4.8 Article

A genome and gene catalog of glacier microbiomes

Related references

Note: Only part of the references are listed.
Article Biotechnology & Applied Microbiology

A unified catalog of 204,938 reference genomes from the human gut microbiome

Alexandre Almeida et al.

Summary: The Unified Human Gastrointestinal Genome (UHGG) and Protein (UHGP) collections include a large number of non-redundant genomes and protein sequences, which are crucial for studying the relationship between genotypes and phenotypes in the human gut microbiome.

NATURE BIOTECHNOLOGY (2021)

Article Biotechnology & Applied Microbiology

Improved metagenome binning and assembly using deep variational autoencoders

Jakob Nybo Nissen et al.

Summary: Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop variational autoencoders for metagenomic binning (VAMB), a program that outperforms existing state-of-the-art binners in reconstructing near-complete genomes on simulated and real data. VAMB is able to separate closely related strains with high accuracy and showcase different geographical distribution patterns of human gut microbiome species.

NATURE BIOTECHNOLOGY (2021)

Article Geography, Physical

Core handling, transportation and processing for the South Pole ice core (SPICEcore) project

Joseph M. Souney et al.

Summary: The South Pole ice core, drilled using the US Intermediate Depth Drill, is the highest-resolution interior East Antarctic ice core that extends into the glacial period and shows minimal brittle ice.

ANNALS OF GLACIOLOGY (2021)

Article Microbiology

PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data

Laura de Nies et al.

Summary: PathoFact is a tool that accurately predicts virulence factors, bacterial toxins, and antimicrobial resistance genes in metagenomic data. It outperforms existing workflows in predicting virulence factors and toxin genes, and performs well in predicting antimicrobial resistance. This tool can be applied independently for each module, making it flexible and versatile.

MICROBIOME (2021)

Article Microbiology

Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean

Marta Royo-Llonch et al.

Summary: Using genome-resolved metagenomics, this study identified uncultured Arctic bacterial and archaeal metagenome-assembled genomes (MAGs) and analyzed their gene expression patterns, habitat preferences, and metabolic potential. The results suggest that marine microorganisms in the Arctic Ocean play a crucial role in climate regulation, and the adaptation of Arctic MAGs to a copiotrophic lifestyle in nutrient-rich waters may influence the ecosystem. The Arctic MAGs catalogue provides insights into polar microorganisms driving global biogeochemical cycles.

NATURE MICROBIOLOGY (2021)

Article Biochemical Research Methods

Sensitive protein alignments at tree-of-life scale using DIAMOND

Benjamin Buchfink et al.

Summary: We are at the beginning of a genomic revolution where all known species are planned to be sequenced. The improved version of DIAMOND allows for quick tree-of-life scale protein alignments.

NATURE METHODS (2021)

Article Biotechnology & Applied Microbiology

A genomic catalog of Earth's microbiomes

Stephen Nayfach et al.

Summary: Reconstructing bacterial and archaeal genomes from shotgun metagenomes has led to the creation of a comprehensive catalog representing a significant expansion of the known phylogenetic diversity of bacteria and archaea. This resource is available for streamlined comparative analyses, interactive exploration, metabolic modeling, and bulk download, demonstrating the utility of genome-centric approaches for understanding genomic properties of uncultivated microorganisms.

NATURE BIOTECHNOLOGY (2021)

Article Biochemistry & Molecular Biology

A computational framework to explore large-scale biosynthetic diversity

Jorge C. Navarro-Munoz et al.

NATURE CHEMICAL BIOLOGY (2020)

Article Environmental Sciences

Potentially pathogenic bacteria isolated from diverse habitats in Spitsbergen, Svalbard

Diana C. Mogrovejo-Arias et al.

ENVIRONMENTAL EARTH SCIENCES (2020)

Article Biochemistry & Molecular Biology

Inhibition of histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing

Bin Liu et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biotechnology & Applied Microbiology

A complete domain-to-species taxonomy for Bacteria and Archaea

Donovan H. Parks et al.

NATURE BIOTECHNOLOGY (2020)

Editorial Material Ecology

Glacial ecosystems are essential to understanding biodiversity responses to glacier retreat

Marek Stibal et al.

NATURE ECOLOGY & EVOLUTION (2020)

Article Biochemistry & Molecular Biology

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

Ivica Letunic et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

Kai Blin et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Ecology

A global synthesis of biodiversity responses to glacier retreat

Sophie Cauvy-Fraunie et al.

NATURE ECOLOGY & EVOLUTION (2019)

Article Biochemistry & Molecular Biology

VFDB 2019: a comparative pathogenomic platform with an interactive web interface

Bo Liu et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Evolutionary Biology

Back to the future in a petri dish: Origin and impact of resurrected microbes in natural populations

Shira Houwenhuyse et al.

EVOLUTIONARY APPLICATIONS (2018)

Article Biochemistry & Molecular Biology

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

Ioanna Kalvari et al.

NUCLEIC ACIDS RESEARCH (2018)

Review Meteorology & Atmospheric Sciences

Climatic and associated cryospheric, biospheric, and hydrological changes on the Tibetan Plateau: a review

Sadia Bibi et al.

INTERNATIONAL JOURNAL OF CLIMATOLOGY (2018)

Article Biochemistry & Molecular Biology

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

Baofeng Jia et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

KEGG: new perspectives on genomes, pathways, diseases and drugs

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

Jaime Huerta-Cepas et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Biotechnology & Applied Microbiology

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Robert M. Bowers et al.

NATURE BIOTECHNOLOGY (2017)

Letter Biotechnology & Applied Microbiology

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

Martin Steinegger et al.

NATURE BIOTECHNOLOGY (2017)

Article Biochemical Research Methods

Salmon provides fast and bias-aware quantification of transcript expression

Rob Patro et al.

NATURE METHODS (2017)

Review Biotechnology & Applied Microbiology

The microbiome of glaciers and ice sheets

Alexandre M. Anesio et al.

NPJ BIOFILMS AND MICROBIOMES (2017)

Article Biochemical Research Methods

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

Yu-Wei Wu et al.

BIOINFORMATICS (2016)

Article Microbiology

ProCarDB: a database of bacterial carotenoids

L. N. U. Nupur et al.

BMC MICROBIOLOGY (2016)

Article Biochemistry & Molecular Biology

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Donovan H. Parks et al.

GENOME RESEARCH (2015)

Review Genetics & Heredity

Horizontal gene transfer: building the web of life

Shannon M. Soucy et al.

NATURE REVIEWS GENETICS (2015)

Review Microbiology

Microbial ecology of the cryosphere: sea ice and glacial habitats

Antje Boetius et al.

NATURE REVIEWS MICROBIOLOGY (2015)

Article Biochemical Research Methods

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

Baris E. Suzek et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

Prokka: rapid prokaryotic genome annotation

Torsten Seemann

BIOINFORMATICS (2014)

Article Biotechnology & Applied Microbiology

An integrated catalog of reference genes in the human gut microbiome

Junhua Li et al.

NATURE BIOTECHNOLOGY (2014)

Article Biotechnology & Applied Microbiology

Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes

Anthony Levasseur et al.

BIOTECHNOLOGY FOR BIOFUELS (2013)

Review Biochemistry & Molecular Biology

The impact of transposable elements in environmental adaptation

Elena Casacuberta et al.

MOLECULAR ECOLOGY (2013)

Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Geosciences, Multidisciplinary

Biological processes on glacier and ice sheet surfaces

Marek Stibal et al.

NATURE GEOSCIENCE (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Ecology

Glaciers and ice sheets as a biome

Alexandre M. Anesio et al.

TRENDS IN ECOLOGY & EVOLUTION (2012)

Article Environmental Sciences

Different glacier status with atmospheric circulations in Tibetan Plateau and surroundings

Tandong Yao et al.

NATURE CLIMATE CHANGE (2012)

Article Biochemical Research Methods

Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt et al.

BMC BIOINFORMATICS (2010)

Article Biochemical Research Methods

Infernal 1.0: inference of RNA alignments

Eric P. Nawrocki et al.

BIOINFORMATICS (2009)

Review Ecology

Glacial ecosystems

Andy Hodson et al.

ECOLOGICAL MONOGRAPHS (2008)

Review Biochemistry & Molecular Biology

Life at low temperatures: is disorder the driving force?

Georges Feller

EXTREMOPHILES (2007)

Article Biochemical Research Methods

The COG database: an updated version includes eukaryotes

RL Tatusov et al.

BMC BIOINFORMATICS (2003)

Article Microbiology

Bacterial recovery from ancient glacial ice

BC Christner et al.

ENVIRONMENTAL MICROBIOLOGY (2003)

Article Biochemistry & Molecular Biology

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

B Boeckmann et al.

NUCLEIC ACIDS RESEARCH (2003)