Related papers: GlobDB: A comprehensive species-dereplicated micro…
With the reduction of sequencing costs and the pervasiveness of computing devices, genomic data collection is continually growing. However, data collection is highly fragmented and the data is still siloed across different repositories.…
In this research, we have been constructing a large database of molecules by {\it ab initio} calculations. Currently, we have over 1.53 million entries of 6-31G* B3LYP optimized geometries and ten excited states by 6-31+G* TDDFT…
Genomic approaches have revolutionized medical research, providing valuable insights into human physiology and disease. Despite major benefits from large collections of genomes, the lack of diversity in genomic data represents a significant…
We present an update on CRDB (https://lpsc.in2p3.fr/crdb), the cosmic-ray database for charged species. CRDB is based on MySQL, queried and sorted by jquery and table-sorter libraries, and displayed via PHP web pages through the AJAX…
Locating recombination hotspots in genomic data is an important but difficult task. Current methods frequently rely on estimating complicated models at high computational cost. In this paper we develop an extremely fast, scalable method for…
The new World Wide Web site "GOLDMine" (Galaxy On Line Database Milano Network) (http://goldmine.mib.infn.it) contains a multiwavelength data-base of an optically selected sample of 3267 galaxies in the Virgo cluster and in the Coma…
A system-level framework of complex microbe-microbe and host-microbe chemical cross-talk would help elucidate the role of our gut microbiota in health and disease. Here we report a literature-curated interspecies network of the human gut…
Building generative models for relational databases (RDBs) is important for many applications, such as privacy-preserving data release and augmenting real datasets. However, most prior works either focus on single-table generation or adapt…
Metagenomics has lowered the barrier to microbial discovery--enabling the identification of novel microbes without isolation--but cultures remain imperative for the deep study of microbes. Cultivation and isolation of non-model microbes…
We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with…
While the publication of datasets in scientific repositories has become broadly recognised, the repositories tend to have increasing semantic-related problems. For instance, they present various data reuse obstacles for machine-actionable…
Reference population databases are an essential tool in variant and gene interpretation. Their use guides the identification of pathogenic variants amidst the sea of benign variation present in every human genome, and supports the discovery…
Popular online enrichment analysis tools from the field of molecular systems biology provide users with the ability to submit their experimental results as gene sets for individual analysis. Such queries are kept private, and have never…
This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be…
Wolbachia are maternally-inherited symbiotic bacteria commonly found in arthropods, which are able to manipulate the reproduction of their host in order to maximise their transmission. Here we use whole genome resequencing data from 290…
Detached eclipsing binary star systems are our primary source of measured physical properties of normal stars. I introduce DEBCat: a catalogue of detached eclipsing binaries with mass and radius measurements to the 2% precision necessary to…
The ExoMol database (www.exomol.com) provides extensive line lists of molecular transitions which are valid over extended temperatures ranges. The status of the current release of the database is reviewed and a new data structure is…
Being able to store and transmit human genome sequences is an important part in genomic research and industrial applications. The complete human genome has 3.1 billion base pairs (haploid), and storing the entire genome naively takes about…
Even though computational reproducibility is widely accepted as necessary for research validation and reuse, it is often not considered during the research process. This is because reproducibility tools are typically stand-alone and require…
Nowadays, the worlds scientific community has been publishing an enormous number of papers in different scientific fields. In such environment, it is essential to know which databases are equally efficient and objective for literature…