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Scientists today collect, analyze, and generate TeraBytes and PetaBytes of data. These data are often shared and further processed and analyzed among collaborators. In order to facilitate sharing and data interpretations, data need to carry…
Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly…
With advanced imaging, sequencing, and profiling technologies, multiple omics data become increasingly available and hold promises for many healthcare applications such as cancer diagnosis and treatment. Multimodal learning for integrative…
The deep learning revolution is touching all scientific disciplines and corners of our lives as a means of harnessing the power of big data. Marine ecology is no exception. These new methods provide analysis of data from sensors, cameras,…
Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this…
Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse entities in the biosphere. There is accumulating evidence revealing their important roles in shaping the structure of various microbiomes. Thanks to…
Numerous studies have shown that microbial metabolites, which represent the products of bacteria in the human gut, play a key role in shaping cancer risk and response to treatment. However, metabolite data typically contain a large…
Large systems biology projects can encompass several workgroups often located in different countries. An overview about existing data standards in systems biology and the management, storage, exchange and integration of the generated data…
Microorganisms play a vital role in human life. Therefore, microorganism detection is of great significance to human beings. However, the traditional manual microscopic detection methods have the disadvantages of long detection cycle, low…
Spatially-resolved omics-data enable researchers to precisely distinguish cell types in tissue and explore their spatial interactions, enabling deep understanding of tissue functionality. To understand what causes or deteriorates a disease…
Understanding the spread of any disease is a highly complex and interdisciplinary exercise as biological, social, geographic, economic, and medical factors may shape the way a disease moves through a population and options for its eventual…
Graph-based machine learning methods are useful tools in the identification and prediction of variation in genetic data. In particular, the comprehension of phenotypic effects at the cellular level is an accelerating research area in…
In microbiome studies, it is often of great interest to identify clusters or partitions of microbiome profiles within a study population and to characterize the distinctive attributes of each resulting microbial community. While raw counts…
Microbes thrive in diverse porous environments -- from soil and riverbeds to human lungs and cancer tissues -- spanning multiple scales and conditions. Short- to long-term fluctuations in local factors induce spatio-temporal…
MicroRNAs play critical roles in many physiological processes. Their dysregulations are also closely related to the development and progression of various human diseases, including cancer. Therefore, identifying new microRNAs that are…
Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data…
Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. For communities of up to medium diversity,…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Metabonomics time-course experiments provide the opportunity to understand the changes to an organism by observing the evolution of metabolic profiles in response to internal or external stimuli. Along with other omic longitudinal profiling…
It is well recognised that animal and plant pathogens form complex ecological communities of interacting organisms within their hosts. Although community ecology approaches have been applied to determine pathogen interactions at the…