Research graph
References from kMermaid: Ultrafast metagenomic read assignment to protein clusters by hashing of amino acid k-mer frequencies. Local targets link to admitted publications; unresolved targets remain external evidence.
Clinical metagenomics
10.1038/s41576-019-0113-7 · 2019 · External reference
Metagenomics-enabled microbial surveillance
10.1038/s41564-022-01089-w · 2022 · External reference
Microbiome research outlook: past, present, and future
10.1093/procel/pwad031 · 2023 · External reference
Toward Accurate and Quantitative Comparative Metagenomics
10.1016/j.cell.2016.08.007 · 2016 · External reference
Functional assignment of metagenomic data: challenges and applications
10.1093/bib/bbs033 · 2012 · External reference
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
10.1093/molbev/msab293 · 2021 · External reference
PANNZER2: a rapid functional annotation web server
10.1093/nar/gky350 · 2018 · External reference
BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences
10.1016/j.jmb.2015.11.006 · 2016 · External reference
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
10.7554/elife.65088 · 2021 · External reference
Metagenomic functional profiling: to sketch or not to sketch?
2024 · External reference
eggNOG 6.0: enabling comparative genomics across 12 535 organisms
2022 · External reference
Basic local alignment search tool
10.1016/s0022-2836(05)80360-2 · 1990 · External reference
The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples
10.1186/s40793-019-0347-1 · 2019 · External reference
Fast and sensitive protein alignment using DIAMOND
10.1038/nmeth.3176 · 2014 · External reference
Sensitive protein alignments at tree-of-life scale using DIAMOND
10.1038/s41592-021-01101-x · 2021 · External reference
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
10.1038/nbt.3988 · 2017 · External reference
In silico benchmarking of metagenomic tools for coding sequence detection reveals the limits of sensitivity and precision
10.1186/s12859-020-03802-0 · 2020 · External reference
Pseudoalignment for metagenomic read assignment
10.1093/bioinformatics/btx106 · 2017 · External reference
Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression
10.1093/bioinformatics/bty078 · 2018 · External reference
10.1016/j.csbj.2024.05.025 · 2024 · Admitted local publication
Kraken: ultrafast metagenomic sequence classification using exact alignments
2014 · External reference
Improved metagenomic analysis with Kraken 2
10.1186/s13059-019-1891-0 · 2019 · External reference
KrakenUniq: confident and fast metagenomics classification using unique k-mer counts
10.1186/s13059-018-1568-0 · 2018 · External reference
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
10.1186/s12864-015-1419-2 · 2015 · External reference
Centrifuge: rapid and sensitive classification of metagenomic sequences
10.1101/gr.210641.116 · 2016 · External reference
Fast and sensitive taxonomic classification for metagenomics with Kaiju
10.1038/ncomms11257 · 2016 · External reference
HH-suite3 for fast remote homology detection and deep protein annotation
10.1186/s12859-019-3019-7 · 2019 · External reference
The National Center for Biotechnology Information’s Protein Clusters Database
10.1093/nar/gkn734 · 2009 · External reference
Lyophilised oral faecal microbiota transplantation for ulcerative colitis (LOTUS): a randomised, double-blind, placebo-controlled trial
10.1016/s2468-1253(21)00400-3 · 2022 · External reference
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
10.1093/nar/25.17.3389 · 1997 · External reference
Metagenomic biomarker discovery and explanation
10.1186/gb-2011-12-6-r60 · 2011 · External reference
Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights
10.1371/journal.pcbi.1004977 · 2016 · External reference
MetaPheno: A critical evaluation of deep learning and machine learning in metagenome-based disease prediction
10.1016/j.ymeth.2019.03.003 · 2019 · External reference
Spaced seeds improve k-mer-based metagenomic classification
10.1093/bioinformatics/btv419 · 2015 · External reference
Libra: scalable k-mer-based tool for massive all-vs-all metagenome comparisons
10.1093/gigascience/giy165 · 2019 · External reference
KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping
10.1093/bioinformatics/btac845 · 2022 · External reference
Binning metagenomic contigs by coverage and composition
10.1038/nmeth.3103 · 2014 · External reference
Recognition of microorganisms and activation of the immune response
10.1038/nature06246 · 2007 · External reference
Molecular mimicry as a mechanism of autoimmune disease
10.1007/s12016-011-8294-7 · 2012 · External reference
A deep learning approach reveals unexplored landscape of viral expression in cancer
10.1038/s41467-023-36336-z · 2023 · External reference
Bacteriophage classification for assembled contigs using graph convolutional network
10.1093/bioinformatics/btab293 · 2021 · External reference
MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation
10.1093/femsle/fnw049 · 2016 · External reference
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
10.1093/bioinformatics/btl158 · 2006 · External reference
CD-HIT: accelerated for clustering the next-generation sequencing data
10.1093/bioinformatics/bts565 · 2012 · External reference
RefSeq microbial genomes database: new representation and annotation strategy
10.1093/nar/gkt1274 · 2014 · External reference
The Protein Data Bank
10.1093/nar/28.1.235 · 2000 · External reference
Uniclust databases of clustered and deeply annotated protein sequences and alignments
10.1093/nar/gkw1081 · 2017 · External reference
Bacterial DNA Mutations.
2023 · External reference
Analysis of error profiles in deep next-generation sequencing data
10.1186/s13059-019-1659-6 · 2019 · External reference
Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients
10.1186/s13073-019-0672-4 · 2019 · External reference
