On the public citation graph
Fungal Phylogeny in the Age of Genomics: Insights Into Phylogenetic Inference From Genome-Scale Datasets
0 signed · 103 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.
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known work and none has been retracted — and get a dated CiteStamped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.
What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/bies.201100110openalex-snapshot
No jacket required – new fungal lineage defies dress code
inferredcites →https://doi.org/10.1007/s00239-011-9461-4openalex-snapshot
Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom
inferredcites →https://doi.org/10.1016/j.cub.2013.06.057openalex-snapshot
Shared Signatures of Parasitism and Phylogenomics Unite Cryptomycota and Microsporidia
inferredcites →https://doi.org/10.1016/j.cub.2016.05.007openalex-snapshot
The Genome of Intoshia linei Affirms Orthonectids as Highly Simplified Spiralians
inferredcites →https://doi.org/10.1016/j.fgb.2006.05.001openalex-snapshot
A phylogenomic analysis of the Ascomycota
inferredcites →https://doi.org/10.1016/j.fgb.2012.01.007openalex-snapshot
The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction
inferredcites →https://doi.org/10.1016/j.funbio.2015.10.002openalex-snapshot
The genome of Xylona heveae provides a window into fungal endophytism
inferredcites →https://doi.org/10.1016/j.mycres.2007.03.004openalex-snapshot
A higher-level phylogenetic classification of the Fungi
inferredcites →https://doi.org/10.1016/j.protis.2012.08.001openalex-snapshot
Obligately Phagotrophic Aphelids Turned out to Branch with the Earliest-diverging Fungi
inferredcites →https://doi.org/10.1016/j.tig.2006.02.003openalex-snapshot
Phylogenomics: the beginning of incongruence?
inferredcites →https://doi.org/10.1016/j.tpb.2014.12.005openalex-snapshot
Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
inferredcites →https://doi.org/10.1016/j.ympev.2006.08.024openalex-snapshot
Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi)
inferredcites →https://doi.org/10.1016/j.ympev.2012.06.019openalex-snapshot
Culture-based study of endophytes associated with rubber trees in Peru reveals a new class of Pezizomycotina: Xylonomycetes
inferredcites →https://doi.org/10.1038/nature02053openalex-snapshot
Genome-scale approaches to resolving incongruence in molecular phylogenies
inferredcites →https://doi.org/10.1038/nature05110openalex-snapshot
Reconstructing the early evolution of Fungi using a six-gene phylogeny
inferredcites →https://doi.org/10.1038/nature13805openalex-snapshot
Origins of major archaeal clades correspond to gene acquisitions from bacteria
inferredcites →https://doi.org/10.1038/ncomms5471openalex-snapshot
Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts
inferredcites →https://doi.org/10.1038/ng.3223openalex-snapshot
Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists
inferredcites →https://doi.org/10.1038/nrg1603openalex-snapshot
Phylogenomics and the reconstruction of the tree of life
inferredcites →https://doi.org/10.1038/s41559-018-0525-3openalex-snapshot
Gene transfers can date the tree of life
inferredcites →https://doi.org/10.1038/srep22262openalex-snapshot
Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches
inferredcites →https://doi.org/10.1073/pnas.1202997109openalex-snapshot
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations
inferredcites →https://doi.org/10.1073/pnas.1400592111openalex-snapshot
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi
inferredcites →https://doi.org/10.1073/pnas.1410442111openalex-snapshot
Evolution of a morphological novelty occurred before genome compaction in a lineage of extreme parasites
inferredcites →https://doi.org/10.1073/pnas.1618463114openalex-snapshot
Integrative modeling of gene and genome evolution roots the archaeal tree of life
inferredcites →https://doi.org/10.1080/10635150390218330openalex-snapshot
Missing Data, Incomplete Taxa, and Phylogenetic Accuracy
inferredcites →https://doi.org/10.1080/10635150500234583openalex-snapshot
Can Incomplete Taxa Rescue Phylogenetic Analyses from Long-Branch Attraction?
inferredcites →https://doi.org/10.1080/10635150701499563openalex-snapshot
Experimental Design Criteria in Phylogenetics: Where to Add Taxa
inferredcites →https://doi.org/10.1080/10635150802306527openalex-snapshot
Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btm015openalex-snapshot
Assessment of phylogenomic and orthology approaches for phylogenetic inference
inferredcites →https://doi.org/10.1093/bioinformatics/btv234openalex-snapshot
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
inferredcites →https://doi.org/10.1093/gbe/evv090openalex-snapshot
Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants
inferredcites →https://doi.org/10.1093/gbe/evw196openalex-snapshot
Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes
inferredcites →https://doi.org/10.1093/molbev/msh137openalex-snapshot
Genome-Scale Phylogeny and the Detection of Systematic Biases
inferredcites →https://doi.org/10.1093/molbev/msh182openalex-snapshot
Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments
inferredcites →https://doi.org/10.1093/molbev/msp123openalex-snapshot
Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model
inferredcites →https://doi.org/10.1093/molbev/msr202openalex-snapshot
Statistics and Truth in Phylogenomics
inferredcites →https://doi.org/10.1093/molbev/msr285openalex-snapshot
A Consistent Phylogenetic Backbone for the Fungi
inferredcites →https://doi.org/10.1093/molbev/mss075openalex-snapshot
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
inferredcites →https://doi.org/10.1093/molbev/mss208openalex-snapshot
Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets
inferredcites →https://doi.org/10.1093/molbev/msu305openalex-snapshot
Toward More Accurate Ancestral Protein Genotype–Phenotype Reconstructions with the Use of Species Tree-Aware Gene Trees
inferredcites →https://doi.org/10.1093/molbev/msv249openalex-snapshot
Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated
inferredcites →https://doi.org/10.1093/molbev/msv337openalex-snapshot
Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities
inferredcites →https://doi.org/10.1093/sysbio/27.4.401openalex-snapshot
Cases in which Parsimony or Compatibility Methods will be Positively Misleading
inferredcites →https://doi.org/10.1093/sysbio/syq025openalex-snapshot
Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships
inferredcites →https://doi.org/10.1093/sysbio/syq097openalex-snapshot
Taxon Sampling and the Optimal Rates of Evolution for Phylogenetic Inference
inferredcites →https://doi.org/10.1093/sysbio/syt054openalex-snapshot
Efficient Exploration of the Space of Reconciled Gene Trees
inferredcites →https://doi.org/10.1093/sysbio/syu048openalex-snapshot
The Inference of Gene Trees with Species Trees
inferredcites →https://doi.org/10.1098/rspb.2012.0683openalex-snapshot
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
inferredcites →https://doi.org/10.1098/rstb.2014.0335openalex-snapshot
Genome-scale phylogenetic analysis finds extensive gene transfer among fungi
inferredcites →https://doi.org/10.1101/gr.141978.112openalex-snapshot
Genome-scale coestimation of species and gene trees
inferredcites →https://doi.org/10.1111/jse.12160openalex-snapshot
Coalescent methods for estimating species trees from phylogenomic data
inferredcites →https://doi.org/10.1126/science.1221748openalex-snapshot
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
inferredcites →https://doi.org/10.1126/science.1250463openalex-snapshot
Statistical binning enables an accurate coalescent-based estimation of the avian tree
inferredcites →https://doi.org/10.1126/science.aaa7343openalex-snapshot
Comment on “Statistical binning enables an accurate coalescent-based estimation of the avian tree”
inferredcites →https://doi.org/10.1128/9781555816636openalex-snapshot
Cellular and Molecular Biology of Filamentous Fungi
inferredcites →https://doi.org/10.1128/9781555816636.ch4openalex-snapshot
Phylogenetics and Phylogenomics of the Fungal Tree of Life
inferredcites →https://doi.org/10.1139/b06-128openalex-snapshot
Resolving the phylogenetic position of the Wallemiomycetes: an enigmatic major lineage of Basidiomycota
inferredcites →https://doi.org/10.1146/annurev.micro.56.012302.160854openalex-snapshot
Microsporidia: Biology and Evolution of Highly Reduced Intracellular Parasites
inferredcites →https://doi.org/10.1186/1471-2105-14-s15-s4openalex-snapshot
Lateral gene transfer, rearrangement, reconciliation
inferredcites →https://doi.org/10.1186/1471-2148-10-302openalex-snapshot
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
inferredcites →https://doi.org/10.1186/1471-2148-6-99openalex-snapshot
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis.
inferredcites →https://doi.org/10.1186/1471-2148-9-272openalex-snapshot
Phylogenomic analyses predict sistergroup relationship of nucleariids and Fungi and paraphyly of zygomycetes with significant support
inferredcites →https://doi.org/10.1186/1741-7007-10-47openalex-snapshot
Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi
inferredcites →https://doi.org/10.1371/currents.tol.8d41ac0f13d1abedf4c4a59f5d17b1f7openalex-snapshot
Concatenation Analyses in the Presence of Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1371/journal.pbio.1000602openalex-snapshot
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
inferredcites →https://doi.org/10.1371/journal.pone.0022783openalex-snapshot
Addressing Inter-Gene Heterogeneity in Maximum Likelihood Phylogenomic Analysis: Yeasts Revisited
inferredcites →https://doi.org/10.1371/journal.pone.0128183openalex-snapshot
Entorrhizomycota: A New Fungal Phylum Reveals New Perspectives on the Evolution of Fungi
inferredcites →https://doi.org/10.1371/journal.pone.0129183openalex-snapshot
Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
inferredcites →https://doi.org/10.2307/2412923openalex-snapshot
Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
inferredcites →https://doi.org/10.3389/fmicb.2014.00112openalex-snapshot
Morphology, phylogeny, and ecology of the aphelids (Aphelidea, Opisthokonta) and proposal for the new superphylum Opisthosporidia
inferredcites →https://doi.org/10.3852/16-042openalex-snapshot
A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data
inferredcites →https://doi.org/10.3852/mycologia.98.6.896openalex-snapshot
An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences
inferredcites →https://doi.org/10.48550/arxiv.1409.2051openalex-snapshot
Likelihood-based tree reconstruction on a concatenation of alignments can be positively misleading
inferredcites →https://doi.org/10.5852/ejt.2017.283openalex-snapshot
Pitfalls in supermatrix phylogenomics
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.11646/megataxa.1.2.2zenodo-depositor-declared
Hurdles in fungal taxonomy: Effectiveness of recent methods in discriminating taxa
inferred← citeshttps://doi.org/10.1007/s13225-020-00447-5openalex-snapshot
High quality genome sequences of thirteen Hypoxylaceae (Ascomycota) strengthen the phylogenetic family backbone and enable the discovery of new taxa
inferred← citeshttps://doi.org/10.1007/s13225-024-00535-wopenalex-snapshot
Phylogenomics, divergence times and notes of orders in Basidiomycota
inferred← citeshttps://doi.org/10.1007/s13225-025-00568-9openalex-snapshot
Disentangling taxonomic chaos in Agaricaceae s.l.: an integrative phylogenomic framework with divergence dating reconstructs classification
inferred← citeshttps://doi.org/10.1016/j.fbr.2018.02.001openalex-snapshot
Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal development
inferred← citeshttps://doi.org/10.1016/j.funbio.2020.11.011openalex-snapshot
Root fungal endophytes: identity, phylogeny and roles in plant tolerance to metal stress
inferred← citeshttps://doi.org/10.1016/j.funbio.2025.101551openalex-snapshot
Phytopathogenic fungi and oomycetes causing diseases in Theobroma cacao: Chemical and genetic features
inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108310openalex-snapshot
Deciphering the distribution and types of Multicopper oxidases in Basidiomycota fungi
inferred← citeshttps://doi.org/10.1093/molbev/msab365openalex-snapshot
SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss
inferred← citeshttps://doi.org/10.1093/sysbio/syz029openalex-snapshot
Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships
inferred← citeshttps://doi.org/10.1126/sciadv.abd0079openalex-snapshot
Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota
inferred← citeshttps://doi.org/10.1186/s12864-018-5334-1openalex-snapshot
Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi
inferred← citeshttps://doi.org/10.1371/journal.ppat.1007692openalex-snapshot
Multi-omics characterization of the necrotrophic mycoparasite Saccharomycopsis schoenii
inferred← citeshttps://doi.org/10.1515/ijfe-2023-0073openalex-snapshot
Value addition of mushrooms by incorporation in the food products: an overview
inferred← citeshttps://doi.org/10.21203/rs.3.rs-9058008/v1openalex-snapshot
Fungi classification from metagenomic data using CNN_FunBar: A simulation study
inferred← citeshttps://doi.org/10.22541/au.167845826.61933731/v1openalex-snapshot
Phylogenetics and phylogenomics to understand fungal diversity
inferred← citeshttps://doi.org/10.2478/s11756-020-00642-4openalex-snapshot
Where are the basal fungi? Current status on diversity, ecology, evolution, and taxonomy
inferred← citeshttps://doi.org/10.3389/fmicb.2023.1199144openalex-snapshot
Insight into the phylogeny and metabolic divergence of Monascus species (M. pilosus, M. ruber, and M. purpureus) at the genome level
inferred← citeshttps://doi.org/10.3390/genes14030634openalex-snapshot
CNN_FunBar: Advanced Learning Technique for Fungi ITS Region Classification
inferred← citeshttps://doi.org/10.3390/ijms20246317openalex-snapshot
Comparative Proteomic Analysis of Pleurotus ostreatus Reveals Great Metabolic Differences in the Cap and Stipe Development and the Potential Role of Ca2+ in the Primordium Differentiation
inferred← citeshttps://doi.org/10.5772/intechopen.80671openalex-snapshot
Importance of Molecular and Phylogenetic Analyses for Identification of Basidiomycetes
inferred← citeshttps://doi.org/10.64898/2026.03.30.714540openalex-snapshot
Signal, noise, and bias in phylogenetic inference: potential and limits to the resolution of phylogenetic trees in the phylogenomic era
inferred← citeshttps://doi.org/10.70675/e7767ebfz558ez4643z95dezeb6df847fe7dopenalex-snapshot
Rôles des endophytes fongiques racinaires dans la tolérance de Fallopia aux éléments Traces Métalliques
inferred← citeshttps://doi.org/10.7320/borziana.004.051openalex-snapshot
The macrofungi of Gozo (Maltese Islands): an annotated checklist
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.