Reference health
Metagenomics - a guide from sampling to data analysis
2 of 90 checkable references need attention · checked 2026-07-14
At the dated check, the references listed below either did not resolve in Crossref or DataCite, or carried a publisher retraction notice. Each one is shown with the registry record that put it there.
5 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
References needing attention
does not resolve to a known work10.1093/nar/25.5.0955
does not resolve to a known work10.1101/gr.229202. Article published online before March 2002
The 88 checked references that resolve
resolves10.1016/S1074-5521(98)90108-9
Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products
resolves10.1038/nature02340
Community structure and metabolism through reconstruction of microbial genomes from the environment
resolves10.1016/j.tim.2005.12.006
Metaproteomics: studying functional gene expression in microbial ecosystems
resolves10.1371/journal.pone.0003042
Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities
resolves10.1126/science.289.5486.1902
Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea
resolves10.1016/j.tim.2006.03.004
Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle?
resolves10.1016/j.mimet.2011.06.013
Metagenomic comparison of direct and indirect soil DNA extraction approaches
resolves10.1038/ismej.2010.74
Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis
resolves10.1111/j.1462-2920.2008.01772.x
Coastal
<i>Synechococcus</i>
metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity
resolves10.1042/BST0370450
Genomic DNA amplification by the multiple displacement amplification (MDA) method
resolves10.1016/j.mib.2008.05.006
Genomic sequencing of single microbial cells from environmental samples
resolves10.1128/AEM.02943-08
Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing “
<i>Leptospirillum rubarum</i>
” (Group II) and “
<i>Leptospirillum ferrodiazotrophum</i>
” (Group III) Bacteria in Acid Mine Drainage Biofilms
resolves10.1126/science.1147112
Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer
resolves10.1186/1471-2105-11-187
Artificial and natural duplicates in pyrosequencing reads of metagenomic data
resolves10.1101/pdb.prot5409
Identifying and Removing Artificial Replicates from 454 Pyrosequencing Data
resolves10.1186/1471-2164-10-116
Digital PCR provides sensitive and absolute calibration for high throughput sequencing
resolves10.1186/gb-2010-11-12-r119
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
resolves10.1038/nature07517
Accurate whole human genome sequencing using reversible terminator chemistry
resolves10.1126/science.1200387
Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
resolves10.1038/nature08821
A human gut microbial gene catalogue established by metagenomic sequencing
resolves10.1186/1471-2164-11-512
SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes
resolves10.1094/MPMI-22-12-1624
Confirmation of the Sequence of ‘<i>Candidatus</i> Liberibacter asiaticus’ and Assessment of Microbial Diversity in Huanglongbing-Infected Citrus Phloem Using a Metagenomic Approach
resolves10.1038/msb.2008.35
Millimeter‐scale genetic gradients and community‐level molecular convergence in a hypersaline microbial mat
resolves10.1056/NEJMoa1106920
Origins of the
<i>E. coli</i>
Strain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany
resolves10.1126/science.1181498
Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays
resolves10.1101/gr.074492.107
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
resolves10.1093/bioinformatics/btl158
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
resolves10.1142/S0219720010005051
SHORT PROKARYOTIC DNA FRAGMENT BINNING USING A HIERARCHICAL CLASSIFIER BASED ON LINEAR DISCRIMINANT ANALYSIS AND PRINCIPAL COMPONENT ANALYSIS
resolves10.1186/1471-2105-10-56
TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
resolves10.1093/bioinformatics/btp317
SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
resolves10.1186/1471-2164-12-S2-S4
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
resolves10.1038/nmeth.1358
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
resolves10.1093/bioinformatics/btr186
A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio
resolves10.1093/nar/gkp746
Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion
resolves10.1093/bioinformatics/btp393
IMG ER: a system for microbial genome annotation expert review and curation
resolves10.1093/dnares/dsn027
MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes
resolves10.1186/1471-2105-12-20
Combining gene prediction methods to improve metagenomic gene annotation
resolves10.1186/1471-2105-8-209
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
resolves10.1093/nar/gkm360
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
resolves10.1093/nar/gkm864
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
resolves10.1128/AEM.03006-05
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
resolves10.1093/nar/gkn879
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
resolves10.1093/nar/gkq1102
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource
resolves10.1371/journal.pone.0015545
The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation
resolves10.1371/journal.pbio.0050016
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
resolves10.1093/nar/gkp951
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
resolves10.1093/nar/gkl1043
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
resolves10.1111/j.1442-9993.1993.tb00438.x
Non‐parametric multivariate analyses of changes in community structure
resolves10.1371/journal.pcbi.1000352
Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
resolves10.1093/bioinformatics/btp508
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
resolves10.1073/pnas.1101591108
Bacterial community assembly based on functional genes rather than species
resolves10.1038/nbt.1823
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
resolves10.1101/gr.114819.110
Efficient storage of high throughput DNA sequencing data using reference-based compression
The 5 references without a DOI — listed, not checked
no DOI — not checkedKnight R, Desai N, Field D, Fierer N, Fuhrman J, Gordon J, Hu B, Hugenholtz P, Jansson J, Meyer F, Stevens R, Bailey M, Kowalchuk G, Gilbert J: Designing Better Metagenomic Surveys: The role of experimental design and metadata capture in making useful metagenomic datasets for ecology and biotechnology. Nature Biotechnology. in review
no DOI — not checkedAbbai NS, Govender A, Shaik R, Pillay B: Pyrosequence analysis of unamplified and whole genome amplified DNA from hydrocarbon-contaminated groundwater. Mol Biotechnol. 2011
no DOI — not checkedChevreux B, Wetter T, Suhai S: Genome Sequence Assembly Using Trace Signals and Additional Sequence Information Computer Science and Biology. Proceedings of the German Conference on Bioinformatics. 1999, 99: 45-56.
no DOI — not checkedGlass EM, Wilkening J, Wilke A, Antonopoulos D, Meyer F: Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc. 2010, 2010 (1): pdb prot5368
no DOI — not checkedWilkening J, Desai N, Meyer F, A W: Using clouds for metagenomics - case study. IEEE Cluster. 2009
What this badge says. CiteStamped means the CHECKABLE references of this
work were clean at the dated check: each resolved to a known work in a public registry, and none
carried a publisher retraction notice at that time. It says nothing about the quality, findings,
or importance of the work itself, and nothing about references deposited without a DOI.
checked 2026-07-14 — re-checked daily as this page is visited; titles and statuses come from Crossref and DataCite and are not part of the signed record
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