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Summary: The advent of Web-based tools that assist in the analysis and visualization of macromolecules require application programming interfaces (APIs) designed for modern web frameworks. To this end, we have developed a Node.js module…
The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid…
We describe the Gun Violence Database (GVDB), a large and growing database of gun violence incidents in the United States. The GVDB is built from the detailed information found in local news reports about gun violence, and is constructed…
Recent work on globular cluster systems in dwarf galaxies outside the Local Group is reviewed. Recent large imaging surveys with the Hubble Space Telescope and follow-up spectroscopy with 8-m class telescopes now allow us to compare the…
Colonoscopy is the primary method for examination, detection, and removal of polyps. However, challenges such as variations among the endoscopists' skills, bowel quality preparation, and the complex nature of the large intestine contribute…
As data-driven methods are becoming pervasive in a wide variety of disciplines, there is an urgent need to develop scalable and sustainable tools to simplify the process of data science, to make it easier to keep track of the analyses being…
The reconstruction of microbial genomes from large metagenomic datasets is a critical procedure for finding uncultivated microbial populations and defining their microbial functional roles. To achieve that, we need to perform metagenomic…
Open-source libraries are have a catalytic role in research pipelines, where new methods must be compared against up-to-date baselines. We present the GLobal Optimization Benchmark (GLOBe) modular Python library that unifies classical and…
Discrete data such as counts of microbiome taxa resulting from next-generation sequencing are routinely encountered in bioinformatics. Taxa count data in microbiome studies are typically high-dimensional, over-dispersed, and can only reveal…
High-throughput sequencing technology provides unprecedented opportunities to quantitatively explore human gut microbiome and its relation to diseases. Microbiome data are compositional, sparse, noisy, and heterogeneous, which pose serious…
The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific…
This paper describes a prototype of extended XDB. XDB is an open-source and extensible database architecture developed by National Aeronautics and Space Administration (NASA) to provide integration of heterogeneous and distributed…
String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher…
Microbes can affect processes from food production to human health. Such microbes are not isolated, but rather interact with each other and establish connections with their living environments. Understanding these interactions is essential…
Cell-cell communication is essential for tissue development, regeneration and function, and its disruption can lead to diseases and developmental abnormalities. The revolution of single-cell genomics technologies offers unprecedented…
Microbial communities play important roles in the function and maintenance of various biosystems, ranging from human body to the environment. Current methods for analysis of microbial communities are typically based on taxonomic…
Identification of every single genome present in a microbial sample is an important and challenging task with crucial applications. It is challenging because there are typically millions of cells in a microbial sample, the vast majority of…
The diversity revealed by large scale genomics in microbiology is calling into question long held beliefs about genome stability, evolutionary rate, even the definition of a species. MacArthur and Wilson's theory of insular biogeography…
Accurate estimates of Above Ground Biomass (AGB) are essential in addressing two of humanity's biggest challenges: climate change and biodiversity loss. Existing datasets for AGB estimation from satellite imagery are limited. Either they…
The Intelligence Studies Network is a comprehensive resource database for publications, events, conferences, and calls for papers in the field of intelligence studies. It offers a novel solution for monitoring, indexing, and visualising…