Related papers: ChloroScan: Recovering plastid genome bins from me…
Metagenomics enables the reconstruction of microbial genomes in complex microbial communities without the need for culturing. Since assembly typically results in fragmented genomes the grouping of genome fragments (contigs) belonging to the…
The reconstruction of microbial genomes from large metagenomic datasets is a critical procedure for finding uncultivated microbial populations and defining their microbial functional roles. To achieve that, we need to perform metagenomic…
Clustering algorithms can help reconstruct the assembly history of the Milky Way by identifying groups of stars sharing similar properties in a kinematical or chemical abundance space. Despite being promising tools, their efficiency has not…
Chromosome analysis and identification from metaphase images is a critical part of cytogenetics based medical diagnosis. It is mainly used for identifying constitutional, prenatal and acquired abnormalities in the diagnosis of genetic…
Background: Convolutional Neural Networks can be effectively used only when data are endowed with an intrinsic concept of neighbourhood in the input space, as is the case of pixels in images. We introduce here Ph-CNN, a novel deep learning…
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
Prokaryotic organisms usually possess compact genomes, which are particularly suitable to complete sequencing with existing technologies, which led to an escalating accumulation of available genome data. In response to this ever-expanding…
The marine environment is one of the most important sources for microbial biodiversity on the planet. These microbes are drivers for many biogeochemical processes, and their enormous genetic potential is still not fully explored or…
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 large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires…
The recent development of metagenomic sequencing makes it possible to sequence microbial genomes including viruses in an environmental sample. Identifying viral sequences from metagenomic data is critical for downstream virus analyses. The…
Metagenomic binning aims to cluster DNA fragments from mixed microbial samples into their respective genomes, a critical step for downstream analyses of microbial communities. Existing methods rely on deterministic representations, such as…
Metagenomic taxonomic annotation aims to identify the microbial origins of DNA fragments in environmental samples. Traditional methods that rely on sequence similarity are often constrained by the high microbial diversity and the…
Background: In the metagenome assembly of a microbiome community, we may think abundant species would be easier to assemble due to their deeper coverage. However, this conjucture is rarely tested. We often do not know how many abundant…
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:…
Current methods for microplastic identification in water samples are costly and require expert analysis. Here, we propose a deep learning segmentation model to automatically identify microplastics in microscopic images. We labeled images of…
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…
For nearly 50 years microbiologists have been determining prokaryotic genome relatedness by means of nucleic acid reassociation kinetics. These methods, however, are technically challenging, difficult to reproduce, and - given the time and…
Motivation: Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and…