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Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical…
Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in…
The biological significance of genomic features is often context-dependent. We present CruzDB, a fast and intuitive programmatic interface to the UCSC genome browser that facilitates integrative analyses of diverse local and remotely hosted…
Geographically distributed database systems use remote replication to protect against regional failures. These systems are sensitive to severe latency penalties caused by centralized transaction management, remote access to sharded data,…
Genetic interactions and protein co-dependencies shape cellular fitness, buffering capacity, and disease vulnerability. However, systematic integration of co-dependency relationships across heterogeneous datasets remains limited. Here, we…
Summary: BGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to hundreds of thousands of samples. On real data, it encodes…
The 1000 Genomes Project provides sequencing data on 3,202 samples from 26 populations spanning five continental regions with no access or use restrictions. The kgp R package provides consistent and comprehensive metadata about samples and…
polyDB is a database for discrete geometric objects. The database is accessible via web and an interface from the software package polymake. It contains various datasets from the area of lattice polytopes, combinatorial polytopes, matroids…
Numerous studies have utilized NCBI data for genomic analysis, gene annotation, and identifying disease-associated variants, yet NCBI's epidemiological potential remains underexplored. This study demonstrates how NCBI datasets can be…
During genomics life science research, the data volume of whole genomics and life science algorithm is going bigger and bigger, which is calculated as TB, PB or EB etc. The key problem will be how to store and analyze the data with…
Botanical specimens are shared as long-term consultable research objects in a global network of specimen repositories. Multiple specimens are generated from a shared field collection event; generated specimens are then managed individually…
Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…
A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a…
Today's sequencing technology allows sequencing an individual genome within a few weeks for a fraction of the costs of the original Human Genome project. Genomics labs are faced with dozens of TB of data per week that have to be…
Cheap high-throughput DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food…
DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…
A short note describing the development of a database providing factual and numerical data on the spectral properties of diatomic molecules. This database is available online for the overall scientific community at the following adress:…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Human genomic data carry unique information about an individual and offer unprecedented opportunities for healthcare. The clinical interpretations derived from large genomic datasets can greatly improve healthcare and pave the way for…