Metagenomics-a guide from sampling to data analysis

T Thomas, J Gilbert, F Meyer - Microbial informatics and experimentation, 2012 - Springer
Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly
access the genetic content of entire communities of organisms. The field of metagenomics …

The present and future of de novo whole-genome assembly

J Sohn, D Kim, JM Paggi, C Park, C Bennett… - Nature biotechnology, 2019 - nature.com
The human reference genome represents only a small number of individuals, which limits its
usefulness for genoty**. We present a method named HISAT2 (hierarchical indexing for …

The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

W Zhuang, H Chen, M Yang, J Wang, MK Pandey… - Nature …, 2019 - nature.com
High oil and protein content make tetraploid peanut a leading oil and food legume. Here we
report a high-quality peanut genome sequence, comprising 2.54 Gb with 20 …

Transcriptional and epigenetic decoding of the microglial aging process

X Li, Y Li, Y **, Y Zhang, J Wu, Z Xu, Y Huang, L Cai… - Nature Aging, 2023 - nature.com
As important immune cells, microglia undergo a series of alterations during aging that
increase the susceptibility to brain dysfunctions. However, the longitudinal characteristics of …

Microplastics reduce nitrogen uptake in peanut plants by damaging root cells and impairing soil nitrogen cycling

Y Liu, F Xu, L Ding, G Zhang, B Bai, Y Han… - Journal of Hazardous …, 2023 - Elsevier
Microplastic (MP) pollution severely impairs the sustainable development of modern
agriculture. However, the mechanisms underlying the effects of MP contaminants on nutrient …

Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements

J Guo, J Li, H Chen, PL Bond, Z Yuan - Water research, 2017 - Elsevier
The intensive use of antibiotics results in their continuous release into the environment and
the subsequent widespread occurrence of antibiotic resistant bacteria (ARB), antibiotic …

Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps

C Belser, B Istace, E Denis, M Dubarry, FC Baurens… - Nature plants, 2018 - nature.com
Plant genomes are often characterized by a high level of repetitiveness and polyploid
nature. Consequently, creating genome assemblies for plant genomes is challenging. The …

Functional and metabolic alterations of gut microbiota in children with new-onset type 1 diabetes

X Yuan, R Wang, B Han, CJ Sun, R Chen… - Nature …, 2022 - nature.com
Gut dysbiosis has been linked to type 1 diabetes (T1D); however, microbial capacity in T1D
remains unclear. Here, we integratively profiled gut microbial functional and metabolic …

Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing

C Belser, FC Baurens, B Noel, G Martin… - Communications …, 2021 - nature.com
Long-read technologies hold the promise to obtain more complete genome assemblies and
to make them easier. Coupled with long-range technologies, they can reveal the architecture …