SemiBin2: self-supervised contrastive learning leads to better MAGs for short-and long-read sequencing

S Pan, XM Zhao, LP Coelho - Bioinformatics, 2023 - academic.oup.com
Motivation Metagenomic binning methods to reconstruct metagenome-assembled genomes
(MAGs) from environmental samples have been widely used in large-scale metagenomic …

A survey on computational strategies for genome-resolved gut metagenomics

L Jia, Y Wu, Y Dong, J Chen, WH Chen… - Briefings in …, 2023 - academic.oup.com
Recovering high-quality metagenome-assembled genomes (HQ-MAGs) is critical for
exploring microbial compositions and microbe–phenotype associations. However, multiple …

Solving genomic puzzles: computational methods for metagenomic binning

V Mallawaarachchi, A Wickramarachchi… - Briefings in …, 2024 - academic.oup.com
Metagenomics involves the study of genetic material obtained directly from communities of
microorganisms living in natural environments. The field of metagenomics has provided …

Metagenomic binning with assembly graph embeddings

A Lamurias, M Sereika, M Albertsen, K Hose… - …, 2022 - academic.oup.com
Motivation Despite recent advancements in sequencing technologies and assembly
methods, obtaining high-quality microbial genomes from metagenomic samples is still not a …

Accurate binning of metagenomic contigs using composition, coverage, and assembly graphs

V Mallawaarachchi, Y Lin - Journal of Computational Biology, 2022 - liebertpub.com
Metagenomics enables the recovery of various genetic materials from different species, thus
providing valuable insights into microbial communities. Metagenomic binning group …

Metagenomics binning of long reads using read-overlap graphs

A Wickramarachchi, Y Lin - RECOMB International Workshop on …, 2022 - Springer
Metagenomics sequencing enables the direct study of microbial communities revealing
important information such as taxonomy and relative abundance of species. Metagenomics …

Improving Metagenomic Binning of Long Reads via Feature Fusion and Graph SAGE

J Nie, H Liu, F Huang, H Chen… - 2024 IEEE International …, 2024 - ieeexplore.ieee.org
The advent of advanced metagenome sequencing techniques has enabled the direct study
of microbial communities in their natural habitats, thereby facilitating the acquisition of …

Separating DNA Sequences of Microbes Using Apache Spark

TT Pham, TH Pham, VV Le - International Conference on Green …, 2024 - Springer
Metagenomic projects focus on analyzing microbial communities which contain a huge
amount of DNA sequences. Therefore, utilizing high performance computing for analysis of …

[PDF][PDF] Multi-label Deep Learning Models for Virus Genome DNA Sequence Classification

PS Hossain - 2022 - researchgate.net
There are 39 trillion microbial cells in the globe, including bacteria, viruses, and fungus,
which live on and in us. Because of the effects of globalisation and high mobilization of the …

Models and Algorithms for Metagenomics Analysis and Plasmid Classification

A Wickramarachchi - 2022 - search.proquest.com
Metagenomics studies have provided key insights into the composition and structure of
microbial communities found in different environments. Among the techniques used to …