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Motivation: Peptide-protein interactions (PepPIs) are central to cellular regulation and peptide therapeutics, but experimental characterization remains too slow for large-scale screening. Existing methods usually emphasize either…
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…
The prospect of new biological and industrial applications that require communication in micro-scale, encourages research on the design of bio-compatible communication networks using networking primitives already available in nature. One of…
Motivation: Receptor-binding proteins (RBPs) initiate viral infection and determine host specificity, serving as key targets for phage engineering and therapy. However, the identification of RBPs is complicated by their extreme sequence…
As antibiotic resistance grows more frequent for common bacterial infections, alternative treatment strategies such as phage therapy have become more widely studied in the medical field. While many studies have explored the efficacy of…
Ecologists have long suspected that species are more likely to interact if their traits match in a particular way. For example, a pollination interaction may be more likely if the proportions of a bee's tongue fit a plant's flower shape.…
Gene regulatory network of lambda phage is one the best studied model systems in molecular biology. More 50 years of experimental study has provided a tremendous amount of data at all levels: physics, chemistry, DNA, protein, and function.…
Metadata are general characteristics of the data in a well-curated and condensed format, and have been proven to be useful for decision making, knowledge discovery, and also heterogeneous data organization of biobank. Among all data types…
Biological data sets are often high-dimensional, noisy, and governed by complex interactions among sparse signals. This poses major challenges for interpretability and reliable feature selection. Tasks such as identifying motif interactions…
A significant advancement in bioinformatics is using genome graph techniques to improve variation discovery across organisms. Traditional approaches, such as bwa mem, rely on linear reference genomes for genomic analyses but may introduce…
Self-organizing complex systems typically are comprised of a large number of frequently similar components or events. Through their process, a pattern at the global-level of a system emerges solely from numerous interactions among the…
The bacterial microbiome is increasingly being recognised as a key factor in human health, driven in large part by datasets collected using 16S rRNA (ribosomal ribonucleic acid) gene sequencing, which enable cost-effective quantification of…
Feature management is essential for many online machine learning applications and can often become the performance bottleneck (e.g., taking up to 70% of the overall latency in sales prediction service). Improper feature configurations…
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…
Quantification of heritability is a fundamental desideratum in genetics, which allows an assessment of the contribution of additive genetic variation to the variability of a trait of interest. The traditional computational approaches for…
Host-response-based diagnostics can improve the accuracy of diagnosing bacterial and viral infections, thereby reducing inappropriate antibiotic prescriptions. However, the existing cohorts with limited sample size and coarse infections…
The combination of Deep Learning techniques and Raman spectroscopy shows great potential offering precise and prompt identification of pathogenic bacteria in clinical settings. However, the traditional closed-set classification approaches…
Bacteriophage viruses, one of the most abundant entities in our planet, lack the ability to move independently. Instead, they crowd fluid environments in anticipation of a random encounter with a bacterium. Once they land on the cell body…
Machine learning strategies like multi-task learning, meta-learning, and transfer learning enable efficient adaptation of machine learning models to specific applications in healthcare, such as prediction of various diseases, by leveraging…
The outcomes of evolution are determined by which mutations occur and fix. In rapidly adapting microbial populations, this process is particularly hard to predict because lineages with different beneficial mutations often spread…