On the public citation graph

TaxonKit: a cross-platform and efficient NCBI taxonomy toolkit

https://doi.org/10.1101/513523
0 signed · 69 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.
Claim with ORCID
Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.
See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1093/bioinformatics/btp163openalex-snapshot
Biopython: freely available Python tools for computational molecular biology and bioinformatics
inferredcites →https://doi.org/10.1093/molbev/msw046openalex-snapshot
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
inferredcites →https://doi.org/10.1093/nar/gkh073openalex-snapshot
Database resources of the National Center for Biotechnology Information: update
inferredcites →https://doi.org/10.1093/nar/gkx1095openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferredcites →https://doi.org/10.1186/gb-2011-12-6-r60openalex-snapshot
Metagenomic biomarker discovery and explanation

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/edn3.235openalex-snapshot
One size does not fit all: Tuning eDNA protocols for high‐ and low‐turbidity water sampling
inferred← citeshttps://doi.org/10.1002/edn3.479openalex-snapshot
Optimizing a metabarcoding marker portfolio for species detection from complex mixtures of globally diverse fishes
inferred← citeshttps://doi.org/10.1007/978-1-0716-2380-0_18openalex-snapshot
Computational Methods for the Discovery and Annotation of Viral Integrations
inferred← citeshttps://doi.org/10.1007/978-1-4939-9173-0_16openalex-snapshot
Choosing the Best Gene Predictions with GeneValidator
inferred← citeshttps://doi.org/10.1007/s00253-023-12993-4openalex-snapshot
Biogeographic patterns of meio- and micro-eukaryotic communities in dam-induced river-reservoir systems
inferred← citeshttps://doi.org/10.1007/s00338-026-02832-zopenalex-snapshot
Assessment of antibiotic resistance genes in Caribbean corals, including those treated with amoxicillin
inferred← citeshttps://doi.org/10.1007/s10815-019-01672-xopenalex-snapshot
What human sperm RNA-Seq tells us about the microbiome
inferred← citeshttps://doi.org/10.1007/s11356-024-34077-0openalex-snapshot
A study of bacteria producing carbonic anhydrase enzyme for CaCO3 precipitation and soil biocementation
inferred← citeshttps://doi.org/10.1007/s11427-021-2081-6openalex-snapshot
Building the Chordata Olfactory Receptor Database using more than 400,000 receptors annotated by Genome2OR
inferred← citeshttps://doi.org/10.1007/s12539-021-00493-wopenalex-snapshot
Consistent Clustering Pattern of Prokaryotic Genes Based on Base Frequency at the Second Codon Position and its Association with Functional Category Preference
inferred← citeshttps://doi.org/10.1016/j.cub.2020.03.011openalex-snapshot
Parallel Evolution in the Integration of a Co-Obligate Aphid Symbiosis
inferred← citeshttps://doi.org/10.1016/j.cub.2020.08.061openalex-snapshot
New Lineage of Microbial Predators Adds Complexity to Reconstructing the Evolutionary Origin of Animals
inferred← citeshttps://doi.org/10.1016/j.jmoldx.2022.01.011openalex-snapshot
Defining Novel DNA Virus-Tumor Associations and Genomic Correlates Using Prospective Clinical Tumor/Normal Matched Sequencing Data
inferred← citeshttps://doi.org/10.1017/s0031182022001688openalex-snapshot
Revisiting fecal metatranscriptomics analyses of macaques with idiopathic chronic diarrhoea with a focus on trichomonad parasites
inferred← citeshttps://doi.org/10.1038/s41477-021-01031-8openalex-snapshot
Representation and participation across 20 years of plant genome sequencing
inferred← citeshttps://doi.org/10.1038/s41587-022-01494-wopenalex-snapshot
Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome
inferred← citeshttps://doi.org/10.1038/s41598-021-00865-8openalex-snapshot
Venatorbacter cucullus gen. nov sp. nov a novel bacterial predator
inferred← citeshttps://doi.org/10.1038/s41598-022-14893-5openalex-snapshot
The first long-read nuclear genome assembly of Oryza australiensis, a wild rice from northern Australia
inferred← citeshttps://doi.org/10.1073/pnas.2109019118openalex-snapshot
Toward a genome sequence for every animal: Where are we now?
inferred← citeshttps://doi.org/10.1073/pnas.2122957119openalex-snapshot
Physicochemical classification of organisms
inferred← citeshttps://doi.org/10.1089/phage.2024.0049openalex-snapshot
Escherichia Phage Ge15, NRG-P0073: Genomic Characterization and Host Range Analysis Against the ECOR Reference Library
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz188openalex-snapshot
GToTree: a user-friendly workflow for phylogenomics
inferred← citeshttps://doi.org/10.1093/evolinnean/kzad001openalex-snapshot
Wolbachia and Spiroplasma endosymbionts in the Anurida maritima (Collembola) species group
inferred← citeshttps://doi.org/10.1093/gbe/evab105openalex-snapshot
The Presence of Ancient Core Genes Reveals Endogenization from Diverse Viral Ancestors in Parasitoid Wasps
inferred← citeshttps://doi.org/10.1093/gbe/evad148openalex-snapshot
Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats
inferred← citeshttps://doi.org/10.1093/nargab/lqac080openalex-snapshot
AsgeneDB: a curated orthology arsenic metabolism gene database and computational tool for metagenome annotation
inferred← citeshttps://doi.org/10.1099/mgen.0.000624openalex-snapshot
High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts
inferred← citeshttps://doi.org/10.1101/2020.03.16.994376openalex-snapshot
Microbial contaminants cataloged as novel human sequences in recent human pan-genomes
inferred← citeshttps://doi.org/10.1101/2020.05.28.119461openalex-snapshot
Taxallnomy: Closing gaps in the NCBI Taxonomy
inferred← citeshttps://doi.org/10.1101/2020.09.09.290502openalex-snapshot
Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus
inferred← citeshttps://doi.org/10.1101/2020.10.18.344572openalex-snapshot
Codependence in the Nephromyces species swarm depends on heterospecific bacterial endosymbionts
inferred← citeshttps://doi.org/10.1101/2021.05.31.446451openalex-snapshot
Lessons from 20 years of plant genome sequencing: an unprecedented resource in need of more diverse representation
inferred← citeshttps://doi.org/10.1101/2021.12.21.473765openalex-snapshot
Plant growth promoting activity of bacteria isolated from Asian rice ( Oryza sativa L.) are plant subspecies dependent
inferred← citeshttps://doi.org/10.1101/2022.07.10.499467openalex-snapshot
Highly accurate long reads are crucial for realizing the potential of biodiversity genomics
inferred← citeshttps://doi.org/10.1101/2024.11.01.621504openalex-snapshot
Assessment of antimicrobial resistance genes in Caribbean corals, including those treated with amoxicillin
inferred← citeshttps://doi.org/10.1111/1755-0998.13407openalex-snapshot
Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes
inferred← citeshttps://doi.org/10.1111/mec.15620openalex-snapshot
Modelling technical and biological biases in macroinvertebrate community assessment from bulk preservative using multiple metabarcoding markers
inferred← citeshttps://doi.org/10.1111/mec.16673openalex-snapshot
Complete metamorphosis and microbiota turnover in insects
inferred← citeshttps://doi.org/10.1128/jb.00491-19openalex-snapshot
The Mechanism of Bidirectional pH Taxis in Bacillus subtilis
inferred← citeshttps://doi.org/10.1128/mbio.00918-22openalex-snapshot
Two Different Species of Mycoplasma Endosymbionts Can Influence Trichomonas vaginalis Pathophysiology
inferred← citeshttps://doi.org/10.1128/mra.00354-20openalex-snapshot
Draft Genome Sequences of Bacillus glennii V44-8, Bacillus saganii V47-23a, Bacillus sp. Strain V59.32b, Bacillus sp. Strain MER_TA_151, and Paenibacillus sp. Strain MER_111, Isolated from Cleanrooms Where the Viking and Mars Exploration Rover Spacecraft Were Assembled
inferred← citeshttps://doi.org/10.1128/spectrum.01404-23openalex-snapshot
Multiomics Reveals Symbionts, Pathogens, and Tissue-Specific Microbiome of Blacklegged Ticks (Ixodes scapularis) from a Lyme Disease Hot Spot in Southeastern Ontario, Canada
inferred← citeshttps://doi.org/10.1128/spectrum.02787-21openalex-snapshot
Plant Growth-Promoting Activity of Bacteria Isolated from Asian Rice (Oryza sativa L.) Depends on Rice Genotype
inferred← citeshttps://doi.org/10.1128/spectrum.04102-22openalex-snapshot
Metagenomic Insight into Microbiome and Antibiotic Resistance Genes of High Clinical Concern in Urban and Rural Hospital Wastewater of Northern India Origin: a Major Reservoir of Antimicrobial Resistance
inferred← citeshttps://doi.org/10.1177/1176934319862245openalex-snapshot
Applications and Considerations of GToTree: A User-Friendly Workflow for Phylogenomics
inferred← citeshttps://doi.org/10.1186/s12859-020-3507-9openalex-snapshot
Blast2Fish: a reference-based annotation web tool for transcriptome analysis of non-model teleost fish
inferred← citeshttps://doi.org/10.1186/s12864-023-09193-9openalex-snapshot
Highly accurate long reads are crucial for realizing the potential of biodiversity genomics
inferred← citeshttps://doi.org/10.1186/s42523-022-00208-6openalex-snapshot
Effect of Mannan-rich fraction supplementation on commercial broiler intestinum tenue and cecum microbiota
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1008214openalex-snapshot
Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation
inferred← citeshttps://doi.org/10.1371/journal.pone.0266720openalex-snapshot
Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary
inferred← citeshttps://doi.org/10.1534/g3.120.401309openalex-snapshot
CeMbio - The Caenorhabditis elegans Microbiome Resource
inferred← citeshttps://doi.org/10.21203/rs.3.rs-539338/v1openalex-snapshot
Identification of hidden N4-like viruses and their interactions with hosts in global metagenomes
inferred← citeshttps://doi.org/10.22541/au.163861686.62434613/v1openalex-snapshot
Optimizing a metabarcoding primer portfolio for species-level detection of taxa in complex mixtures of diverse fishes
inferred← citeshttps://doi.org/10.26686/wgtn.17147699.v1openalex-snapshot
Discovery and Biosynthesis of Natural Products from New Zealand Soil Metagenome Libraries
inferred← citeshttps://doi.org/10.3389/fcimb.2022.911563openalex-snapshot
Untangling an AGS Outbreak Caused by the Recombinant GII.12[P16] Norovirus With Nanopore Sequencing
inferred← citeshttps://doi.org/10.3389/fmars.2021.695236openalex-snapshot
Molecular Mechanisms of Coral Persistence Within Highly Urbanized Locations in the Port of Miami, Florida
inferred← citeshttps://doi.org/10.3389/fmicb.2019.01805openalex-snapshot
Fishing in the Soup – Pathogen Detection in Food Safety Using Metabarcoding and Metagenomic Sequencing
inferred← citeshttps://doi.org/10.3389/fmicb.2020.596626openalex-snapshot
High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies
inferred← citeshttps://doi.org/10.3390/biom10040612openalex-snapshot
Novel Apoptotic Mediators Identified by Conservation of Vertebrate Caspase Targets
inferred← citeshttps://doi.org/10.3390/plants10020251openalex-snapshot
A Transcriptomic Approach Provides Insights on the Mycorrhizal Symbiosis of the Mediterranean Orchid Limodorum abortivum in Nature
inferred← citeshttps://doi.org/10.70675/fe7a7f41z710bz471cz9b7fz8337110de97eopenalex-snapshot
Caractérisation de l'holobionte des isopodes par des approches omiques : exemple du processus de dégradation de la lignocellulose
inferred← citeshttps://doi.org/10.7287/peerj.12198v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.12198v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets (v0.1)"
inferred← citeshttps://doi.org/10.7717/peerj.12198openalex-snapshot
Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.