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Shape complementarity of molecular surfaces at the interfaces is a well-known characteristic of protein-protein binding regions, and it is critical in influencing the stability of the complex. Measuring such complementarity is at the basis…
Protein phosphorylation involves the reversible modification of a protein (substrate) residue by another protein (kinase). Liquid chromatography-mass spectrometry studies are rapidly generating massive protein phosphorylation datasets…
Edge/Fog computing is a novel computing paradigm that provides resource-limited Internet of Things (IoT) devices with scalable computing and storage resources. Compared to cloud computing, edge/fog servers have fewer resources, but they can…
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…
Microbial genome web portals have a broad range of capabilities that address a number of information-finding and analysis needs for scientists. This article compares the capabilities of the major microbial genome web portals to aid…
Web applications require exchanging parameters between a client and a server to function properly. In real-world systems such as online banking transfer, traversing multiple pages with parameters contributed by both the user and server is a…
Bacteriophages are promising alternative antimicrobial agents due to their high specificity for host bacteria and minimal immunogenicity in humans. However, their therapeutic application is limited by their nature as biological entities,…
Background: Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular…
Computational analyses of, e.g., genomic, proteomic, or metabolomic data, commonly result in one or more sets of candidate genes, proteins, or enzymes. These sets are often the outcome of clustering algorithms. Subsequently, it has to be…
Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of analyzing extracellular metabolomic data in the context of the…
Metagenomics offers a way to analyze biotopes at the genomic level and to reach functional and taxonomical conclusions. The bio-analyzes of large metagenomic projects face critical limitations: complex metagenomes cannot be assembled and…
Cell-free DNA (cfDNA) analysis is a powerful, minimally invasive tool for monitoring disease progression, treatment response, and early detection. A major challenge, however, is accurately determining the tissue of origin, especially in…
We present zea (pronounced ze-yah), a Python package for cognitive ultrasound imaging that offers a flexible, modular, and differentiable pipeline for ultrasound data processing. Additionally, it includes a collection of pre-defined models…
We present a new software pipeline -- PyMorph -- for automated estimation of structural parameters of galaxies. Both parametric fits through a two dimensional bulge disk decomposition as well as structural parameter measurements like…
Analyzing machine learning model performance stratified by patient and recording properties is becoming the accepted norm and often yields crucial insights about important model failure modes. Performing such analyses in a statistically…
Mutation-based fuzzing is popular and effective in discovering unseen code and exposing bugs. However, only a few studies have concentrated on quantifying the importance of input bytes, which refers to the degree to which a byte contributes…
Microbiome data analyses require statistical tools that can simultaneously decode microbes' reactions to the environment and interactions among microbes. We introduce CARlasso, the first user-friendly open-source and publicly available R…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
There is a keen interest in characterizing variation in the microbiome across cancer patients, given increasing evidence of its important role in determining treatment outcomes. Here our goal is to discover subgroups of patients with…
Cloud applications are increasingly shifting from large monolithic services to complex graphs of loosely-coupled microservices. Despite the advantages of modularity and elasticity microservices offer, they also complicate cluster management…