The soil microbiome—from metagenomics to metaphenomics

JK Jansson, KS Hofmockel - Current opinion in microbiology, 2018 - Elsevier
Soil microorganisms carry out important processes, including support of plant growth and
cycling of carbon and other nutrients. However, the majority of soil microbes have not yet …

Dynamics of ecological communities following current retreat of glaciers

GF Ficetola, S Marta, A Guerrieri… - Annual Review of …, 2021 - annualreviews.org
Glaciers are retreating globally, and the resulting ice-free areas provide an experimental
system for understanding species colonization patterns, community formation, and …

Multi-view low-rank sparse subspace clustering

M Brbić, I Kopriva - Pattern recognition, 2018 - Elsevier
Most existing approaches address multi-view subspace clustering problem by constructing
the affinity matrix on each view separately and afterwards propose how to extend spectral …

Gcfagg: Global and cross-view feature aggregation for multi-view clustering

W Yan, Y Zhang, C Lv, C Tang… - Proceedings of the …, 2023 - openaccess.thecvf.com
Multi-view clustering can partition data samples into their categories by learning a
consensus representation in unsupervised way and has received more and more attention …

Gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models

J Zimmermann, C Kaleta, S Waschina - Genome biology, 2021 - Springer
Genome-scale metabolic models of microorganisms are powerful frameworks to predict
phenotypes from an organism's genotype. While manual reconstructions are laborious …

Application and challenge of 3rd generation sequencing for clinical bacterial studies

M Ben Khedher, K Ghedira, JM Rolain… - International Journal of …, 2022 - mdpi.com
Over the past 25 years, the powerful combination of genome sequencing and bioinformatics
analysis has played a crucial role in interpreting information encoded in bacterial genomes …

A host–microbiota interactome reveals extensive transkingdom connectivity

ND Sonnert, CE Rosen, AR Ghazi, EA Franzosa… - Nature, 2024 - nature.com
The myriad microorganisms that live in close association with humans have diverse effects
on physiology, yet the molecular bases for these impacts remain mostly unknown …

A positive correlation between GC content and growth temperature in prokaryotes

EZ Hu, XR Lan, ZL Liu, J Gao, DK Niu - BMC genomics, 2022 - Springer
Background GC pairs are generally more stable than AT pairs; GC-rich genomes were
proposed to be more adapted to high temperatures than AT-rich genomes. Previous studies …

High‐throughput identification and diagnostics of pathogens and pests: overview and practical recommendations

L Tedersoo, R Drenkhan, S Anslan… - Molecular ecology …, 2019 - Wiley Online Library
High‐throughput identification technologies provide efficient tools for understanding the
ecology and functioning of microorganisms. Yet, these methods have been only rarely used …

Collaborative feature-weighted multi-view fuzzy c-means clustering

MS Yang, KP Sinaga - Pattern Recognition, 2021 - Elsevier
Fuzzy c-means (FCM) clustering had been extended for handling multi-view data with
collaborative idea. However, these collaborative multi-view FCM treats multi-view data …