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The problem addressed here is that of simultaneous treatment of several gene expression datasets, possibly collected under different experimental conditions and/or platforms. Using robust statistics, a large scale statistical analysis has…
Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is:…
Comparing strains within the same microbial species has proven effective in the identification of genes and genomic regions responsible for virulence, as well as in the diagnosis and treatment of infectious diseases. In this paper, we…
Population analysis is persistently challenging but important, leading to the determination of diversity and function prediction of microbial community members. Here we detail our bioinformatics methods for analyzing population distribution…
GitHub repositories consist of various detailed information about the project contributors, the number of commits and its contributors, releases, pull requests, programming languages, and issues. However, no systematic dataset of open…
The code of nature, embedded in DNA and RNA genomes since the origin of life, holds immense potential to impact both humans and ecosystems through genome modeling. Genomic Foundation Models (GFMs) have emerged as a transformative approach…
Novel technologies in genomics allow creating data in exascale dimension with relatively minor effort of human and laboratory and thus monetary resources compared to capabilities only a decade ago. While the availability of this data…
Leveraging the vast genetic diversity within microbiomes offers unparalleled insights into complex phenotypes, yet the task of accurately predicting and understanding such traits from genomic data remains challenging. We propose a framework…
A new family of Intensional RDBs (IRDBs), introduced in [1], extends the traditional RDBs with the Big Data and flexible and 'Open schema' features, able to preserve the user-defined relational database schemas and all preexisting user's…
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…
In this systems paper, we present MillenniumDB: a novel graph database engine that is modular, persistent, and open source. MillenniumDB is based on a graph data model, which we call domain graphs, that provides a simple abstraction upon…
This paper introduces the recent work of Nebula Graph, an open-source, distributed, scalable, and native graph database. We present a system design trade-off and a comprehensive overview of Nebula Graph internals, including graph data…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
Research resources (RRs) such as data, software, and tools are essential pillars of scientific research. The field of biomedicine, a critical scientific discipline, is witnessing a surge in research publications resulting in the…
Science is a social process with far-reaching impact on our modern society. In the recent years, for the first time we are able to scientifically study the science itself. This is enabled by massive amounts of data on scientific…
Microbes have a profound impact on our health and environment, but our understanding of the diversity and function of microbial communities is severely limited. Through DNA sequencing of microbial communities (metagenomics), DNA fragments…
Motivation: Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of disparate bioinformatics tools. Results: To provide an…
The article presents the theoretical foundations of the algorithm for calculating the number of different genomes in the medium under study and of two algorithms for determining the presence of a particular (known) genome in this medium.…
In this research, we consider a mixture of genome fragments of a certain bacteria set. The problem of mixture separation is studied under the assumption that all the genomes present in the mixture are completely sequenced or are close to…
In the big data era, the relationship between entries becomes more and more complex. Many graph (or network) algorithms have already paid attention to dynamic networks, which are more suitable than static ones for fitting the complex…