Related papers: Accurate identification of bacteriophages from met…

Bacteriophages, phages for short, are viruses of bacteria. The majority of phages contain a double-stranded DNA genome packaged in a capsid at a density of ~500 mg/ml. This high density requires substantial compression of the normal B form…

Various machine-learning models, including deep neural network models, have already been developed to predict deleteriousness of missense (non-synonymous) mutations. Potential improvements to the current state of the art, however, may still…

Bacteriophages are viruses infecting bacteria and archaea. Many phage species cause infections which lead to the certain death of the infected prokaryotic host cell and the release of a large batch of phage progeny, yet they have been able…

Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…

The ability to quickly and accurately identify microbial species in a sample, known as metagenomic profiling, is critical across various fields, from healthcare to environmental science. This paper introduces a novel method to profile…

While metagenomics has emerged as a technology of choice for analyzing bacterial populations, assembly of metagenomic data remains difficult thus stifling biological discoveries. metaSPAdes is a new assembler that addresses the challenge of…

Current metagenomic analysis algorithms require significant computing resources, can report excessive false positives (type I errors), may miss organisms (type II errors / false negatives), or scale poorly on large datasets. This paper…

Specialised transformers-based models (such as BioBERT and BioMegatron) are adapted for the biomedical domain based on publicly available biomedical corpora. As such, they have the potential to encode large-scale biological knowledge. We…

Background: Phage therapy shows promise for treating antibiotic-resistant Klebsiella infections. Identifying phage depolymerases that target Klebsiella capsular polysaccharides is crucial, as these capsules contribute to biofilm formation…

Insertion Sequences (ISs) are small DNA segments that have the ability of moving themselves into genomes. These types of mobile genetic elements (MGEs) seem to play an essential role in genomes rearrangements and evolution of prokaryotic…

Electrocardiogram (ECG) is one of the most important diagnostic tools in clinical applications. With the advent of advanced algorithms, various deep learning models have been adopted for ECG tasks. However, the potential of Transformer for…

In biological experiments researchers often have information in the form of a graph that supplements observed numerical data. Incorporating the knowledge contained in these graphs into an analysis of the numerical data is an important and…

Identification of features is a critical task in microbiome studies that is complicated by the fact that microbial data are high dimensional and heterogeneous. Masked by the complexity of the data, the problem of separating signals from…

Medical time series (MedTS) data, such as Electroencephalography (EEG) and Electrocardiography (ECG), play a crucial role in healthcare, such as diagnosing brain and heart diseases. Existing methods for MedTS classification primarily rely…

The term bacteriophage means killer or eater of bacteria. They were initially discovered by F.W. Twort and later on, Felix d'Herelle unveiled them to the world in 1910. Phage therapy has arisen as a favorable option to conventional…

Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this…

Classification of malware families is crucial for a comprehensive understanding of how they can infect devices, computers, or systems. Thus, malware identification enables security researchers and incident responders to take precautions…

Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows us…

Breast cancer detection through mammography interpretation remains difficult because of the minimal nature of abnormalities that experts need to identify alongside the variable interpretations between readers. The potential of CNNs for…

The research reported in this paper identifies the epigenetic biomarker (methylation beta pattern) of breast cancer. Many cancers are triggered by abnormal gene expression levels caused by aberrant methylation of CpG sites in the DNA. In…