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Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…
Molecular ecology uses molecular genetic data to answer traditional ecological questions in biogeography and biodiversity among others. Several ecological principles, such as the niche hypothesis and the competitive exclusions, are based on…
Since the advent of next-generation sequencing in the early 2000s, the volume of bioinformatics software tools and databases has exploded and continues to grow rapidly. Documenting this evolution on a global and time-dependent scale is a…
One of the central questions of metacommunity theory is how dispersal of organisms affects species diversity. Here we show that the diversity-dispersal relationship should not be studied in isolation of other abiotic and biotic flows in the…
Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common…
Biodiversity research requires complete and detailed information to study ecosystem dynamics at different scales. Employing data-driven methods like Machine Learning is getting traction in ecology and more specific biodiversity, offering…
High throughput genome sequencing technologies such as RNA-Seq and Microarray have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level.…
Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
Massive Multi-Omics Microbiome Database (M3DB) is a data warehousing and analytics solution designed to handle diverse, complex, and unprecedented volumes of sequence and taxonomic classification data obtained in a typical microbiome…
In recent years the research community has accumulated overwhelming evidence for the emergence of complex and heterogeneous connectivity patterns in a wide range of biological and sociotechnical systems. The complex properties of real-world…
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…
With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families…
The human gastrointestinal tract is an environment that hosts an ecosystem of microorganisms essential to human health. Vital biological processes emerge from fundamental inter- and intra-species molecular interactions that influence the…
Today's distributed and pervasive computing addresses large-scale cyber-physical ecosystems, characterised by dense and large networks of devices capable of computation, communication and interaction with the environment and people. While…
A significant advancement in bioinformatics is using genome graph techniques to improve variation discovery across organisms. Traditional approaches, such as bwa mem, rely on linear reference genomes for genomic analyses but may introduce…
Advances in cellular imaging technologies, especially those based on fluorescence in situ hybridization (FISH) now allow detailed visualization of the spatial organization of human or bacterial cells. Quantifying this spatial organization…
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…
Many scientific datasets are compositional in nature. Important biological examples include species abundances in ecology, cell-type compositions derived from single-cell sequencing data, and amplicon abundance data in microbiome research.…
Current metagenomic analysis algorithms require significant computing resources, can report excessive false positives (type I errors), may miss organisms (type II errors / false negatives), or scale poorly on large datasets. This paper…