology that estimates sequence as an emergent property of the binding and localization of a repertoire of short oligonucleotide probes. SEQE…
Bam-readcount is a utility for generating low-level information about sequencing data at specific nucleotide positions. Originally designed to help filter genomic mutation calls, the metrics it outputs are useful as input for variant…
Combining different modalities of data from human tissues has been critical in advancing biomedical research and personalised medical care. In this study, we leverage a graph embedding model (i.e VGAE) to perform link prediction on…
Whole genome sequencing (WGS) is quickly becoming the customary means for identification of antimicrobial resistance (AMR) due to its ability to obtain high resolution information about the genes and mechanisms that are causing resistance…
Genomic selection (GS) is a technique that plant breeders use to select individuals to mate and produce new generations of species. Allocation of resources is a key factor in GS. At each selection cycle, breeders are facing the choice of…
In the machine learning culture, an independent test set is required for proper model verification. Failures in model verification, including test set omission and test set leakage, make it impossible to know whether or not a trained model…
Motivation: With the development of third-generation sequencing technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow protein domain annotation without assembly, thus can produce…
Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods…
MicroRNAs (miRNAs) are a class of small noncoding RNAs that can regulate many genes by base pairing to sites in mRNAs. The functionality of miRNAs overlaps that of short interfering RNAs (siRNAs), and many features of miRNA targeting have…