[HTML][HTML] A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data

C Yang, D Chowdhury, Z Zhang, WK Cheung… - Computational and …, 2021 - Elsevier
Metagenomic sequencing provides a culture-independent avenue to investigate the
complex microbial communities by constructing metagenome-assembled genomes (MAGs) …

Metagenomic data assembly–the way of decoding unknown microorganisms

AL Lapidus, AI Korobeynikov - Frontiers in Microbiology, 2021 - frontiersin.org
Metagenomics is a segment of conventional microbial genomics dedicated to the
sequencing and analysis of combined genomic DNA of entire environmental samples. The …

Phables: from fragmented assemblies to high-quality bacteriophage genomes

V Mallawaarachchi, MJ Roach, P Decewicz… - …, 2023 - academic.oup.com
Motivation Microbial communities have a profound impact on both human health and
various environments. Viruses infecting bacteria, known as bacteriophages or phages, play …

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 …

RepBin: constraint-based graph representation learning for metagenomic binning

H Xue, V Mallawaarachchi, Y Zhang… - Proceedings of the AAAI …, 2022 - ojs.aaai.org
Mixed communities of organisms are found in many environments--from the human gut to
marine ecosystems--and can have profound impact on human health and the environment …

Disinfectant-induced ammonia oxidation disruption in microbial N-cycling process in aquatic ecosystem after the COVID-19 outbreak

L Yang, P Han, Q Wang, H Lin, D Wang, J Mao, W Qi… - Water Research, 2024 - Elsevier
Anthropogenic activities significantly impact the elemental cycles in aquatic ecosystems,
with the N-cycling playing a critical role in potential nutrient turnover and substance cycling …

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 …

Classgraph: improving metagenomic read classification with overlap graphs

M Cavattoni, M Comin - Journal of Computational Biology, 2023 - liebertpub.com
Current technologies allow the sequencing of microbial communities directly from the
environment without prior culturing. One of the major problems when analyzing a microbial …

MetaCoAG: binning metagenomic contigs via composition, coverage and assembly graphs

V Mallawaarachchi, Y Lin - International Conference on Research in …, 2022 - Springer
Metagenomics has allowed us to obtain various genetic material from different species and
gain valuable insights into microbial communities. Binning plays an important role in the …

Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2

B Papudeshi, AA Vega, C Souza… - Microbial …, 2023 - microbiologyresearch.org
Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading
complex polysaccharides. Their abundance is influenced by phages belonging to the …