Salvaging high-quality genomes of microbial species from a meromictic lake using a hybrid sequencing approach

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)

(2021) Renaud Van Damme et al.   PLoS Computational Biology

Complete, closed bacterial genomes from microbiomes using nanopore sequencing

(2020) Eli L. Moss et al.   NATURE BIOTECHNOLOGY

Global airborne sampling reveals a previously unobserved dimethyl sulfide oxidation mechanism in the marine atmosphere

(2020) Patrick R. Veres et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate and complete genomes from metagenomes

(2020) Lin-Xing Chen et al.   GENOME RESEARCH

Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan

(2020) Andreas Sichert et al.   Nature Microbiology

Assembly methods for nanopore-based metagenomic sequencing: a comparative study

(2020) Adriel Latorre-Pérez et al.   Scientific Reports

Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community

(2020) Ga Gong et al.   BMC MICROBIOLOGY

metaFlye: scalable long-read metagenome assembly using repeat graphs

(2020) Mikhail Kolmogorov et al.   NATURE METHODS

Isolation of a member of the candidate phylum ‘Atribacteria’ reveals a unique cell membrane structure

(2020) Taiki Katayama et al.   Nature Communications

Microbial dark matter coming to light: challenges and opportunities

(2020) Jian-Yu Jiao et al.   National Science Review

Genetic Evidence for Two Carbon Fixation Pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in Symbiotic and Free-Living Bacteria

(2019) Maxim Rubin-Blum et al.   mSphere

Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing

(2019) You Che et al.   Microbiome

Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates

(2019) Girish Beedessee et al.   Scientific Reports

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

New approaches for metagenome assembly with short reads

(2019) Martin Ayling et al.   BRIEFINGS IN BIOINFORMATICS

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

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

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae

(2019) Michaela M. Salcher et al.   ISME Journal

Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes

(2019) Denis Bertrand et al.   NATURE BIOTECHNOLOGY

Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments

(2019) Xiyang Dong et al.   Nature Communications

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

(2019) Charlotte D. Vavourakis et al.   BMC BIOLOGY

KEGG Mapper for inferring cellular functions from protein sequences

(2019) Minoru Kanehisa et al.   PROTEIN SCIENCE

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat

(2019) Pedro J. Cabello‐Yeves et al.   LIMNOLOGY AND OCEANOGRAPHY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Flux of the biogenic volatiles isoprene and dimethyl sulfide from an oligotrophic lake

(2018) Michael Steinke et al.   Scientific Reports

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia

(2018) Yu-Ting Wu et al.   Frontiers in Microbiology

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

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

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs

(2017) Pedro J. Cabello-Yeves et al.   Frontiers in Microbiology

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes

(2017) Shaomei He et al.   mSphere

Heatmapper: web-enabled heat mapping for all

(2016) Sasha Babicki et al.   NUCLEIC ACIDS RESEARCH

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Cold Shock Proteins: A Minireview with Special Emphasis on Csp-family of Enteropathogenic Yersinia

(2016) Riikka Keto-Timonen et al.   Frontiers in Microbiology

Bacterial Communities of Three Saline Meromictic Lakes in Central Asia

(2016) Bayanmunkh Baatar et al.   PLoS One

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

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

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

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Computational approaches to natural product discovery

(2015) Marnix H Medema et al.   Nature Chemical Biology

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine

(2014) Guillaume Borrel et al.   BMC GENOMICS

A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights

(2014) Q.-L. Qin et al.   JOURNAL OF BACTERIOLOGY

Diversity of Glycosyl Hydrolase Enzymes from Metagenome and Their Application in Food Industry

(2014) T.A. Sathya et al.   JOURNAL OF FOOD SCIENCE

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

Role of glutamate metabolism in bacterial responses towards acid and other stresses

(2012) C. Feehily et al.   JOURNAL OF APPLIED MICROBIOLOGY

A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem

(2012) Hideto Takami et al.   PLoS One

Vertical Distribution of Archaea and Bacteria in a Meromictic Lake as Determined by Fluorescent In Situ Hybridization

(2011) Valeria Lentini et al.   CURRENT MICROBIOLOGY

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

An integrative study of a meromictic lake ecosystem in Antarctica

(2010) Federico M Lauro et al.   ISME Journal

Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica

(2010) Charmaine Ng et al.   ISME Journal

Anaerobic phototrophic nitrite oxidation by Thiocapsa sp. strain KS1 and Rhodopseudomonas sp. strain LQ17

(2010) J. Schott et al.   MICROBIOLOGY-SGM

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Prediction of enzyme function by combining sequence similarity and protein interactions

(2008) Jordi Espadaler et al.   BMC BIOINFORMATICS

"Candidatus Cloacamonas Acidaminovorans": Genome Sequence Reconstruction Provides a First Glimpse of a New Bacterial Division

(2008) E. Pelletier et al.   JOURNAL OF BACTERIOLOGY

Domain-Based and Family-Specific Sequence Identity Thresholds Increase the Levels of Reliable Protein Function Transfer

(2008) Sarah Addou et al.   JOURNAL OF MOLECULAR BIOLOGY

The CGView Server: a comparative genomics tool for circular genomes

(2008) J. R. Grant et al.   NUCLEIC ACIDS RESEARCH