Community standards and future opportunities for synthetic communities in plant–microbiota research
Harnessing beneficial microorganisms is seen as a promising approach to enhance
sustainable agriculture production. Synthetic communities (SynComs) are increasingly …
sustainable agriculture production. Synthetic communities (SynComs) are increasingly …
BUSCO: assessing genomic data quality and beyond
Abstract Evaluation of the quality of genomic “data products” such as genome assemblies or
gene sets is of critical importance in order to recognize possible issues and correct them …
gene sets is of critical importance in order to recognize possible issues and correct them …
ColabFold: making protein folding accessible to all
ColabFold offers accelerated prediction of protein structures and complexes by combining
the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold's 40− 60 …
the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold's 40− 60 …
Protein-to-genome alignment with miniprot
H Li - Bioinformatics, 2023 - academic.oup.com
Motivation Protein-to-genome alignment is critical to annotating genes in non-model
organisms. While there are a few tools for this purpose, all of them were developed over 10 …
organisms. While there are a few tools for this purpose, all of them were developed over 10 …
BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes
Methods for evaluating the quality of genomic and metagenomic data are essential to aid
genome assembly procedures and to correctly interpret the results of subsequent analyses …
genome assembly procedures and to correctly interpret the results of subsequent analyses …
xTrimoPGLM: unified 100B-scale pre-trained transformer for deciphering the language of protein
Protein language models have shown remarkable success in learning biological information
from protein sequences. However, most existing models are limited by either autoencoding …
from protein sequences. However, most existing models are limited by either autoencoding …
compleasm: a faster and more accurate reimplementation of BUSCO
Motivation Evaluating the gene completeness is critical to measuring the quality of a
genome assembly. An incomplete assembly can lead to errors in gene predictions …
genome assembly. An incomplete assembly can lead to errors in gene predictions …
Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean
Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate.
However, their poor representation in culture collections limits our understanding of the …
However, their poor representation in culture collections limits our understanding of the …
Anammox bacteria adapt to long-term light irradiation in photogranules
L Kong, R Zheng, Y Feng, W Du, C Xie, Y Gu, S Liu - Water Research, 2023 - Elsevier
Photogranules composed of algae, nitrifiers, and anammox bacteria are promising for
nitrogen removal from wastewater with reduced aeration and carbon emissions. However, it …
nitrogen removal from wastewater with reduced aeration and carbon emissions. However, it …
High-resolution metagenomic reconstruction of the freshwater spring bloom
Background The phytoplankton spring bloom in freshwater habitats is a complex, recurring,
and dynamic ecological spectacle that unfolds at multiple biological scales. Although …
and dynamic ecological spectacle that unfolds at multiple biological scales. Although …