Standout Papers
Citation Impact
Citing Papers
Tackling soil diversity with the assembly of large, complex metagenomes
2014
CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus
2015
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
2015 Standout
QUAST: quality assessment tool for genome assemblies
2013 Standout
Longitudinal analysis of microbial interaction between humans and the indoor environment
2014 Science
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
2014
Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle
2023 StandoutNobel
Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism
2016 Standout
Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems
2016
Diverse uncultivated ultra-small bacterial cells in groundwater
2015
Exploring the rice dispensable genome using a metagenome-like assembly strategy
2015
Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins
2022 StandoutNobel
Expanded diversity of Asgard archaea and their relationships with eukaryotes
2021 Nature
Hundreds of Circular Novel Plasmids and DNA Elements Identified in a Rat Cecum Metamobilome
2014
Metagenomic microbial community profiling using unique clade-specific marker genes
2012
Interactions between the microbiota, immune and nervous systems in health and disease
2017 Standout
A scoutRNA Is Required for Some Type V CRISPR-Cas Systems
2020 StandoutNobel
Human Genetics Shape the Gut Microbiome
2014 Standout
Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling
2013
Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study
2017
New CRISPR–Cas systems from uncultivated microbes
2016 StandoutNatureNobel
A new coronavirus associated with human respiratory disease in China
2020 StandoutNature
DNA Targeting by a Minimal CRISPR RNA-Guided Cascade
2016 StandoutNobel
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
2015 Standout
PHASTER: a better, faster version of the PHAST phage search tool
2016 Standout
Accurate identification of centromere locations in yeast genomes using Hi-C
2015
RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes
2017 StandoutNobel
Bioinformatics for the Human Microbiome Project
2012
Complete nitrification by Nitrospira bacteria
2015 StandoutNature
Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations
2015
A Functional Mini-Integrase in a Two-Protein Type V-C CRISPR System
2019 StandoutNobel
The Science of Antibiotic Discovery
2020 Standout
Asgard archaea illuminate the origin of eukaryotic cellular complexity
2017 Nature
Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning
2015
Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis
2018 Nature
A Broad-Spectrum Inhibitor of CRISPR-Cas9
2017 StandoutNobel
Crohn's disease
2016 Standout
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
2018 Standout
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
2016
The pangenome of an agronomically important crop plant Brassica oleracea
2016 Standout
Unusual biology across a group comprising more than 15% of domain Bacteria
2015 Nature
Meta'omic Analytic Techniques for Studying the Intestinal Microbiome
2014
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
2017 Standout
Current understanding of the human microbiome
2018 Standout
TruSPAdes: barcode assembly of TruSeq synthetic long reads
2016
MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
2016
Recent advances in genomic DNA sequencing of microbial species from single cells
2014
A roadmap for natural product discovery based on large-scale genomics and metabolomics
2014
A thermostable Cas9 with increased lifetime in human plasma
2017 StandoutNobel
Broad-spectrum enzymatic inhibition of CRISPR-Cas12a
2019 StandoutNobel
Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample
2015
Assembly of long, error-prone reads using repeat graphs
2019 Standout
Gut microbiota, metabolites and host immunity
2016 Standout
Biology and Applications of CRISPR Systems: Harnessing Nature’s Toolbox for Genome Engineering
2016 StandoutNobel
Chemistry of Class 1 CRISPR-Cas effectors: Binding, editing, and regulation
2020 StandoutNobel
The Biology of CRISPR-Cas: Backward and Forward
2018 StandoutNobel
Adaptation in CRISPR-Cas Systems
2016 StandoutNobel
metaSPAdes: a new versatile metagenomic assembler
2017 Standout
The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle
2015
CasX enzymes comprise a distinct family of RNA-guided genome editors
2019 StandoutNatureNobel
Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
2015
Evolutionary history of Coleoptera revealed by extensive sampling of genes and species
2018 Standout
Sequence assembly demystified
2013
Accurate, multi-kb reads resolve complex populations and detect rare microorganisms
2015
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
2017 Standout
Advances and Applications of Single-Cell Sequencing Technologies
2015
The pros, cons, and many unknowns of probiotics
2019 Standout
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
2015 Standout
The microbial nitrogen-cycling network
2018 Standout
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis
2011
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products
2013
STAMP: statistical analysis of taxonomic and functional profiles
2014 Standout
Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach
2013 Standout
Assembling short reads from jumping libraries with large insert sizes
2015
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
2019 Standout
Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease
2015
2015
GroopM: an automated tool for the recovery of population genomes from related metagenomes
2014
Computational meta'omics for microbial community studies
2013
Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption
2015
VirSorter: mining viral signal from microbial genomic data
2015
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
2017 StandoutScience
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
2012
Systematic discovery of natural CRISPR-Cas12a inhibitors
2018 StandoutScienceNobel
MetaQUAST: evaluation of metagenome assemblies
2015
Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
2013
CRISPR-CasΦ from huge phages is a hypercompact genome editor
2020 StandoutScienceNobel
Bambus 2: scaffolding metagenomes
2011
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
2012
Programmed DNA destruction by miniature CRISPR-Cas14 enzymes
2018 StandoutScienceNobel
Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold
2013
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
2015 Standout
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
2013
Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla
2015
ExSPAnder: a universal repeat resolver for DNA fragment assembly
2014
The commensal microbiome is associated with anti–PD-1 efficacy in metastatic melanoma patients
2018 StandoutScience
Omega: an Overlap-graphde novoAssembler for Metagenomics
2014
Ray Meta: scalable de novo metagenome assembly and profiling
2012
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
2013
Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development
2015
PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes
2016
Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO 2 concentrations
2016
The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level
2018
Genomes from Metagenomics
2013 Science
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)
2022 Standout
SAR11 bacteria linked to ocean anoxia and nitrogen loss
2016 Nature
Works of Yu Peng being referenced
Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers
2010
Meta-IDBA: a de Novo assembler for metagenomic data
2011
A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio
2011
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
2012 Standout