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The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
The collection of immunoglobulin genes in an individual's germline, which gives rise to B cell receptors via recombination, is known to vary significantly across individuals. In humans, for example, each individual has only a fraction of…
The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires…
We developed an online database, ExprTargetDB, of human miRNA targets predicted by an approach that integrates gene expression profiling into a broader framework involving important features of miRNA target site predictions.
Background: In the metagenome assembly of a microbiome community, we may think abundant species would be easier to assemble due to their deeper coverage. However, this conjucture is rarely tested. We often do not know how many abundant…
Useful information about scientific collaboration structures and patterns can be inferred from computer databases of published papers. The genetic programming bibliography is the most complete reference of papers on GP\@. In addition to…
Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of genomic data that populates several online databases and repositories. Here, we…
We have collected the largest existing set of radio source lists in machine-readable form: 320 tables with 1.75 million records. Only a minor fraction of these is accessible via public databases. We describe our plans to make this huge…
Low-mass X-ray binaries (LMXBs) are high-energy sources that require multi-wavelength follow up campaigns to be fully characterized. New transients associated to LMXBs are regularly discovered, and previously known systems are often…
Globular clusters are stellar dynamical systems which evolve on stellar evolutionary and both internal and external dynamical timescales. Quantitative comparison of cluster properties with realistic evolutionary dynamical models is becoming…
The astorb database at Lowell Observatory is an actively curated catalog of all known asteroids in the Solar System. astorb has heritage dating back to the 1970's and has been publicly accessible since the 1990's. Beginning in 2015 work…
A computational engine applied to different representations of the same data can produce different discrete outcomes, with some representations preserving the result and others changing it entirely. A decision-valued map records which…
Distributed databases, as the core infrastructure software for internet applications, play a critical role in modern cloud services. However, existing distributed databases frequently experience system failures and performance degradation,…
Graph theory and graph mining constitute rich fields of computational techniques to study the structures, topologies and properties of graphs. These techniques constitute a good asset in bioinformatics if there exist efficient methods for…
Factorised databases are relational databases that use compact factorised representations at the physical layer to reduce data redundancy and boost query performance. This paper introduces FDB, an in-memory query engine for…
Summary: PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, PDBImages provides a means to…
We present SemRepo, an RDF knowledge graph comprising over 81 million triples describing nearly 200,000 GitHub repositories associated with scientific research. SemRepo captures repository-level metadata, such as contributors, issues, and…
Gene co-expression databases in model plants such as Arabidopsis and rice have been extensively developed and utilised for predicting gene function and identifying functional modules for underlying biological processes. However, such tools…
High-throughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major…
Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical…